The University of Queensland

Relative time inference using lateral gene transfers

Davín, Adrián A., Schrempf, Dominik, Williams, Tom A., Hugenholtz, Philip and Szöllősi, Gergely J. (2022). Relative time inference using lateral gene transfers. Environmental microbial evolution: methods and protocols. (pp. 75-94) edited by Haiwei Luo. New York, United States: Humana Press. doi: 10.1007/978-1-0716-2691-7_4

Design and evaluation of 16S rRNA-targeted oligonucleotide probes for fluorescence in situ hybridization

Hugenholtz, Philip, Tyson, Gene W. and Blackall, Linda L. (2018). Design and evaluation of 16S rRNA-targeted oligonucleotide probes for fluorescence in situ hybridization. Gene probes: principles and protocols. (pp. 029-042) edited by Marilena Aquino de Muro and Ralph Rapley. New Jersey, United States: Humana Press. doi: 10.1385/1-59259-238-4:029

Blastobacter: ProteobacteriaAlphaproteobacteriaRhizobialesBradyrhizobiaceae

Sly, Lindsay I. and Hugenholtz, Philip (2015). Blastobacter: ProteobacteriaAlphaproteobacteriaRhizobialesBradyrhizobiaceae. Bergey's manual of systematics of archaea and bacteria. (pp. 1-11) Chichester, United Kingdom: John Wiley & Sons. doi: 10.1002/9781118960608.gbm00800

Blastomonas: ProteobacteriaAlphaproteobacteriaSphingomonadalesSphingomonadaceae

Sly, Lindsay I. and Hugenholtz, Philip (2015). Blastomonas: ProteobacteriaAlphaproteobacteriaSphingomonadalesSphingomonadaceae. Bergey's manual of systematics of archaea and bacteria. (pp. 1-7) Chichester, United Kingdom: John Wiley & Sons. doi: 10.1002/9781118960608.gbm00918

Anaerobaculum

Patel, Bharat K. C. and Hugenholtz, Philip (2015). Anaerobaculum. Bergey's Manual of Systematics of Archaea and Bacteria. (pp. 1-7) Chichester, United Kingdom: John Wiley & Sons. doi: 10.1002/9781118960608.gbm01254

The enduring legacy of small subunit rRNA in microbiology

Tringe, Susannah G. and Hugenholtz, Philip (2011). The enduring legacy of small subunit rRNA in microbiology. Handbook of molecular microbial ecology I: metagenomics and complementary approaches. (pp. 123-128) Hoboken, New Jersey, USA: John Wiley & Sons. doi: 10.1002/9781118010518.ch15

Single cell whole genome amplification of uncultivated organisms

Podar, Mircea, Keller, Martin and Hugenholtz, Philip (2009). Single cell whole genome amplification of uncultivated organisms. Uncultivated microorganisms. (pp. 241-256) edited by Slava S. Epstein. Heidelberg, Germany: Springer . doi: 10.1007/978-3-540-85465-4_10

Single cell whole genome amplifications of uncultivated organisms

Podar, Mircea, Keller, Martin and Hugenholtz, Philip (2009). Single cell whole genome amplifications of uncultivated organisms. Uncultivated microorganisms. (pp. 83-100) edited by Slava S. Epstein. Heidelberg, Germany: Springer. doi: 10.1007/7171_2008_10

Environmental shotgun sequencing

Tyson, Gene W. and Hugenholtz, Philip (2005). Environmental shotgun sequencing. Encyclopedia of genetics, genomics, proteomics, and bioinformatics. (pp. 1386-1391) edited by Lynn B. Jorde. West Sussex, U.K.: John Wiley & Sons. doi: 10.1002/047001153X.g205313

Genus II. Blastomonas. Sly and Cahill 1997, 567VP emend. Hiraishi, Kuraishi and Kawahara 2000a. 1117

Sly, Lindsay I. and Hugenholtz, Philip (2005). Genus II. Blastomonas. Sly and Cahill 1997, 567VP emend. Hiraishi, Kuraishi and Kawahara 2000a. 1117. Bergey's manual of systematic bacteriology: The proteobacteria. Part C. The alpha-, beta-, delta-, and epsilonproteobacteria. (pp. 258-263) edited by D. J. Brenner, N. R. Krieg and J. T. Staley. New York, U.S.A.: Springer. doi: 10.1007/0-387-29298-5_70

Genus IV. Blastobacter Zavarzin 1961, 962AL emend. Sly 1985, 44

Sly, Lindsay I. and Hugenholtz, Philip (2005). Genus IV. Blastobacter Zavarzin 1961, 962AL emend. Sly 1985, 44. Bergey's manual of systematic bacteriology. (pp. 452-459) edited by D. J. Brenner, N. R. Krieg and J. T. Staley. New York, U.S.A.: Springer.

The tree of life: An overview

Baldauf, S.L., Bhattacharya, D., Cockrill, J., Hugenholtz, Philip, Pawlowski, J. and Simpson, A.G. (2004). The tree of life: An overview. Assembling the tree of life. (pp. 43-75) New York: Oxford University Press.

Design and evaluation of 16S rRNA-targeted oligonucleotide probes for fluorescence in situ hybridisation (FISH)

Hugenholtz, P., Tyson, G. and Blackall, L. L. (2002). Design and evaluation of 16S rRNA-targeted oligonucleotide probes for fluorescence in situ hybridisation (FISH). Gene Probes - Principles and Protocols. (pp. 1-17) edited by Aquino de Muro. M and Rapley. R. London: Humana Press.

Characterization of the skin microbiome in normal and cutaneous squamous cell carcinoma affected cats and dogs

Bromfield, Jacoba I., Zaugg, Julian, Straw, Rodney C., Cathie, Julia, Krueger, Annika, Sinha, Debottam, Chandra, Janin, Hugenholtz, Philip and Frazer, Ian H. (2024). Characterization of the skin microbiome in normal and cutaneous squamous cell carcinoma affected cats and dogs. mSphere. doi: 10.1128/msphere.00555-23

Novel spore-forming species exhibiting intrinsic resistance to third- and fourth-generation cephalosporins and description of <i>Tigheibacillus jepli</i> gen. nov., sp. nov

Miliotis, Georgios, Sengupta, Pratyay, Hameed, Asif, Chuvochina, Maria, McDonagh, Francesca, Simpson, Anna C., Parker, Ceth W., Singh, Nitin K., Rekha, Punchappady D., Morris, Dearbháile, Raman, Karthik, Kyrpides, Nikos C., Hugenholtz, Philip and Venkateswaran, Kasthuri (2024). Novel spore-forming species exhibiting intrinsic resistance to third- and fourth-generation cephalosporins and description of Tigheibacillus jepli gen. nov., sp. nov. mBio. doi: 10.1128/mbio.00181-24

Faecal microbial transfer and complex carbohydrates mediate protection against COPD

Budden, Kurtis F, Shukla, Shakti D, Bowerman, Kate L, Vaughan, Annalicia, Gellatly, Shaan L, Wood, David L A, Lachner, Nancy, Idrees, Sobia, Rehman, Saima Firdous, Faiz, Alen, Patel, Vyoma K, Donovan, Chantal, Alemao, Charlotte A, Shen, Sj, Amorim, Nadia, Majumder, Rajib, Vanka, Kanth S, Mason, Jazz, Haw, Tatt Jhong, Tillet, Bree, Fricker, Michael, Keely, Simon, Hansbro, Nicole, Belz, Gabrielle T, Horvat, Jay, Ashhurst, Thomas, van Vreden, Caryn, McGuire, Helen, Fazekas de St Groth, Barbara ... Hansbro, Philip M (2024). Faecal microbial transfer and complex carbohydrates mediate protection against COPD. Gut, gutjnl-2023. doi: 10.1136/gutjnl-2023-330521

Anaerobic gut fungal communities in marsupial hosts

Jones, Adrienne L., Pratt, Carrie J., Meili, Casey H., Soo, Rochelle M., Hugenholtz, Philip, Elshahed, Mostafa S. and Youssef, Noha H. (2024). Anaerobic gut fungal communities in marsupial hosts. Mbio, 15 (2), e0337023. doi: 10.1128/mbio.03370-23

Multiple independent losses of sporulation and peptidoglycan in the Mycoplasmatales and related orders of the class Bacilli

Field, Christian J., Bowerman, Kate L. and Hugenholtz, Philip (2024). Multiple independent losses of sporulation and peptidoglycan in the Mycoplasmatales and related orders of the class Bacilli. Microbial Genomics, 10 (1) 001176. doi: 10.1099/mgen.0.001176

- Invited Review - Identification of the mechanism for dehalorespiration of monofluoroacetate in the phylum Synergistota

Leong, Lex E X, Denman, Stuart E, Kang, Seungha, Mondot, Stanislas, Hugenholtz, Philip and McSweeney, Chris S (2023). - Invited Review - Identification of the mechanism for dehalorespiration of monofluoroacetate in the phylum Synergistota. Animal bioscience, 37 (2), 396-403. doi: 10.5713/ab.23.0351

A long-awaited taxogenomic investigation of the family Halomonadaceae

de la Haba, Rafael R., Arahal, David R., Sánchez-Porro, Cristina, Chuvochina, Maria, Wittouck, Stijn, Hugenholtz, Philip and Ventosa, Antonio (2023). A long-awaited taxogenomic investigation of the family Halomonadaceae. Frontiers in Microbiology, 14 1293707, 1-28. doi: 10.3389/fmicb.2023.1293707

Draft genome sequence of two “Candidatus Intestinicoccus colisanans” strains isolated from faeces of healthy humans

Zhou, Joyce, Boyd, Joel A., Nyeverecz, Bozica, Vivian, Charlotte, Angel, Nicola, Wood, David L. A., Hugenholtz, Philip, Tyson, Gene W., Krause, Lutz and Ó Cuív, Páraic (2023). Draft genome sequence of two “Candidatus Intestinicoccus colisanans” strains isolated from faeces of healthy humans. BMC Research Notes, 16 (1) 174, 1-4. doi: 10.1186/s13104-023-06447-3

Corrigendum: 'A comparative genome analysis of the Bacillota (Firmicutes) class Dehalobacteriia'

Song, Young C., Holland, Sophie I., Lee, Matthew, Chen, Gao, Zaugg, Julian, Löffler, Frank E., Manefield, Michael J., Hugenholtz, Philip and Kappler, Ulrike (2023). Corrigendum: 'A comparative genome analysis of the Bacillota (Firmicutes) class Dehalobacteriia'. Microbial Genomics, 9 (8) 001092. doi: 10.1099/mgen.0.001092

Greengenes2 unifies microbial data in a single reference tree

McDonald, Daniel, Jiang, Yueyu, Balaban, Metin, Cantrell, Kalen, Zhu, Qiyun, Gonzalez, Antonio, Morton, James T., Nicolaou, Giorgia, Parks, Donovan H., Karst, Søren M., Albertsen, Mads, Hugenholtz, Philip, DeSantis, Todd, Song, Se Jin, Bartko, Andrew, Havulinna, Aki S., Jousilahti, Pekka, Cheng, Susan, Inouye, Michael, Niiranen, Teemu, Jain, Mohit, Salomaa, Veikko, Lahti, Leo, Mirarab, Siavash and Knight, Rob (2023). Greengenes2 unifies microbial data in a single reference tree. Nature Biotechnology. doi: 10.1038/s41587-023-01845-1

Proposal of names for 329 higher rank taxa defined in the Genome Taxonomy Database under two prokaryotic codes

Chuvochina, Maria, Mussig, Aaron J., Chaumeil, Pierre-Alain, Skarshewski, Adam, Rinke, Christian, Parks, Donovan H. and Hugenholtz, Philip (2023). Proposal of names for 329 higher rank taxa defined in the Genome Taxonomy Database under two prokaryotic codes. FEMS Microbiology Letters, 370 fnad071, 1-33. doi: 10.1093/femsle/fnad071

Parameter estimation and species tree rooting using ALE and GeneRax

Williams, Tom A., Davín, Adrián A., Morel, Benoit, Szánthó, Lénárd L., Spang, Anja, Stamatakis, Alexandros, Hugenholtz, Philip and Szöllősi, Gergely J. (2023). Parameter estimation and species tree rooting using ALE and GeneRax. Genome Biology and Evolution, 15 (7) evad134. doi: 10.1093/gbe/evad134

Structure, function, and evolution of metallo-β-lactamases from the B3 subgroup—emerging targets to combat antibiotic resistance

Krco, Stefan, Davis, Samuel J., Joshi, Pallav, Wilson, Liam A., Monteiro Pedroso, Marcelo, Douw, Andrew, Schofield, Christopher J., Hugenholtz, Philip, Schenk, Gerhard and Morris, Marc T. (2023). Structure, function, and evolution of metallo-β-lactamases from the B3 subgroup—emerging targets to combat antibiotic resistance. Frontiers in Chemistry, 11 1196073, 1196073. doi: 10.3389/fchem.2023.1196073

A comparative genome analysis of the Bacillota (Firmicutes) class Dehalobacteriia

Song, Young C., Holland, Sophie I., Lee, Matthew, Chen, Gao, Löffler, Frank E., Manefield, Michael J., Hugenholtz, Philip and Kappler, Ulrike (2023). A comparative genome analysis of the Bacillota (Firmicutes) class Dehalobacteriia. Microbial Genomics, 9 (6) 001039, 1-15. doi: 10.1099/mgen.0.001039

Isolation and characterisation of novel Methanocorpusculum species indicates the genus is ancestrally host-associated

Volmer, James G., Soo, Rochelle M., Evans, Paul N., Hoedt, Emily C., Astorga Alsina, Ana L., Woodcroft, Benjamin J., Tyson, Gene W., Hugenholtz, Philip and Morrison, Mark (2023). Isolation and characterisation of novel Methanocorpusculum species indicates the genus is ancestrally host-associated. BMC Biology, 21 (1) 59, 1-17. doi: 10.1186/s12915-023-01524-2

The koala gut microbiome is largely unaffected by host translocation but rather influences host diet

Blyton, Michaela D. J., Pascoe, Jack, Hynes, Emily, Soo, Rochelle M., Hugenholtz, Philip and Moore, Ben D. (2023). The koala gut microbiome is largely unaffected by host translocation but rather influences host diet. Frontiers in Microbiology, 14 1085090, 1-13. doi: 10.3389/fmicb.2023.1085090

Targeting Staphylococcus aureus dominated skin dysbiosis in actinic keratosis to prevent the onset of cutaneous squamous cell carcinoma: Outlook for future therapies?

Bromfield, Jacoba Isobella, Hugenholtz, Philip, Frazer, Ian Hector, Khosrotehrani, Kiarash and Chandra, Janin (2023). Targeting Staphylococcus aureus dominated skin dysbiosis in actinic keratosis to prevent the onset of cutaneous squamous cell carcinoma: Outlook for future therapies?. Frontiers in Oncology, 13 1091379, 1091379. doi: 10.3389/fonc.2023.1091379

Author Correction: Greengenes2 unifies microbial data in a single reference tree (Nature Biotechnology, (2023), 10.1038/s41587-023-01845-1)

McDonald, Daniel, Jiang, Yueyu, Balaban, Metin, Cantrell, Kalen, Zhu, Qiyun, Gonzalez, Antonio, Morton, James T., Nicolaou, Giorgia, Parks, Donovan H., Karst, Søren M., Albertsen, Mads, Hugenholtz, Philip, DeSantis, Todd, Song, Se Jin, Bartko, Andrew, Havulinna, Aki S., Jousilahti, Pekka, Cheng, Susan, Inouye, Michael, Niiranen, Teemu, Jain, Mohit, Salomaa, Veikko, Lahti, Leo, Mirarab, Siavash and Knight, Rob (2023). Author Correction: Greengenes2 unifies microbial data in a single reference tree (Nature Biotechnology, (2023), 10.1038/s41587-023-01845-1). Nature Biotechnology. doi: 10.1038/s41587-023-02026-w

Toward a universal unit for quantification of antibiotic resistance genes in environmental samples

Yin, Xiaole, Chen, Xi, Jiang, Xiao-Tao, Yang, Ying, Li, Bing, Shum, Marcus Ho-Hin, Lam, Tommy T. Y., Leung, Gabriel M., Rose, Joan, Sanchez-Cid, Concepcion, Vogel, Timothy M., Walsh, Fiona, Berendonk, Thomas U., Midega, Janet, Uchea, Chibuzor, Frigon, Dominic, Wright, Gerard D., Bezuidenhout, Carlos, Picão, Renata C., Ahammad, Shaikh Z., Nielsen, Per Halkjær, Hugenholtz, Philip, Ashbolt, Nicholas J., Corno, Gianluca, Fatta-Kassinos, Despo, Bürgmann, Helmut, Schmitt, Heike, Cha, Chang-Jun, Pruden, Amy ... Zhang, Tong (2023). Toward a universal unit for quantification of antibiotic resistance genes in environmental samples. Environmental Science and Technology, 57 (26), 9713-9721. doi: 10.1021/acs.est.3c00159

Probiotic Bifidobacterium longum subsp. longum protects against cigarette smoke-induced inflammation in mice

Budden, Kurtis F., Gellatly, Shaan L., Vaughan, Annalicia, Amorim, Nadia, Horvat, Jay C., Hansbro, Nicole G., Wood, David L. A., Hugenholtz, Philip, Dennis, Paul G., Wark, Peter A. B. and Hansbro, Philip M. (2022). Probiotic Bifidobacterium longum subsp. longum protects against cigarette smoke-induced inflammation in mice. International Journal of Molecular Sciences, 24 (1) 252, 1-12. doi: 10.3390/ijms24010252

GTDB-Tk v2: memory friendly classification with the genome taxonomy database

Chaumeil, Pierre-Alain, Mussig, Aaron J., Hugenholtz, Philip and Parks, Donovan H. (2022). GTDB-Tk v2: memory friendly classification with the genome taxonomy database. Bioinformatics, 38 (23), 5315-5316. doi: 10.1093/bioinformatics/btac672

SeqCode: a nomenclatural code for prokaryotes described from sequence data

Hedlund, Brian P., Chuvochina, Maria, Hugenholtz, Philip, Konstantinidis, Konstantinos T., Murray, Alison E., Palmer, Marike, Parks, Donovan H., Probst, Alexander J., Reysenbach, Anna-Louise, Rodriguez-R, Luis M., Rossello-Mora, Ramon, Sutcliffe, Iain C., Venter, Stephanus N. and Whitman, William B. (2022). SeqCode: a nomenclatural code for prokaryotes described from sequence data. Nature Microbiology, 7 (10), 1702-1708. doi: 10.1038/s41564-022-01214-9

Development of the SeqCode: A proposed nomenclatural code for uncultivated prokaryotes with DNA sequences as type

Whitman, William B., Chuvochina, Maria, Hedlund, Brian P., Hugenholtz, Philip, Konstantinidis, Konstantinos T., Murray, Alison E., Palmer, Marike, Parks, Donovan H., Probst, Alexander J., Reysenbach, Anna-Louise, Rodriguez-R, Luis M., Rossello-Mora, Ramon, Sutcliffe, Iain and Venter, Stephanus N. (2022). Development of the SeqCode: A proposed nomenclatural code for uncultivated prokaryotes with DNA sequences as type. Systematic and Applied Microbiology, 45 (5) 126305, 1-8. doi: 10.1016/j.syapm.2022.126305

Persistence and resistance: survival mechanisms of Candidatus Dormibacterota from nutrient‐poor Antarctic soils

Montgomery, Kate, Williams, Timothy J., Brettle, Merryn, Berengut, Jonathan F., Ray, Angelique E. , Zhang, Eden, Zaugg, Julian, Hugenholtz, Philip and Ferrari, Belinda C. (2022). Persistence and resistance: survival mechanisms of Candidatus Dormibacterota from nutrient‐poor Antarctic soils. Environmental Microbiology, 24 (9), 4491-4491. doi: 10.1111/1462-2920.16191

Atmospheric chemosynthesis is phylogenetically and geographically widespread and contributes significantly to carbon fixation throughout cold deserts

Ray, Angelique E., Zaugg, Julian, Benaud, Nicole, Chelliah, Devan S., Bay, Sean, Wong, Hon Lun, Leung, Pok Man, Ji, Mukan, Terauds, Aleks, Montgomery, Kate, Greening, Chris, Cowan, Don A., Kong, Weidong, Williams, Timothy J., Hugenholtz, Philip and Ferrari, Belinda C. (2022). Atmospheric chemosynthesis is phylogenetically and geographically widespread and contributes significantly to carbon fixation throughout cold deserts. The ISME Journal, 16 (11), 1-14. doi: 10.1038/s41396-022-01298-5

Chemotaxis may assist marine heterotrophic bacterial diazotrophs to find microzones suitable for N2 fixation in the pelagic ocean

Hallstrøm, Søren, Raina, Jean-Baptiste, Ostrowski, Martin, Parks, Donovan H., Tyson, Gene W., Hugenholtz, Philip, Stocker, Roman, Seymour, Justin R. and Riemann, Lasse (2022). Chemotaxis may assist marine heterotrophic bacterial diazotrophs to find microzones suitable for N2 fixation in the pelagic ocean. The ISME Journal, 16 (11), 2525-2534. doi: 10.1038/s41396-022-01299-4

A genome and gene catalog of glacier microbiomes

Liu, Yongqin, Ji, Mukan, Yu, Tao, Zaugg, Julian, Anesio, Alexandre M., Zhang, Zhihao, Hu, Songnian, Hugenholtz, Philip, Liu, Keshao, Liu, Pengfei, Chen, Yuying, Luo, Yingfeng and Yao, Tandong (2022). A genome and gene catalog of glacier microbiomes. Nature Biotechnology, 40 (9), 1341-1348. doi: 10.1038/s41587-022-01367-2

Skin cancer-associated S. aureus strains can induce DNA damage in human keratinocytes by downregulating DNA repair and promoting oxidative stress

Krueger, Annika, Mohamed, Ahmed, Kolka, Cathryn M., Stoll, Thomas, Zaugg, Julian, Linedale, Richard, Morrison, Mark, Soyer, H. Peter, Hugenholtz, Philip, Frazer, Ian H. and Hill, Michelle M. (2022). Skin cancer-associated S. aureus strains can induce DNA damage in human keratinocytes by downregulating DNA repair and promoting oxidative stress. Cancers, 14 (9) 2143. doi: 10.3390/cancers14092143

Chemotaxis shapes the microscale organization of the ocean’s microbiome

Raina, Jean-Baptiste, Lambert, Bennett S., Parks, Donovan H., Rinke, Christian, Siboni, Nachshon, Bramucci, Anna, Ostrowski, Martin, Signal, Brandon, Lutz, Adrian, Mendis, Himasha, Rubino, Francesco, Fernandez, Vicente I., Stocker, Roman, Hugenholtz, Philip, Tyson, Gene W. and Seymour, Justin R. (2022). Chemotaxis shapes the microscale organization of the ocean’s microbiome. Nature, 605 (7908), 132-138. doi: 10.1038/s41586-022-04614-3

Changes in the skin microbiome associated with squamous cell carcinoma in transplant recipients

Krueger, Annika, Zaugg, Julian, Lachner, Nancy, Bialasiewicz, Seweryn, Lin, Lynlee L., Gabizon, Sharon, Sobarun, Priyamvada, Morrison, Mark, Soyer, H. Peter, Hugenholtz, Philip and Frazer, Ian H. (2022). Changes in the skin microbiome associated with squamous cell carcinoma in transplant recipients. ISME Communications, 2 (1) 13, 13. doi: 10.1038/s43705-022-00095-7

Secreted toxins from Staphylococcus aureus strains isolated from keratinocyte skin cancers mediate pro-tumorigenic inflammatory responses in the skin

Krueger, Annika, Zaugg, Julian, Chisholm, Sarah, Linedale, Richard, Lachner, Nancy, Teoh, Siok Min, Tuong, Zewen K., Lukowski, Samuel W., Morrison, Mark, Soyer, H. Peter, Hugenholtz, Philip, Hill, Michelle M. and Frazer, Ian H. (2022). Secreted toxins from Staphylococcus aureus strains isolated from keratinocyte skin cancers mediate pro-tumorigenic inflammatory responses in the skin. Frontiers in Microbiology, 12 789042, 789042. doi: 10.3389/fmicb.2021.789042

Correction: Recoding of stop codons expands the metabolic potential of two novel Asgardarchaeota

Sun, Jiarui, Evans, Paul N., Gagen, Emma J., Woodcroft, Ben J., Hedlund, Brian P., Woyke, Tanja, Hugenholtz, Philip and Rinke, Christian (2022). Correction: Recoding of stop codons expands the metabolic potential of two novel Asgardarchaeota. ISME Communications, 2 (1) 6, 6. doi: 10.1038/s43705-021-00048-6

Characterization of the juvenile koala gut microbiome across wild populations

Blyton, Michaela D. J., Soo, Rochelle M., Hugenholtz, Philip and Moore, Ben D. (2022). Characterization of the juvenile koala gut microbiome across wild populations. Environmental Microbiology, 24 (9), 4209-4219. doi: 10.1111/1462-2920.15884

GTDB: an ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalized and complete genome-based taxonomy

Parks, Donovan H., Chuvochina, Maria, Rinke, Christian, Mussig, Aaron J., Chaumeil, Pierre-Alain and Hugenholtz, Philip (2022). GTDB: an ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalized and complete genome-based taxonomy. Nucleic Acids Research, 50 (D1), D785-D794. doi: 10.1093/nar/gkab776

Maternal inheritance of the koala gut microbiome and its compositional and functional maturation during juvenile development

Blyton, Michaela D.J, Soo, Rochelle M., Hugenholtz, Philip and Moore, Ben D. (2022). Maternal inheritance of the koala gut microbiome and its compositional and functional maturation during juvenile development. Environmental Microbiology, 24 (1), 475-493. doi: 10.1111/1462-2920.15858

Microvolume DNA extraction methods for microscale amplicon and metagenomic studies

Bramucci, Anna R., Focardi, Amaranta, Rinke, Christian, Hugenholtz, Philip, Tyson, Gene W., Seymour, Justin R. and Raina, Jean-Baptiste (2021). Microvolume DNA extraction methods for microscale amplicon and metagenomic studies. ISME Communications, 1 (1) 79. doi: 10.1038/s43705-021-00079-z

Successional dynamics and alternative stable states in a saline activated sludge microbial community over 9 years

Wang, Yulin, Ye, Jun, Ju, Feng, Liu, Lei, Boyd, Joel A., Deng, Yu, Parks, Donovan H., Jiang, Xiaotao, Yin, Xiaole, Woodcroft, Ben J., Tyson, Gene W., Hugenholtz, Philip, Polz, Martin F. and Zhang, Tong (2021). Successional dynamics and alternative stable states in a saline activated sludge microbial community over 9 years. Microbiome, 9 (1) 199, 199. doi: 10.1186/s40168-021-01151-5

Kinetic and structural characterization of the first B3 metallo-β-lactamase with an active site glutamic acid

Wilson, Liam A., Knaven, Esmée G., Morris, Marc T., Monteiro Pedroso, Marcelo, Schofield, Christopher J., Brück, Thomas, Boden, Mikael, Waite, David W., Hugenholtz, Philip, Guddat, Luke and Schenk, Gerhard (2021). Kinetic and structural characterization of the first B3 metallo-β-lactamase with an active site glutamic acid. Antimicrobial Agents and Chemotherapy, 65 (10) e00936-21, e0093621. doi: 10.1128/aac.00936-21

Effects of laboratory domestication on the rodent gut microbiome

Bowerman, Kate L., Knowles, Sarah C. L., Bradley, Janette E., Baltrūnaitė, Laima, Lynch, Michael D. J., Jones, Kathryn M. and Hugenholtz, Philip (2021). Effects of laboratory domestication on the rodent gut microbiome. ISME Communications, 1 (1) 49, 49. doi: 10.1038/s43705-021-00053-9

Persistence and resistance: survival mechanisms of Candidatus Dormibacterota from nutrient-poor Antarctic soils

Montgomery, Kate, Williams, Timothy J., Brettle, Merryn, Berengut, Jonathan F., Zhang, Eden, Zaugg, Julian, Hugenholtz, Philip and Ferrari, Belinda C. (2021). Persistence and resistance: survival mechanisms of Candidatus Dormibacterota from nutrient-poor Antarctic soils. Environmental Microbiology, 23 (8), 4276-4294. doi: 10.1111/1462-2920.15610

Termite gas emissions select for hydrogenotrophic microbial communities in termite mounds

Chiri, Eleonora, Nauer, Philipp A., Lappan, Rachael, Jirapanjawat, Thanavit, Waite, David W., Handley, Kim M., Hugenholtz, Philip, Cook, Perran L.M., Arndt, Stefan K. and Greening, Chris (2021). Termite gas emissions select for hydrogenotrophic microbial communities in termite mounds. Proceedings of the National Academy of Sciences of the United States of America, 118 (30) e2102625118, 1-8. doi: 10.1073/pnas.2102625118

Recoding of stop codons expands the metabolic potential of two novel Asgardarchaeota lineages

Sun, Jiarui, Evans, Paul N., Gagen, Emma J., Woodcroft, Ben J., Hedlund, Brian P., Woyke, Tanja, Hugenholtz, Philip and Rinke, Christian (2021). Recoding of stop codons expands the metabolic potential of two novel Asgardarchaeota lineages. ISME Communications, 1 (1) 30, 1-14. doi: 10.1038/s43705-021-00032-0

A standardized archaeal taxonomy for the Genome Taxonomy Database

Rinke, Christian, Chuvochina, Maria, Mussig, Aaron J., Chaumeil, Pierre-Alain, Davín, Adrián A., Waite, David W., Whitman, William B., Parks, Donovan H. and Hugenholtz, Philip (2021). A standardized archaeal taxonomy for the Genome Taxonomy Database. Nature Microbiology, 6 (7), 946-959. doi: 10.1038/s41564-021-00918-8

Metagenomic compendium of 189,680 DNA viruses from the human gut microbiome

Nayfach, Stephen, Páez-Espino, David, Call, Lee, Low, Soo Jen, Sberro, Hila, Ivanova, Natalia N., Proal, Amy D., Fischbach, Michael A., Bhatt, Ami S., Hugenholtz, Philip and Kyrpides, Nikos C. (2021). Metagenomic compendium of 189,680 DNA viruses from the human gut microbiome. Nature Microbiology, 6 (7), 960-970. doi: 10.1038/s41564-021-00928-6

Chemosynthetic and photosynthetic bacteria contribute differentially to primary production across a steep desert aridity gradient

Bay, Sean K., Waite, David W., Dong, Xiyang, Gillor, Osnat, Chown, Steven L., Hugenholtz, Philip and Greening, Chris (2021). Chemosynthetic and photosynthetic bacteria contribute differentially to primary production across a steep desert aridity gradient. The ISME Journal, 15 (11), 3339-3356. doi: 10.1038/s41396-021-01001-0

A rooted phylogeny resolves early bacterial evolution

Coleman, Gareth A., Davín, Adrián A., Mahendrarajah, Tara A., Szánthó, Lénárd L., Spang, Anja, Hugenholtz, Philip, Szöllősi, Gergely J. and Williams, Tom A. (2021). A rooted phylogeny resolves early bacterial evolution. Science, 372 (6542) eabe0511, eabe0511-+. doi: 10.1126/science.abe0511

Critical evaluation of faecal microbiome preservation using metagenomic analysis

Pribyl, Alena L., Parks, Donovan H., Angel, Nicola Z., Boyd, Joel A., Hasson, Alexander G., Fang, Liang, MacDonald, Samantha L., Wills, Blake A., Wood, David L. A., Krause, Lutz, Tyson, Gene W. and Hugenholtz, Philip (2021). Critical evaluation of faecal microbiome preservation using metagenomic analysis. ISME Communications, 1 (1) 14, 14. doi: 10.1038/s43705-021-00014-2

IFN-λ therapy prevents severe gastrointestinal graft-versus-host disease

Henden, Andrea S., Koyama, Motoko, Robb, Renee J., Forero, Adriana, Kuns, Rachel D., Chang, Karshing, Ensbey, Kathleen S., Varelias, Antiopi, Kazakoff, Stephen H., Waddell, Nicole, Clouston, Andrew D., Giri, Rabina, Begun, Jakob, Blazar, Bruce R., Degli-Esposti, Mariapia A., Kotenko, Sergei V., Lane, Steven W., Bowerman, Kate L., Savan, Ram, Hugenholtz, Philip, Gartlan, Kate H. and Hill, Geoffrey R. (2021). IFN-λ therapy prevents severe gastrointestinal graft-versus-host disease. Blood, 138 (8), 722-737. doi: 10.1182/blood.2020006375

Metabolic flexibility allows bacterial habitat generalists to become dominant in a frequently disturbed ecosystem

Chen, Ya-Jou, Leung, Pok Man, Wood, Jennifer L., Bay, Sean K., Hugenholtz, Philip, Kessler, Adam J., Shelley, Guy, Waite, David W., Franks, Ashley E., Cook, Perran L. M. and Greening, Chris (2021). Metabolic flexibility allows bacterial habitat generalists to become dominant in a frequently disturbed ecosystem. The ISME Journal, 15 (10), 2986-3004. doi: 10.1038/s41396-021-00988-w

Evaluation of the microba community profiler for taxonomic profiling of metagenomic datasets from the human gut microbiome

Parks, Donovan H., Rigato, Fabio, Vera-Wolf, Patricia, Krause, Lutz, Hugenholtz, Philip, Tyson, Gene W. and Wood, David L. A. (2021). Evaluation of the microba community profiler for taxonomic profiling of metagenomic datasets from the human gut microbiome. Frontiers in Microbiology, 12 643682, 1-15. doi: 10.3389/fmicb.2021.643682

Prokaryotic taxonomy and nomenclature in the age of big sequence data

Hugenholtz, Philip, Chuvochina, Maria, Oren, Aharon, Parks, Donovan H. and Soo, Rochelle M. (2021). Prokaryotic taxonomy and nomenclature in the age of big sequence data. The ISME Journal, 15 (7), 1879-1892. doi: 10.1038/s41396-021-00941-x

Candidatus Eremiobacterota, a metabolically and phylogenetically diverse terrestrial phylum with acid-tolerant adaptations

Ji, Mukan, Williams, Timothy J., Montgomery, Kate, Wong, Hon Lun, Zaugg, Julian, Berengut, Jonathan F., Bissett, Andrew, Chuvochina, Maria, Hugenholtz, Philip and Ferrari, Belinda C. (2021). Candidatus Eremiobacterota, a metabolically and phylogenetically diverse terrestrial phylum with acid-tolerant adaptations. The ISME Journal, 15 (9), 2692-2707. doi: 10.1038/s41396-021-00944-8

Streptococcus species enriched in the oral cavity of patients with RA are a source of peptidoglycan-polysaccharide polymers that can induce arthritis in mice

Moentadj, Rabia, Wang, Yiwen, Bowerman, Kate, Rehaume, Linda, Nel, Hendrik, O Cuiv, Paraic, Stephens, Juliette, Baharom, Amalina, Maradana, Muralidhara, Lakis, Vanessa, Morrison, Mark, Wells, Timothy, Hugenholtz, Philip, Benham, Helen, Le Cao, Kim-Anh and Thomas, Ranjeny (2021). Streptococcus species enriched in the oral cavity of patients with RA are a source of peptidoglycan-polysaccharide polymers that can induce arthritis in mice. Annals of the Rheumatic Diseases, 80 (5) annrheumdis-2020-219009, annrheumdis-2020. doi: 10.1136/annrheumdis-2020-219009

Wastewater monitoring for SARS-CoV-2

Donner, Erica, Zamyadi, Arash, Jex, Aaron, Short, Michael, Drigo, Barbara, McCarthy, David, Crosbie, Nicholas, Ahmed, Warish, Mueller, Jochen, Thomas, Kevin, Monis, Paul, Keegan, Alex, Ginige, Maneesha, Hugenholtz, Philip, Tyson, Gene, Hill, Kelly and Blackall, Linda (2021). Wastewater monitoring for SARS-CoV-2. Microbiology Australia, 42 (1), 18-22. doi: 10.1071/ma21006

Tracking seasonal changes in diversity of pollen allergen exposure: targeted metabarcoding of a subtropical aerobiome

Campbell, B. C., Al Kouba, J., Timbrell, V., Noor, M. J., Massel, K., Gilding, E. K., Angel, N., Kemish, B., Hugenholtz, P., Godwin, I. D. and Davies, J. M. (2020). Tracking seasonal changes in diversity of pollen allergen exposure: targeted metabarcoding of a subtropical aerobiome. Science of the Total Environment, 747 141189, 141189. doi: 10.1016/j.scitotenv.2020.141189

COVID-19 pandemic reveals the peril of ignoring metadata standards

Schriml, Lynn M., Chuvochina, Maria, Davies, Neil, Eloe-Fadrosh, Emiley A., Finn, Robert D., Hugenholtz, Philip, Hunter, Christopher I., Hurwitz, Bonnie L., Kyrpides, Nikos C., Meyer, Folker, Mizrachi, Ilene Karsch, Sansone, Susanna-Assunta, Sutton, Granger, Tighe, Scott and Walls, Ramona (2020). COVID-19 pandemic reveals the peril of ignoring metadata standards. Scientific Data, 7 (1) 188, 188. doi: 10.1038/s41597-020-0524-5

Fluconazole resistance in Candida albicans is induced by Pseudomonas aeruginosa quorum sensing

Bandara, H. M.H.N., Wood, D. L.A., Vanwonterghem, I., Hugenholtz, P., Cheung, B. P.K. and Samaranayake, L. P. (2020). Fluconazole resistance in Candida albicans is induced by Pseudomonas aeruginosa quorum sensing. Scientific Reports, 10 (1) 7769, 7769. doi: 10.1038/s41598-020-64761-3

Disease-associated gut microbiome and metabolome changes in patients with chronic obstructive pulmonary disease

Bowerman, Kate L., Rehman, Saima Firdous, Vaughan, Annalicia, Lachner, Nancy, Budden, Kurtis F., Kim, Richard Y., Wood, David L. A., Gellatly, Shaan L., Shukla, Shakti D., Wood, Lisa G., Yang, Ian A., Wark, Peter A., Hugenholtz, Philip and Hansbro, Philip M. (2020). Disease-associated gut microbiome and metabolome changes in patients with chronic obstructive pulmonary disease. Nature Communications, 11 (1) 5886, 1-15. doi: 10.1038/s41467-020-19701-0

Author Correction: Roadmap for naming uncultivated Archaea and Bacteria

Murray, Alison E., Freudenstein, John, Gribaldo, Simonetta, Hatzenpichler, Roland, Hugenholtz, Philip, Kämpfer, Peter, Konstantinidis, Konstantinos T., Lane, Christopher E., Papke, R. Thane, Parks, Donovan H., Rossello-Mora, Ramon, Stott, Matthew B., Sutcliffe, Iain C., Thrash, J. Cameron, Venter, Stephanus N., Whitman, William B., Acinas, Silvia G., Amann, Rudolf I., Anantharaman, Karthik, Armengaud, Jean, Baker, Brett J., Barco, Roman A., Bode, Helge B., Boyd, Eric S., Brady, Carrie L., Carini, Paul, Chain, Patrick S. G., Colman, Daniel R., DeAngelis, Kristen M. ... Reysenbach, Anna-Louise (2020). Author Correction: Roadmap for naming uncultivated Archaea and Bacteria. Nature Microbiology, 6 (1), 136-136. doi: 10.1038/s41564-020-00827-2

Author Correction: A complete domain-to-species taxonomy for Bacteria and Archaea (Nature Biotechnology, (2020), 38, 9, (1079-1086), 10.1038/s41587-020-0501-8)

Parks, Donovan H., Chuvochina, Maria, Chaumeil, Pierre-Alain, Rinke, Christian, Mussig, Aaron J. and Hugenholtz, Philip (2020). Author Correction: A complete domain-to-species taxonomy for Bacteria and Archaea (Nature Biotechnology, (2020), 38, 9, (1079-1086), 10.1038/s41587-020-0501-8). Nature Biotechnology, 38 (9), 1098-1098. doi: 10.1038/s41587-020-0539-7

First confirmed detection of SARS-CoV-2 in untreated wastewater in Australia: a proof of concept for the wastewater surveillance of COVID-19 in the community

Ahmed, Warish, Angel, Nicola, Edson, Janette, Bibby, Kyle, Bivins, Aaron, O'Brien, Jake W., Choi, Phil M., Kitajima, Masaaki, Simpson, Stuart L., Li, Jiaying, Tscharke, Ben, Verhagen, Rory, Smith, Wendy J.M., Zaugg, Julian, Dierens, Leanne, Hugenholtz, Philip, Thomas, Kevin V. and Mueller, Jochen F. (2020). First confirmed detection of SARS-CoV-2 in untreated wastewater in Australia: a proof of concept for the wastewater surveillance of COVID-19 in the community. Science of the Total Environment, 728 138764, 138764. doi: 10.1016/j.scitotenv.2020.138764

A unified catalog of 204,938 reference genomes from the human gut microbiome

Almeida, Alexandre, Nayfach, Stephen, Boland, Miguel, Strozzi, Francesco, Beracochea, Martin, Shi, Zhou Jason, Pollard, Katherine S., Sakharova, Ekaterina, Parks, Donovan H., Hugenholtz, Philip, Segata, Nicola, Kyrpides, Nikos C. and Finn, Robert D. (2020). A unified catalog of 204,938 reference genomes from the human gut microbiome. Nature Biotechnology, 39 (1), 105-114. doi: 10.1038/s41587-020-0603-3

Detection of SARS-CoV-2 RNA in commercial passenger aircraft and cruise ship wastewater: a surveillance tool for assessing the presence of COVID-19 infected travelers

Ahmed, Warish, Bertsch, Paul M., Angel, Nicola, Bibby, Kyle, Bivins, Aaron, Dierens, Leanne, Edson, Janette, Ehret, John, Gyawali, Pradip, Hamilton, Kerry, Hosegood, Ian, Hugenholtz, Philip, Jiang, Guangming, Kitajima, Masaaki, Sichani, Homa T., Shi, Jiahua, Shimko, Katja M., Simpson, Stuart L., Smith, Wendy J. M., Symonds, Erin M., Thomas, Kevin V., Verhagen, Rory, Zaugg, Julian and Mueller, Jochen F (2020). Detection of SARS-CoV-2 RNA in commercial passenger aircraft and cruise ship wastewater: a surveillance tool for assessing the presence of COVID-19 infected travelers. Journal of Travel Medicine, 27 (5) ARTN taaa116, 1-11. doi: 10.1093/jtm/taaa116

Broad spectrum antibiotic-degrading metallo-β-lactamases are phylogenetically diverse

Pedroso, Marcelo Monteiro, Waite, David W., Melse, Okke, Wilson, Liam, Mitić, Nataša, McGeary, Ross P., Antes, Iris, Guddat, Luke W., Hugenholtz, Philip and Schenk, Gerhard (2020). Broad spectrum antibiotic-degrading metallo-β-lactamases are phylogenetically diverse. Protein and Cell, 11 (8), 613-617. doi: 10.1007/s13238-020-00736-4

A complete domain-to-species taxonomy for bacteria and archaea

Parks, Donovan H., Chuvochina, Maria, Chaumeil, Pierre-Alain, Rinke, Christian, Mussig, Aaron J. and Hugenholtz, Philip (2020). A complete domain-to-species taxonomy for bacteria and archaea. Nature Biotechnology, 38 (9), 1098-1098. doi: 10.1038/s41587-020-0501-8

Draft genome sequence of Limisphaera ngatamarikiensis NGM72.4(T), a moderately alkaliphilic thermophile belonging to the class Verrucomicrobiae

Carere, Carlo R., Steen, Jason A., Hugenholtz, Philip and Stott, Matthew B. (2020). Draft genome sequence of Limisphaera ngatamarikiensis NGM72.4(T), a moderately alkaliphilic thermophile belonging to the class Verrucomicrobiae. Microbiology Resource Announcements, 9 (18) e00225-20. doi: 10.1128/MRA.00225-20

GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database

Chaumeil, Pierre-Alain, Mussig, Aaron J., Hugenholtz, Philip and Parks, Donovan H. (2020). GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database. Bioinformatics, 36 (6), 1925-1927. doi: 10.1093/bioinformatics/btz848

Correction: A phylogenomic and ecological analysis of the globally abundant Marine Group II archaea (Ca. Poseidoniales ord. nov.)

Rinke, Christian, Rubino, Francesco, Messer, Lauren F., Youssef, Noha, Parks, Donovan H., Chuvochina, Maria, Brown, Mark, Jeffries, Thomas, Tyson, Gene W., Seymour, Justin R. and Hugenholtz, Philip (2020). Correction: A phylogenomic and ecological analysis of the globally abundant Marine Group II archaea (Ca. Poseidoniales ord. nov.). The ISME Journal, 14 (3), 878-878. doi: 10.1038/s41396-019-0556-z

Continuous pre- and post-transplant exposure to a disease-associated gut microbiome promotes hyper-acute graft-versus-host disease in wild-type mice

Bowerman, Kate L., Varelias, Antiopi, Lachner, Nancy, Kuns, Rachel D., Hill, Geoffrey R. and Hugenholtz, Philip (2020). Continuous pre- and post-transplant exposure to a disease-associated gut microbiome promotes hyper-acute graft-versus-host disease in wild-type mice. Gut Microbes, 11 (4), 1-17. doi: 10.1080/19490976.2019.1705729

Proposal to reclassify the proteobacterial classes Deltaproteobacteria and Oligoflexia, and the phylum Thermodesulfobacteria into four phyla reflecting major functional capabilities

Waite, David W., Chuvochina, Maria, Pelikan, Claus, Parks, Donovan H., Yilmaz, Pelin, Wagner, Michael, Loy, Alexander, Naganuma, Takeshi, Nakai, Ryosuke, Whitman, William B., Hahn, Martin W., Kuever, Jan and Hugenholtz, Philip (2020). Proposal to reclassify the proteobacterial classes Deltaproteobacteria and Oligoflexia, and the phylum Thermodesulfobacteria into four phyla reflecting major functional capabilities. International Journal of Systematic and Evolutionary Microbiology, 70 (11) 004213, 5972-6016. doi: 10.1099/ijsem.0.004213

Roadmap for naming uncultivated Archaea and Bacteria

Murray, Alison E., Freudenstein, John, Gribaldo, Simonetta, Hatzenpichler, Roland, Hugenholtz, Philip, Kämpfer, Peter, Konstantinidis, Konstantinos T., Lane, Christopher E., Papke, R. Thane, Parks, Donovan H., Rossello-Mora, Ramon, Stott, Matthew B., Sutcliffe, Iain C., Thrash, J. Cameron, Venter, Stephanus N., Whitman, William B., Acinas, Silvia G., Amann, Rudolf I., Anantharaman, Karthik, Armengaud, Jean, Baker, Brett J., Barco, Roman A., Bode, Helge B., Boyd, Eric S., Brady, Carrie L., Carini, Paul, Chain, Patrick S. G., Colman, Daniel R., DeAngelis, Kristen M. ... Reysenbach, Anna-Louise (2020). Roadmap for naming uncultivated Archaea and Bacteria. Nature Microbiology, 5 (8), 987-994. doi: 10.1038/s41564-020-0733-x

Functional effects of the microbiota in chronic respiratory disease

Budden, Kurtis F., Shukla, Shakti D., Rehman, Saima Firdous, Bowerman, Kate L., Keely, Simon, Hugenholtz, Philip, Armstrong-James, Darius P. H., Adcock, Ian M., Chotirmall, Sanjay H., Chung, Kian Fan and Hansbro, Philip M. (2019). Functional effects of the microbiota in chronic respiratory disease. Lancet Respiratory Medicine, 7 (10), 907-920. doi: 10.1016/S2213-2600(18)30510-1

Genomic Encyclopedia of Bacteria and Archaea (GEBA) VI: learning from type strains

Whitman, William B., Klenk, Hans-Peter, Arahal, David R., Aznar, Rosa, Garrity, George, Pester, Michael and Hugenholtz, Philip (2019). Genomic Encyclopedia of Bacteria and Archaea (GEBA) VI: learning from type strains. Microbiology Australia, 40 (3), 125-129. doi: 10.1071/MA19034

Faecal inoculations alter the gastrointestinal microbiome and allow dietary expansion in a wild specialist herbivore, the koala

Blyton, Michaela D. J., Soo, Rochelle M., Whisson, Desley, Marsh, Karen J., Pascoe, Jack, Le Pla, Mark, Foley, William, Hugenholtz, Philip and Moore, Ben D. (2019). Faecal inoculations alter the gastrointestinal microbiome and allow dietary expansion in a wild specialist herbivore, the koala. Animal Microbiome, 1 (1) 6, 6. doi: 10.1186/s42523-019-0008-0

Defining the human gut host–phage network through single-cell viral tagging

Džunková, Mária, Low, Soo Jen, Daly, Joshua N., Deng, Li, Rinke, Christian and Hugenholtz, Philip (2019). Defining the human gut host–phage network through single-cell viral tagging. Nature Microbiology, 4 (12), 2192-2203. doi: 10.1038/s41564-019-0526-2

Evaluation of a concatenated protein phylogeny for classification of tailed double-stranded DNA viruses belonging to the order Caudovirales

Low, Soo Jen, Džunková, Mária, Chaumeil, Pierre-Alain, Parks, Donovan H. and Hugenholtz, Philip (2019). Evaluation of a concatenated protein phylogeny for classification of tailed double-stranded DNA viruses belonging to the order Caudovirales. Nature Microbiology, 4 (8), 1306-1315. doi: 10.1038/s41564-019-0448-z

Consent insufficient for data release Response

Amann, Rudolf I., Baichoo, Shakuntala, Blencowe, Benjamin J., Bork, Peer, Borodovsky, Mark, Brooksbank, Cath, Chain, Patrick S. G., Colwell, Rita R., Daffonchio, Daniele G., Danchin, Antoine, de Lorenzo, Victor, Dorrestein, Pieter C., Finn, Robert D., Fraser, Claire M., Gilbert, Jack A., Hallam, Steven J., Hugenholtz, Philip, Ioannidis, John P. A., Jansson, Janet K., Kim, Jihyun F., Klenk, Hans-Peter, Klotz, Martin G., Knight, Rob, Konstantinidis, Konstantinos T., Kyrpides, Nikos C., Mason, Christopher E., McHardy, Alice C., Meyer, Folker, Ouzounis, Christos A. ... Xenarios, Ioannis (2019). Consent insufficient for data release Response. Science, 364 (6439), 446-446. doi: 10.1126/science.aax7509

Bacterial fermentation and respiration processes are uncoupled in anoxic permeable sediments

Kessler, Adam J., Chen, Ya-Jou, Waite, David W., Hutchinson, Tess, Koh, Sharlynn, Popa, M. Elena, Beardall, John, Hugenholtz, Philip, Cook, Perran L. M. and Greening, Chris (2019). Bacterial fermentation and respiration processes are uncoupled in anoxic permeable sediments. Nature Microbiology, 4 (6), 1014-1023. doi: 10.1038/s41564-019-0391-z

IL-23 favours outgrowth of spondyloarthritis-associated pathobionts and suppresses host support for homeostatic microbiota

Rehaume, Linda M., Matigian, Nicholas, Mehdi, Ahmed M., Lachner, Nancy, Bowerman, Kate L., Daly, Joshua, Lê Cao, Kim-Anh, Hugenholtz, Philip and Thomas, Ranjeny (2019). IL-23 favours outgrowth of spondyloarthritis-associated pathobionts and suppresses host support for homeostatic microbiota. Annals of the Rheumatic Diseases, 78 (4), 494-503. doi: 10.1136/annrheumdis-2018-214381

Toward unrestricted use of public genomic data

Amann, Rudolf I., Baichoo, Shakuntala, Blencowe, Benjamin J., Bork, Peer, Borodovsky, Mark, Brooksbank, Cath, Chain, Patrick S. G., Colwell, Rita R., Daffonchio, Daniele G., Danchin, Antoine, de Lorenzo, Victor, Dorrestein, Pieter C., Finn, Robert D., Fraser, Claire M., Gilbert, Jack A., Hallam, Steven J., Hugenholtz, Philip, Ioannidis, John P. A., Jansson, Janet K., Kim, Jihyun F., Klenk, Hans-Peter, Klotz, Martin G., Knight, Rob, Konstantinidis, Konstantinos T., Kyrpides, Nikos C., Mason, Christopher E., McHardy, Alice C., Meyer, Folker, Ouzounis, Christos A. ... Xenarios, Ioannis (2019). Toward unrestricted use of public genomic data. Science, 363 (6425), 350-352. doi: 10.1126/science.aaw1280

An evolving view of methane metabolism in the Archaea

Evans, Paul N., Boyd, Joel A., Leu, Andy O., Woodcroft, Ben J., Parks, Donovan H., Hugenholtz, Philip and Tyson, Gene W. (2019). An evolving view of methane metabolism in the Archaea. Nature Reviews Microbiology, 17 (4), 219-232. doi: 10.1038/s41579-018-0136-7

Evolution of photosynthesis and aerobic respiration in the cyanobacteria

Soo, Rochelle M., Hemp, James and Hugenholtz, Philip (2019). Evolution of photosynthesis and aerobic respiration in the cyanobacteria. Free Radical Biology and Medicine, 140, 200-205. doi: 10.1016/j.freeradbiomed.2019.03.029

The importance of designating type material for uncultured taxa

Chuvochina, Maria, Rinke, Christian, Parks, Donovan H., Rappé, Michael S., Tyson, Gene W., Yilmaz, Pelin, Whitman, William B. and Hugenholtz, Philip (2019). The importance of designating type material for uncultured taxa. Systematic and Applied Microbiology, 42 (1), 15-21. doi: 10.1016/j.syapm.2018.07.003

Minimum information about an uncultivated virus genome (MIUViG)

Roux, Simon, Adriaenssens, Evelien M, Dutilh, Bas E, Koonin, Eugene V, Kropinski, Andrew M, Krupovic, Mart, Kuhn, Jens H, Lavigne, Rob, Brister, J Rodney, Varsani, Arvind, Amid, Clara, Aziz, Ramy K, Bordenstein, Seth R, Bork, Peer, Breitbart, Mya, Cochrane, Guy R, Daly, Rebecca A, Desnues, Christelle, Duhaime, Melissa B, Emerson, Joanne B, Enault, François, Fuhrman, Jed A, Hingamp, Pascal, Hugenholtz, Philip, Hurwitz, Bonnie L, Ivanova, Natalia N, Labonté, Jessica M, Lee, Kyung-Bum, Malmstrom, Rex R ... Eloe-Fadrosh, Emiley A (2018). Minimum information about an uncultivated virus genome (MIUViG). Nature Biotechnology, 37 (1), 29-37. doi: 10.1038/nbt.4306

A phylogenomic and ecological analysis of the globally abundant Marine Group II archaea (Ca. Poseidoniales ord. nov.)

Rinke, Christian, Rubino, Francesco, Messer, Lauren F., Youssef, Noha, Parks, Donovan H., Chuvochina, Maria, Brown, Mark, Jeffries, Thomas, Tyson, Gene W., Seymour, Justin R. and Hugenholtz, Philip (2018). A phylogenomic and ecological analysis of the globally abundant Marine Group II archaea (Ca. Poseidoniales ord. nov.). The ISME Journal, 13 (3), 663-675. doi: 10.1038/s41396-018-0282-y

A natural history of actinic keratosis and cutaneous squamous cell carcinoma microbiomes

Wood, David L. A., Lachner, Nancy, Tan, Jean-Marie, Tang, Stephanie, Angel, Nicola, Laino, Antonia, Linedale, Richard, Lê Cao, Kim-Anh, Morrison, Mark, Frazer, Ian H., Soyer, H. Peter and Hugenholtz, Philip (2018). A natural history of actinic keratosis and cutaneous squamous cell carcinoma microbiomes. MBio, 9 (5) e01432-18. doi: 10.1128/mBio.01432-18

A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life

Parks, Donovan H., Chuvochina, Maria, Waite, David W., Rinke, Christian, Skarshewski, Adam, Chaumeil, Pierre-Alain and Hugenholtz, Philip (2018). A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life. Nature Biotechnology, 36 (10), 996-1004. doi: 10.1038/nbt.4229

Culture- and metagenomics-enabled analyses of the Methanosphaera genus reveals their monophyletic origin and differentiation according to genome size

Hoedt, Emily C., Parks, Donovan H., Volmer, James G., Rosewarne, Carly P., Denman, Stuart E., McSweeney, Christopher S., Muir, Jane G., Gibson, Peter R., Cuív, Páraic Ó, Hugenholtz, Philip, Tyson, Gene W. and Morrison, Mark (2018). Culture- and metagenomics-enabled analyses of the Methanosphaera genus reveals their monophyletic origin and differentiation according to genome size. ISME Journal, 12 (12), 2942-2953. doi: 10.1038/s41396-018-0225-7

Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea (Nature Biotechnology (2017) 35 (725-731) DOI: 10.1038/nbt.3893)

Bowers, Robert M., Kyrpides, Nikos C., Stepanauskas, Ramunas, Harmon-Smith, Miranda, Doud, Devin, Reddy, T. B.K., Schulz, Frederik, Jarett, Jessica, Rivers, Adam R, Eloe-Fadrosh, Emiley A., Tringe, Susannah G., Ivanova, Natalia N., Copeland, Alex, Clum, Alicia, Becraft, Eric D., Malmstrom, Rex R., Birren, Bruce, Podar, Mircea, Bork, Peer, Weinstock, George M., Garrity, George M., Dodsworth, Jeremy A., Yooseph, Shibu, Sutton, Granger, Glöckner, Frank O., Gilbert, Jack A, Nelson, William C., Hallam, Steven J., Jungbluth, Sean P. ... Woyke, Tanja (2018). Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea (Nature Biotechnology (2017) 35 (725-731) DOI: 10.1038/nbt.3893). Nature Biotechnology, 36 (7), 660-660. doi: 10.1038/nbt0718-660a

Network-guided genomic and metagenomic analysis of the faecal microbiota of the critically endangered kakapo

Waite, David W., Dsouza, Melissa, Sekiguchi, Yuji, Hugenholtz, Philip and Taylor, Michael W. (2018). Network-guided genomic and metagenomic analysis of the faecal microbiota of the critically endangered kakapo. Scientific Reports, 8 (1) 8128, 8128. doi: 10.1038/s41598-018-26484-4

American gut: an open platform for citizen science microbiome research

McDonald, Daniel, Hyde, Embriette, Debelius, Justine W., Morton, James T., Gonzalez, Antonio, Ackermann, Gail, Aksenov, Alexander A., Behsaz, Bahar, Brennan, Caitriona, Chen, Yingfeng, DeRight Goldasich, Lindsay, Dorrestein, Pieter C., Dunn, Robert R., Fahimipour, Ashkaan K., Gaffney, James, Gilbert, Jack A., Gogul, Grant, Green, Jessica L, Hugenholtz, Philip, Humphrey, Greg, Huttenhower, Curtis, Jackson, Matthew A., Janssen, Stefan, Jeste, Dilip V., Jiang, Lingjing, Kelley, Scott T., Knights, Dan, Kosciolek, Tomasz, Ladau, Joshua ... Knight, Rob (2018). American gut: an open platform for citizen science microbiome research. mSystems, 3 (3) e00031-18. doi: 10.1128/mSystems.00031-18

Mechanisms of persistence of the ammonia-oxidizing bacteria Nitrosomonas to the biocide free nitrous acid

Laloo, Andrew E., Wei, Justin, Wang, Dongbo, Narayanasamy, Shaman, Vanwonterghem, Inka, Waite, David, Steen, Jason, Kaysen, Anne, Heintz-Buschart, Anna, Wang, Qilin, Schulz, Benjamin, Nouwens, Amanda, Wilmes, Paul, Hugenholtz, Philip, Yuan, Zhiguo and Bond, Philip L. (2018). Mechanisms of persistence of the ammonia-oxidizing bacteria Nitrosomonas to the biocide free nitrous acid. Environmental science & technology, 52 (9), 5386-5397. doi: 10.1021/acs.est.7b04273

Addendum: Comparative genomic analysis of the class Epsilonproteobacteria and proposed reclassification to Epsilonbacteraeota (phyl. nov.) (vol 8, 682, 2017)

Waite, David W., Vanwonterghem, Inka, Rinke, Christian, Parks, Donovan H., Zhang, Ying, Takai, Ken, Sievert, Stefan M., Simon, Jorg, Campbell, Barbara J., Hanson, Thomas E., Woyke, Tanja, Klotz, Martin G. and Hugenholtz, Philip (2018). Addendum: Comparative genomic analysis of the class Epsilonproteobacteria and proposed reclassification to Epsilonbacteraeota (phyl. nov.) (vol 8, 682, 2017). Frontiers in Microbiology, 9 (APR) 772, 772. doi: 10.3389/fmicb.2018.00772

Recipient mucosal-associated invariant T cells control GVHD within the colon

Varelias, Antiopi, Bunting, Mark D., Ormerod, Kate L., Koyama, Motoko, Olver, Stuart D., Straube, Jasmin, Kuns, Rachel D., Robb, Renee J., Henden, Andrea S., Cooper, Leanne, Lachner, Nancy, Gartlan, Kate H., Lantz, Olivier, Kjer-Nielsen, Lars, Mak, Jeffrey Y. W., Fairlie, David P., Clouston, Andrew D., McCluskey, James, Rossjohn, Jamie, Lane, Steven W., Hugenholtz, Philip and Hill, Geoffrey R. (2018). Recipient mucosal-associated invariant T cells control GVHD within the colon. Journal of Clinical Investigation, 128 (5), 1919-1936. doi: 10.1172/JCI91646

1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life (vol 35, pg 676, 2017)

Mukherjee, Supratim, Seshadri, Rekha, Varghese, Neha J., Eloe-Fadrosh, Emiley A., Meier-Kolthoff, Jan P., Goeker, Markus, Coates, R. Cameron, Hadjithomas, Michalis, Pavlopoulos, Georgios A., Paez-Espino, David, Yoshikuni, Yasuo, Visel, Axel, Whitman, William B., Garrity, George M., Eisen, Jonathan A., Hugenholtz, Philip, Pati, Amrita, Ivanova, Natalia N., Woyke, Tanja, Klenk, Hans-Peter and Kyrpides, Nikos C. (2018). 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life (vol 35, pg 676, 2017). Nature Biotechnology, 36 (4), 368-368. doi: 10.1038/nbt0418-368c

Beneficial changes in rumen bacterial community profile in sheep and dairy calves as a result of feeding the probiotic Bacillus amyloliquefaciens H57

Schofield, Benjamin J., Lachner, Nancy, Le, Oanh T., McNeill, David M., Dart, Peter, Ouwerkerk, Diane, Hugenholtz, Philip and Klieve, Athol V. (2018). Beneficial changes in rumen bacterial community profile in sheep and dairy calves as a result of feeding the probiotic Bacillus amyloliquefaciens H57. Journal of Applied Microbiology, 124 (3), 855-866. doi: 10.1111/jam.13688

Author correction: recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life

Parks, Donovan H., Rinke, Christian, Chuvochina, Maria, Chaumeil, Pierre-Alain, Woodcroft, Ben J., Evans, Paul N., Hugenholtz, Philip and Tyson, Gene W. (2017). Author correction: recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life. Nature Microbiology, 3 (2), 253-253. doi: 10.1038/s41564-017-0083-5

Atmospheric trace gases support primary production in Antarctic desert surface soil

Ji, Mukan, Greening, Chris, Vanwonterghem, Inka, Carere, Carlo R., Bay, Sean K., Steen, Jason A., Montgomery, Kate, Lines, Thomas, Beardall, John, van Dorst, Josie, Snape, Ian, Stott, Matthew B., Hugenholtz, Philip and Ferrari, Belinda C. (2017). Atmospheric trace gases support primary production in Antarctic desert surface soil. Nature, 552 (7685), 400-403. doi: 10.1038/nature25014

Evolutionary conservation of a core root microbiome across plant phyla along a tropical soil chronosequence

Yeoh, Yun Kit, Dennis, Paul G., Paungfoo-Lonhienne, Chanyarat, Weber, Lui, Brackin, Richard, Ragan, Mark A., Schmidt, Susanne and Hugenholtz, Philip (2017). Evolutionary conservation of a core root microbiome across plant phyla along a tropical soil chronosequence. Nature Communications, 8 (1) 002628, 215. doi: 10.1038/s41467-017-00262-8

Gene and genome-centric analyses of koala and wombat fecal microbiomes point to metabolic specialization for Eucalyptus digestion

Shiffman, Miriam E, Soo, Rochelle M, Dennis, Paul G, Morrison, Mark, Tyson, Gene W and Hugenholtz, Philip (2017). Gene and genome-centric analyses of koala and wombat fecal microbiomes point to metabolic specialization for Eucalyptus digestion. PeerJ, 5, 1-32. doi: 10.7717/peerj.4075

Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life

Parks, Donovan H., Rinke, Christian, Chuvochina, Maria, Chaumeil, Pierre-Alain, Woodcroft, Ben J., Evans, Paul N., Hugenholtz, Philip and Tyson, Gene W. (2017). Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life. Nature Microbiology, 2 (11), 1533-1542. doi: 10.1038/s41564-017-0012-7

A microfluidics-based in situ chemotaxis assay to study the behaviour of aquatic microbial communities

Lambert, Bennett S., Raina, Jean-Baptiste, Fernandez, Vicente I., Rinke, Christian, Siboni, Nachshon, Rubino, Francesco, Hugenholtz, Philip, Tyson, Gene W., Seymour, Justin R. and Stocker, Roman (2017). A microfluidics-based in situ chemotaxis assay to study the behaviour of aquatic microbial communities. Nature Microbiology, 2 (10), 1344-1349. doi: 10.1038/s41564-017-0010-9

Characterization of a highly efficient antibiotic-degrading metallo-β-lactamase obtained from an uncultured member of a permafrost community

Pedroso, Marcelo Monteiro, Selleck, Christopher, Enculescu, Charmaine, Harmer, Jeffrey R., Mitic, Natasa, Craig, Whitney R., Helweh, Waleed, Hugenholtz, Philip, Tyson, Gene W., Tierney, David L., Larrabee, James A. and Schenk, Gerhard (2017). Characterization of a highly efficient antibiotic-degrading metallo-β-lactamase obtained from an uncultured member of a permafrost community. Metallomics, 9 (8), 1157-1168. doi: 10.1039/c7mt00195a

Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea

Bowers, Robert M., Kyrpides, Nikos C., Stepanauskas, Ramunas, Harmon-Smith, Miranda, Doud, Devin, Reddy, T. B. K., Schulz, Frederik, Jarett, Jessica, Rivers, Adam R., Eloe-Fadrosh, Emiley A., Tringe, Susannah G., Ivanova, Natalia N., Copeland, Alex, Clum, Alicia, Becraft, Eric D., Malmstrom, Rex R., Birren, Bruce, Podar, Mircea, Bork, Peer, Weinstock, George M., Garrity, George M., Dodsworth, Jeremy A., Yooseph, Shibu, Sutton, Granger, Gloeckner, Frank O., Gilbert, Jack A., Nelson, William C., Hallam, Steven J., Jungbluth, Sean P. ... Woyke, Tanja (2017). Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea. Nature Biotechnology, 35 (8), 725-731. doi: 10.1038/nbt.3893

1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life.

Mukherjee, Supratim, Seshadri, Rekha, Varghese, Neha J., Eloe-Fadrosh, Emiley A., Meier-Kolthoff, Jan P., Göker, Markus, Coates, R Cameron, Hadjithomas, Michalis, Pavlopoulos, Georgios A., Paez-Espino, David, Yoshikuni, Yasuo, Visel, Axel, Whitman, William B., Garrity, George M., Eisen, Jonathan A., Hugenholtz, Philip, Pati, Amrita, Ivanova, Natalia N., Woyke, Tanja, Klenk, Hans-Peter and Kyrpides, Nikos C. (2017). 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life.. Nature Biotechnology, 35 (7), 676-683. doi: 10.1038/nbt.3886

Introducing BASE: the Biomes of Australian Soil Environments soil microbial diversity database (vol 5, 1, 2016)

Bissett, Andrew, Fitzgerald, Anna, Court, Leon, Meintjes, Thys, Mele, Pauline M., Reith, Frank, Dennis, Paul G., Breed, Martin F., Brown, Belinda, Brown, Mark V., Brugger, Joel, Byrne, Margaret, Caddy-Retalic, Stefan, Carmody, Bernie, Coates, David J., Correa, Carolina, Ferrari, Belinda C., Gupta, Vadakattu V. S. R., Hamonts, Kelly, Haslem, Asha, Hugenholtz, Philip, Karan, Mirko, Koval, Jason, Lowe, Andrew J., Macdonald, Stuart, McGrath, Leanne, Martin, David, Morgan, Matt, North, Kristin I. ... Young, Andrew (2017). Introducing BASE: the Biomes of Australian Soil Environments soil microbial diversity database (vol 5, 1, 2016). Gigascience, 6 (5) gix021, 1-1. doi: 10.1093/gigascience/gix021

Acute graft-versus-host disease is regulated by an IL-17-sensitive microbiome

Varelias, Antiopi, Ormerod, Kate L, Bunting, Mark D, Koyama, Motoko, Gartlan, Kate H, Kuns, Rachel D, Lachner, Nancy, Locke, Kelly R, Lim, Chun Y, Henden, Andrea S, Zhang, Ping, Clouston, Andrew D, Hasnain, Sumaira Z, McGuckin, Michael A, Blazar, Bruce R, MacDonald, Kelli PA, Hugenholtz, Philip and Hill, Geoff R (2017). Acute graft-versus-host disease is regulated by an IL-17-sensitive microbiome. The Journal of Immunology, 198 (1_Supplement), 82.8-82.8. doi: 10.4049/jimmunol.198.supp.82.8

Comparative genomic analysis of the class Epsilonproteobacteria and proposed reclassification to Epsilonbacteraeota (phyl. nov.)

Waite, David W., Vanwonterghem, Inka, Rinke, Christian, Parks, Donovan H. , Zhang, Ying, Takai, Ken, Sievert, Stefan M. , Simon, Joerg, Campbell, Barbara J. , Hanson, Thomas E. , Woyke, Tanja, Klotz, Martin G. and Hugenholtz, Philip (2017). Comparative genomic analysis of the class Epsilonproteobacteria and proposed reclassification to Epsilonbacteraeota (phyl. nov.). Frontiers in Microbiology, 8 (APR) 682 doi: 10.3389/fmicb.2017.00682.

On the origins of oxygenic photosynthesis and aerobic respiration in Cyanobacteria

Soo, Rochelle M. , Hemp, James, Parks, Donovan H. , Fischer, Woodward W. and Hugenholtz, Philip (2017). On the origins of oxygenic photosynthesis and aerobic respiration in Cyanobacteria. Science, 355 (6332), 1436-1440. doi: 10.1126/science.aal3794

Microbiomes in respiratory health and disease: an Asia-Pacific perspective

Chotirmall, Sanjay H., Gellatly, Shaan L., Budden, Kurtis F., Mac Aogain, Micheál, Shukla, Shakti D., Wood, David L. A., Hugenholtz, Philip, Pethe, Kevin and Hansbro, Philip M. (2017). Microbiomes in respiratory health and disease: an Asia-Pacific perspective. Respirology, 22 (2), 240-250. doi: 10.1111/resp.12971

Acute graft-versus-host disease is regulated by an IL-17-sensitive microbiome

Varelias, Antiopi, Ormerod, Kate L., Bunting, Mark D., Koyama, Motoko, Gartlan, Kate H., Kuns, Rachel D., Lachner, Nancy, Locke, Kelly R., Lim, Chun Y., Henden, Andrea S., Zhang, Ping, Clouston, Andrew D., Hasnain, Sumaira Z., McGuckin, Michael A., Blazar, Bruce R., MacDonald, Kelli P. A ., Hugenholtz, Philip and Hill, Geoffrey R. (2017). Acute graft-versus-host disease is regulated by an IL-17-sensitive microbiome. Blood, 129 (15), 2172-2185. doi: 10.1182/blood-2016-08-732628

Anode potential influences the structure and function of anodic electrode and electrolyte-associated microbiomes

Dennis, Paul G., Virdis, Bernardino, Vanwonterghem, Inka, Hassan, Alif, Hugenholtz, Phil, Tyson, Gene W. and Rabaey, Korneel (2016). Anode potential influences the structure and function of anodic electrode and electrolyte-associated microbiomes. Scientific Reports, 6 (1) 39114, 39114. doi: 10.1038/srep39114

Crosstalk between sugarcane and a plant-growth promoting Burkholderia species

Paungfoo-Lonhienne, Chanyarat, Lonhienne, Thierry G. A., Yeoh, Yun Kit, Donose, Bogdan C., Webb, Richard I., Parsons, Jeremy, Liao, Webber, Sagulenko, Evgeny, Lakshmanan, Prakash, Hugenholtz, Philip, Schmidt, Susanne and Ragan, Mark A. (2016). Crosstalk between sugarcane and a plant-growth promoting Burkholderia species. Scientific Reports, 6 (1) 37389, 37389. doi: 10.1038/srep37389

Emerging pathogenic links between microbiota and the gut-lung axis.

Budden, Kurtis F. , Gellatly, Shaan L. , Wood, David L., Cooper, Matthew A. , Morrison, Mark, Hugenholtz, Philip and Hansbro, Philip M. (2016). Emerging pathogenic links between microbiota and the gut-lung axis.. Nature Reviews Microbiology, 15 (1), 55-63. doi: 10.1038/nrmicro.2016.142

Methylotrophic methanogenesis discovered in the archaeal phylum Verstraetearchaeota

Vanwonterghem, Inka, Evans, Paul N., Parks, Donovan H., Jensen, Paul D., Woodcroft, Ben J., Hugenholtz, Philip and Tyson, Gene W. (2016). Methylotrophic methanogenesis discovered in the archaeal phylum Verstraetearchaeota. Nature Microbiology, 1 (16170) 16170, 16170. doi: 10.1038/nmicrobiol.2016.170

Validation of picogram- and femtogram-input DNA libraries for microscale metagenomics

Rinke, Christian, Low, Serene, Woodcroft, Ben J., Raina, Jean-Baptista, Skarshewski, Adam, Le, Xuyen H., Butler, Margaret K., Stocker, Roman, Seymour, Justin, Tyson, Gene W. and Hugenholtz, Philip (2016). Validation of picogram- and femtogram-input DNA libraries for microscale metagenomics. PeerJ, 4 (9) e2486, 1-28. doi: 10.7717/peerj.2486

Near complete genome sequence of the animal feed probiotic, Bacillus amyloliquefaciens H57

Schofield, Benjamin J., Skarshewski, Adam, Lachner, Nancy, Ouwerkerk, Diane, Klieve, Athol V., Dart, Peter and Hugenholtz, Philip (2016). Near complete genome sequence of the animal feed probiotic, Bacillus amyloliquefaciens H57. Standards in Genomic Sciences, 11 (1) 60, 60. doi: 10.1186/s40793-016-0189-z

'Candidatus Adiutrix intracellularis', an endosymbiont of termite gut flagellates, is the first representative of a deep-branching clade of Deltaproteobacteria and a putative homoacetogen

Ikeda-Ohtsubo, Wakako, Strassert, Juergen F. H., Kohler, Tim, Mikaelyan, Aram, Gregor, Ivan, Mchardy, Alice C., Tringe, Susannah Green, Hugenholtz, Phil, Radek, Renate and Brune, Andreas (2016). 'Candidatus Adiutrix intracellularis', an endosymbiont of termite gut flagellates, is the first representative of a deep-branching clade of Deltaproteobacteria and a putative homoacetogen. Environmental Microbiology, 18 (8), 2548-2564. doi: 10.1111/1462-2920.13234

Genomic characterization of the uncultured Bacteroidales family S24-7 inhabiting the guts of homeothermic animals

Ormerod, Kate L., Wood, David L. A., Lachner, Nancy, Gellatly, Shaan L., Daly, Joshua N., Parsons, Jeremy D., Dal’Molin, Cristiana G. O., Palfreyman, Robin W., Nielsen, Lars K., Cooper, Matthew A., Morrison, Mark, Hansbro, Philip M. and Hugenholtz, Philip (2016). Genomic characterization of the uncultured Bacteroidales family S24-7 inhabiting the guts of homeothermic animals. Microbiome, 4 (1) 36, 36.1-36.17. doi: 10.1186/s40168-016-0181-2

A catalogue of 136 microbial draft genomes from Red Sea metagenomes

Haroon, Mohamed F., Thompson, Luke R., Parks, Donovan H., Hugenholtz, Philip and Stingl, Ulrich (2016). A catalogue of 136 microbial draft genomes from Red Sea metagenomes. Scientific Data, 3 (1) 160050, 160050.1-160050.6. doi: 10.1038/sdata.2016.50

Introducing BASE: the Biomes of Australian Soil Environments soil microbial diversity database

Bissett, Andrew, Fitzgerald, Anna, Meintjes, Thys, Mele, Pauline M., Reith, Frank, Dennis, Paul G., Breed, Martin F., Brown, Belinda, Brown, Mark V., Brugger, Joel, Byrne, Margaret, Caddy-Retalic, Stefan, Carmody, Bernie, Coates, David J., Correa, Carolina, Ferrari, Belinda C., Gupta, Vadakattu V. S. R., Hamonts, Kelly, Haslem, Asha, Hugenholtz, Philip, Karan, Mirko, Koval, Jason, Lowe, Andrew J., Macdonald, Stuart, McGrath, Leanne, Martin, David, Morgan, Matt, North, Kristin I., Paungfoo-Lonhienne, Chanyarat ... Young, Andrew (2016). Introducing BASE: the Biomes of Australian Soil Environments soil microbial diversity database. Gigascience, 5 (1) 21, 21.1-21.11. doi: 10.1186/s13742-016-0126-5

Genome-based microbial taxonomy coming of age

Hugenholtz, Philip, Skarshewski, Adam and Parks, Donovan H. (2016). Genome-based microbial taxonomy coming of age. Cold Spring Harbor Perspectives in Biology, 8 (6) a018085, a018085. doi: 10.1101/cshperspect.a018085

Airway dysbiosis: Haemophilus influenzae and Tropheryma in poorly controlled asthma

Simpson, Jodie L., Daly, Joshua, Baines, Katherine J., Yang, Ian A., Upham, John W., Reynolds, Paul N., Hodge, Sandra, James, Alan L., Hugenholtz, Philip, Willner, Dana and Gibson, Peter G. (2016). Airway dysbiosis: Haemophilus influenzae and Tropheryma in poorly controlled asthma. European Respiratory Journal, 47 (3), 792-800. doi: 10.1183/13993003.00405-2015

Metagenomic insights into the uncultured diversity and physiology of microbes in four hypersaline soda lake brines

Vavourakis, Charlotte D., Ghai, Rohit, Rodriguez-Valera, Francisco, Sorokin, Dimitry Y., Tringe, Susannah G., Hugenholtz, Philip and Muyzer, Gerard (2016). Metagenomic insights into the uncultured diversity and physiology of microbes in four hypersaline soda lake brines. Frontiers in Microbiology, 7 (FEB) 211, 211.1-211.18. doi: 10.3389/fmicb.2016.00211

High-resolution phylogenetic microbial community profiling

Singer, Esther, Bushnell, Brian, Coleman-Derr, Devin, Bowman, Brett, Bowers, Robert M., Levy, Asaf, Gies, Esther A., Cheng, Jan-Fang, Copeland, Alex, Klenk, Hans-Peter, Hallam, Steven J., Hugenholtz, Philip, Tringe, Susannah G. and Woyke, Tanja (2016). High-resolution phylogenetic microbial community profiling. ISME Journal, 10 (8), 2020-2032. doi: 10.1038/ismej.2015.249

A phylogenomic analysis of the bacterial phylum fibrobacteres

Abdul Rahman, Nurdyana, Parks, Donovan H., Vanwonterghem, Inka, Morrison, Mark, Tyson, Gene W. and Hugenholtz, Philip (2016). A phylogenomic analysis of the bacterial phylum fibrobacteres. Frontiers in Microbiology, 6 (JAN) 1469, 1469.1-1469.15. doi: 10.3389/fmicb.2015.01469

Comparative genomics of candidate phylum TM6 suggests that parasitism is widespread and ancestral in this lineage

Yeoh, Yun Kit, Sekiguchi, Yuji, Parks, Donovan H. and Hugenholtz, Philip (2015). Comparative genomics of candidate phylum TM6 suggests that parasitism is widespread and ancestral in this lineage. Molecular Biology and Evolution, 33 (4), 915-927. doi: 10.1093/molbev/msv281

Evaluating DNA Extraction Methods for Community Profiling of Pig Hindgut Microbial Community

Lu, Yang, Hugenholtz, Phillip and Batstone, Damien John (2015). Evaluating DNA Extraction Methods for Community Profiling of Pig Hindgut Microbial Community. PLoS One, 10 (11) e0142720, e0142720.1-e0142720.10. doi: 10.1371/journal.pone.0142720

Draft genome sequences of Anaerolinea thermolimosa IMO-1, Bellilinea caldifistulae GOMI-1, Leptolinea tardivitalis YMTK-2, Levilinea saccharolytica KIBI-1, Longilinea arvoryzae KOME-1, previously described as members of the class Anaerolineae (Chloroflexi

Matsuura, Norihisa, Tourlousse, Dieter M., Ohashi, Akiko, Hugenholtz, Philip and Sekiguchia, Yuji (2015). Draft genome sequences of Anaerolinea thermolimosa IMO-1, Bellilinea caldifistulae GOMI-1, Leptolinea tardivitalis YMTK-2, Levilinea saccharolytica KIBI-1, Longilinea arvoryzae KOME-1, previously described as members of the class Anaerolineae (Chloroflexi. Genome Announcements, 3 (5) e00975-15. doi: 10.1128/genomeA.00975-15

Comparative genomics of non-pseudomonal bacterial species colonising paediatric cystic fibrosis patients

Ormerod, Kate L., George, Narelle M., Fraser, James A., Wainwright, Claire and Hugenholtz, Philip (2015). Comparative genomics of non-pseudomonal bacterial species colonising paediatric cystic fibrosis patients. PeerJ, 3 (9) e1223, e1223.1-e1223.27. doi: 10.7717/peerj.1223

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes

Parks, Donovan H., Imelfort, Michael, Skennerton, Connor T., Hugenholtz, Philip and Tyson, Gene W. (2015). CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Research, 25 (7), 1043-1055. doi: 10.1101/gr.186072.114

Amino acid and peptide utilization profiles of the fluoroacetate-degrading bacterium synergistetes strain MFA1 under varying conditions

Leong, Lex E. X., Denman, Stuart E., Hugenholtz, Philip and McSweeney, Christopher S. (2015). Amino acid and peptide utilization profiles of the fluoroacetate-degrading bacterium synergistetes strain MFA1 under varying conditions. Microbial Ecology, 71 (2), 494-504. doi: 10.1007/s00248-015-0641-4

The core root microbiome of sugarcanes cultivated under varying nitrogen fertiliser application.

Yeoh, Yun Kit, Paungfoo-Lonhienne, Chanyarat, Dennis, Paul G., Robinson, Nicole, Ragan, Mark A., Schmidt, Susanne and Hugenholtz, Philip (2015). The core root microbiome of sugarcanes cultivated under varying nitrogen fertiliser application.. Environmental Microbiology, 18 (5), 1338-1351. doi: 10.1111/1462-2920.12925

Genomic Encyclopedia of Bacterial and Archaeal Type Strains, Phase III: the genomes of soil and plant-associated and newly described type strains

Whitman, William B., Woyke, Tanja, Klenk, Hans-Peter, Zhou, Yuguamg, Lilburn, Timothy G., Beck, Brian J., De Vos, Paul, Vandamme, Peter, Eisen, Jonathan A., Garrity, George, Hugenholtz, Philip and Kyrpides, Nikos C. (2015). Genomic Encyclopedia of Bacterial and Archaeal Type Strains, Phase III: the genomes of soil and plant-associated and newly described type strains. Standards in Genomic Sciences, 10 (26) 26, 26. doi: 10.1186/s40793-015-0017-x

Do You Kiss Your Mother with That Mouth? An Authentic Large-Scale Undergraduate Research Experience in Mapping the Human Oral Microbiome

Wang, Jack T.H., Daly, Joshua N., Willner, Dana L., Patil, Jayee, Hall, Roy A., Schembri, Mark A., Tyson, Gene W. and Hugenholtz, Philip (2015). Do You Kiss Your Mother with That Mouth? An Authentic Large-Scale Undergraduate Research Experience in Mapping the Human Oral Microbiome. Journal of Microbiology and Biology Education, 16 (1), 50-60. doi: 10.1128/jmbe.v16i1.816

Back from the dead; the curious tale of the predatory cyanobacterium Vampirovibrio chlorellavorus.

Soo, Rochelle M., Woodcroft, Ben J., Parks, Donovan H., Tyson, Gene W. and Hugenholtz, Philip (2015). Back from the dead; the curious tale of the predatory cyanobacterium Vampirovibrio chlorellavorus.. PeerJ, 2015 (5) e968, Art. No.: e968-Art. No.: e968. doi: 10.7717/peerj.968

Nitrogen fertilizer dose alters fungal communities in sugarcane soil and rhizosphere.

Paungfoo-Lonhienne, Chanyarat, Yeoh, Yun Kit, Kasinadhuni, Naga Rup Pinaki, Lonhienne, Thierry G. A., Robinson, Nicole, Hugenholtz, Philip, Ragan, Mark A. and Schmidt, Susanne (2015). Nitrogen fertilizer dose alters fungal communities in sugarcane soil and rhizosphere.. Scientific Reports, 5 (8678) 8678, 1-6. doi: 10.1038/srep08678

A molecular survey of Australian and North American termite genera indicates that vertical inheritance is the primary force shaping termite gut microbiomes

Abdul Rahman, Nurdyana, Parks, Donovan H., Willner, Dana L., Engelbrektson, Anna L., Goffredi, Shana K., Warnecke, Falk, Scheffrahn, Rudolf H. and Hugenholtz, Philip (2015). A molecular survey of Australian and North American termite genera indicates that vertical inheritance is the primary force shaping termite gut microbiomes. Microbiome, 3 (5) 5, 1-16. doi: 10.1186/s40168-015-0067-8

First genomic insights into members of a candidate bacterial phylum responsible for wastewater bulking

Sekiguchi, Yuji, Ohashi, Akiko, Parks, Donovan H., Yamauchi, Toshihiro, Tyson, Gene W. and Hugenholtz, Philip (2015). First genomic insights into members of a candidate bacterial phylum responsible for wastewater bulking. PeerJ, 3 (e740) e740, 1-24. doi: 10.7717/peerj.740

Complete genome sequence of Planctomyces brasiliensis type strain (DSM 5305T), phylogenomic analysis and reclassification of Planctomycetes including the descriptions of Gimesia gen. nov., Planctopirus gen. nov. and Rubinisphaera gen. nov. and emended descriptions of the order Planctomycetales and the family Planctomycetaceae

Scheuner, Carmen, Tindall, Brian J., Lu, Megan, Nolan, Matt, Lapidus, Alla, Cheng, Jan-Fang, Goodwin, Lynne, Pitluck, Sam, Huntemann, Marcel, Liolios, Konstantinos, Pagani, Ioanna, Mavromatis, Konstantinos, Ivanova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Jeffries, Cynthia D., Hauser, Loren, Land, Miriam, Mwirichia, Romano, Rohde, Manfred, Abt, Birte, Detter, John C., Woyke, Tanja, Eisen, Jonathan A., Markowitz, Victor, Hugenholtz, Philip, Goker, Markus, Kyrpides, Nikos C. and Klenk, Hans-Peter (2014). Complete genome sequence of Planctomyces brasiliensis type strain (DSM 5305T), phylogenomic analysis and reclassification of Planctomycetes including the descriptions of Gimesia gen. nov., Planctopirus gen. nov. and Rubinisphaera gen. nov. and emended descriptions of the order Planctomycetales and the family Planctomycetaceae. Standards in Genomic Sciences, 9 (1) 10, 10. doi: 10.1186/1944-3277-9-10

JTD special edition 'Hot Topics in COPD'- the microbiome in COPD

Chambers, Daniel C., Gellatly, Shaan L., Hugenholtz, Philip and Hansbro, Philip M. (2014). JTD special edition 'Hot Topics in COPD'- the microbiome in COPD. Journal of Thoracic Disease, 6 (11), 1525-1531. doi: 10.3978/j.issn.2072-1439.2014.11.08

GroopM: an automated tool for the recovery of population genomes from related metagenomes

Imelfort, Michael, Parks, Donovan, Woodcroft, Ben J., Dennis, Paul, Hugenholtz, Philip and Tyson, Gene W. (2014). GroopM: an automated tool for the recovery of population genomes from related metagenomes. PeerJ, 2014 (1) e603, 1-16. doi: 10.7717/peerj.603

Genomic encyclopedia of bacteria and archaea: sequencing a myriad of type strains

Kyrpides, Nikos C., Hugenholtz, Philip, Eisen, Jonathan A., Woyke, Tanja, Goker, Markus, Parker, Charles T., Amann, Rudolf, Beck, Brian J., Chun, Jongsik, Colwell, Rita R., Danchin, Antoine, Dawyndt, Peter, Dedeurwaerdere, Tom, DeLong, Edward F., Detter, John C., De Vos, Paul, Donohue, Timothy J., Dong, Xiu-Zhu, Ehrlich, Dusko S., Fraser, Claire, Gibbs, Richard, Gilbert, Jack, Gilna, Paul, Glockner, Frank Oliver, Jansson, Janet K., Keasling, Jay D., Knight, Rob, Labeda, David, Lapidus, Alla ... Klenk, Hans-Peter (2014). Genomic encyclopedia of bacteria and archaea: sequencing a myriad of type strains. PLoS Biology, 12 (8) e1001920, e1001920.1-e1001920.7. doi: 10.1371/journal.pbio.1001920

STAMP: Statistical analysis of taxonomic and functional profiles.

Parks, Donovan H., Tyson, Gene W., Hugenholtz, Philip and Beiko, Robert G. (2014). STAMP: Statistical analysis of taxonomic and functional profiles.. Bioinformatics., 30 (21), 3123-3124. doi: 10.1093/bioinformatics/btu494

Deterministic processes guide long-term synchronised population dynamics in replicate anaerobic digesters

Vanwonterghem, Inka, Jensen, Paul D., Dennis, Paul G., Hugenholtz, Philip, Rabaey, Korneel and Tyson, Gene W. (2014). Deterministic processes guide long-term synchronised population dynamics in replicate anaerobic digesters. ISME Journal, Advance Online (10), 1-14. doi: 10.1038/ismej.2014.50

An expanded genomic representation of the phylum Cyanobacteria

Soo, Rochelle M., Skennerton, Connor T., Sekiguchi, Yuji, Imelfort, Michael, Paech, Samuel J., Dennis, Paul G., Steen, Jason A., Parks, Donovan H., Tyson, Gene W. and Hugenholtz, Philip (2014). An expanded genomic representation of the phylum Cyanobacteria. Genome Biology and Evolution, Advance Access (5), 1-42. doi: 10.1093/gbe/evu073

CopyRighter: a rapid tool for improving the accuracy of microbial community profiles through lineage-specific gene copy number correction

Angly, Florent E., Dennis, Paul G., Skarshewski, Adam, Vanwonterghem, Inka, Hugenholtz, Philip and Tyson, Gene W. (2014). CopyRighter: a rapid tool for improving the accuracy of microbial community profiles through lineage-specific gene copy number correction. Microbiome, 2 (11) 11, 11. doi: 10.1186/2049-2618-2-11

A new species of Burkholderia isolated from sugarcane roots promotes plant growth

Paungfoo-Lonhienne, Chanyarat, Lonhienne, Thierry G. A., Yeoh, Yun Kit, Webb, Richard I., Lakshmanan, Prakash, Chan, Cheong Xin, Lim, Phaik-Eem, Ragan, Mark A., Schmidt, Susanne and Hugenholtz, Philip (2014). A new species of Burkholderia isolated from sugarcane roots promotes plant growth. Microbial Biotechnology, 7 (2), 142-154. doi: 10.1111/1751-7915.12105

Single clinical isolates from acute uncomplicated urinary tract infections are representative of dominant In Situ populations

Willner, Dana, Low, Serene, Steen, Jason A., George, Narelle, Nimmo, Graeme R., Schembri, Mark A. and Hugenholtz, Philip (2014). Single clinical isolates from acute uncomplicated urinary tract infections are representative of dominant In Situ populations. mBio, 5 (2) e01064-13, e01064-13.1-e01064-13.10. doi: 10.1128/mBio.01064-13

Discovery of a novel methanogen prevalent in thawing permafrost

Mondav, Rhiannon, Woodcroft, Ben J., Kim, Eun-Hae, McCalley, Carmody K., Hodgkins, Suzanne B., Crill, Patrick M., Chanton, Jeffrey, Hurst, Gregory B., VerBerkmoes, Nathan C., Saleska, Scott R., Hugenholtz, Philip, Rich, Virginia I. and Tyson, Gene W. (2014). Discovery of a novel methanogen prevalent in thawing permafrost. Nature Communications, 5 (1) 3212, 3212.1-3212.7. doi: 10.1038/ncomms4212

Effects of sample treatments on genome recovery via single-cell genomics

Clingenpeel, Scott, Schwientek, Patrick, Hugenholtz, Philip and Woyke, Tanja (2014). Effects of sample treatments on genome recovery via single-cell genomics. The ISME Journal, 8 (12), 2546-2549. doi: 10.1038/ismej.2014.92

Genome sequence of enterotoxigenic Escherichia coli strain B2C

Vipin Madhavan, T. P., Steen, Jason A., Hugenholtz, Philip and Sakellaris, Harry (2014). Genome sequence of enterotoxigenic Escherichia coli strain B2C. Genome Announcements, 2 (2) e00247-14. doi: 10.1128/genomeA.00247-14

Genome sequence of the Thermotoga thermarum type strain (LA3T) from an African solfataric spring

Göker, Markus, Spring, Stefan, Scheuner, Carmen, Anderson, Iain, Zeytun, Ahmet, Nolan, Matt, Lucas, Susan, Tice, Hope, Del Rio, Tijana Glavina, Cheng, Jan-Fang, Han, Cliff, Tapia, Roxanne, Goodwin, Lynne A., Pitluck, Sam, Liolios, Konstantinos, Mavromatis, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-juan, Jeffries, Cynthia D., Rohde, Manfred, Detter, John C., Woyke, Tanja ... Lapidus, Alla (2014). Genome sequence of the Thermotoga thermarum type strain (LA3T) from an African solfataric spring. Standards in Genomic Sciences, 9 (3), 1105-1117. doi: 10.4056/sigs.3016383

Genome sequence of the mud-dwelling archaeon Methanoplanus limicola type strain (DSM 2279 (T)), reclassification of Methanoplanus petrolearius as Methanolacinia petrolearia and emended descriptions of the genera Methanoplanus and Methanolacinia

Goeker, Markus, Lu, Megan, Fiebig, Anne, Nolan, Matt, Lapidus, Alla, Tice, Hope, Glavina Del Rio, Tijana, Cheng, Jan-Feng, Han, Cliff, Tapia, Roxanne, Goodwin, Lynne A., Pitluck, Sam, Liolios, Konstantinos, Mavromatis, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Mayilraj, Shanmugam, Rohde, Manfred, Detter, John C., Bunk, Boyke, Spring, Stefan, Wirth, Reinhard, Woyke, Tanja, Bristow, James ... Klenk, Hans-Peter (2014). Genome sequence of the mud-dwelling archaeon Methanoplanus limicola type strain (DSM 2279 (T)), reclassification of Methanoplanus petrolearius as Methanolacinia petrolearia and emended descriptions of the genera Methanoplanus and Methanolacinia. Standards in Genomic Sciences, 9 (3), 1076-1088. doi: 10.4056/sigs.5138968

Viral tagging reveals discrete populations in Synechococcus viral genome sequence space.

Deng, Li, Ignacio-Espinoza, J. Cesar, Gregory, Ann C., Poulos, Bonnie T., Weitz, Joshua S., Hugenholtz, Philip and Sullivan, Matthe B. (2014). Viral tagging reveals discrete populations in Synechococcus viral genome sequence space.. Nature, 513 (7517), 242-245 + 13. doi: 10.1038/nature13459

Yeast as a biofertilizer alters plant growth and morphology

Lonhienne, Thierry, Mason, Michael G., Ragan, Mark A., Hugenholtz, Philip, Schmidt, Susanne and Paungfoo-Lonhienne, Chanyarat (2014). Yeast as a biofertilizer alters plant growth and morphology. Crop Science, 54 (2), 785-790. doi: 10.2135/cropsci2013.07.0488

Dielectrophoresis-based discrimination of bacteria at the strain level based on their surface properties

Braff, William A., Willner, Dana, Hugenholtz, Philip, Rabaey, Korneel and Buie, Cullen R. (2013). Dielectrophoresis-based discrimination of bacteria at the strain level based on their surface properties. PLoS ONE, 8 (1) e76751, e76751.1-e76751.7. doi: 10.1371/journal.pone.0076751

Defining the core Arabidopsis thaliana root microbiome

Lundberg, Derek S., Lebeis, Sarah L., Paredes, Sur Herrera, Yourstone, Scott, Gehring, Jase, Malfatti, Stephanie, Tremblay, Julien, Engelbrektson, Anna, Kunin, Victor, Del Rio, Tijana Glavina, Edgar, Robert C., Eickhorst, Thilo, Ley, Ruth E., Hugenholtz, Philip, Tringe, Susannah Green and Dangl, Jeffery L. (2013). Defining the core Arabidopsis thaliana root microbiome. Nature, 501 (7468 SUPPL.).

Erratum: Anaerobic oxidation of methane coupled to nitrate reduction in a novel archaeal lineage

Haroon, Mohamed F., Hu, Shihu, Shi, Ying, Imelfort, Michael, Keller, Jurg, Hugenholtz, Philip, Yuan, Zhiguo and Tyson, Gene W. (2013). Erratum: Anaerobic oxidation of methane coupled to nitrate reduction in a novel archaeal lineage. Nature, 501 (7468), 578-578. doi: 10.1038/nature12619

Insights into the phylogeny and coding potential of microbial dark matter

Rinke, Christian, Schwientek, Patrick, Sczyrba, Alexander, Ivanova, Natalia N., Anderson, Iain J., Cheng, Jan-Fang, Darling, Aaron, Malfatti, Stephanie, Swan, Brandon K., Gies, Esther A., Dodsworth, Jeremy A., Hedlund, Brian P., Tsiamis, George, Sievert, Stefan M., Liu, Wen-Tso, Eisen, Jonathan A., Hallam, Steven J., Kyrpides, Nikos C., Stepanauskas, Ramunas, Rubin, Edward M., Hugenholtz, Philip and Woyke, Tanja (2013). Insights into the phylogeny and coding potential of microbial dark matter. Nature, 499 (7459), 431-437. doi: 10.1038/nature12352

Proteogenomic Analysis of a Thermophilic Bacterial Consortium Adapted to Deconstruct Switchgrass

D'haeseleer, Patrik, Gladden, John M., Allgaier, Martin, Chain, Patrik S. G., Tringe, Susannah G., Malfatti, Stephanie A., Aldrich, Joshua T., Nicora, Carrie D., Robinson, Errol W., Pasa-Tolic, Ljiljana, Hugenholtz, Philip, Simmons, Blake A. and Singer, Steven W. (2013). Proteogenomic Analysis of a Thermophilic Bacterial Consortium Adapted to Deconstruct Switchgrass. Plos One, 8 (7) e68465, e68465.1-e68465.11. doi: 10.1371/journal.pone.0068465

Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes

Albertsen, Mads, Hugenholtz, Philip, Skarshewski, Adam, Nielsen, Kare L., Tyson, Gene W. and Nielsen, Per H. (2013). Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes. Nature Biotechnology, 31 (6), 533-538+. doi: 10.1038/nbt.2579

From deep sequencing to viral tagging: recent advances in viral metagenomics

Willner, Dana and Hugenholtz, Philip (2013). From deep sequencing to viral tagging: recent advances in viral metagenomics. Bioessays, 35 (5), 436-442. doi: 10.1002/bies.201200174

Comparative metagenomic and metatranscriptomic analysis of hindgut paunch microbiota in wood- and dung-feeding higher termites

He, Shaomei, Ivanova, Natalia, Kirton, Edward, Allgaier, Martin, Bergin, Claudia, Scheffrahn, Rudolf H., Kyrpides, Nikos C., Warnecke, Falk, Tringe, Susannah G. and Hugenholtz, Philip (2013). Comparative metagenomic and metatranscriptomic analysis of hindgut paunch microbiota in wood- and dung-feeding higher termites. PLoS One, 8 (4) e61126, e61126. doi: 10.1371/journal.pone.0061126

Shining a light on dark sequencing: characterising errors in Ion Torrent PGM data

Bragg, Lauren M., Stone, Glenn, Butler, Margaret K., Hugenholtz, Philip and Tyson, Gene W. (2013). Shining a light on dark sequencing: characterising errors in Ion Torrent PGM data. Plos Computational Biology, 9 (4) e1003031, e1003031.1-e1003031.18. doi: 10.1371/journal.pcbi.1003031

Contrasting Life Strategies of Viruses That Infect Photo- and Heterotrophic Bacteria, as Revealed by Viral Tagging (vol 3, e00373, 2012)

Deng, Li, Gregory, Ann, Yilmaz, Suzan, Poulos, Bonnie T., Hugenholtz, Philip and Sullivan, Matthew B. (2013). Contrasting Life Strategies of Viruses That Infect Photo- and Heterotrophic Bacteria, as Revealed by Viral Tagging (vol 3, e00373, 2012). Mbio, 4 (1). doi: 10.1128/mBio.00516-12

Anaerobic oxidation of methane coupled to nitrate reduction in a novel archaeal lineage

Haroon, Mohamed F., Hu, Shihu, Shi, Ying, Imelfort, Michael, Keller, Jurg, Hugenholtz, Philip, Yuan, Zhiguo and Tyson, Gene W. (2013). Anaerobic oxidation of methane coupled to nitrate reduction in a novel archaeal lineage. Nature, 500 (7464), 567-570. doi: 10.1038/nature12375

Comparative genomics of two 'Candidatus Accumulibacter' clades performing biological phosphorus removal

Flowers, Jason J., He, Shaomei, Malfatti, Stephanie, Glavina del Rio, Tijana, Tringe, Susannah G., Hugenholtz, Philip and McMahon, Katherine D. (2013). Comparative genomics of two 'Candidatus Accumulibacter' clades performing biological phosphorus removal. ISME Journal, 7 (12), 2301-2314. doi: 10.1038/ismej.2013.117

Complete genome sequence of Coriobacterium glomerans type strain (PW2(T)) from the midgut of Pyrrhocoris apterus L. (red soldier bug)

Stackebrandt, Erko, Zeytun, Ahmet, Lapidus, Alla, Nolan, Matt, Lucas, Susan, Hammon, Nancy, Deshpande, Shweta, Cheng, Jan-Fang, Tapia, Roxanne, Goodwin, Lynne A., Pitluck, Sam, Liolios, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Huntemann, Marcel, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Chang, Yun-juan, Land, Miriam, Hauser, Loren, Rohde, Manfred, Pukall, Ruediger, Goeker, Markus, Detter, John C., Woyke, Tanja, Bristow, James ... Klenk, Hans-Peter (2013). Complete genome sequence of Coriobacterium glomerans type strain (PW2(T)) from the midgut of Pyrrhocoris apterus L. (red soldier bug). Standards in Genomic Sciences, 8 (1), 15-25. doi: 10.4056/sigs.3507020

Complete genome sequence of the bile-resistant pigment-producing anaerobe Alistipes finegoldii type strain (AHN2437(T))

Mavromatis, Konstantinos, Stackebrandt, Erko, Munk, Christine, Lapidus, Alla, Nolan, Matt, Lucas, Susan, Hammon, Nancy, Deshpande, Shweta, Cheng, Jan-Fang, Tapia, Roxanne, Goodwin, Lynne A., Pitluck, Sam, Liolios, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Mikhailova, Natalia, Huntemann, Marcel, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Rohde, Manfred, Gronow, Sabine, Goeker, Markus, Detter, John C., Bristow, James, Eisen, Jonathan A., Markowitz, Victor ... Woyke, Tanja (2013). Complete genome sequence of the bile-resistant pigment-producing anaerobe Alistipes finegoldii type strain (AHN2437(T)). Standards in Genomic Sciences, 8 (1), 26-36. doi: 10.4056/sigs.3527032

Complete genome sequence of the halophilic bacterium Spirochaeta africana type strain (Z-7692(T)) from the alkaline Lake Magadi in the East African Rift

Liolos, Konstantinos, Abt, Birte, Scheuner, Carmen, Teshima, Hazuki, Held, Brittany, Lapidus, Alla, Nolan, Matt, Lucas, Susan, Deshpande, Shweta, Cheng, Jan-Fang, Tapia, Roxanne, Goodwin, Lynne A., Pitluck, Sam, Pagani, Ioanna, Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Huntemann, Marcel, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Rohde, Manfred, Tindall, Brian J., Detter, John C., Goeker, Markus, Bristow, James, Eisen, Jonathan A., Markowitz, Victor ... Kyrpides, Nikos C. (2013). Complete genome sequence of the halophilic bacterium Spirochaeta africana type strain (Z-7692(T)) from the alkaline Lake Magadi in the East African Rift. Standards in Genomic Sciences, 8 (2), 165-176. doi: 10.4056/sigs.3607108

Complete genome sequence of the moderate thermophile Anaerobaculum mobile type strain (NGA(T))

Mavromatis, Konstantinos, Stackebrandt, Erko, Held, Brittany, Lapidus, Alla, Nolan, Matt, Lucas, Susan, Hammon, Nancy, Deshpande, Shweta, Cheng, Jan-Fang, Tapia, Roxanne, Goodwin, Lynne A., Pitluck, Sam, Liolios, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Mikhailova, Natalia, Huntemann, Marcel, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Rohde, Manfred, Spring, Stefan, Goeker, Markus, Woyke, Tanja, Detter, John C., Bristow, James, Eisen, Jonathan A., Markowitz, Victor ... Kyrpides, Nikos C. (2013). Complete genome sequence of the moderate thermophile Anaerobaculum mobile type strain (NGA(T)). Standards in Genomic Sciences, 8 (1), 47-57. doi: 10.4056/sigs.3547050

Genome sequence of Frateuria aurantia type strain (Kondô 67T), a xanthomonade isolated from Lilium auratium Lindl

Anderson, Iain, Teshima, Huzuki, Nolan, Matt, Lapidus, Alla, Tice, Hope, Glavina del Rio, Tijana, Cheng, Jan-Fang, Han, Cliff, Tapia, Roxanne, Goodwin, Lynne A., Pitluck, Sam, Liolios, Konstantinos, Mavromatis, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Rohde, Manfred, Lang, Elke, Detter, John C., Goker, Markus, Woyke, Tanja, Bristow, James, Eisen, Jonathan A., Markowitz, Victor, Hugenholtz, Philip ... Klenk, Hans-Peter (2013). Genome sequence of Frateuria aurantia type strain (Kondô 67T), a xanthomonade isolated from Lilium auratium Lindl. Standards in Genomic Sciences, 9 (1), 83-92. doi: 10.4056/sigs.4338002

Genome sequence of the free-living aerobic spirochete Turneriella parva type strain (H-T), and emendation of the species Turneriella parva

Stackebrandt, Erko, Chertkov, Olga, Lapidus, Alla, Nolan, Matt, Lucas, Susan, Hammon, Nancy, Deshpande, Shweta, Cheng, Jan-Fang, Tapia, Roxanne, Goodwin, Lynne A., Pitluck, Sam, Liolios, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Huntemann, Marcel, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Pan, Chongle, Rohde, Manfred, Gronow, Sabine, Goeker, Markus, Detter, John C., Bristow, James, Eisen, Jonathan A., Markowitz, Victor ... Klenk, Hans-Peter (2013). Genome sequence of the free-living aerobic spirochete Turneriella parva type strain (H-T), and emendation of the species Turneriella parva. Standards in Genomic Sciences, 8 (2), 228-238. doi: 10.4056/sigs.3617113

Genome sequence of the moderately thermophilic sulfur-reducing bacterium Thermanaerovibrio velox type strain (Z-9701T) and emended description of the genus Thermanaerovibrio

Palaniappan, Krishna, Meier-Kolthoff, Jan P., Teshima, Hazuki, Nolan, Matt, Lapidus, Alla, Tice, Hope, Glavina del Rio, Tijana, Cheng, Jan-Fang, Han, Cliff, Tapia, Roxanne, Goodwin, Lynne A., Pitluck, Sam, Liolios, Konstantinos, Mavromatis, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Rohde, Manfred, Mayilraj, Shanmugam, Spring, Stefan, Detter, John C., Goker, Markus, Bristow, James, Eisen, Jonathan A., Markowitz, Victor, Hugenholtz, Philip, Kyrpides, Nikos C. ... Woyke, Tanja (2013). Genome sequence of the moderately thermophilic sulfur-reducing bacterium Thermanaerovibrio velox type strain (Z-9701T) and emended description of the genus Thermanaerovibrio. Standards in Genomic Sciences, 9 (1), 57-70. doi: 10.4056/sigs.4237901

Genome sequence of the phylogenetically isolated spirochete Leptonema illini type strain (3055(T))

Huntemann, Marcel, Stackebrandt, Erko, Held, Brittany, Nolan, Matt, Lucas, Susan, Hammon, Nancy, Deshpande, Shweta, Cheng, Jan-Fang, Tapia, Roxanne, Goodwin, Lynne A., Pitluck, Sam, Liolios, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Rohde, Manfred, Gronow, Sabine, Goeker, Markus, Detter, John C., Bristow, James, Eisen, Jonathan A., Markowitz, Victor, Woyke, Tanja, Hugenholtz, Philip ... Lapidus, Alla (2013). Genome sequence of the phylogenetically isolated spirochete Leptonema illini type strain (3055(T)). Standards in Genomic Sciences, 8 (2), 177-187. doi: 10.4056/sigs.3637201

Genome sequence of the thermophilic fresh-water bacterium Spirochaeta caldaria type strain (H1(T)), reclassification of Spirochaeta caldaria, Spirochaeta stenostrepta, and Spirochaeta zuelzerae in the genus Treponema as Treponema caldaria comb. nov., Trep

Abt, Birte, Goeker, Markus, Scheuner, Carmen, Han, Cliff, Lu, Megan, Misra, Monica, Lapidus, Alla, Nolan, Matt, Lucas, Susan, Hammon, Nancy, Deshpande, Shweta, Cheng, Jan-Fang, Tapia, Roxanne, Goodwin, Lynne A., Pitluck, Sam, Liolios, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Huntemann, Marcel, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Jeffries, Cynthia D., Rohde, Manfred, Spring, Stefan ... Klenk, Hans-Peter (2013). Genome sequence of the thermophilic fresh-water bacterium Spirochaeta caldaria type strain (H1(T)), reclassification of Spirochaeta caldaria, Spirochaeta stenostrepta, and Spirochaeta zuelzerae in the genus Treponema as Treponema caldaria comb. nov., Trep. Standards in Genomic Sciences, 8 (1), 88-105. doi: 10.4056/sigs.3096473

Genomic Encyclopedia of Type Strains, Phase I: The one thousand microbial genomes (KMG-I) project

Kyrpides, Nikos C., Woyke, Tanja, Eisen, Jonathan A., Garrity, George, Lilburn, Timothy G., Beck, Brian J., Whitman, William B., Hugenholtz, Phil and Klenk, Hans-Peter (2013). Genomic Encyclopedia of Type Strains, Phase I: The one thousand microbial genomes (KMG-I) project. Standards in Genomic Sciences, 9 (3), 628-634. doi: 10.4056/sigs.5068949

High-quality-draft genome sequence of the yellow-pigmented flavobacterium Joostella marina type strain (En5(T))

Stackebrandt, Erko, Chertkov, Olga, Lapidus, Alla, Nolan, Matt, Lucas, Susan, Han, Cliff, Cheng, Jan-Fang, Tapia, Roxanne, Goodwin, Lynne A., Bruce, David, Pitluck, Sam, Liolios, Konstantinos, Mavromatis, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Mikhailova, Natalia, Huntemann, Marcel, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Rohde, Manfred, Tindall, Brian J., Goeker, Markus, Woyke, Tanja, Detter, John C., Bristow, James, Eisen, Jonathan A., Markowitz, Victor, Hugenholtz, Philip ... Kyrpides, Nikos C. (2013). High-quality-draft genome sequence of the yellow-pigmented flavobacterium Joostella marina type strain (En5(T)). Standards in Genomic Sciences, 8 (1), 37-46. doi: 10.4056/sigs.3537045

In-solution fluorescence in situ hybridization and fluorescence-activated cell sorting for single cell and population genome recovery

Haroon, Mohamed F., Skennerton, Connor T., Steen, Jason A., Lachner, Nancy, Hugenholtz, Philip and Tyson, Gene W. (2013). In-solution fluorescence in situ hybridization and fluorescence-activated cell sorting for single cell and population genome recovery. Methods in Enzymology, 531, 3-19. doi: 10.1016/B978-0-12-407863-5.00001-0

Metagenomics and community profiling: culture-independent techniques in the clinical laboratory

Willner, Dana and Hugenholtz, Phil (2013). Metagenomics and community profiling: culture-independent techniques in the clinical laboratory. Clinical Microbiology Newsletter, 35 (1), 1-9. doi: 10.1016/j.clinmicnews.2012.12.001

Phylogenetic stratigraphy in the Guerrero Negro hypersaline microbial mat

Harris, J. Kirk, Caporaso, J. Gregory, Walker, Jeffrey J., Spear, John R., Gold, Nicholas J., Robertson, Charles E., Hugenholtz, Philip, Goodrich, Julia, McDonald, Daniel, Knights, Dan, Marshall, Paul, Tufo, Henry, Knight, Rob and Pace, Norman R. (2013). Phylogenetic stratigraphy in the Guerrero Negro hypersaline microbial mat. ISME Journal, 7 (1), 50-60. doi: 10.1038/ismej.2012.79

Prokaryotic super program advisory committee DOE joint genome institute, Walnut Creek, CA, March 27, 2013

Garrity, George M., Banfield, Jill, Eisen, Jonathan, van der Lelie, Niels, McMahon, Trina, Rusch, Doug, Delong, Edward, Moran, Mary Ann, Currie, Cameron, Furhman, Jed, Hallam, Steve, Hugenholtz, Phil, Moran, Nancy, Nelson, Karen, Roberts, Richard and Stepanauskas, Ramunas (2013). Prokaryotic super program advisory committee DOE joint genome institute, Walnut Creek, CA, March 27, 2013. Standards in Genomic Sciences, 8 (3), 561-570. doi: 10.4056/sigs.4638348

Reestablishment of recipient-associated microbiota in the lung allograft is linked to reduced risk of bronchiolitis obliterans syndrome

Willner, Dana L., Hugenholtz, Philip, Yerkovich, Stephanie T., Tan, Maxine E., Daly, Joshua N., Lachner, Nancy, Hopkins, Peter M. and Chambers, Daniel C. (2013). Reestablishment of recipient-associated microbiota in the lung allograft is linked to reduced risk of bronchiolitis obliterans syndrome. American Journal of Respiratory and Critical Care Medicine, 187 (6), 640-647. doi: 10.1164/rccm.201209-1680OC

Respiratory syncytial virus infection is associated with increased bacterial load in the upper respiratory tract in young children

Chappell, K.J., Brealey, J.C., Mackay, I.M., Bletchly, C., Hugenholtz, P., Sloots, T.P., Sly, P.D. and Young, P.R. (2013). Respiratory syncytial virus infection is associated with increased bacterial load in the upper respiratory tract in young children. Journal of Medical Microbiology & Diagnosis, S (1), 1-9. doi: 10.4172/2161-0703.S1-005

Genome sequence of the flexirubin-pigmented soil bacterium Niabella soli type strain (JS13-8(T))

Anderson, Iain, Munk, Christine, Lapidus, Alla, Nolan, Matt, Lucas, Susan, Tice, Hope, Del Rio, Tijana Glavina, Cheng, Jan-Fang, Han, Cliff, Tapia, Roxanne, Goodwin, Lynne, Pitluck, Sam, Liolios, Konstantinos, Mavromatis, Konstantinos, Pagani, Ioanna, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Rohde, Manfred, Tindall, Brian J., Goeker, Markus, Detter, John C., Woyke, Tanja, Bristow, James, Eisen, Jonathan A., Markowitz, Victor, Hugenholtz, Philip ... Ivanova, Natalia (2012). Genome sequence of the flexirubin-pigmented soil bacterium Niabella soli type strain (JS13-8(T)). Standards in Genomic Sciences, 7 (2), 210-220. doi: 10.4056/sigs.3117229

Contrasting Life Strategies of Viruses that Infect Photo- and Heterotrophic Bacteria, as Revealed by Viral Tagging

Deng, Li, Gregory, Ann, Yilmaz, Suzan, Poulos, Bonnie T., Hugenholtz, Philip and Sullivan, Matthew B. (2012). Contrasting Life Strategies of Viruses that Infect Photo- and Heterotrophic Bacteria, as Revealed by Viral Tagging. Mbio, 3 (6) e00373-12. doi: 10.1128/mBio.00373-12

Guest commentary: the human microbiome and the promise of clinical ecology

Hugenholtz, Phil (2012). Guest commentary: the human microbiome and the promise of clinical ecology. Microbiology Australia, 33 (3), 90-90.

Defining the core Arabidopsis thaliana root microbiome

Lundberg, Derek S., Lebeis, Sarah L., Paredes, Sut Herrera, Yourstone, Scott, Gehring, Jase, Malfatti, Stephanie, Tremblay, Julien, Engelbrektson, Anna, Kunin, Victor, del Rio, Tijana Glavina, Edgar, Robert C., Eickhorst, Thilo, Ley, Ruth E., Hugenholtz, Philip, Tringe, Susannah Green and Dangl, Jeffery L. (2012). Defining the core Arabidopsis thaliana root microbiome. Nature, 488 (7409), 86-90. doi: 10.1038/nature11237

Complete genome sequence of the moderately thermophilic mineral-sulfide-oxidizing firmicute Sulfobacillus acidophilus type strain (NAL(T))

Anderson, Iain, Chertkov, Olga, Chen, Amy, Saunders, Elizabeth, Lapidus, Alla, Nolan, Matt, Lucas, Susan, Hammon, Nancy, Deshpande, Shweta, Cheng, Jan-Fang, Han, Cliff, Tapia, Roxanne, Goodwin, Lynne A., Pitluck, Sam, Liolios, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Mikhailova, Natalia, Pati, Amrita, Palaniappan, Krishna, Land, Miriam, Pan, Chongle, Rohde, Manfred, Pukall, Ruediger, Goeker, Markus, Detter, John C., Woyke, Tanja, Bristow, James, Eisen, Jonathan A. ... Mavromatis, Konstantinos (2012). Complete genome sequence of the moderately thermophilic mineral-sulfide-oxidizing firmicute Sulfobacillus acidophilus type strain (NAL(T)). Standards in Genomic Sciences, 6 (3), 293-303. doi: 10.4056/sigs.2736042

Grinder: a versatile amplicon and shotgun sequence simulator

Angly, Florent E., Willner, Dana, Rohwer, Forest, Hugenholtz, Philip and Tyson, Gene W. (2012). Grinder: a versatile amplicon and shotgun sequence simulator. Nucleic Acids Research, 40 (12), e94.1-e94.8. doi: 10.1093/nar/gks251

Unlocking the potential of metagenomics through replicated experimental design

Knight, Rob, Jansson, Janet, Field, Dawn, Fierer, Noah, Desai, Narayan, Fuhrman, Jed A., Hugenholtz, Phil, van der Lelie, Daniel, Meyer, Folker, Stevens, Rick, Bailey, Mark J., Gordon, Jeffrey I., Kowalchuk, George A. and Gilbert, Jack A. (2012). Unlocking the potential of metagenomics through replicated experimental design. Nature Biotechnology, 30 (6), 513-520. doi: 10.1038/nbt.2235

Fast, accurate error-correction of amplicon pyrosequences using Acacia

Bragg, Lauren, Stone, Glenn, Imelfort, Michael, Hugenholtz, Philip and Tyson, Gene W. (2012). Fast, accurate error-correction of amplicon pyrosequences using Acacia. Nature Methods, 9 (5), 245-246. doi: 10.1038/nmeth.1990

Comparison of DNA extraction methods for microbial community profiling with an application to pediatric bronchoalveolar lavage samples

Willner, Dana, Daly, Joshua, Whiley, David, Grimwood, Keith, Wainwright, Claire E. and Hugenholtz, Philip (2012). Comparison of DNA extraction methods for microbial community profiling with an application to pediatric bronchoalveolar lavage samples. PLoS One, 7 (4) e34605, e34605.1-e34605.12. doi: 10.1371/journal.pone.0034605

An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea

McDonald, Daniel, Price, Morgan N., Goodrich, Julia, Nawrocki, Eric P., DeSantis, Todd Z, Probst, Alexander, Andersen, Gary L, Knight, Rob and Hugenholtz, Philip (2012). An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea. ISME Journal, 6 (3), 610-618. doi: 10.1038/ismej.2011.139

Comparative analyses of foregut and hindgut bacterial communities in hoatzins and cows

Godoy-Vitorino, Filipa, Goldfarb, Katherine C., Karaoz, Ulas, Leal, Sara, Garcia-Amado, Maria A., Hugenholtz, Philip, Tringe, Susannah G., Brodie, Eoin L. and Dominguez-Bello, Maria Gloria (2012). Comparative analyses of foregut and hindgut bacterial communities in hoatzins and cows. ISME Journal, 6 (3), 531-541. doi: 10.1038/ismej.2011.131

Complete genome sequence of the aerobic, heterotroph Marinithermus hydrothermalis type strain (T1(T)) from a deep-sea hydrothermal vent chimney

Copeland, Alex, Gu, Wei, Yasawong, Montri, Lapidus, Alla, Lucas, Susan, Deshpande, Shweta, Pagani, Ioanna, Tapia, Roxanne, Cheng, Jan-Fang, Goodwin, Lynne, Pitluck, Sam, Liolios, Konstantinos, Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Pan, Chongle, Brambilla, Evelyne-Marie, Rohde, Manfred, Tindall, Brian J., Sikorski, Johannes, Goker, Markus, Detter, John C., Bristow, James, Eisen, Jonathan A., Markowitz, Victor ... Woyke, Tanja (2012). Complete genome sequence of the aerobic, heterotroph Marinithermus hydrothermalis type strain (T1(T)) from a deep-sea hydrothermal vent chimney. Standards in Genomic Sciences, 6 (1), 21-30. doi: 10.4056/sigs.2435521

Complete genome sequence of the aquatic bacterium Runella slithyformis type strain (LSU 4(T))

Copeland, Alex, Zhang, Xiaojing, Misra, Monica, Lapidus, Alla, Nolan, Matt, Lucas, Susan, Deshpande, Shweta, Cheng, Jan-Fang, Tapia, Roxanne, Goodwin, Lynne A., Pitluck, Sam, Liolios, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Pan, Chongle, Jeffries, Cynthia D., Detter, John C., Brambilla, Evelyne-Marie, Rohde, Manfred, Djao, Olivier D. Ngatchou, Goeker, Markus, Sikorski, Johannes, Tindall, Brian J. ... Mavromatis, Konstantinos (2012). Complete genome sequence of the aquatic bacterium Runella slithyformis type strain (LSU 4(T)). Standards in Genomic Sciences, 6 (2), 145-154. doi: 10.4056/sigs.2475579

Complete genome sequence of the facultatively anaerobic, appendaged bacterium Muricauda ruestringensis type strain (B1(T))

Huntemann, Marcel, Teshima, Hazuki, Lapidus, Alla, Nolan, Matt, Lucas, Susan, Hammon, Nancy, Deshpande, Shweta, Cheng, Jan-Fang, Tapia, Roxanne, Goodwin, Lynne A., Pitluck, Sam, Liolios, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Pan, Chongle, Brambilla, Evelyne-Marie, Rohde, Manfred, Spring, Stefan, Goeker, Markus, Detter, John C., Bristow, James, Eisen, Jonathan A. ... Woyke, Tanja (2012). Complete genome sequence of the facultatively anaerobic, appendaged bacterium Muricauda ruestringensis type strain (B1(T)). Standards in Genomic Sciences, 6 (2), 185-193. doi: 10.4056/sigs.2786069

Complete genome sequence of the orange-red pigmented, radioresistant Deinococcus proteolyticus type strain (MRPT)

Copeland, Alex, Zeytun, Ahmet, Yassawong, Montri, Nolan, Matt, Lucas, Susan, Hammon, Nancy, Deshpande, Shweta, Cheng, Jan-Fang, Han, Cliff, Tapia, Roxanne, Goodwin, Lynne A., Pitluck, Sam, Mavromatis, Konstantinos, Liolios, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Jeffries, Cynthia D., Brambilla, Evelyne-Marie, Rohde, Manfred, Sikorski, Johannes, Pukall, Ruediger, Goeker, Markus, Detter, John C. ... Lapidus, Alla (2012). Complete genome sequence of the orange-red pigmented, radioresistant Deinococcus proteolyticus type strain (MRPT). Standards in Genomic Sciences, 6 (2), 240-250. doi: 10.4056/sigs.2756060

Complete genome sequence of the sulfur compounds oxidizing chemolithoautotroph Sulfuricurvum kujiense type strain (YK-1(T))

Han, Cliff, Kotsyurbenko, Oleg, Chertkov, Olga, Held, Brittany, Lapidus, Alla, Nolan, Matt, Lucas, Susan, Hammon, Nancy, Deshpande, Shweta, Cheng, Jan-Fang, Tapia, Roxanne, Goodwin, Lynne, Pitluck, Sam, Liolios, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-juan, Jeffries, Cynthia D., Brambilla, Evelyne-Marie, Rohde, Manfred, Spring, Stefan, Sikorski, Johannes ... Detter, John C. (2012). Complete genome sequence of the sulfur compounds oxidizing chemolithoautotroph Sulfuricurvum kujiense type strain (YK-1(T)). Standards in Genomic Sciences, 6 (1), 94-103. doi: 10.4056/sigs.2456004

Complete genome sequence of the termite hindgut bacterium Spirochaeta coccoides type strain (SPN1(T)), reclassification in the genus Sphaerochaeta as Sphaerochaeta coccoides comb. nov and emendations of the family Spirochaetaceae and the genus Sphaerochae

Abt, Birte, Han, Cliff, Scheuner, Carmen, Lu, Megan, Lapidus, Alla, Nolan, Matt, Lucas, Susan, Hammon, Nancy, Deshpande, Shweta, Cheng, Jan-Fang, Tapia, Roxanne, Goodwin, Lynne A., Pitluck, Sam, Liolios, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Huntemann, Marcel, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Brambilla, Evelyne-Marie, Rohde, Manfred, Spring, Stefan, Gronow, Sabine, Goeker, Markus ... Detter, John C. (2012). Complete genome sequence of the termite hindgut bacterium Spirochaeta coccoides type strain (SPN1(T)), reclassification in the genus Sphaerochaeta as Sphaerochaeta coccoides comb. nov and emendations of the family Spirochaetaceae and the genus Sphaerochae. Standards in Genomic Sciences, 6 (2), 194-209. doi: 10.4056/sigs.2796069

Complete genome sequence of the thermophilic sulfate-reducing ocean bacterium Thermodesulfatator indicus type strain (CIR29812(T))

Anderson, Iain, Saunders, Elizabeth, Lapidus, Alla, Nolan, Matt, Lucas, Susan, Tice, Hope, Del Rio, Tijana Glavina, Cheng, Jan-Fang, Han, Cliff, Tapia, Roxanne, Goodwin, Lynne A., Pitluck, Sam, Liolios, Konstantinos, Mavromatis, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Jeffries, Cynthia D., Chang, Yun-juan, Brambilla, Evelyne-Marie, Rohde, Manfred, Spring, Stefan, Goeker, Markus, Detter, John C. ... Klenk, Hans-Peter (2012). Complete genome sequence of the thermophilic sulfate-reducing ocean bacterium Thermodesulfatator indicus type strain (CIR29812(T)). Standards in Genomic Sciences, 6 (2), 155-164. doi: 10.4056/sigs.2665915

Genome sequence of the Antarctic rhodopsins-containing flavobacterium Gillisia limnaea type strain (R-8282(T))

Riedel, Thomas, Held, Brittany, Nolan, Matt, Lucas, Susan, Lapidus, Alla, Tice, Hope, Del Rio, Tijana Glavina, Cheng, Jan-Fang, Han, Cliff, Tapia, Roxanne, Goodwin, Lynne A., Pitluck, Sam, Liolios, Konstantinos, Mavromatis, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Rohde, Manfred, Tindall, Brian J., Detter, John C., Goeker, Markus, Bristow, James, Eisen, Jonathan A., Markowitz, Victor, Hugenholtz, Philip ... Woyke, Tanja (2012). Genome sequence of the Antarctic rhodopsins-containing flavobacterium Gillisia limnaea type strain (R-8282(T)). Standards in Genomic Sciences, 7 (1), 107-119. doi: 10.4056/sigs.3216895

Genome sequence of the homoacetogenic bacterium holophaga foetida type strain (TMBS4(T))

Anderson, Iain, Held, Brittany, Lapidus, Alla, Nolan, Matt, Lucas, Susan, Tice, Hope, Del Rio, Tijana Glavina, Cheng, Jan-Fang, Han, Cliff, Tapia, Roxanne, Goodwin, Lynne A., Pitluck, Sam, Liolios, Konstantinos, Mavromatis, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Brambilla, Evelyne-Marie, Rohde, Manfred, Spring, Stefan, Goeker, Markus, Detter, John C., Woyke, Tanja, Bristow, James, Eisen, Jonathan A. ... Kyrpides, Nikos C. (2012). Genome sequence of the homoacetogenic bacterium holophaga foetida type strain (TMBS4(T)). Standards in Genomic Sciences, 6 (2), 174-184. doi: 10.4056/sigs.2746047

Genome sequence of the moderately thermophilic, amino-acid-degrading and sulfur-reducing bacterium Thermovirga lienii type strain (Cas60314(T))

Goeker, Markus, Saunders, Elisabeth, Lapidus, Alla, Nolan, Matt, Lucas, Susan, Hammon, Nancy, Deshpande, Shweta, Cheng, Jan-Fang, Han, Cliff, Tapia, Roxanne, Goodwin, Lynne A., Pitluck, Sam, Liolios, Konstantinos, Mavromatis, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Chang, Yun-juan, Jeffries, Cynthia D., Brambilla, Evelyne-Marie, Rohde, Manfred, Spring, Stefan, Detter, John C., Woyke, Tanja, Bristow, James ... Klenk, Hans-Peter (2012). Genome sequence of the moderately thermophilic, amino-acid-degrading and sulfur-reducing bacterium Thermovirga lienii type strain (Cas60314(T)). Standards in Genomic Sciences, 6 (2), 230-239. doi: 10.4056/sigs.2726028

Genome sequence of the orange-pigmented seawater bacterium Owenweeksia hongkongensis type strain (UST20020801(T))

Riedel, Thomas, Held, Brittany, Nolan, Matt, Lucas, Susan, Lapidus, Alla, Tice, Hope, Del Rio, Tijana Glavina, Cheng, Jan-Fang, Han, Cliff, Tapia, Roxanne, Goodwin, Lynne A., Pitluck, Sam, Liolios, Konstantinos, Mavromatis, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Rohde, Manfred, Tindall, Brian J., Detter, John C., Goeker, Markus, Woyke, Tanja, Bristow, James, Eisen, Jonathan A., Markowitz, Victor, Hugenholtz, Philip ... Kyrpides, Nikos C. (2012). Genome sequence of the orange-pigmented seawater bacterium Owenweeksia hongkongensis type strain (UST20020801(T)). Standards in Genomic Sciences, 7 (1), 120-130. doi: 10.4056/sigs.3296896

Impact of training sets on classification of high-throughput bacterial 16s rRNA gene surveys

Werner, Jeffrey J., Koren, Omry, Hugenholtz, Philip, DeSantis, Todd Z., Walters, William A., Caporaso, J. Gregory, Angenent, Largus T., Knight, Rob and Ley, Ruth E (2012). Impact of training sets on classification of high-throughput bacterial 16s rRNA gene surveys. ISME Journal, 6 (1), 94-103. doi: 10.1038/ismej.2011.82

Permanent draft genome sequence of the gliding predator Saprospira grandis strain Sa g1 (=HR1)

Mavromatis, Konstantinos, Chertkov, Olga, Lapidus, Alla, Nolan, Matt, Lucas, Susan, Tice, Hope, Del Rio, Tijana Glavina, Cheng, Jan-Fang, Han, Cliff, Tapia, Roxanne, Bruce, David, Goodwin, Lynne A., Pitluck, Sam, Huntemann, Marcel, Liolios, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Brambilla, Evelyne-Marie, Rohde, Manfred, Spring, Stefan, Goeker, Markus, Detter, John C., Bristow, James, Eisen, Jonathan A. ... Woyke, Tanja (2012). Permanent draft genome sequence of the gliding predator Saprospira grandis strain Sa g1 (=HR1). Standards in Genomic Sciences, 6 (2), 210-219. doi: 10.4056/sigs.2816096

Genome sequence of the filamentous, gliding Thiothrix nivea neotype strain (JP2(T))

Lapidus, Alla, Nolan, Matt, Lucas, Susan, Del Rio, Tijana Glavina, Tice, Hope, Cheng, Jan-Fang, Tapia, Roxanne, Han, Cliff, Goodwin, Lynne, Pitluck, Sam, Liolios, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Huntemann, Marcel, Mavromatis, Konstantinos, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Brambilla, Evelyne-Marie, Rohde, Manfred, Abt, Birte, Verbarg, Susanne, Goeker, Markus, Bristow, James, Eisen, Jonathan A., Markowitz, Victor, Hugenholtz, Philip ... Woyke, Tanja (2011). Genome sequence of the filamentous, gliding Thiothrix nivea neotype strain (JP2(T)). Standards in Genomic Sciences, 5 (3), 398-406. doi: 10.4056/sigs.2344929

Complete genome sequence of Syntrophobotulus glycolicus type strain (FlGlyR T)

Han, Cliff, Mwirichia, Romano, Chertkov, Olga, Held, Brittany, Lapidus, Alla, Nolan, Matt, Lucas, Susan, Hammon, Nancy, Deshpande, Shweta, Cheng, Jan-Fang, Tapia, Roxanne, Goodwin, Lynne, Pitluck, Sam, Huntemann, Marcel, Liolios, Konstantinos, Ivanova, Natalia, Pagani, Ioanna, Mavromatis, Konstantinos, Ovchinikova, Galina, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Brambilla, Evelyne-Marie, Rohde, Manfred, Spring, Stefan, Sikorski, Johannes, Göker, Markus ... Detter, John C. (2011). Complete genome sequence of Syntrophobotulus glycolicus type strain (FlGlyR T). Standards in Genomic Sciences, 4 (3), 371-380. doi: 10.4056/sigs.2004648

Bioenergy feedstock-specific enrichment of microbial populations during high-solids thermophilic deconstruction

Reddy, Amitha P., Allgaier, Martin, Singer, Steven W., Hazen, Terry C., Simmons, Blake A., Hugenholtz, Philip and VanderGheynst, Jean S. (2011). Bioenergy feedstock-specific enrichment of microbial populations during high-solids thermophilic deconstruction. Biotechnology and Bioengineering, 108 (9), 2088-2098. doi: 10.1002/bit.23176

Glycoside hydrolase activities of thermophilic bacterial consortia adapted to switchgrass

Gladden, John M., Allgaier, Martin, Miller, Christopher S., Hazen, Terry C., VanderGheynst, Jean S., Hugenholtz, Philip, Simmons, Blake A. and Singer, Steven W. (2011). Glycoside hydrolase activities of thermophilic bacterial consortia adapted to switchgrass. Applied and Environmental Microbiology, 77 (16), 5804-5812. doi: 10.1128/AEM.00032-11

Isolation of Succinivibrionaceae implicated in low methane emissions from Tammar wallabies

Pope, P. B., Smith, W., Denman, S. E., Tringe, S. G., Barry, K., Hugenholtz, P., McSweeney, C. S., McHardy, A. C. and Morrison, M. (2011). Isolation of Succinivibrionaceae implicated in low methane emissions from Tammar wallabies. Science, 333 (6042), 646-648. doi: 10.1126/science.1205760

Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications

Yilmaz, Pelin, Kottmann, Renzo, Field, Dawn, Knight, Rob, Cole, James R., Amaral-Zettler, Linda, Gilbert, Jack A., Karsch-Mizrachi, Ilene, Johnston, Anjanette, Cochrane, Guy, Vaughan, Robert, Hunter, Christopher, Park, Joonhong, Morrison, Norman, Rocca-Serra, Philippe, Sterk, Peter, Arumugam, Manimozhiyan, Bailey, Mark, Baumgartner, Laura, Birren, Bruce W., Blaser, Martin J., Bonazzi, Vivien, Booth, Tim, Bork, Peer, Bushman, Frederic D., Buttigieg, Pier Luigi., Chain, Patrick S. G., Charlson, Emily, Costello, Elizabeth K. ... Glockner, Frank Oliver (2011). Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications. Nature Biotechnology, 29 (5), 415-420. doi: 10.1038/nbt.1823

Phage encoded H-NS: A potential Achilles heel in the bacterial defence system

Skennerton, Connor T., Angly, Florent E., Breitbart, Mya, Bragg, Lauren, He, Shaomei, McMahon, Katherine D., Hugenholtz, Philip and Tyson, Gene W. (2011). Phage encoded H-NS: A potential Achilles heel in the bacterial defence system. Plos One, 6 (5) e20095, e20095-1-e20095-7. doi: 10.1371/journal.pone.0020095

Complete genome sequence of Bacteroides salanitronis type strain (BL78(T))

Gronow, Sabine, Held, Brittany, Lucas, Susan, Lapidus, Alla, Del Rio, Tijana Glavina, Nolan, Matt, Tice, Hope, Deshpande, Shweta, Cheng, Jan-Fang, Pitluck, Sam, Liolios, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Mavromatis, Konstantinos, Pati, Amrita, Tapia, Roxane, Han, Cliff, Goodwin, Lynne, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Brambilla, Evelyne-Marie, Rohde, Manfred, Göker, Markus, Detter, John C., Woyke, Tanja ... Eisen, Jonathan A. (2011). Complete genome sequence of Bacteroides salanitronis type strain (BL78(T)). Standards in Genomic Sciences, 4 (2), 191-199. doi: 10.4056/sigs.1704212

Complete genome sequence of Cellulophaga lytica type strain (LIM-21(T))

Pati, Amrita, Abt, Birte, Teshima, Hazuki, Nolan, Matt, Lapidus, Alla, Lucas, Susan, Hammon, Nancy, Deshpande, Shweta, Cheng, Jan-Fang, Tapia, Roxane, Han, Cliff, Goodwin, Lynne, Pitluck, Sam, Liolios, Konstantinos, Pagani, Ioanna, Mavromatis, Konstantinos, Ovchinikova, Galina, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Jeffries, Cynthia D., Detter, John C., Brambilla, Evelyne-Marie, Kannan, K. Palani, Rohde, Manfred, Spring, Stefan, Göker, Markus, Woyke, Tanja ... Ivanova, Natalia (2011). Complete genome sequence of Cellulophaga lytica type strain (LIM-21(T)). Standards in Genomic Sciences, 4 (2), 221-232. doi: 10.4056/sigs.1774329

Complete genome sequence of Deinococcus maricopensis type strain (LB-34(T))

Pukall, Rüdiger, Zeytun, Ahmet, Lucas, Susan, Lapidus, Alla, Hammon, Nancy, Deshpande, Shweta, Nolan, Matt, Cheng, Jan-Fang, Pitluck, Sam, Liolios, Konstantinos, Pagani, Ioanna, Mikhailova, Natalia, Ivanova, Natalia, Mavromatis, Konstantinos, Pati, Amrita, Tapia, Roxane, Han, Cliff, Goodwin, Lynne, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Brambilla, Evelyne-Marie, Rohde, Manfred, Göker, Markus, Detter, J. Chris, Woyke, Tanja ... Klenk, Hans-Peter (2011). Complete genome sequence of Deinococcus maricopensis type strain (LB-34(T)). Standards in Genomic Sciences, 4 (2), 163-172. doi: 10.4056/sigs.1633949

Complete genome sequence of Desulfurococcus mucosus type strain (O7/1(T))

Wirth, Reinhard, Chertkov, Olga, Held, Brittany, Lapidus, Alla, Nolan, Matt, Lucas, Susan, Hammon, Nancy, Deshpande, Shweta, Cheng, Jan-Fang, Tapia, Roxane, Han, Cliff, Goodwin, Lynne, Pitluck, Sam, Liolios, Konstantinos, Ioanna, Pagani, Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Bilek, Yvonne, Hader, Thomas, Rohde, Manfred, Spring, Stefan ... Klenk, Hans-Peter (2011). Complete genome sequence of Desulfurococcus mucosus type strain (O7/1(T)). Standards in Genomic Sciences, 4 (2), 173-182. doi: 10.4056/sigs.1644004

Complete genome sequence of Hydrogenobacter thermophilus type strain (TK-6(T))

Zeytun, Ahmet, Sikorski, Johannes, Nolan, Matt, Lapidus, Alla, Lucas, Susan, Han, James, Tice, Hope, Cheng, Jan-Fang, Tapia, Roxanne, Goodwin, Lynne, Pitluck, Sam, Liolios, Konstantinos, Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Ovchinnikova, Galina, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Ngatchou-Djao, Olivier D., Land, Miriam, Hauser, Loren, Jeffries, Cynthia D., Han, Cliff, Detter, John C., Übler, Susanne, Rohde, Manfred, Tindall, Brian J., Göker, Markus ... Kyrpides, Nikos C. (2011). Complete genome sequence of Hydrogenobacter thermophilus type strain (TK-6(T)). Standards in Genomic Sciences, 4 (2), 131-143. doi: 10.4056/sigs.1463589

Complete genome sequence of Marivirga tractuosa type strain (H-43(T))

Pagani, Ioanna, Chertkov, Olga, Lapidus, Alla, Lucas, Susan, Del Rio, Tijana Glavina, Tice, Hope, Copeland, Alex, Cheng, Jan-Fang, Nolan, Matt, Saunders, Elizabeth, Pitluck, Sam, Held, Brittany, Goodwin, Lynne, Liolios, Konstantinos, Ovchinikova, Galina, Ivanova, Natalia, Mavromatis, Konstantinos, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Jeffries, Cynthia D., Detter, John C., Han, Cliff, Tapia, Roxanne, Ngatchou-Djao, Olivier D., Rohde, Manfred, Göker, Markus ... Kyrpides, Nikos C. (2011). Complete genome sequence of Marivirga tractuosa type strain (H-43(T)). Standards in Genomic Sciences, 4 (2), 154-162. doi: 10.4056/sigs.1623941

Complete genome sequence of Oceanithermus profundus type strain (506(T))

Pati, Amrita, Zhang, Xiaojing, Lapidus, Alla, Nolan, Matt, Lucas, Susan, Del Rio, Tijana Glavina, Tice, Hope, Cheng, Jan-Fang, Tapia, Roxane, Han, Cliff, Goodwin, Lynne, Pitluck, Sam, Liolios, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Mavromatis, Konstantinos, Chen, Amy, Palaniappan, Krishna, Hauser, Loren, Jeffries, Cynthia D., Brambilla, Evelyne-Marie, Röhl, Alina, Mwirichia, Romano, Rohde, Manfred, Tindall, Brian J., Sikorski, Johannes, Wirth, Reinhard, Göker, Markus, Woyke, Tanja ... Land, Miriam (2011). Complete genome sequence of Oceanithermus profundus type strain (506(T)). Standards in Genomic Sciences, 4 (2), 210-220. doi: 10.4056/sigs.1734292

Complete genome sequence of Odoribacter splanchnicus type strain (1651/6(T))

Göker, Markus, Gronow, Sabine, Zeytun, Ahmet, Nolan, Matt, Lucas, Susan, Lapidus, Alla, Hammon, Nancy, Deshpande, Shweta, Cheng, Jan-Fang, Pitluck, Sam, Liolios, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Mavromatis, Konstantinos, Ovchinikova, Galina, Pati, Amrita, Tapia, Roxane, Han, Cliff, Goodwin, Lynne, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Jeffries, Cynthia D., Brambilla, Evelyne-Marie, Rohde, Manfred, Detter, John C., Woyke, Tanja, Bristow, James ... Klenk, Hans-Peter (2011). Complete genome sequence of Odoribacter splanchnicus type strain (1651/6(T)). Standards in Genomic Sciences, 4 (2), 200-209. doi: 10.4056/sigs.1714269

Complete genome sequence of Riemerella anatipestifer type strain (ATCC 11845(T))

Mavromatis, Konstantinos, Lu, Megan, Misra, Monica, Lapidus, Alla, Nolan, Matt, Lucas, Susan, Hammon, Nancy, Deshpande, Shweta, Cheng, Jan-Fang, Tapia, Roxane, Han, Cliff, Goodwin, Lynne, Pitluck, Sam, Liolios, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Jeffries, Cynthia D., Detter, John C., Brambilla, Evelyne-Marie, Rohde, Manfred, Göker, Markus, Gronow, Sabine, Woyke, Tanja ... Kyrpides, Nikos C. (2011). Complete genome sequence of Riemerella anatipestifer type strain (ATCC 11845(T)). Standards in Genomic Sciences, 4 (2), 144-153. doi: 10.4056/sigs.1553865

Non-contiguous finished genome sequence of Bacteroides coprosuis type strain (PC139(T))

Land, Miriam, Held, Brittany, Gronow, Sabine, Abt, Birte, Lucas, Susan, Del Rio, Tijana Glavina, Nolan, Matt, Tice, Hope, Cheng, Jan-Fang, Pitluck, Sam, Liolios, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Pati, Amrita, Tapia, Roxane, Han, Cliff, Goodwin, Lynne, Chen, Amy, Palaniappan, Krishna, Hauser, Loren, Brambilla, Evelyne-Marie, Rohde, Manfred, Göker, Markus, Detter, John C., Woyke, Tanja, Bristow, James, Eisen, Jonathan A. ... Lapidus, Alla (2011). Non-contiguous finished genome sequence of Bacteroides coprosuis type strain (PC139(T)). Standards in Genomic Sciences, 4 (2), 233-243. doi: 10.4056/sigs.1784330

Characterization of trapped lignin-degrading microbes in tropical forest soil

Deangelis, Kristen M., Allgaier, Martin, Chavarria, Yaucin, Fortney, Julian L., Hugenholtz, Philip, Simmons, Blake, Sublette, Kerry, Silver, Whendee L. and Hazen, Terry C. (2011). Characterization of trapped lignin-degrading microbes in tropical forest soil. Plos One, 6 (4) e19306, e19306.1-e19306.9. doi: 10.1371/journal.pone.0019306

Complete genome sequence of Bacteroides helcogenes type strain (P 36-108T)

Pati, Amrita, Gronow, Sabine, Zeytun, Ahmet, Lapidus, Alla, Nolan, Matt, Hammon, Nancy, Deshpande, Shweta, Cheng, Jan-Fang, Tapia, Roxane, Han, Cliff, Goodwin, Lynne, Pitluck, Sam, Liolios, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Mavromatis, Konstantinos, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Detter, John C., Brambilla, Evelyne, Rohde, Manfred, Goeker, Markus, Woyke, Tanja, Bristow, James, Eisen, Jonathan A. ... Lucas, Susan (2011). Complete genome sequence of Bacteroides helcogenes type strain (P 36-108T). Standards in Genomic Sciences, 4 (1), 45-53. doi: 10.4056/sigs.1513795

Complete genome sequence of Calditerrivibrio nitroreducens type strain (Yu37-1 T)

Pitluck, Sam, Sikorski, Johannes, Zeytun, Ahmet, Lapidus, Alla, Nolan, Matt, Lucas, Susan, Hammon, Nancy, Deshpande, Shweta, Cheng, Jan-Fang, Tapia, Roxane, Han, Cliff, Goodwin, Lynne, Liolios, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Mavromatis, Konstantinos, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Detter, John C., Brambilla, Evelyne, Djao, Oliver D. Ngatchou, Rohde, Manfred, Spring, Stefan, Goker, Markus, Woyke, Tanja ... Land, Miriam (2011). Complete genome sequence of Calditerrivibrio nitroreducens type strain (Yu37-1 T). Standards in Genomic Sciences, 4 (1), 54-62. doi: 10.4056/sigs.1523807

Complete genome sequence of Cellulophaga algicola type strain (IC166(T))

Abt, Birte, Lu, Megan, Misra, Monica, Han, Cliff, Nolan, Matt, Lucas, Susan, Hammon, Nancy, Deshpande, Shweta, Cheng, Jan-Fang, Tapia, Roxane, Goodwin, Lynne, Pitluck, Sam, Liolios, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Mavromatis, Konstantinos, Ovchinikova, Galina, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Detter, John C., Brambilla, Evelyne, Rohde, Manfred, Tindall, Brian J., Goeker, Markus ... Lapidus, Alla (2011). Complete genome sequence of Cellulophaga algicola type strain (IC166(T)). Standards in Genomic Sciences, 4 (1), 72-80. doi: 10.4056/sigs.1543845

Complete genome sequence of Desulfobulbus propionicus type strain (1pr3 T)

Pagani, Ioanna, Lapidus, Alla, Nolan, Matt, Lucas, Susan, Hammon, Nancy, Desh-Pande, Shweta, Cheng, Jan-Fang, Chertkov, Olga, Davenport, Karen, Tapia, Roxane, Han, Cliff, Goodwin, Lynne, Pitluck, Sam, Liolios, Konstantinos, Mavromatis, Konstantinos, Ivanova, Natalia, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Detter, John C., Brambilla, Evelyne, Kannan, K. Palani, Djao, Olivier D. Ngatchou, Rohde, Manfred ... Klenk, Hans-Peter (2011). Complete genome sequence of Desulfobulbus propionicus type strain (1pr3 T). Standards in Genomic Sciences, 4 (1), 100-110. doi: 10.4056/sigs.1613929

Complete genome sequence of Haliscomenobacter hydrossis type strain (O-T)

Daligault, Hajnalka, Lapidus, Alla, Zeytun, Ahmet, Nolan, Matt, Lucas, Susan, Del Rio, Tijana Galvina, Tice, Hope, Cheng, Jan-Feng, Tapia, Roxanne, Han, Cliff, Goodwin, Lynne, Pitluck, Sam, Liolios, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Huntemann, Marcel, Mavromatis, Konstantinos, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Brambilla, Evelyne-Marie, Rohde, Manfred, Verbarg, Susanne, Goker, Markus, Bristow, James, Eisen, JA ... Woyke, Tanja (2011). Complete genome sequence of Haliscomenobacter hydrossis type strain (O-T). Standards in Genomic Sciences, 4 (3), 352-360. doi: 10.4056/sigs.1964579

Complete genome sequence of Isosphaera pallida type strain (IS1BT)

Goker, Markus, Cleland, David, Saunders, Elizabeth, Lapidus, Alla, Nolan, Matt, Lucas, Susan, Hammon, Nancy, Deshpande, Shweta, Cheng, Jan-Fang, Tapia, Roxane, Han, Cliff, Goodwin, Lynne, Pitluck, Sam, Liolios, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Mavromatis, Konstantinos, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Detter, John C., Beck, Brian, Woyke, Tanja, Bristow, James, Eisen, Jonathan A. ... Klenk, Hans-Peter (2011). Complete genome sequence of Isosphaera pallida type strain (IS1BT). Standards in Genomic Sciences, 4 (1), 63-71. doi: 10.4056/sigs.1533840

Complete genome sequence of Nitratifractor salsuginis type strain (E9I37-1(T))

Anderson, Iain, Sikorski, Johannes, Zeytun, Ahmet, Nolan, Matt, Lapidus, Alla, Lucas, Susan, Hammon, Nancy, Deshpande, Shweta, Cheng, Jan-Feng, Tapia, Roxanne, Han, Cliff, Goodwin, Lynne, Pitluck, Sam, Liolios, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Huntemann, Marcel, Mavromatis, Konstantinos, Ovchinikova, Galina, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Brambilla, Evelyne-Marie, Ngatchou-Djao, Oliver D., Rohde, Manfred, Tindall, Brian J., Goker, Markus ... Kyrpides, Nikos C. (2011). Complete genome sequence of Nitratifractor salsuginis type strain (E9I37-1(T)). Standards in Genomic Sciences, 4 (3), 322-330. doi: 10.4056/sigs.1844518

Complete genome sequence of Paludibacter propionicigenes type strain (WB4 T)

Gronow, Sabine, Munk, Christine, Lapidus, Alla, Nolan, Matt, Lucas, Susan, Hammon, Nancy, Deshpande, Shweta, Cheng, Jan-Fang, Tapia, Roxane, Han, Cliff, Goodwin, Lynn, Pitluck, Sam, Liolios, Konstantinos, Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Brambilla, Evelyne, Rohde, Manfred, Goker, Markus, Detter, John C., Woyke, Tanja, Bristow, James ... Klenk, Hans-Peter (2011). Complete genome sequence of Paludibacter propionicigenes type strain (WB4 T). Standards in Genomic Sciences, 4 (1), 36-44. doi: 10.4056/sigs.1503846

Complete genome sequence of Syntrophobotulus glycolicus type strain (FlGlyR(T))

Han, Cliffe, Mwirichia, Romano, Chertkov, Olga, Held, Brittany, Lapidus, Alla, Nolan, Matt, Lucas, Susan, Hammon, Nancy, Deshpande, Shweta, Cheng, Jan-Fang, Tapia, Roxanne, Goodwin, Lynne, Pitluck, Sam, Huntemann, Marcel, Liolios, Konstantinos, Ivanova, Natalia, Pagani, Ioanna, Mavromatis, Konstantinos, Ovchinikova, Galina, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Brambilla, Evelyne, Rohde, Manfred, Spring, Stefan, Sikorski, Johannes, Goker, Markus ... Detter, John C. (2011). Complete genome sequence of Syntrophobotulus glycolicus type strain (FlGlyR(T)). Standards in Genomic Sciences, 4 (3), 371-380. doi: 10.4056/sigs.2004684

Complete genome sequence of Thermomonospora curvata type strain (B9 T)

Chertkov, Olga, Sikorski, Johannes, Nolan, Matt, Lapidus, Alla, Lucas, Susan, del Rio, Tijana Glavina, Tice, Hope, Cheng, Jan-Fang, Goodwin, Lynne, Pitluck, Sam, Liolios, Konstantinos, Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Ovchinnikova, Galina, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Djao, Oliver D. N., Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Brettin, Thomas, Han, Cliff, Detter, John C., Rohde, Manfred, Goker, Markus, Woyke, Tanja ... Kyrpides, Nikos C. (2011). Complete genome sequence of Thermomonospora curvata type strain (B9 T). Standards in Genomic Sciences, 4 (1), 13-22. doi: 10.4056/sigs.1453580

Complete genome sequence of Treponema succinifaciens type strain (6091(T))

Han, Cliff, Gronow, Sabine, Teshima, Hazuki, Lapidus, Alla, Nolan, Matt, Lucas, Susan, Hammon, Nancy, Deshpande, Shweta, Cheng, Jan-Feng, Zeytun, Ahmed, Tapia, Roxanne, Goodwin, Lynne, Pitluck, Sam, Liolios, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Huntemann, Marcel, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Brambilla, Evelyne-Marie, Rohde, Manfred, Goker, Markus, Woyke, Tanja, Bristow, James ... Detter, John C. (2011). Complete genome sequence of Treponema succinifaciens type strain (6091(T)). Standards in Genomic Sciences, 4 (3), 361-370. doi: 10.4056/sigs.1984594

Complete genome sequence of Truepera radiovictrix type strain (RQ-24 T)

Ivanova, Natalia, Rohde, Christine, Munk, Christine, Nolan, Matt, Lucas, Susan, del Rio,Tijana Glavina, Tice, Hope, Deshpande, Shweta, Cheng, Jan-Fang, Tapia, Roxane, Han, Cliff, Goodwin, Lynne, Pitluck. Sam, Liolios, Konstantinos, Mavromatis, Konstantinos, Mikhailova,Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Brambilla, Evelyne, Rohde, , Manfred, Goker, Markus, Tindall, Brian J., Woyke, Tanja, Bristow, James ... Lapidus,Alla (2011). Complete genome sequence of Truepera radiovictrix type strain (RQ-24 T). Standards in Genomic Sciences, 4 (1), 91-96. doi: 10.4056/sigs.1563919

Complete genome sequence of Tsukamurella paurometabola type strain (no. 33(T))

Munk, A. Christine, Lapidus, Alla, Lucas, Susan, Nolan, Matt, Tice, Hope, Cheng, Jan-Fang, Del Rio, Tijana Glavina, Goodwin, Lynne, Pitluck, Sam, Liolios, Konstantinos, Huntemann, Marcel, Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Tapia, Roxanne, Han, Cliff, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Brettin, Thomas, Yasawong, Montri, Brambilla, Evelyne-Marie, Rohde, Manfred, Sikorski, Johannes, Goker, Markus ... Klenk, Hans-Peter (2011). Complete genome sequence of Tsukamurella paurometabola type strain (no. 33(T)). Standards in Genomic Sciences, 4 (3), 342-351. doi: 10.4056/sigs.1894556

Complete genome sequence of Weeksella virosa type strain (9751 T)

Lang, Elke, Teshima, Hazuki, Lucas, Susan, Lapidus, Alla, Hammon, Nancy, Deshpande, Shweta, Nolan, Matt, Cheng, Jan-Fang, Pitluck, Sam, Liolios, Konstantinos, Pagani, Ioanna, Mikhailova, Natalia, Ivanova, Natalia, Mavromatis, Konstantinos, Pati, Amrita, Tapia, Roxane, Han, Cliff, Goodwin, Lynne, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Brambilla, Evelyne-Marie, Kopitz, Markus, Rohde, Manfred, Goker, Markus, Tindall, Brian J. ... Kyrpides, Nikos C. (2011). Complete genome sequence of Weeksella virosa type strain (9751 T). Standards in Genomic Sciences, 4 (1), 81-90. doi: 10.4056/sigs.1603927

Complete genome sequence of leadbetterella byssophila type strain (4M15 T)

Abt, Birte, Teshima, Hazuki, Lucas, Susan, Lapidus, Alla, del Rio, Tijana Glavina, Nolan, Matt, Tice, Hope, Cheng, Jan-Fang, Pitluck, Sam, Liolios, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Mavromatis, Konstantinos, Pati, Amrita, Tapia, Roxane, Han, Cliff, Goodwin, Lynne, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Rohde, Manfred, Goker, Markus, Tindall, Brian J., Detter, John C., Woyke, Tanja, Bristow, James ... Kyrpides, Nikos C. (2011). Complete genome sequence of leadbetterella byssophila type strain (4M15 T). Standards in Genomic Sciences, 4 (1), 2-12. doi: 10.4056/sigs.1413518

Complete genome sequence of mahella australiensis type strain (50-1 BONT)

Sikorski, Johannes, Teshima, Hazuki, Nolan, Matt, Lucas, Susan, Hammon, Nancy, Deshpande, Shweta, Cheng, Jan-Fang, Pitluck, Sam, Liolios, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Huntemann, Marcel, Mavromatis, Konstantinos, Ovchinikova, Galina, Pati, Amrita, Tapia, Roxane, Han, Cliff, Goodwin, Lynne, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Ngatchou-Djao, Oliver Duplex, Rohde, Manfred, Pukall, Rudiger, Spring, Stefan, Abt, Birte, Goker, Markus, Detter, John C. ... Lapidus, Alla (2011). Complete genome sequence of mahella australiensis type strain (50-1 BONT). Standards in Genomic Sciences, 4 (3), 331-341. doi: 10.4056/sigs.1864526

Complete genome sequence of the acetate-degrading sulfate reducer Desulfobacca acetoxidans type strain (ASRB2(T))

Goker, Markus, Teshima, Hazuki, Lapidus, Alla, Nolan, Matt, Lucas, Susan, Hammon, Nancy, Deshpande, Shweta, Cheng, Jan-Fang, Tapia, Roxane, Han, Cliff, Goodwin, Lynne, Pitluck, Sam, Huntemann, Marcel, Liolios, Konstantinos, Ivanova, Natalia, Pagani, Ioanna, Mavromatis, Konstantinos, Ovchinikova, Galina, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Brambilla, Evelyne, Rohde, Manfred, Spring, Stefan, Detter, John C., Woyke, Tanja, Bristow, James ... Klenk, Hans-Peter (2011). Complete genome sequence of the acetate-degrading sulfate reducer Desulfobacca acetoxidans type strain (ASRB2(T)). Standards in Genomic Sciences, 4 (3), 393-401. doi: 10.4056/sigs.2064705

Complete genome sequence of the extremely halophilic Halanaerobium praevalens type strain (GSL(T))

Ivanova, Natalia, Sikorski, Johannes, Chertkov, Olga, Nolan, Matt, Lucas, Susan, Hammon, Nancy, Deshpande, Shweta, Cheng, Jan-Feng, Tapia, Roxanne, Han, Cliff, Goodwin, Lynne, Pitluck, Sam, Huntemann, Marcel, Liolios, Konstantinos, Pagani, Ioanna, Mavromatis, Konstantinos, Ovchinikova, Galina, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Brambilla, Evelyne-Marie, Kannan, K. Palani, Rohde, Manfred, Tindall, Brian J., Goker, Markus, Detter, John C., Woyke, Tanja ... Lapidus, Alla (2011). Complete genome sequence of the extremely halophilic Halanaerobium praevalens type strain (GSL(T)). Standards in Genomic Sciences, 4 (3), 312-321. doi: 10.4056/sigs.1824509

Complete genome sequence of the gliding freshwater bacterium Fluviicola taffensis type strain (RW262(T))

Woyke, Tanja, Chertkov, Olga, Lapidus, Alla, Nolan, Matt, Lucas, Susan, Del Rio, Tijana Glavina, Tice, Hope, Cheng, Jan-Feng, Tapia, Roxanne, Han, Cliff, Goodwin, Lynne, Pitluck, Sam, Liolios, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Huntemann, Marcel, Mavromatis, Konstantinos, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Brambilla, Evelyne-Marie, Rohde, Manfred, Mwirichia, Romano, Sikorski, Johannes, Tindall, Brian J., Goker, Markus ... Kyrpides, Nikos C. (2011). Complete genome sequence of the gliding freshwater bacterium Fluviicola taffensis type strain (RW262(T)). Standards in Genomic Sciences, 5 (1), 21-29. doi: 10.4056/sigs.2124912

Complete genome sequence of the gliding, heparinolytic Pedobacter saltans type strain (113(T))

Liolios, Konstantinos, Sikorski, Johannes, Lu, Meagan, Nolan, Matt, Lapidus, Alla, Lucas, Susan, Hammon, Nancy, Deshpande, Shweta, Cheng, Jan-Feng, Tapia, Roxanne, Han, Cliff, Goodwin, Lynne, Pitluck, Sam, Huntemann, Marcel, Ivanova, Natalia, Pagani, Ioanna, Mavromatis, Konstantinos, Ovchinikova, Galina, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Brambilla, Evelyne-Marie, Kotsyurbenko, Oleg, Rohde, Manfred, Tindall, Brian J., Abt, Birte, Goker, Markus ... Kyrpides, Nikos C. (2011). Complete genome sequence of the gliding, heparinolytic Pedobacter saltans type strain (113(T)). Standards in Genomic Sciences, 5 (1), 30-40. doi: 10.4056/sigs.2154937

Complete genome sequence of the hyperthermophilic chemolithoautotroph Pyrolobus fumarii type strain (1A(T))

Anderson, Iain, Goker, Markus, Nolan, Matt, Lucas, Susan, Hammon, Nancy, Deshpande, Shweta, Cheng, Jan-Fang, Tapia, Roxanne, Han, Cliff, Goodwin, Lynne, Pitluck, Sam, Huntemann, Marcel, Liolios, Konstantinos, Ivanova, Natalia, Pagani, Ioanna, Mavromatis, Konstantinos, Ovchinikova, Galina, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Brambilla, Evelyne-Marie, Huber, Harald, Yasawong, Montri, Rohde, Manfred, Spring, Stefan, Abt, Birte, Sikorski, Johannes ... Lapidus, Alla (2011). Complete genome sequence of the hyperthermophilic chemolithoautotroph Pyrolobus fumarii type strain (1A(T)). Standards in Genomic Sciences, 4 (3), 381-392. doi: 10.4056/sigs.2014648

Complete genome sequence of the thermophilic sulfur-reducer Desulfurobacterium thermolithotrophum type strain (BSA(T)) from a deep-sea hydrothermal vent

Goker, Markus, Daligault, Hajnalka, Mwirichia, Romano, Lapidus, Alla, Lucas, Susan, Deshpande, Shweta, Pagani, Ioanna, Tapia, Roxanne, Cheng, Jan-Fang, Goodwin, Lynne, Pitluck, Sam, Liolios, Konstantinos, Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Han, Cliff, Land, Miriam, Hauser, Loren, Pan, Chongle, Brambilla, Evelyne, Rohde, Manfred, Spring, Stefan, Sikorski, Johannes, Wirth, Reinhard, Detter, John C., Woyke, Tanja ... Klenk, Hans-Peter (2011). Complete genome sequence of the thermophilic sulfur-reducer Desulfurobacterium thermolithotrophum type strain (BSA(T)) from a deep-sea hydrothermal vent. Standards in Genomic Sciences, 5 (3), 407-415. doi: 10.4056/sigs.2465574

Complete genome sequence of the thermophilic sulfur-reducer Hippea maritima type strain (MH2T)

Huntemann, Marcel, Lu, Megan, Nolan, Matt, Lapidus, Alla, Lucas, Susan, Hammon, Nancy, Deshpande, Shweta, Cheng, Jan-Feng, Tapia, Roxanne, Han, Cliff, Goodwin, Lynne, Pitluck, Sam, Liolios, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Ovchinikova, Galina, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Jeffries, Cynthia D., Detter, John C., Brambilla, Evelynne-Marie, Rohde, Manfred, Spring, Stefan, Goker, Markus, Woyke, Tanja, Bristow, James ... Mavromatis, Konstantinos (2011). Complete genome sequence of the thermophilic sulfur-reducer Hippea maritima type strain (MH2T). Standards in Genomic Sciences, 4 (3), 303-311. doi: 10.4056/sigs.1814460

Complete genome sequence of the thermophilic, hydrogen-oxidizing Bacillus tusciae type strain (T2(T)) and reclassification in the new genus, Kyrpidia gen. nov. as Kyrpidia tusciae comb. nov. and emendation of the family Alicyclobacillaceae da Costa and Ra

Klenk, Hans-Peter, Lapidus, Alla, Chertkov, Olga, Copeland, Alex, Del Rio, Tijana Glavina, Nolan, Matt, Lucas, Susan, Chen, Feng, Tice, Hope, Cheng, Jan-Fang, Han, Cliff, Bruce, David, Goodwin, Lynne, Pitluck, Sam, Pati, Amrita, Ivanova, Natalia, Mavromatis, Konstantinos, Daum, Chris, Chen, Amy, Palaniappan, Krishna, Chang, Yun-juan, Land, Miriam, Hauser, Loren, Jeffries, Cynthia D., Detter, John C., Rohde, Manfred, Abt, Birte, Pukall, Rüdiger, Göker, Markus ... Eisen, Jonathan A. (2011). Complete genome sequence of the thermophilic, hydrogen-oxidizing Bacillus tusciae type strain (T2(T)) and reclassification in the new genus, Kyrpidia gen. nov. as Kyrpidia tusciae comb. nov. and emendation of the family Alicyclobacillaceae da Costa and Ra. Standards in Genomic Sciences, 5 (1), 121-134. doi: 10.4056/sigs.2144922

Genome sequence of the moderately thermophilic halophile Flexistipes sinusarabici strain (MAS10(T))

Lapidus, Alla, Chertkov, Olga, Nolan, Matt, Lucas, Susan, Hammon, Nancy, Deshpande, Shweta, Cheng, Jan-Fang, Tapia, Roxanne, Han, Cliff, Goodwin, Lynne, Pitluck, Sam, Liolios, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Huntemann, Marcel, Mavromatis, Konstantinos, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Brambilla, Evelyne, Rohde, Manfred, Abt, Birte, Spring, Stefan, Goker, Markus, Bristow, James, Eisen, Jonathan A. ... Woyke, Tanja (2011). Genome sequence of the moderately thermophilic halophile Flexistipes sinusarabici strain (MAS10(T)). Standards in Genomic Sciences, 5 (1), 86-96. doi: 10.4056/sigs.2235024

Identification of a haloalkaliphilic and thermostable cellulase with improved ionic liquid tolerance

Zhang, Tao, Datta, Supratim, Eichler, Jerry, Ivanova, Natalia, Axen, Seth D., Kerfeld, Cheryl A., Chen, Feng, Kyrpides, Nikos, Hugenholtz, Philip, Cheng, Jan-Fang, Sale, Kenneth L., Simmons, Blake and Rubin, Eddy (2011). Identification of a haloalkaliphilic and thermostable cellulase with improved ionic liquid tolerance. Green Chemistry, 13 (8), 2083-2090. doi: 10.1039/c1gc15193b

Multiple syntrophic interactions in a terephthalate-degrading methanogenic consortium

Lykidis, Athanasios, Chen, Chia-Lung, Tringe, Susannah G., McHardy, Alice C., Copeland, Alex, Kyrpides, Nikos C., Hugenholtz, Philip, Macarie, Hervé, Olmos, Alejandro, Monroy, Oscar and Liu, Wen-Tso (2011). Multiple syntrophic interactions in a terephthalate-degrading methanogenic consortium. ISME Journal, 5 (1), 122-130. doi: 10.1038/ismej.2010.125

Non-contiguous finished genome sequence and contextual data of the filamentous soil bacterium Ktedonobacter racemifer type strain (SOSP1-21(T))

Chang, Yun-Juan, Land, Miriam, Hauser, Loren, Chertkov, Olga, Del Rio, Tijana Galvina, Nolan, Matt, Copeland, Alex, Tice, Hope, Cheng, Jan-Feng, Lucas, Susan, Han, Cliff, Goodwin, Lynne, Pitluck, Sam, Ivanova, Natalia, Ovchinikova, Galina, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Mavromatis, Konstantinos, Liolios, Konstantinos, Brettin, Thomas, Fiebig, Anne, Rohde, Manfred, Abt, Birte, Goker, Markus, Detter, John C., Woyke, Tanja, Bristow, James, Eisen, Jonathan A. ... Lapidus, Alla (2011). Non-contiguous finished genome sequence and contextual data of the filamentous soil bacterium Ktedonobacter racemifer type strain (SOSP1-21(T)). Standards in Genomic Sciences, 5 (1), 97-111. doi: 10.4056/sigs.2114901

Non-contiguous finished genome sequence of the opportunistic oral pathogen Prevotella multisaccharivorax type strain (PPPA20(T))

Pati, Amrita, Gronow, Sabine, Lu, Megan, Lapidus, Alla, Nolan, Matt, Lucas, Susan, Hammon, Nancy, Deshpande, Shweta, Cheng, Jan-Feng, Tapia, Roxanne, Han, Cliff, Goodwin, Lynne, Pitluck, Sam, Liolios, Konstantinos, Pagani, Ioanna, Mavromatis, Konstantinos, Mikhailova, N, Huntemann, Marcel, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Detter, John C., Brambilla, Evelyne-Marie, Rohde, Manfred, Goker, Markus, Woyke, Tanja, Bristow, James, Eisen, Jonathan A. ... Ivanova, Natalia (2011). Non-contiguous finished genome sequence of the opportunistic oral pathogen Prevotella multisaccharivorax type strain (PPPA20(T)). Standards in Genomic Sciences, 5 (1), 41-49. doi: 10.4056/sigs.2164949

Proteome insights into the symbiotic relationship between a captive colony of Nasutitermes corniger and its hindgut microbiome

Burnum, Kristin E., Callister, Stephen J., Nicora, Carrie D., Purvine, Samuel O., Hugenholtz, Philip, Warnecke, Falk, Scheffrahn. Rudolf H., Smith, Richard D. and Lipton, Mary S. (2011). Proteome insights into the symbiotic relationship between a captive colony of Nasutitermes corniger and its hindgut microbiome. ISME Journal, 5 (1), 161-164. doi: 10.1038/ismej.2010.97

Complete genome sequence of Desulfarculus baarsii type strain (2st14(T))

Sun, Hui, Spring, Stefan, Lapidus, Alla, Davenport, Karen, Del Rio, Tijana Glavina, Tice, Hope, Nolan, Matt, Copeland, Alex, Cheng, Jan-Fang, Lucas, Susan, Tapia, Roxanne, Goodwin, Lynne, Pitluck, Sam, Ivanova, Natalia, Pagani, Ionna, Mavromatis, Konstantinos, Ovchinnikova, Galina, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Detter, John C., Han, Cliff, Rohde, Manfred, Brambilla, Evelyne, Goeker, Markus, Woyke, Tanja ... Land, Miriam (2010). Complete genome sequence of Desulfarculus baarsii type strain (2st14(T)). Standards in Genomic Sciences, 3 (3), 276-284. doi: 10.4056/sigs.1243258

Complete genome sequence of Ilyobacter polytropus type strain (CuHbu1(T))

Sikorski, Johannes, Chertkov, Olga, Lapidus, Alla, Nolan, Matt, Lucas, Susan, Del Rio, Tijana Glavina, Tice, Hope, Cheng, Jan-Fang, Tapia, Roxane, Han, Cliff, Goodwin, Lynne, Pitluck, Sam, Liolios, Konstantinos, Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Brambilla, Evelyne, Yasawong, Montri, Rohde, Manfred, Pukall, Ruediger, Spring, Stefan, Goeker, Markus ... Klenk, Hans-Peter (2010). Complete genome sequence of Ilyobacter polytropus type strain (CuHbu1(T)). Standards in Genomic Sciences, 3 (3), 304-314. doi: 10.4056/sigs.1273360

Non-contiguous finished genome sequence of Aminomonas paucivorans type strain (GLU-3(T))

Pitluck, Sam, Yasawong, Montri, Held, Brittany, Lapidus, Alla, Nolan, Matt, Copeland, Alex, Lucas, Susan, Del Rio, Tijana Glavina, Tice, Hope, Cheng, Jan-Fang, Chertkov, Olga, Goodwin, Lynne, Tapia, Roxane, Han, Cliff, Liolios, Konstantinos, Ivanova, Natalia, Mavromatis, Konstantinos, Ovchinnikova, Galina, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Pukall, Ruediger, Spring, Stefan, Rohde, Manfred, Sikorski, Johannes ... Klenk, Hans-Peter (2010). Non-contiguous finished genome sequence of Aminomonas paucivorans type strain (GLU-3(T)). Standards in Genomic Sciences, 3 (3), 285-293. doi: 10.4056/sigs.1253298

Complete genome sequence of Haloterrigena turkmenica type strain (4k T)

Saunders, Elisabeth, Tindall, Brian J., Fähnrich, Regine, Lapidus, Alla, Copeland, Alex, del Rio, Tijana Glavina, Lucas, Susan, Chen, Feng, Tice, Hope, Cheng, Jan-Fang, Han, Cliff, Detter, John C., Bruce, David, Goodwin, Lynne, Chain, Patrick, Pitluck, Sam, Pati, Amrita, Ivanova, Natalia, Mavromatis, Konstantinos, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Brettin, Thomas, Rohde, Manfred, Göker, Markus, Bristow, James ... Kyrpides, Nikos C. (2010). Complete genome sequence of Haloterrigena turkmenica type strain (4k T). Standards in Genomic Sciences, 2 (1), 107-116. doi: 10.4056/sigs.681272

Erratum to: Complete genome sequence of Pirellula staleyi type strain (ATCC 27377 T)

Clum, Alicia, Tindall, Brian J., Sikorski, Johannes, Ivanova, Natalia, Mavromatis, Konstantinos, Lucas, Susan, Glavina Del Rio, Tijana, Nolan, Matt, Chen, Feng, Tice, Hope, Pitluck, Sam, Cheng, Jan-Fang, Chertkov, Olga, Thomas, Brettin, Han, Cliff, Detter, John C., Kuske, Cheryl, Bruce, David, Goodwin, Lynne, Ovchinikova, Galina, Pati, Amrita, Mikhailova, Natalia, Chen, Amy, Palaniappan, Krishna, Land, Miram, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Chain, Patrick ... Lapidus, Alla (2010). Erratum to: Complete genome sequence of Pirellula staleyi type strain (ATCC 27377 T). Standards in Genomic Sciences, 2 (2). doi: 10.4056/sigs.88.1234

Multiple displacement amplification compromises quantitative analysis of metagenomes

Yilmaz, S, Allgaier, M and Hugenholtz, P (2010). Multiple displacement amplification compromises quantitative analysis of metagenomes. Nature Methods, 7 (12), 943-944. doi: 10.1038/nmeth1210-943

Complete genome sequence of Methanothermus fervidus type strain (V24S)

Anderson, Iain, Djao, Olivier Duplex, Misra, Monica, Chertkov, Olga, Nolan, Matt, Lucas, Susan, Lapidus, Alla, Giavina Del Rio, Tijana, Tice, Hope, Cheng, Jan-Fang, Tapia, Roxanne, Han. Cliff, Goodwin, Lynne, Pitluck, Sam, Liolios, Konstantinos, Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Pati, Amrita, Brambilla, Evelyne, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Sikorski, Johannes, Spring, Stefan, Rohde, Manfred ... Kyrpides, Nikos C. (2010). Complete genome sequence of Methanothermus fervidus type strain (V24S). Standards in Genomic Sciences, 3 (3), 315-324. doi: 10.4056/sigs.1283367

Evolutionary relationships of wild hominids recapitulated by gut microbial communities

Ochman, Howard, Worobey, Michael, Kuo, Chih-Horng, Ndjango, Jean-Bosco N., Peeters, Jean-Bosco N., Hahn, Beatrice H. and Hugenholtz, Philip (2010). Evolutionary relationships of wild hominids recapitulated by gut microbial communities. PLoS Biology, 8 (11 Article number e1000546) e1000546, e1000546. doi: 10.1371/journal.pbio.1000546

Complete genome sequence of Methanoplanus petrolearius type strain (SEBR 4847)

Brambilla, Evelyne, Djao, Olivier Duplex, Daligault, Hajnalka, Lapidus, Alla, Lucas, Susan, Hammon, Nancy, Nolan , Matt, Tice, Hope, Cheng, Jan-Fang, Han, Cliff, Tapia, Roxanne, Goodwin, Lynne, Pitluck, Sam, Liolios, Konstantinos, Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Rohde, Manfred, Spring, Stefan, Sikorski, Johannes, Goker, Markus, Woyke, Tanja ... Klenk, Hans-Peter (2010). Complete genome sequence of Methanoplanus petrolearius type strain (SEBR 4847). Standards in Genomic Sciences, 3 (2), 203-211. doi: 10.4056/sigs.1183143

Complete genome sequence of Thermosediminibacter oceani type strain (JW/IW-1228P(T))

Pitluck, Sam, Yasawong, Montri, Munk, Christine, Nolan, Matt, Lapidus, Alla, Lucas, Susan, Del Rio, Tijana Glavina, Tice, Hope, Cheng, Jan-Fang, Bruce, David, Detter, Chris, Tapia, Roxanne, Han, Cliff, Goodwin, Lynne, Liolios, Konstantinos, Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Rohde, Manfred, Spring, Stefan, Sikorski, Johannes, Goeker, Markus ... Klenk, Hans-Peter (2010). Complete genome sequence of Thermosediminibacter oceani type strain (JW/IW-1228P(T)). Standards in Genomic Sciences, 3 (2), 108-116. doi: 10.4056/sigs.1133078

Fixation-free fluorescence in situ hybridization for targeted enrichment of microbial populations

Yilmaz, S, Haroon, MF, Rabkin, BA, Tyson, GW and Hugenholtz, P (2010). Fixation-free fluorescence in situ hybridization for targeted enrichment of microbial populations. The ISME Journal, 4 (10), 1352-1356. doi: 10.1038/ismej.2010.73

Validation of two ribosomal RNA removal methods for microbial metatranscriptomics

He, Shaomei, Wurtzel, Omri, Singh, Kanwar, Froula, Jeff L., Yilmaz, Suzan, Tringe, Susannah G., Wang, Zhong, Chen, Feng, Lindquist, Erika A., Sorek, Rotem and Hugenholtz, Philip (2010). Validation of two ribosomal RNA removal methods for microbial metatranscriptomics. Nature Methods, 7 (10), 807-812. doi: 10.1038/NMETH.1507

Complete genome sequence of Olsenella uli type strain (VPI D76D-27C(T))

Goeker, Markus, Held, Brittany, Lucas, Susan, Nolan, Matt, Yasawong, Montri, Del Rio, Tijana Glavina, Tice, Hope, Cheng, Jan-Fang, Bruce, David, Detter, John C., Tapia, Roxanne, Han, Cliff, Goodwin, Lynne, Pitluck, Sam, Liolios, Konstantinos, Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Rohde, Manfred, Sikorski, Johannes, Pukall, Ruediger, Woyke, Tanja ... Lapidus, Alla (2010). Complete genome sequence of Olsenella uli type strain (VPI D76D-27C(T)). Standards in Genomic Sciences, 3 (1), 76-84. doi: 10.4056/sigs.1082860

Adaptation to herbivory by the Tammar wallaby includes bacterial and glycoside hydrolase profiles different from other herbivores

Pope, P. B., Denman, S. E., Jones, M., Tringe, S. G., Barry, K., Malfatti, S. A., McHardy, A. C., Cheng, J. F., Hugenholtz, P., McSweeney, C. S. and Morrison, M. (2010). Adaptation to herbivory by the Tammar wallaby includes bacterial and glycoside hydrolase profiles different from other herbivores. Proceedings of the National Academy of Sciences of the United States of America, 107 (33), 14793-1-14798-6. doi: 10.1073/pnas.1005297107

Complete genome sequence of Acidaminococcus fermentans type strain (VR4)

Chang, Yun-Juan, Pukall, Rüdiger, Saunders, Elizabeth, Lapidus, Alla, Copeland, Alex, Nolan, Matt, Glavina Del Rio, Tijana, Lucas, Susan, Chen, Feng, Tice, Hope, Cheng, Jan-Fang, Han. Cliff, Detter, John C., Bruce, David, Goodwin, Lynne, Pitluck, Sam, Mikhailova, Natalia, Liolios, Konstantinos, Pati, Amrita, Ivanova, Natalia, Mavromatis, Konstantinos, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Jeffries, Cynthia D., Brettin, Thomas, Rohde, Manfred, Goker, Markus ... Klenk, Hans-Peter (2010). Complete genome sequence of Acidaminococcus fermentans type strain (VR4). Standards in Genomic Sciences, 3 (1), 1-14. doi: 10.4056/sigs.1002553

Complete genome sequence of Cellulomonas flavigena type strain (134)

Abt, Birte, Foster, Brian, Lapidus, Alla, Clum, Alicia, Sun, Hui, Pukall, Rüdiger, Lucas, Susan, Giavina Del Rio, Tijana, Nolan, Matt, Tice, Hope, Cheng, Jan-Fang, Pitluck, Sam, Liolios, Konstantinos, Ivanova, Natalia, Mavromatis, Konstantinos, Ovchinnikova, Galina, Pati, Amrita, Goodwin, Lynne, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Rohde, Manfred, Goker, Markus, Woyke, Tanja, Bristow, James, Elsen, Jonathan A. ... Klenk, Hans-Peter (2010). Complete genome sequence of Cellulomonas flavigena type strain (134). Standards in Genomic Sciences, 3 (1), 15-25. doi: 10.4056/sigs.1012662

A call for standardized classification of metagenome projects

Ivanova, Natalia, Tringe, Susannah G., Liolios, Konstantinos, Liu, Wen-Tso, Morrison, Norman, Hugenholtz, Philip and Kyrpides, Nikos C. (2010). A call for standardized classification of metagenome projects. Environmental Microbiology, 12 (7), 1803-1805. doi: 10.1111/j.1462-2920.2010.02270.x

Complete genome sequence of Aminobacterium colombiense type strain (ALA-1)

Chertkov, Olga, Sikorski, Johannes, Brambilla, Evelyne, Lapidus, Alla, Copeland, Alex, Glavina Del Rio, Tijana, Nolan, Matt, Lucas, Susan, Tice, Hope, Cheng, Jan-Fang, Han, Cliff, Detter, John C., Bruce, David, Tapia, Roxanne, Goodwin, Lynne, Pitluck, Sam, Liolios, Konstantinos, Ivanova, Natalia, Mavromatis, Konstantinos, Ovchinnikova, Galina, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Spring, Stefan, Rohde, Manfred ... Klenk, Hans-Peter (2010). Complete genome sequence of Aminobacterium colombiense type strain (ALA-1). Standards in Genomic Sciences, 2 (3), 280-289. doi: 10.4056/sigs.902116

Complete genome sequence of Archaeoglobus profundus type strain (AV18(T))

von Jan, Mathias, Lapidus, Alla, Del Rio, Tijana Glavina, Copeland, Alex, Tice, Hope, Cheng, Jan-Fang, Lucas, Susan, Chen, Feng, Nolan, Matt, Goodwin, Lynne, Han, Cliff, Pitluck, Sam, Liolios, Konstantinos, Ivanova, Natalia, Mavromatis, Konstantinos, Ovchinnikova, Galina, Chertkov, Olga, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Saunders, Elizabeth, Brettin, Thomas, Detter, John C., Chain, Patrick, Eichinger, Konrad ... Klenk, Hans-Peter (2010). Complete genome sequence of Archaeoglobus profundus type strain (AV18(T)). Standards in Genomic Sciences, 2 (3), 327-346. doi: 10.4056/sigs.942153

Complete genome sequence of Brachyspira murdochii type strain (56-150(T))

Pati, Amrita, Sikorski, Johannes, Gronow, Sabine, Munk, Christine, Lapidus, Alla, Copeland, Alex, Del Tio, Tijana Glavina, Nolan, Matt, Lucas, Susan, Chen, Feng, Tice, Hope, Cheng, Jan-Fang, Han, Cliff, Detter, John C., Bruce, David, Tapia, Roxanne, Goodwin, Lynne, Pitluck, Sam, Liolios, Konstantinos, Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Spring, Stefan ... Klenk, Hans-Peter (2010). Complete genome sequence of Brachyspira murdochii type strain (56-150(T)). Standards in Genomic Sciences, 2 (3), 260-269. doi: 10.4056/sigs.831993

Complete genome sequence of Thermobispora bispora type strain (R51(T))

Liolios, Konstantinos, Sikorski, Johannes, Jando, Marlen, Lapidus, Alla, Copeland, Alex, Del Rio, Tijana Glavina, Nolan, Matt, Lucas, Susan, Tice, Hope, Cheng, Jan-Fang, Han, Cliff, Woyke, Tanja, Goodwin, Lynne, Pitluck, Sam, Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Chertkov, Olga, Kuske, Cheryl, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Detter, John C., Brettin, Thomas, Rohde, Manfred, Goeker, Markus ... Kyrpides, Nikos C. (2010). Complete genome sequence of Thermobispora bispora type strain (R51(T)). Standards in Genomic Sciences, 2 (3), 318-326. doi: 10.4056/sigs.962171

Complete genome sequence of Thermosphaera aggregans type strain (M11TL(T))

Spring, Stefan, Rachel, Reinhard, Lapidus, Alla, Davenport, Karen, Tice, Hope, Copeland, Alex, Cheng, Jan-Fang, Lucas, Susan, Chen, Feng, Nolan, Matt, Bruce, David, Goodwin, Lynne, Pitluck, Sam, Ivanova, Natalia, Mavromatis, Konstantinos, Ovchinnikova, Galina, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia C., Brettin, Thomas, Detter, John C., Tapia, Roxanne, Han, Cliff, Heimerl, Thomas, Weikl, Fabian ... Klenk, Hans-Peter (2010). Complete genome sequence of Thermosphaera aggregans type strain (M11TL(T)). Standards in Genomic Sciences, 2 (3), 245-259. doi: 10.4056/sigs.821804

Strategies for enhancing the effectiveness of metagenomic-based enzyme discovery in lignocellulolytic microbial communities

DeAngelis, Kristen M., Gladden, John M., Allgaier, Martin, D'haeseleer, Patrik, Fortney, Julian L., Reddy, Amitha, Hugenholtz, Philip, Singer, Steven W., Vander Gheynst, Jean S., Silver, Whendee L., Simmons, Blake A. and Hazen, Terry C. (2010). Strategies for enhancing the effectiveness of metagenomic-based enzyme discovery in lignocellulolytic microbial communities. BioEnergy Research, 3 (2), 146-158. doi: 10.1007/s12155-010-9089-z

Experimental factors affecting PCR-based estimates of microbial species richness and evenness

Engelbrektson, Anna, Kunin, Victor, Wrighton, Kelly C., Zvenigorodsky, Natasha, Chen, Feng, Ochman, Howard and Hugenholtz, Philip (2010). Experimental factors affecting PCR-based estimates of microbial species richness and evenness. ISME Journal, 4 (5), 642-647. doi: 10.1038/ismej.2009.153

Metatranscriptomic array analysis of 'Candidatus Accumulibacter phosphatis'-enriched enhanced biological phosphorus removal sludge

He, Shaomei, Kunin, Victor, Haynes, Matthew, Martin, Hector Garcia, Ivanova, Natalia, Rohwer, Forest, Hugenholtz, Philip and McMahon, Katherine D. (2010). Metatranscriptomic array analysis of 'Candidatus Accumulibacter phosphatis'-enriched enhanced biological phosphorus removal sludge. Environmental Microbiology, 12 (5), 1205-1217. doi: 10.1111/j.1462-2920.2010.02163.x

Complete genome sequence of Nakamurella multipartita type strain (Y-104(T))

Tice, Hope, Mayilraj, Shanmugam, Sims, David, Lapidus, Alla, Nolan, Matt, Lucas, Susan, Del Rio, Tijana Glavina, Copeland, Alex, Cheng, Jan-Fang, Meincke, Linda, Bruce, David, Goodwin, Lynne, Pitluck, Sam, Ivanova, Natalia, Mavromatis, Konstantinos, Ovchinnikova, Galina, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Detter, John C., Brettin, Thomas, Rohde, Manfred, Goeker, Markus, Bristow, Jim, Eisen, Jonathan A. ... Chen, Feng (2010). Complete genome sequence of Nakamurella multipartita type strain (Y-104(T)). Standards in Genomic Sciences, 2 (2), 168-175. doi: 10.4056/sigs.721316

Complete genome sequence of Sebaldella termitidis type strain (NCTC 11300(T))

Harmon-Smith, Miranda, Celia, Laura, Chertkov, Olga, Lapidus, Alla, Copeland, Alex, Del Rio, Tijana Glavina, Nolan, Matt, Lucas, Susan, Tice, Hope, Cheng, Jan-Fang, Han, Cliff, Detter, John C., Bruce, David, Goodwin, Lynne, Pitluck, Sam, Pati, Amrita, Liolios, Konstantinos, Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Brettin, Thomas, Goeker, Markus, Beck, Brian ... Chen, Feng (2010). Complete genome sequence of Sebaldella termitidis type strain (NCTC 11300(T)). Standards in Genomic Sciences, 2 (2), 220-227. doi: 10.4056/sigs.811799

Complete genome sequence of Segniliparus rotundus type strain (CDC 1076(T))

Sikorski, Johannes, Lapidus, Alla, Copeland, Alex, Misra, Monica, Del Rio, Tijana Glavina, Nolan, Matt, Lucas, Susan, Chen, Feng, Tice, Hope, Cheng, Jan-Fang, Jando, Marlen, Schneider, Susanne, Bruce, David, Goodwin, Lynne, Pitluck, Sam, Liolios, Konstantinos, Mikhailova, Natalia, Pati, Amrita, Ivanova, Natalia, Mavromatis, Konstantinos, Chen, Amy, Palaniappan, Krishna, Chertkov, Olga, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Brettin, Thomas, Detter, John C. ... Klenk, Hans-Peter (2010). Complete genome sequence of Segniliparus rotundus type strain (CDC 1076(T)). Standards in Genomic Sciences, 2 (2), 203-211. doi: 10.4056/sigs.791633

Complete genome sequence of Spirosoma linguale type strain (1(T))

Lail, Kathleen, Sikorski, Johannes, Saunders, Elizabeth, Lapidus, Alla, Del Rio, Tijana Glavina, Copeland, Alex, Tice, Hope, Cheng, Jan-Fang, Lucas, Susan, Nolan, Matt, Bruce, David, Goodwin, Lynne, Pitluck, Sam, Ivanova, Natalia, Mavromatis, Konstantinos, Ovchinnikova, Galina, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Chain, Patrick, Brettin, Thomas, Detter, John C., Schuetze, Andrea, Rohde, Manfred, Tindall, Brian J. ... Chen, Feng (2010). Complete genome sequence of Spirosoma linguale type strain (1(T)). Standards in Genomic Sciences, 2 (2), 176-185. doi: 10.4056/sigs.741334

Complete genome sequence of Xylanimonas cellulosilytica type strain (XIL07(T))

Foster, Brian, Pukall, Ruediger, Abt, Birte, Nolan, Matt, Del Rio, Tijana Glavina, Chen, Feng, Lucas, Susan, Tice, Hope, Pitluck, Sam, Cheng, Jan-Fang, Chertkov, Olga, Brettin, Thomas, Han, Cliff, Detter, John C., Bruce, David, Goodwin, Lynne, Ivanova, Natalia, Mavromatis, Konstantinos, Pati, Amrita, Mikhailova, Natalia, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Chain, Patrick, Rohde, Manfred, Goeker, Markus ... Lapidus, Alla (2010). Complete genome sequence of Xylanimonas cellulosilytica type strain (XIL07(T)). Standards in Genomic Sciences, 2 (1), 1-8. doi: 10.4056/sigs.571102

Complete genome sequence of Vulcanisaeta distributa type strain (IC-017(T))

Mavromatis, Konstantinos, Sikorski, Johannes, Pabst, Elke, Teshima, Hazuki, Lapidus, Alla, Lucas, Susan, Nolan, Matt, Del Rio, Tijana Glavina, Cheng, Jan-Fang, Bruce, David, Goodwin, Lynne, Pitluck, Sam, Liolios, Konstantinos, Ivanova, Natalia, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Rohde, Manfred, Spring, Stefan, Goeker, Markus, Wirth, Reinhard, Woyke, Tanja, Bristow, James, Eisen, Jonathan A. ... Kyrpides, Nikos C. (2010). Complete genome sequence of Vulcanisaeta distributa type strain (IC-017(T)). Standards in Genomic Sciences, 3 (2), 117-125. doi: 10.4056/sigs.1113067

Targeted discovery of glycoside hydrolases from a switchgrass-adapted compost community

Allagier, Martin, Reddy, Amitha, Park, Joshua I., Ivanova, Natalia, D'haeseleer, Patrik, Lowry, Steve, Sapra, Rajat, Hazen, Terry C., Simmons, Blake A., VanderGheynst, Jean S. and Hugenholtz, Philip (2010). Targeted discovery of glycoside hydrolases from a switchgrass-adapted compost community. PLoS One, 5 (1) e8812, e8812-1-e8812-9. doi: 10.1371/journal.pone.0008812

Complete genome sequence of 'Thermobaculum terrenum' type strain (YNP1(T))

Kiss, Hajnalka, Cleland, David, Lapidus, Alla, Lucas, Susan, Del Rio, Tijana Glavina, Nolan, Matt, Tice, Hope, Han, Cliff, Goodwin, Lynne, Pitluck, Sam, Liolios, Konstantinos, Ivanova, Natalia, Mavromatis, Konstantinos, Ovchinnikova, Galina, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Lu, Megan, Brettin, Thomas, Detter, John C., Goeker, Markus, Tindall, Brian J., Beck, Brian, McDermott, Timothy R., Woyke, Tanja ... Cheng, Jan-Fang (2010). Complete genome sequence of 'Thermobaculum terrenum' type strain (YNP1(T)). Standards in Genomic Sciences, 3 (2), 153-162. doi: 10.4056/sigs.1153107

Complete genome sequence of Acetohalobium arabaticum type strain (Z-7288(T))

Sikorski, Johannes, Lapidus, Alla, Chertkov, Olga, Lucas, Susan, Copeland, Alex, Del Rio, Tijana Glavina, Nolan, Matt, Tice, Hope, Cheng, Jan-Fang, Han, Cliff, Brambilla, Evelyne, Pitluck, Sam, Liolios, Konstantinos, Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Pati, Amrita, Bruce, David, Detter, Chris, Tapia, Roxanne, Goodwin, Lynne, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Rohde, Manfred, Goeker, Markus ... Klenk, Hans-Peter (2010). Complete genome sequence of Acetohalobium arabaticum type strain (Z-7288(T)). Standards in Genomic Sciences, 3 (1), 57-65. doi: 10.4056/sigs.1062906

Complete genome sequence of Alicyclobacillus acidocaldarius type strain (104-IA(T))

Mavromatis, Konstantinos, Sikorski, Johannes, Lapidus, Alla, Del Rio, Tijana Glavina, Copeland, Alex, Tice, Hope, Cheng, Jan-Fang, Lucas, Susan, Chen, Feng, Nolan, Matt, Bruce, David, Goodwin, Lynne, Pitluck, Sam, Ivanova, Natalia, Ovchinnikova, Galina, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Chain, Patrick, Meincke, Linda, Sims, David, Chertkov, Olga, Han, Cliff, Brettin, Thomas, Detter, John C. ... Kyrpides, Nikos C. (2010). Complete genome sequence of Alicyclobacillus acidocaldarius type strain (104-IA(T)). Standards in Genomic Sciences, 2 (1), 9-18. doi: 10.4056/sigs.591104

Complete genome sequence of Arcanobacterium haemolyticum type strain (11018(T))

Yasawong, Montri, Teshima, Hazuki, Lapidus, Alla, Nolan, Matt, Lucas, Susan, Del Rio, Tijana Glavina, Tice, Hope, Cheng, Jan-Fang, Bruce, David, Detter, Chris, Tapia, Roxanne, Han, Cliff, Goodwin, Lynne, Pitluck, Sam, Liolios, Konstantinos, Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Rohde, Manfred, Sikorski, Johannes, Pukall, Ruediger, Goeker, Markus ... Klenk, Hans-Peter (2010). Complete genome sequence of Arcanobacterium haemolyticum type strain (11018(T)). Standards in Genomic Sciences, 3 (2), 126-135. doi: 10.4056/sigs.1123072

Complete genome sequence of Arcobacter nitrofigilis type strain (CIT)

Pati, Amrita, Gronow, Sabine, Lapidus, Alla, Copeland, Alex, Del Rio, Tijana Glavina, Nolan, Matt, Lucas, Susan, Tice, Hope, Cheng, Jan-Fang, Han, Cliff, Chertkov, Olga, Bruce, David, Tapia, Roxanne, Goodwin, Lynne, Pitluck, Sam, Liolios, Konstantinos, Ivanova, Natalia, Mavromatis, Konstantinos, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Detter, John C., Rohde, Manfred, Goeker, Markus, Bristow, James, Eisen, Jonathan A. ... Kyrpides, Nikos C. (2010). Complete genome sequence of Arcobacter nitrofigilis type strain (CIT). Standards in Genomic Sciences, 2 (3), 300-308. doi: 10.4056/sigs.912121

Complete genome sequence of Atopobium parvulum type strain (IPP 1246(T)) (vol 1, pg 166, 2009)

Copeland, Alex, Sikorski, Johannes, Lapidus, Alla, Nolan, Matt, Del Rio, Tijana Glavina, Lucas, Susan, Chen, Feng, Tice, Hope, Pitluck, Sam, Cheng, Jan-Fang, Pukall, Ruediger, Chertkov, Olga, Brettin, Thomas, Han, Cliff, Kuske, Cheryl, Bruce, David, Goodwin, Lynne, Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Chen, Amy, Palaniappan, Krishna, Chain, Patrick, Rohde, Manfred, Goeker, Markus, Bristow, James, Eisen, Jonathan A., Markowitz, Victor, Hugenholtz, Philip ... Detter, John C. (2010). Complete genome sequence of Atopobium parvulum type strain (IPP 1246(T)) (vol 1, pg 166, 2009). Standards in Genomic Sciences, 2 (3), 361-362. doi: 10.4056/sigs.992408

Complete genome sequence of Chitinophaga pinensis type strain (UQM 2034(T))

Del Rio, Tijana Glavina, Abt, Birte, Spring, Stefan, Lapidus, Alla, Nolan, Matt, Tice, Hope, Copeland, Alex, Cheng, Jan-Fang, Chen, Feng, Bruce, David, Goodwin, Lynne, Pitluck, Sam, Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Chain, Patrick, Saunders, Elizabeth, Detter, John C., Brettin, Thomas, Rohde, Manfred, Goeker, Markus, Bristow, Jim ... Lucas, Susan (2010). Complete genome sequence of Chitinophaga pinensis type strain (UQM 2034(T)). Standards in Genomic Sciences, 2 (1), 87-95. doi: 10.4056/sigs.661199

Complete genome sequence of Conexibacter woesei type strain (ID131577(T))

Pukall, Ruediger, Lapidus, Alla, Del Rio, Tijana Glavina, Copeland, Alex, Tice, Hope, Cheng, Jan-Fang, Lucas, Susan, Chen, Feng, Nolan, Matt, Bruce, David, Goodwin, Lynne, Pitluck, Sam, Mavromatis, Konstantinos, Ivanova, Natalia, Ovchinnikova, Galina, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Chain, Patrick, Meincke, Linda, Sims, David, Brettin, Thomas, Detter, John C., Rohde, Manfred, Goeker, Markus ... Hugenholtz, Philip (2010). Complete genome sequence of Conexibacter woesei type strain (ID131577(T)). Standards in Genomic Sciences, 2 (2), 212-219. doi: 10.4056/sigs.751339

Complete genome sequence of Coraliomargarita akajimensis type strain (04OKA010-24(T))

Mavromatis, Konstantinos, Abt, Birte, Brambilla, Evelyne, Lapidus, Alla, Copeland, Alex, Deshpande, Shweta, Nolan, Matt, Lucas, Susan, Tice, Hope, Cheng, Jan-Fang, Han, Cliff, Detter, John C., Woyke, Tanja, Goodwin, Lynne, Pitluck, Sam, Held, Brittany, Brettin, Thomas, Tapia, Roxanne, Ivanova, Natalia, Mikhailova, Natalia, Pati, Amrita, Liolios, Konstantinos, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Rohde, Manfred ... Kyrpides, Nikos C. (2010). Complete genome sequence of Coraliomargarita akajimensis type strain (04OKA010-24(T)). Standards in Genomic Sciences, 2 (3), 290-299. doi: 10.4056/sigs.952166

Complete genome sequence of Denitrovibrio acetiphilus type strain (N2460(T))

Kiss, Hajnalka, Lang, Elke, Lapidus, Alla, Copeland, Alex, Nolan, Matt, Del Rio, Tijana Glavina, Chen, Feng, Lucas, Susan, Tice, Hope, Cheng, Jan-Fang, Han, Cliff, Goodwin, Lynne, Pitluck, Sam, Liolios, Konstantinos, Pati, Amrita, Ivanova, Natalia, Mavromatis, Konstantinos, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Detter, John C., Brettin, Thomas, Spring, Stefan, Rohde, Manfred, Goeker, Markus, Woyke, Tanja ... Klenk, Hans-Peter (2010). Complete genome sequence of Denitrovibrio acetiphilus type strain (N2460(T)). Standards in Genomic Sciences, 2 (3), 270-279. doi: 10.4056/sigs.892105

Complete genome sequence of Desulfohalobium retbaense type strain (HR100T)

Spring, Stefan, Nolan, Matt, Lapidus, Alla, Del Rio, Tijana Glavina, Copeland, Alex, Tice, Hope, Cheng, Jan-Fang, Lucas, Susan, Land, Miriam, Chen, Feng, Bruce, David, Goodwin, Lynne, Pitluck, Sam, Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Munk, Christine, Kiss, Hajnalka, Chain, Patrick, Han, Cliff, Brettin, Thomas, Detter, John C., Schueler, Esther ... Klenk, Hans-Peter (2010). Complete genome sequence of Desulfohalobium retbaense type strain (HR100T). Standards in Genomic Sciences, 2 (1), 38-48. doi: 10.4056/sigs.581048

Complete genome sequence of Ferrimonas balearica type strain (PAT(T))

Nolan, Matt, Sikorski, Johannes, Davenport, Karen, Lucas, Susan, Del Rio, Tijana Glavina, Tice, Hope, Cheng, Jan-Fang, Goodwin, Lynne, Pitluck, Sam, Liolios, Konstantinos, Ivanova, Natalia, Mavromatis, Konstantinos, Ovchinnikova, Galina, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Tapia, Roxanne, Brettin, Thomas, Detter, John C., Han, Cliff, Yasawong, Montri, Rohde, Manfred, Tindall, Brian J., Goeker, Markus, Woyke, Tanja ... Lapidus, Alla (2010). Complete genome sequence of Ferrimonas balearica type strain (PAT(T)). Standards in Genomic Sciences, 3 (2), 174-182. doi: 10.4056/sigs.1161239

Complete genome sequence of Geodermatophilus obscurus type strain (G-20(T))

Ivanova, Natalia, Sikorski, Johannes, Jando, Marlen, Munk, Christine, Lapidus, Alla, Del Rio, Tijana Glavina, Copeland, Alex, Tice, Hope, Cheng, Jan-Fang, Lucas, Susan, Chen, Feng, Nolan, Matt, Bruce, David, Goodwin, Lynne, Pitluck, Sam, Mavromatis, Konstantinos, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Meincke, Linda, Brettin, Thomas, Detter, John C., Rohde, Manfred, Goeker, Markus ... Klenk, Hans-Peter (2010). Complete genome sequence of Geodermatophilus obscurus type strain (G-20(T)). Standards in Genomic Sciences, 2 (2), 158-167. doi: 10.4056/sigs.711311

Complete genome sequence of Gordonia bronchialis type strain (3410(T))

Ivanova, Natalia, Sikorski, Johannes, Jando, Marlen, Lapidus, Alla, Nolan, Matt, Lucas, Susan, Del Rio, Tijana Glavina, Tice, Hope, Copeland, Alex, Cheng, Jan-Fang, Chen, Feng, Bruce, David, Goodwin, Lynne, Pitluck, Sam, Mavromatis, Konstantinos, Ovchinnikova, Galina, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Chain, Patrick, Saunders, Elizabeth, Han, Cliff, Detter, John C., Brettin, Thomas, Rohde, Manfred ... Kyrpides, Nikos C. (2010). Complete genome sequence of Gordonia bronchialis type strain (3410(T)). Standards in Genomic Sciences, 2 (1), 19-28. doi: 10.4056/sigs.611106

Complete genome sequence of Haliangium ochraceum type strain (SMP-2(T))

Ivanova, Natalia, Daum, Chris, Lang, Elke, Abt, Birte, Kopitz, Markus, Saunders, Elizabeth, Lapidus, Alla, Lucas, Susan, Del Rio, Tijana Glavina, Nolan, Matt, Tice, Hope, Copeland, Alex, Cheng, Jan-Fang, Chen, Feng, Bruce, David, Goodwin, Lynne, Pitluck, Sam, Mavromatis, Konstantinos, Pati, Amrita, Mikhailova, Natalia, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Detter, John C., Brettin, Thomas, Rohde, Manfred ... Klenk, Hans-Peter (2010). Complete genome sequence of Haliangium ochraceum type strain (SMP-2(T)). Standards in Genomic Sciences, 2 (1), 96-106. doi: 10.4056/sigs.69.1277

Complete genome sequence of Haloterrigena turkmenica type strain (4k(T))

Saunders, Elisabeth, Tindall, Brian J., Faehnrich, Regine, Lapidus, Alla, Copeland, Alex, Del Rio, Tijana Glavina, Lucas, Susan, Chen, Feng, Tice, Hope, Cheng, Jan-Fang, Han, Cliff, Detter, John C., Bruce, David, Goodwin, Lynne, Chain, Patrick, Pitluck, Sam, Pati, Amrita, Ivanova, Natalia, Mavromatis, Konstantinos, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Brettin, Thomas, Rohde, Manfred, Goeker, Markus, Bristow, James ... Kyrpides, Nikos C. (2010). Complete genome sequence of Haloterrigena turkmenica type strain (4k(T)). Standards in Genomic Sciences, 2 (1), 107-116. doi: 10.4056/sigs.68923

Complete genome sequence of Ignisphaera aggregans type strain (AQ1.S1(T))

Goeker, Markus, Held, Brittany, Lapidus, Alla, Nolan, Matt, Spring, Stefan, Yasawong, Montri, Lucas, Susan, Del Rio, Tijana Glavina, Tice, Hope, Cheng, Jan-Fang, Goodwin, Lynne, Tapia, Roxanne, Pitluck, Sam, Liolios, Konstantinos, Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Brambilla, Evelyne, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Brettin, Thomas, Detter, John C., Han, Cliff, Rohde, Manfred ... Klenk, Hans-Peter (2010). Complete genome sequence of Ignisphaera aggregans type strain (AQ1.S1(T)). Standards in Genomic Sciences, 3 (1), 66-75. doi: 10.4056/sigs.1072907

Complete genome sequence of Intrasporangium calvum type strain (7 KIPT)

Del Rio, Tijana Glavina, Chertkov, Olga, Yasawong, Montri, Lucas, Susan, Deshpande, Shweta, Cheng, Jan-Fang, Detter, Chris, Tapia, Roxanne, Han, Cliff, Goodwin, Lynne, Pitluck, Sam, Liolios, Konstantinos, Ivanova, Natalia, Mavromatis, Konstantinos, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Rohde, Manfred, Pukall, Ruediger, Sikorski, Johannes, Goeker, Markus, Woyke, Tanja, Bristow, James, Eisen, Jonathan A., Markowitz, Victor ... Lapidus, Alla (2010). Complete genome sequence of Intrasporangium calvum type strain (7 KIPT). Standards in Genomic Sciences, 3 (3), 294-303. doi: 10.4056/sigs.1263355

Complete genome sequence of Kribbella flavida type strain (IFO 14399(T))

Pukall, Ruediger, Lapidus, Alla, Del Rio, Tijana Glavina, Copeland, Alex, Tice, Hope, Cheng, Jan-Fang, Lucas, Susan, Chen, Feng, Nolan, Matt, LaButti, Kurt, Pati, Amrita, Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Pitluck, Sam, Bruce, David, Goodwin, Lynne, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Chen, Amy, Palaniappan, Krishna, Chain, Patrick, Rohde, Manfred, Goeker, Markus, Bristow, Jim, Eisen, Jonathan A., Markowitz, Victor ... Brettin, Thomas (2010). Complete genome sequence of Kribbella flavida type strain (IFO 14399(T)). Standards in Genomic Sciences, 2 (2), 186-193. doi: 10.4056/sigs.731321

Complete genome sequence of Meiothermus ruber type strain (21(T))

Tindall, Brian J., Sikorski, Johannes, Lucas, Susan, Goltsman, Eugene, Copeland, Alex, Del Rio, Tijana Glavina, Nolan, Matt, Tice, Hope, Cheng, Jan-Fang, Han, Cliff, Pitluck, Sam, Liolios, Konstantinos, Ivanova, Natalia, Mavromatis, Konstantinos, Ovchinnikova, Galina, Pati, Amrita, Faehnrich, Regine, Goodwin, Lynne, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Rohde, Manfred, Goeker, Markus, Woyke, Tanja, Bristow, James, Eisen, Jonathan A. ... Lapidus, Alla (2010). Complete genome sequence of Meiothermus ruber type strain (21(T)). Standards in Genomic Sciences, 3 (1), 26-36. doi: 10.4056/sigs.1032748

Complete genome sequence of Meiothermus silvanus type strain (VI-R2(T))

Sikorski, Johannes, Tindall, Brian J., Lowry, Stephen, Lucas, Susan, Nolan, Matt, Copeland, Alex, Del Rio, Tijana Glavina, Tice, Hope, Cheng, Jan-Fang, Han, Cliff, Pitluck, Sam, Liolios, Konstantinos, Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Pati, Amrita, Goodwin, Lynne, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Rohde, Manfred, Goeker, Markus, Woyke, Tanja, Bristow, James, Eisen, Jonathan A., Markowitz, Victor ... Lapidus, Alla (2010). Complete genome sequence of Meiothermus silvanus type strain (VI-R2(T)). Standards in Genomic Sciences, 3 (1), 37-46. doi: 10.4056/sigs.1042812

Complete genome sequence of Nocardiopsis dassonvillei type strain (IMRU 509(T))

Sun, Hui, Lapidus, Alla, Nolan, Matt, Lucas, Susan, Del Rio, Tijana Glavina, Tice, Hope, Cheng, Jan-Fang, Tapia, Roxane, Han, Cliff, Goodwin, Lynne, Pitluck, Sam, Pagani, Ioanna, Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Djao, Olivier Duplex Ngatchou, Rohde, Manfred, Sikorski, Johannes, Goeker, Markus, Woyke, Tanja, Bristow, James, Eisen, Jonathan A. ... Klenk, Hans-Peter (2010). Complete genome sequence of Nocardiopsis dassonvillei type strain (IMRU 509(T)). Standards in Genomic Sciences, 3 (3), 325-336. doi: 10.4056/sigs.1363462

Complete genome sequence of Planctomyces limnophilus type strain (Mu 290(T))

LaButti, Kurt, Sikorski, Johannes, Schneider, Susanne, Nolan, Matt, Lucas, Susan, Del Rio, Tijana Glavina, Tice, Hope, Cheng, Jan-Fang, Goodwin, Lynne, Pitluck, Sam, Liolios, Konstantinos, Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Tindall, Brian J., Rohde, Manfred, Goeker, Markus, Woyke, Tanja, Bristow, James, Eisen, Jonathan A., Markowitz, Victor, Hugenholtz, Philip ... Lapidus, Alla (2010). Complete genome sequence of Planctomyces limnophilus type strain (Mu 290(T)). Standards in Genomic Sciences, 3 (1), 47-56. doi: 10.4056/sigs.1052813

Complete genome sequence of Sphaerobacter thermophilus type strain (S 6022(T))

Pati, Amrita, LaButti, Kurt, Pukall, Ruediger, Nolan, Matt, Del Rio, Tijana Glavina, Tice, Hope, Cheng, Jan-Fang, Lucas, Susan, Chen, Feng, Copeland, Alex, Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Pitluck, Sam, Bruce, David, Goodwin, Lynne, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Chen, Amy, Palaniappan, Krishna, Chain, Patrick, Brettin, Thomas, Sikorski, Johannes, Rohde, Manfred, Goeker, Markus, Bristow, Jim, Eisen, Jonathan A. ... Lapidus, Alla (2010). Complete genome sequence of Sphaerobacter thermophilus type strain (S 6022(T)). Standards in Genomic Sciences, 2 (1), 49-56. doi: 10.4056/sigs.601105

Complete genome sequence of Spirochaeta smaragdinae type strain (SEBR 4228(T))

Mavromatis, Konstantinos, Yasawong, Montri, Chertkov, Olga, Lapidus, Alla, Lucas, Susan, Nolan, Matt, Del Rio, Tijana Glavina, Tice, Hope, Cheng, Jan-Fang, Pitluck, Sam, Liolios, Konstantinos, Ivanova, Natalia, Tapia, Roxanne, Han, Cliff, Bruce, David, Goodwin, Lynne, Pati, Amrita, Chen, Ami, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Detter, John C., Rohde, Manfred, Brambilla, Evelyne, Spring, Stefan, Goeker, Markus, Sikorski, Johannes ... Kyrpides, Nikos C. (2010). Complete genome sequence of Spirochaeta smaragdinae type strain (SEBR 4228(T)). Standards in Genomic Sciences, 3 (2), 136-144. doi: 10.4056/sigs.1143106

Complete genome sequence of Streptosporangium roseum type strain (NI 9100(T))

Nolan, Matt, Sikorski, Johannes, Jando, Marlen, Lucas, Susan, Lapidus, Alla, Del Rio, Tijana Glavina, Chen, Feng, Tice, Hope, Pitluck, Sam, Cheng, Jan-Fang, Chertkov, Olga, Sims, David, Meincke, Linda, Brettin, Thomas, Han, Cliff, Detter, John C., Bruce, David, Goodwin, Lynne, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Chen, Amy, Palaniappan, Krishna, Chain, Patrick, Rohde, Manfred ... Klenk, Hans-Peter (2010). Complete genome sequence of Streptosporangium roseum type strain (NI 9100(T)). Standards in Genomic Sciences, 2 (1), 29-37. doi: 10.4056/sigs.631049

Complete genome sequence of Sulfurimonas autotrophica type strain (OK10(T))

Sikorski, Johannes, Munk, Christine, Lapidus, Alla, Djao, Olivier Duplex Ngatchou, Lucas, Susan, Del Rio, Tijana Glavina, Nolan, Matt, Tice, Hope, Han, Cliff, Cheng, Jan-Fang, Tapia, Roxanne, Goodwin, Lynne, Pitluck, Sam, Liolios, Konstantinos, Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Pati, Amrita, Sims, David, Meincke, Linda, Brettin, Thomas, Detter, John C., Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Rohde, Manfred ... Klenk, Hans-Peter (2010). Complete genome sequence of Sulfurimonas autotrophica type strain (OK10(T)). Standards in Genomic Sciences, 3 (2), 194-202. doi: 10.4056/sigs.1173118

Complete genome sequence of Sulfurospirillum deleyianum type strain (5175(T))

Sikorski, Johannes, Lapidus, Alla, Copeland, Alex, Del Rio, Tijana Glavina, Nolan, Matt, Lucas, Susan, Chen, Feng, Tice, Hope, Cheng, Jan-Fang, Saunders, Elizabeth, Bruce, David, Goodwin, Lynne, Pitluck, Sam, Ovchinnikova, Galina, Pati, Amrita, Ivanova, Natalia, Mavromatis, Konstantinos, Chen, Amy, Palaniappan, Krishna, Chain, Patrick, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Brettin, Thomas, Detter, John C., Han, Cliff, Rohde, Manfred, Lang, Elke ... Klenk, Hans-Peter (2010). Complete genome sequence of Sulfurospirillum deleyianum type strain (5175(T)). Standards in Genomic Sciences, 2 (2), 149-157. doi: 10.4056/sigs.671209

Complete genome sequence of Syntrophothermus lipocalidus type strain (TGB-C1(T))

Djao, Olivier Duplex Ngatchou, Zhang, Xiaojing, Lucas, Susan, Lapidus, Alla, Del Rio, Tijana Glavina, Nolan, Matt, Tice, Hope, Cheng, Jan-Fang, Han, Cliff, Tapia, Roxanne, Goodwin, Lynne, Pitluck, Sam, Liolios, Konstantinos, Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Ovchinnikova, Galina, Pati, Amrita, Brambilla, Evelyne, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Rohde, Manfred, Sikorski, Johannes, Spring, Stefan, Goeker, Markus ... Klenk, Hans-Peter (2010). Complete genome sequence of Syntrophothermus lipocalidus type strain (TGB-C1(T)). Standards in Genomic Sciences, 3 (3), 267-275. doi: 10.4056/sigs.1233249

Complete genome sequence of Thermaerobacter marianensis type strain (7p75a(T))

Han, Cliff, Gu, Wei, Zhang, Xiaojing, Lapidus, Alla, Nolan, Matt, Copeland, Alex, Lucas, Susan, Del Rio, Tijana Glavina, Tice, Hope, Cheng, Jan-Fang, Tapia, Roxane, Goodwin, Lynne, Pitluck, Sam, Pagani, Ioanna, Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Schneider, Susanne, Rohde, Manfred, Goeker, Markus, Pukall, Ruediger, Woyke, Tanja ... Detter, John C. (2010). Complete genome sequence of Thermaerobacter marianensis type strain (7p75a(T)). Standards in Genomic Sciences, 3 (3), 337-345. doi: 10.4056/sigs.1373474

Complete genome sequence of Thermocrinis albus type strain (HI 11/12(T))

Wirth, Reinhard, Sikorski, Johannes, Brambilla, Evelyne, Misra, Monica, Lapidus, Alla, Copeland, Alex, Nolan, Matt, Lucas, Susan, Chen, Feng, Tice, Hope, Cheng, Jan-Fang, Han, Cliff, Detter, John C., Tapia, Roxane, Bruce, David, Goodwin, Lynne, Pitluck, Sam, Pati, Amrita, Anderson, Iain, Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Chen, Amy, Palaniappan, Krishna, Bilek, Yvonne, Hader, Thomas, Land, Miriam, Hauser, Loren, Chang, Yun-Juan ... Klenk, Hans-Peter (2010). Complete genome sequence of Thermocrinis albus type strain (HI 11/12(T)). Standards in Genomic Sciences, 2 (2), 194-202. doi: 10.4056/sigs.761490

Complete genome sequence of Veillonella parvula type strain (Te3(T))

Gronow, Sabine, Welnitz, Sabine, Lapidus, Alla, Nolan, Matt, Ivanova, Natalia, Del Rio, Tijana Glavina, Copeland, Alex, Chen, Feng, Tice, Hope, Pitluck, Sam, Cheng, Jan-Fang, Saunders, Elizabeth, Brettin, Thomas, Han, Cliff, Detter, John C., Bruce, David, Goodwin, Lynne, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Pati, Amrita, Mavromatis, Konstantinos, Mikhailova, Natalia, Chen, Amy, Palaniappan, Krishna, Chain, Patrick, Rohde, Manfred, Goeker, Markus ... Lucas, Susan (2010). Complete genome sequence of Veillonella parvula type strain (Te3(T)). Standards in Genomic Sciences, 2 (1), 57-65. doi: 10.4056/sigs.521107

Permanent draft genome sequence of Dethiosulfovibrio peptidovorans type strain (SEBR 4207(T))

LaButti, Kurt, Mayilraj, Shanmugam, Clum, Alicia, Lucas, Susan, Del Rio, Tijana Glavina, Nolan, Matt, Tice, Hope, Cheng, Jan-Fang, Pitluck, Sam, Liolios, Konstantinos, Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Pati, Amrita, Goodwin, Lynne, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Rohde, Manfred, Spring, Stefan, Goeker, Markus, Woyke, Tanja, Bristow, James, Eisen, Jonathan A., Markowitz, Victor, Hugenholtz, Philip ... Lapidus, Alla (2010). Permanent draft genome sequence of Dethiosulfovibrio peptidovorans type strain (SEBR 4207(T)). Standards in Genomic Sciences, 3 (1), 85-92. doi: 10.4056/sigs.1092865

The genome sequence of Methanohalophilus mahii SLPT reveals differences in the energy metabolism among members of the Methanosarcinaceae inhabiting freshwater and saline environments

Spring, Stefan, Scheuner, Carmen, Lapidus, Alla, Lucas, Susan, Del Rio, Tijana Glavina, Tice, Hope, Copeland, Alex, Cheng, Jan-Fang, Chen, Feng, Nolan, Matt, Saunders, Elizabeth, Pitluck, Sam, Liolios, Konstantinos, Ivanova, Natalia, Mavromatis, Konstantinos, Lykidis, Athanasios, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Goodwin, Lynne, Detter, John C., Brettin, Thomas, Rohde, Manfred, Goker, Markus, Woyke, Tanja ... Klenk, Hans-Peter (2010). The genome sequence of Methanohalophilus mahii SLPT reveals differences in the energy metabolism among members of the Methanosarcinaceae inhabiting freshwater and saline environments. Archaea- An International Microbiological Journal, 2010 690737, 1-16. doi: 10.1155/2010/690737

A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea

Wu, Dongying, Hugenholtz, Philip, Mavromatis, Konstantinos, Pukall, Ru¨diger, Dalin, Eileen, Ivanova, Natalia N., Kunin, Victor, Goodwin, Lynne, Wu, Martin, Tindall, Brian J., Hooper, Sean D., Pati, Amrita, Lykidis, Athanasios, Spring, Stefan, Anderson, Iain J., D'haeseleer, Patrik, Zemla, Adam, Singer, Mitchell, Lapidus, Alla, Nolan, Matt, Copeland, Alex, Han, Cliff, Chen, Feng, Cheng, Jan-Fang, Lucas, Susan, Kerfeld, Cheryl, Lang, Elke, Gronow, Sabine, Chain, Patrick ... Elsen, Jonathan A. (2009). A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea. Nature, 462 (7276), 1056-1060. doi: 10.1038/nature08656

Complete genome sequence of Atopobium parvulum type strain (IPP 1246 T)

Copeland, Alex, Sikorski, Johannes, Lapidus, Alla, Nolan, Matt, Del Rio, Tijana Glavina, Lucas, Susan, Chen, Feng, Tice, Hope, Pitluck, Sam, Cheng, Jan-Fang, Pukall, Rüdiger, Chertkov, Olga, Brettin, Thomas, Han, Cliff, Kuske, Cheryl, Bruce, David, Goodwin, Lynne, Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Chen, Amy, Palaniappan, Krishna, Chain, Patrick, Rohde, Manfred, Göker, Markus, Bristow, Jim, Eisen, Jonathan A., Markowitz, Victor, Hugenholtz, Philip ... Detter, John C. (2009). Complete genome sequence of Atopobium parvulum type strain (IPP 1246 T). Standards in Genomic Sciences, 1 (2), 166-173. doi: 10.4056/sigs.29547

Complete genome sequence of Pedobacter heparinus type strain (HIM 762-3 T)

Han, Cliff, Spring, Stefan, Lapidus, Alla, del Rio, Tijana Glavina, Tice, Hope, Copeland, Alex, Cheng, Jan-Fang, Lucas, Susan, Chen, Feng, Nolan, Matt, Bruce, David, Goodwin, Lynne, Pitluck, Sam, Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia C., Saunders, Elizabeth, Chertkov, Olga, Brettin, Thomas, Göker, Markus, Rohde, Manfred, Bristow, Jim ... Detter, John C. (2009). Complete genome sequence of Pedobacter heparinus type strain (HIM 762-3 T). Standards in Genomic Sciences, 1 (1), 54-62. doi: 10.4056/sigs.22138

Complete genome sequence of Rhodothermus marinus type strain (R-10 T)

Nolan, Matt, Tindall, Brian J., Pomrenke, Helga, Lapidus, Alla, Copeland, Alex, del Rio, Tijana Glavina, Lucas, Susan, Chen, Feng, Tice, Hope, Cheng, Jan-Fang, Saunders, Elizabeth, Han, Cliff, Bruce, David, Goodwin, Lynne, Chain, Patrick, Pitluck, Sam, Ovchinikova, Galina, Pati, Amrita, Ivanova, Natalia, Mavromatis, Konstantinos, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Brettin, Thomas, Göker, Markus, Bristow, James ... Detter, John C. (2009). Complete genome sequence of Rhodothermus marinus type strain (R-10 T). Standards in Genomic Sciences, 1 (3), 283-291. doi: 10.4056/sigs.46736

Complete genome sequence of anaerococcus prevotii type strain (PC1 T)

Labutti, Kurt, Pukall, Rüdiger, Steenblock, Katja, Del Rio, Tijana Glavina, Tice, Hope, Copeland, Alex, Cheng, Jan-Fang, Lucas, Susan, Chen, Feng, Nolan, Matt, Bruce, David, Goodwin, Lynne, Pitluck, Sam, Ivanova, Natalia, Mavromatis, Konstantinos, Ovchinnikova, Galina, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Chain, Patrick, Saunders, Elizabeth, Brettin, Thomas, Detter, John C., Han, Cliff, Göker, Markus ... Lapidus, Alla (2009). Complete genome sequence of anaerococcus prevotii type strain (PC1 T). Standards in Genomic Sciences, 1 (2), 159-165. doi: 10.4056/sigs.24194

The Genomes On Line Database (GOLD) in 2009: status of genomic and metagenomic projects and their associated metadata

Liolios, Konstantinos, Chen, I-Min A., Mavromatis, Konstantinos, Tavernarakis, Nektarios, Hugenholtz, Philip, Markowitz, Victor M. and Kyrpides, Nikos C. (2009). The Genomes On Line Database (GOLD) in 2009: status of genomic and metagenomic projects and their associated metadata. Nucleic Acids Research, 38 (Supp. 1) gkp848, D346-D354. doi: 10.1093/nar/gkp848

ShotgunFunctionalizeR: An R-package for functional comparison of metagenomes

Kristiansson, Erik, Hugenholtz, Philip and Dalevi, Daniel (2009). ShotgunFunctionalizeR: An R-package for functional comparison of metagenomes. Bioinformatics, 25 (20), 2737-2738. doi: 10.1093/bioinformatics/btp508

Genome project standards in a new era of sequencing

Chain, P. S. G., Grafham, D. V., Fulton, R. S., FitzGerald, M. G., Hostetler, J., Muzny, D., Ali, J., Birren, B., Bruce, D. C., Buhay, C., Cole, J. R., Ding, Y., Dugan, S., Field, D., Garrity, G. M., Gibbs, R., Graves, T., Han, C. S., Harrison, S. H., Highlander, S., Hugenholtz, P., Khouri, H. M., Kodira, C. D., Kolker, E., Kyrpides, N. C., Lang, D., Lapidus, A., Malfatti, S. A., Markowitz, V. ... Detter, J. C. (2009). Genome project standards in a new era of sequencing. Science, 326 (5950), 236-237. doi: 10.1126/science.1180614

Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates

Kunin, Victor, Engelbrekston, Anna, Ochman, Howard and Hugenholtz, Philip (2009). Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates. Environmental Microbiology, 12 (1), 118-123. doi: 10.1111/j.1462-2920.2009.02051.x

Focus: Synergistetes

Hugenholtz, P, Hooper, SD and Kyrpides, NC (2009). Focus: Synergistetes. Environmental Microbiology, 11 (6), 1327-1329. doi: 10.1111/j.1462-2920.2009.01949.x

Genomic analysis of "Elusimicrobium minutum," the first cultivated representative of the phylum "Elusimicrobia" (formerly termite group 1)

Herlemann, D. P. R., Geissinger, O., Ikeda-Ohtsubo, W., Kunin, V., Sun, H., Lapidus, A., Hugenholtz, P. and Brune, A. (2009). Genomic analysis of "Elusimicrobium minutum," the first cultivated representative of the phylum "Elusimicrobia" (formerly termite group 1). Applied and Environmental Microbiology, 75 (9), 2841-2849. doi: 10.1128/AEM.02698-08

Getting to the core of the gut microbiome

Tschop, MH, Hugenholtz, P and Karp, CL (2009). Getting to the core of the gut microbiome. Nature Biotechnology, 27 (4), 344-346. doi: 10.1038/nbt0409-344

A changing of the guard: Genomics update

Hugenholtz, P and Kyrpides, NC (2009). A changing of the guard: Genomics update. Environmental Microbiology, 11 (3), 551-553. doi: 10.1111/j.1462-2920.2009.01888.x

Genome analysis of the anaerobic thermohalophilic bacterium Halothermothrix orenii

Mavromatis, Konstantinos, Ivanova, Natalia, Anderson, Iain, Lykidis, Athanasios, Hooper, Sean D., Sun, Hui, Kunin, Victor, Lapidus, Alla, Hugenholtz, Philip, Patel, Bharat and Kyrpides, Nikos C. (2009). Genome analysis of the anaerobic thermohalophilic bacterium Halothermothrix orenii. PLoS One, 4 (1) e4192, e4192.1-e4192.8. doi: 10.1371/journal.pone.0004192

Complete genome sequence of Acidimicrobium ferrooxidans type strain (ICPT)

Clum, Alicia, Nolan, Matt, Lang, Elke, Del Rio, Tijana Glavina, Tice, Hope, Copeland, Alex, Cheng, Jan-Fang, Lucas, Susan, Chen, Feng, Bruce, David, Goodwin, Lynne, Pitluck, Sam, Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Goeker, Markus, Spring, Stefan, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia C., Chain, Patrick, Bristow, Jim, Eisen, Jonathan A., Markowitz, Victor, Hugenholtz, Philip ... Lapidus, Alla (2009). Complete genome sequence of Acidimicrobium ferrooxidans type strain (ICPT). Standards in Genomic Sciences, 1 (1), 38-45. doi: 10.4056/sigs.1463

Complete genome sequence of Actinosynnema mirum type strain (101(T))

Land, Miriam, Lapidus, Alla, Mayilraj, Shanmugam, Chen, Feng, Copeland, Alex, Del Rio, Tijana Glavina, Nolan, Matt, Lucas, Susan, Tice, Hope, Cheng, Jan-Fang, Chertkov, Olga, Bruce, David, Goodwin, Lynne, Pitluck, Sam, Rohde, Manfred, Goeker, Markus, Pati, Amrita, Ivanova, Natalia, Mavromatis, Konstantinos, Chen, Amy, Palaniappan, Krishna, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia C., Brettin, Thomas, Detter, John C., Han, Cliff, Chain, Patrick, Tindall, Brian J. ... Klenk, Hans-Peter (2009). Complete genome sequence of Actinosynnema mirum type strain (101(T)). Standards in Genomic Sciences, 1 (1), 46-53. doi: 10.4056/sigs.21137

Complete genome sequence of Anaerococcus prevotii type strain (PC1(T))

LaButti, Kurt, Pukall, Ruediger, Steenblock, Katja, Del Rio, Tijana Glavina, Tice, Hope, Copeland, Alex, Cheng, Jan-Fang, Lucas, Susan, Chen, Feng, Nolan, Matt, Bruce, David, Goodwin, Lynne, Pitluck, Sam, Ivanova, Natalia, Mavromatis, Konstantinos, Ovchinnikova, Galina, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Chain, Patrick, Saunders, Elizabeth, Brettin, Thomas, Detter, John C., Han, Cliff, Goeker, Markus ... Lapidus, Alla (2009). Complete genome sequence of Anaerococcus prevotii type strain (PC1(T)). Standards in Genomic Sciences, 1 (2), 159-165. doi: 10.4056/sigs.2494

Complete genome sequence of Beutenbergia cavernae type strain (HKI 0122(T))

Land, Miriam, Pukall, Ruediger, Abt, Birte, Goeker, Markus, Rohde, Manfred, Del Rio, Tijana Glavina, Tice, Hope, Copeland, Alex, Cheng, Jan-Fang, Lucas, Susan, Chen, Feng, Nolan, Matt, Bruce, David, Goodwin, Lynne, Pitluck, Sam, Ivanova, Natalia, Mavromatis, Konstantinos, Ovchinnikova, Galina, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Hauser, Loren, Chang, Yun-Juan, Jefferies, Cynthia C., Saunders, Elizabeth, Brettin, Thomas, Detter, John C., Han, Cliff, Chain, Patrick ... Lapidus, Alla (2009). Complete genome sequence of Beutenbergia cavernae type strain (HKI 0122(T)). Standards in Genomic Sciences, 1 (1), 21-28. doi: 10.4056/sigs.1162

Complete genome sequence of Brachybacterium faecium type strain (Schefferle 6-10(T))

Lapidus, Alla, Pukall, Ruediger, LaButtii, Kurt, Copeland, Alex, Del Rio, Tijana Glavina, Nolan, Matt, Chen, Feng, Lucas, Susan, Tice, Hope, Cheng, Jan-Fang, Bruce, David, Goodwin, Lynne, Pitluck, Sam, Rohde, Manfred, Goeker, Markus, Pati, Amrita, Ivanova, Natalia, Mavromatis, Konstantinos, Chen, Amy, Palaniappan, Krishna, D'haeseleer, Patrik, Chain, Patrick, Bristow, Jim, Eisen, Jonathan A., Markowitz, Victor, Hugenholtz, Philip, Kyrpides, Nikos C. and Klenk, Hans-Peter (2009). Complete genome sequence of Brachybacterium faecium type strain (Schefferle 6-10(T)). Standards in Genomic Sciences, 1 (1), 3-11. doi: 10.4056/sigs.492

Complete genome sequence of Capnocytophaga ochracea type strain (VPI 2845T)

Mavrommatis, Konstantinos, Gronow, Sabine, Saunders, Elizabeth, Land, Miriam, Lapidus, Alla, Copeland, Alex, Del Rio, Tijana Glavina, Nolan, Matt, Lucas, Susan, Chen, Feng, Tice, Hope, Cheng, Jan-Fang, Bruce, David, Goodwin, Lynne, Pitluck, Sam, Pati, Amrita, Ivanova, Natalia, Chen, Amy, Palaniappan, Krishna, Chain, Patrick, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Brettin, Thomas, Detter, John C., Han, Cliff, Bristow, James, Goeker, Markus, Rohde, Manfred ... Hugenholtz, Philip (2009). Complete genome sequence of Capnocytophaga ochracea type strain (VPI 2845T). Standards in Genomic Sciences, 1 (2), 101-109. doi: 10.4056/sigs.15195

Complete genome sequence of Catenulispora acidiphila type strain (ID 139908(T))

Copeland, Alex, Lapidus, Alla, Del Rio, Tijana Glavina, Nolan, Matt, Lucas, Susan, Chen, Feng, Tice, Hope, Cheng, Jan-Fang, Bruce, David, Goodwin, Lynne, Pitluck, Sam, Mikhailova, Natalia, Pati, Amrita, Ivanova, Natalia, Mavromatis, Konstantinos, Chen, Amy, Palaniappan, Krishna, Chain, Patrick, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Chertkov, Olga, Brettin, Thomas, Detter, John C., Han, Cliff, Ali, Zahid, Tindall, Brian J., Goeker, Markus ... Klenk, Hans-Peter (2009). Complete genome sequence of Catenulispora acidiphila type strain (ID 139908(T)). Standards in Genomic Sciences, 1 (2), 119-125. doi: 10.4056/sigs.17259

Complete genome sequence of Cryptobacterium curtum type strain (12-3(T))

Mavrommatis, Konstantinos, Pukall, Ruediger, Rohde, Christine, Chen, Feng, Sims, David, Brettin, Thomas, Kuske, Cheryl, Detter, John C., Han, Cliff, Lapidus, Alla, Copeland, Alex, Del Rio, Tijana Glavina, Nolan, Matt, Lucas, Susan, Tice, Hope, Cheng, Jan-Fang, Bruce, David, Goodwin, Lynne, Pitluck, Sam, Ovchinnikova, Galina, Pati, Amrita, Ivanova, Natalia, Chen, Amy, Palaniappan, Krishna, Chain, Patrick, D'haeseleer, Patrik, Goeker, Markus, Bristow, Jim, Eisen, Jonathan A. ... Kyrpides, Nikos C. (2009). Complete genome sequence of Cryptobacterium curtum type strain (12-3(T)). Standards in Genomic Sciences, 1 (2), 93-100. doi: 10.4056/sigs.12260

Complete genome sequence of Desulfomicrobium baculatum type strain (X-T)

Copeland, Alex, Spring, Stefan, Goeker, Markus, Schneider, Susanne, Lapidus, Alla, Del Rio, Tijana Glavina, Tice, Hope, Cheng, Jan-Fang, Lucas, Susan, Chen, Feng, Nolan, Matt, Bruce, David, Goodwin, Lynne, Pitluck, Sam, Ivanova, Natalia, Mavromatis, Konstantinos, Ovchinnikova, Galina, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia C., Meincke, Linda, Sims, David, Brettin, Thomas, Detter, John C., Han, Cliff ... Lucas, Susan (2009). Complete genome sequence of Desulfomicrobium baculatum type strain (X-T). Standards in Genomic Sciences, 1 (1), 29-37. doi: 10.4056/sigs.13134

Complete genome sequence of Desulfotomaculum acetoxidans type strain (5575(T))

Spring, Stefan, Lapidus, Alla, Schroeder, Maren, Gleim, Dorothea, Sims, David, Meincke, Linda, Del Rio, Tijana Glavina, Tice, Hope, Copeland, Alex, Cheng, Jan-Fang, Lucas, Susan, Chen, Feng, Nolan, Matt, Bruce, David, Goodwin, Lynne, Pitluck, Sam, Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Chain, Patrick, Saunders, Elizabeth, Brettin, Thomas ... Han, Cliff (2009). Complete genome sequence of Desulfotomaculum acetoxidans type strain (5575(T)). Standards in Genomic Sciences, 1 (3), 242-252. doi: 10.4056/sigs.39508

Complete genome sequence of Dyadobacter fermentans type strain (NS114(T))

Lang, Elke, Lapidus, Alla, Chertkov, Olga, Brettin, Thomas, Detter, John C., Han, Cliff, Copeland, Alex, Del Rio, Tijana Glavina, Nolan, Matt, Chen, Feng, Lucas, Susan, Tice, Hope, Cheng, Jan-Fang, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Kopitz, Marcus, Bruce, David, Goodwin, Lynne, Pitluck, Sam, Ovchinnikova, Galina, Pati, Amrita, Ivanova, Natalia, Mavrommatis, Konstantinos, Chen, Amy, Palaniappan, Krishna, Chain, Patrick, Bristow, Jim ... Klenk, Hans-Peter (2009). Complete genome sequence of Dyadobacter fermentans type strain (NS114(T)). Standards in Genomic Sciences, 1 (2), 133-140. doi: 10.4056/sigs.19262

Complete genome sequence of Eggerthella lenta type strain (VPI 0255(T))

Saunders, Elizabeth, Pukall, Ruediger, Abt, Birte, Lapidus, Alla, Del Rio, Tijana Glavina, Copeland, Alex, Tice, Hope, Cheng, Jan-Fang, Lucas, Susan, Chen, Feng, Nolan, Matt, Bruce, David, Goodwin, Lynne, Pitluck, Sam, Ivanova, Natalia, Mavromatis, Konstantinos, Ovchinnikova, Galina, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Chain, Patrick, Meincke, Linda, Sims, David, Brettin, Thomas, Detter, John C. ... Han, Cliff (2009). Complete genome sequence of Eggerthella lenta type strain (VPI 0255(T)). Standards in Genomic Sciences, 1 (2), 174-182. doi: 10.4056/sigs.33592

Complete genome sequence of Halogeometricum borinquense type strain (PR3(T))

Malfatti, Stephanie, Tindall, Brian J., Schneider, Susanne, Faehnrich, Regine, Lapidus, Alla, LaButtii, Kurt, Copeland, Alex, Del Rio, Tijana Glavina, Nolan, Matt, Chen, Feng, Lucas, Susan, Tice, Hope, Cheng, Jan-Fang, Bruce, David, Goodwin, Lynne, Pitluck, Sam, Anderson, Iain, Pati, Amrita, Ivanova, Natalia, Mavromatis, Konstantinos, Chen, Amy, Palaniappan, Krishna, D'haeseleer, Patrik, Goeker, Markus, Bristow, Jim, Eisen, Jonathan A., Markowitz, Victor, Hugenholtz, Philip, Kyrpides, Nikos C. ... Chain, Patrick (2009). Complete genome sequence of Halogeometricum borinquense type strain (PR3(T)). Standards in Genomic Sciences, 1 (2), 150-158. doi: 10.4056/sigs.23264

Complete genome sequence of Halomicrobium mukohataei type strain (arg-2(T))

Tindall, Brian J., Schneider, Susanne, Lapidus, Alla, Copeland, Alex, Del Rio, Tijana Glavina, Nolan, Matt, Lucas, Susan, Chen, Feng, Tice, Hope, Cheng, Jan-Fang, Saunders, Elizabeth, Bruce, David, Goodwin, Lynne, Pitluck, Sam, Mikhailova, Natalia, Pati, Amrita, Ivanova, Natalia, Mavrommatis, Konstantinos, Chen, Amy, Palaniappan, Krishna, Chain, Patrick, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Brettin, Thomas, Han, Cliff, Rohde, Manfred, Goeker, Markus ... Detter, John C. (2009). Complete genome sequence of Halomicrobium mukohataei type strain (arg-2(T)). Standards in Genomic Sciences, 1 (3), 270-277. doi: 10.4056/sigs.42644

Complete genome sequence of Halorhabdus utahensis type strain (AX-2(T))

Anderson, Iain, Tindall, Brian J., Pomrenke, Helga, Goeker, Markus, Lapidus, Alla, Nolan, Matt, Copeland, Alex, Del Rio, Tijana Glavina, Chen, Feng, Tice, Hope, Cheng, Jan-Fang, Lucas, Susan, Chertkov, Olga, Bruce, David, Brettin, Thomas, Detter, John C., Han, Cliff, Goodwin, Lynne, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Pitluck, Sam, Pati, Amrita, Mavromatis, Konstantinos, Ivanova, Natalia, Ovchinnikova, Galina, Chen, Amy, Palaniappan, Krishna ... Klenk, Hans-Peter (2009). Complete genome sequence of Halorhabdus utahensis type strain (AX-2(T)). Standards in Genomic Sciences, 1 (3), 218-225. doi: 10.4056/sigs.31864

Complete genome sequence of Jonesia denitrificans type strain (Prevot 55134(T))

Pukall, Ruedieger, Gehrich-Schroeter, Gabriele, Lapidus, Alla, Nolan, Matt, Del Rio, Tijana Glavina, Lucas, Susan, Chen, Feng, Tice, Hope, Pitluck, Sam, Cheng, Jan-Fang, Copeland, Alex, Saunders, Elizabeth, Brettin, Thomas, Detter, John C., Bruce, David, Goodwin, Lynne, Pati, Amrita, Ivanova, Natalia, Mavrommatis, Konstantinos, Ovchinnikova, Galina, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Chain, Patrick, Goeker, Markus, Bristow, Jim ... Han, Cliff (2009). Complete genome sequence of Jonesia denitrificans type strain (Prevot 55134(T)). Standards in Genomic Sciences, 1 (3), 262-269. doi: 10.4056/sigs.41646

Complete genome sequence of Kangiella koreensis type strain (SW-125(T))

Han, Cliff, Sikorski, Johannes, Lapidus, Alla, Nolan, Matt, Del Rio, Tijana Glavina, Tice, Hope, Cheng, Jan-Fang, Lucas, Susan, Chen, Feng, Copeland, Alex, Ivanova, Natalia, Mavromatis, Konstantinos, Ovchinnikova, Galina, Pati, Amrita, Bruce, David, Goodwin, Lynne, Pitluck, Sam, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Chain, Patrick, Saunders, Elizabeth, Brettin, Thomas, Goeker, Markus, Tindall, Brian J., Bristow, Jim ... Detter, John C. (2009). Complete genome sequence of Kangiella koreensis type strain (SW-125(T)). Standards in Genomic Sciences, 1 (3), 226-233. doi: 10.4056/sigs.36635

Complete genome sequence of Kytococcus sedentarius type strain (541(T))

Sims, David, Brettin, Thomas, Detter, John C., Han, Cliff, Lapidus, Alla, Copeland, Alex, Del Rio, Tijana Glavina, Nolan, Matt, Chen, Feng, Lucas, Susan, Tice, Hope, Cheng, Jan-Fang, Bruce, David, Goodwin, Lynne, Pitluck, Sam, Ovchinnikova, Galina, Pati, Amrita, Ivanova, Natalia, Mavromatis, Konstantinos, Chen, Amy, Palaniappan, Krishna, D'haeseleer, Patrik, Chain, Patrick, Bristow, James, Eisen, Jonathan A., Markowitz, Victor, Hugenholtz, Philip, Schneider, Susanne, Goker, Markus ... Klenk, Hans-Peter (2009). Complete genome sequence of Kytococcus sedentarius type strain (541(T)). Standards in Genomic Sciences, 1 (1), 12-20. doi: 10.4056/sigs.761

Complete genome sequence of Leptotrichia buccalis type strain (C-1013-b(T))

Ivanova, Natalia, Gronow, Sabine, Lapidus, Alla, Copeland, Alex, Del Rio, Tijana Glavina, Nolan, Matt, Lucas, Susan, Chen, Feng, Tice, Hope, Cheng, Jan-Fang, Saunders, Elizabeth, Bruce, David, Goodwin, Lynne, Brettin, Thomas, Detter, John C., Han, Cliff, Pitluck, Sam, Mikhailova, Natalia, Pati, Amrita, Mavrommatis, Konstantinos, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Chain, Patrick, Rohde, Christine, Goeker, Markus ... Klenk, Hans-Peter (2009). Complete genome sequence of Leptotrichia buccalis type strain (C-1013-b(T)). Standards in Genomic Sciences, 1 (2), 126-132. doi: 10.4056/sigs.1854

Complete genome sequence of Pedobacter heparinus type strain (HIM 762-3(T))

Han, Cliff, Spring, Stefan, Lapidus, Alla, Del Rio, Tijana Glavina, Tice, Hope, Copeland, Alex, Cheng, Jan-Fang, Lucas, Susan, Chen, Feng, Nolan, Matt, Bruce, David, Goodwin, Lynne, Pitluck, Sam, Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia C., Saunders, Elizabeth, Chertkov, Olga, Brettin, Thomas, Goeker, Markus, Rohde, Manfred, Bristow, Jim ... Detter, John C. (2009). Complete genome sequence of Pedobacter heparinus type strain (HIM 762-3(T)). Standards in Genomic Sciences, 1 (1), 54-62. doi: 10.4506/sigs.22138

Complete genome sequence of Pirellula staleyi type strain (ATCC 27377T)

Clum, Alicia, Tindall, Brian J., Sikorski, Johannes, Ivanova, Natalia, Mavrommatis, Konstantinos, Lucas, Susan, Del Rio, Tijana Glavina, Nolan, Matt, Chen, Feng, Tice, Hope, Pitluck, Sam, Cheng, Jan-Fang, Chertkov, Olga, Brettin, Thomas, Han, Cliff, Detter, John C., Kuske, Cheryl, Bruce, David, Goodwin, Lynne, Ovchinikova, Galina, Pati, Amrita, Mikhailova, Natalia, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Chain, Patrick ... Lapidus, Alla (2009). Complete genome sequence of Pirellula staleyi type strain (ATCC 27377T). Standards in Genomic Sciences, 1 (3), 308-316. doi: 10.4056/sigs.51657

Complete genome sequence of Rhodothermus marinus type strain (R-10(T))

Nolan, Matt, Gronow, Sabine, Lapidus, Alla, Ivanova, Natalia, Copeland, Alex, Lucas, Susan, Del Rio, Tijana Glavina, Chen, Feng, Tice, Hope, Pitluck, Sam, Cheng, Jan-Fang, Sims, David, Meincke, Linda, Bruce, David, Goodwin, Lynne, Brettin, Thomas, Han, Cliff, Detter, John C., Ovchinikova, Galina, Pati, Amrita, Mavromatis, Konstantinos, Mikhailova, Natalia, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Rohde, Manfred ... Chain, Patrick (2009). Complete genome sequence of Rhodothermus marinus type strain (R-10(T)). Standards in Genomic Sciences, 1 (3), 283-291. doi: 10.4056/sigs46736

Complete genome sequence of Saccharomonospora viridis type strain (P101(T))

Pati, Amrita, Sikorski, Johannes, Nolan, Matt, Lapidus, Alla, Copeland, Alex, Del Rio, Tijana Glavina, Lucas, Susan, Chen, Feng, Tice, Hope, Pitluck, Sam, Cheng, Jan-Fang, Chertkov, Olga, Brettin, Thomas, Han, Cliff, Detter, John C., Kuske, Cheryl, Bruce, David, Goodwin, Lynne, Chain, Patrick, D'haeseleer, Patrik, Chen, Amy, Palaniappan, Krishna, Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Rohde, Manfred, Tindall, Brian J., Goeker, Markus, Bristow, Jim ... Klenk, Hans-Peter (2009). Complete genome sequence of Saccharomonospora viridis type strain (P101(T)). Standards in Genomic Sciences, 1 (2), 141-149. doi: 10.4056/sigs.20263

Complete genome sequence of Sanguibacter keddieii type strain (ST-74(T))

Ivanova, Natalia, Sikorski, Johannes, Sims, David, Brettin, Thomas, Detter, John C., Han, Cliff, Lapidus, Alla, Copeland, Alex, Del Rio, Tijana Glavina, Nolan, Matt, Chen, Feng, Lucas, Susan, Tice, Hope, Cheng, Jan-Fang, Bruce, David, Goodwin, Lynne, Pitluck, Sam, Pati, Amrita, Mavromatis, Konstantinos, Chen, Amy, Palaniappan, Krishna, D'haeseleer, Patrik, Chain, Patrick, Bristow, Jim, Eisen, Jonathan A., Markowitz, Victor, Hugenholtz, Philip, Goeker, Markus, Pukall, Ruediger ... Kyrpides, Nikos C. (2009). Complete genome sequence of Sanguibacter keddieii type strain (ST-74(T)). Standards in Genomic Sciences, 1 (2), 110-118. doi: 10.4056/sigs16197

Complete genome sequence of Slackia heliotrinireducens type strain (RHS 1(T))

Pukall, Ruediger, Lapidus, Alla, Nolan, Matt, Copeland, Alex, Del Rio, Tijana Glavina, Lucas, Susan, Chen, Feng, Tice, Hope, Cheng, Jan-Fang, Chertkov, Olga, Bruce, David, Goodwin, Lynne, Kuske, Cheryl, Brettin, Thomas, Detter, John C., Han, Cliff, Pitluck, Sam, Pati, Amrita, Mavrommatis, Konstantinos, Ivanova, Natalia, Ovchinnikova, Galina, Chen, Amy, Palaniappan, Krishna, Schneider, Susanne, Rohde, Manfred, Chain, Patrick, D'haeseleer, Patrik, Goeker, Markus, Bristow, James ... Hugenholtz, Philip (2009). Complete genome sequence of Slackia heliotrinireducens type strain (RHS 1(T)). Standards in Genomic Sciences, 1 (3), 234-241. doi: 10.4056/sigs.37633

Complete genome sequence of Stackebrandtia nassauensis type strain (LLR-40K-21(T))

Munk, Chris, Lapidus, Alla, Copeland, Alex, Jando, Marlen, Mayilraj, Shanmugam, Del Rio, Tijana Glavina, Nolan, Matt, Chen, Feng, Lucas, Susan, Tice, Hope, Cheng, Jan-Fang, Han, Cliff, Detter, John C., Bruce, David, Goodwin, Lynne, Chain, Patrick, Pitluck, Sam, Goeker, Markus, Ovchinikova, Galina, Pati, Amrita, Ivanova, Natalia, Mavromatis, Konstantinos, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Bristow, Jim ... Klenk, Hans-Peter (2009). Complete genome sequence of Stackebrandtia nassauensis type strain (LLR-40K-21(T)). Standards in Genomic Sciences, 1 (3), 292-299. doi: 10.4056/sigs.47643

Complete genome sequence of Streptobacillus moniliformis type strain (9901(T))

Nolan, Matt, Gronow, Sabine, Lapidus, Alla, Ivanova, Natalia, Copeland, Alex, Lucas, Susan, Del Rio, Tijana Glavina, Chen, Feng, Tice, Hope, Pitluck, Sam, Cheng, Jan-Fang, Sims, David, Meincke, Linda, Bruce, David, Goodwin, Lynne, Brettin, Thomas, Han, Cliff, Detter, John C., Ovchinikova, Galina, Pati, Amrita, Mavromatis, Konstantinos, Mikhailova, Natalia, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Rohde, Manfred ... Chain, Patrick (2009). Complete genome sequence of Streptobacillus moniliformis type strain (9901(T)). Standards in Genomic Sciences, 1 (3), 300-307. doi: 10.4056/sigs.48727

Complete genome sequence of Thermanaerovibrio acidaminovorans type strain (Su883(T))

Chovatia, Mansi, Sikorski, Johannes, Schroeder, Maren, Lapidus, Alla, Nolan, Matt, Tice, Hope, Del Rio, Tijana Glavina, Copeland, Alex, Cheng, Jan-Fang, Lucas, Susan, Chen, Feng, Bruce, David, Goodwin, Lynne, Pitluck, Sam, Ivanova, Natalia, Mavromatis, Konstantinos, Ovchinnikova, Galina, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Chain, Patrick, Saunders, Elizabeth, Detter, John C., Brettin, Thomas, Rohde, Manfred ... Eisen, Jonathan A. (2009). Complete genome sequence of Thermanaerovibrio acidaminovorans type strain (Su883(T)). Standards in Genomic Sciences, 1 (3), 254-261. doi: 10.4056/sigs.40645

Correlative tem and fish imaging of microbial communities

Knierim, B., Webb, R., Wilmes, P., Hugenholtz, P., Liphardt, J., McDonald, K., Banfield, J. and Auer, M. (2009). Correlative tem and fish imaging of microbial communities. Microscopy and Microanalysis, 15 (Suppl. 2), 834-835. doi: 10.1017/S1431927609098250

A bioinformatician's guide to metagenomics

Kunin, V., Copeland, A., Lapidus, A., Mavromatis, K. and Hugenholtz, P. (2008). A bioinformatician's guide to metagenomics. Microbiology and Molecular Biology Reviews, 72 (4), 557-578. doi: 10.1128/MMBR.00009-08

A novel ecological role of the Firmicutes identified in thermophilic microbial fuel cells

Wrighton, Kelly C., Agbo, Peter, Warnecke, Falk, Weber, Karrie A., Brodie, Eoin L., DeSantis, Todd Z., Hugenholtz, Philip, Andersen, Gary L. and Coates, John D. (2008). A novel ecological role of the Firmicutes identified in thermophilic microbial fuel cells. The ISME Journal, 2 (11), 1146-1156. doi: 10.1038/ismej.2008.48

A renaissance for the pioneering 16S rRNA gene

Tringe, SG and Hugenholtz, P (2008). A renaissance for the pioneering 16S rRNA gene. Current Opinions in Microbiology, 11 (5), 442-446. doi: 10.1016/j.mib.2008.09.011

Environmental distribution and population biology of Candidatus Accumulibacter, a primary agent of biological phosphorus removal

Peterson, S. Brook, Warnecke, Falk, Madejska, Julita, McMahon, Katherine D. and Hugenholtz, Philip (2008). Environmental distribution and population biology of Candidatus Accumulibacter, a primary agent of biological phosphorus removal. Environmental Microbiology, 10 (10), 2692-2703. doi: 10.1111/j.1462-2920.2008.01690.x

Microbiology: Metagenomics

Hugenhotz, Philip and Tyson, Gene W. (2008). Microbiology: Metagenomics. Nature, 455 (7212), 481-483. doi: 10.1038/455481a

Evolution of Hyaluronic Acid Synthesis (has) Operon in Streptococcus zooepidemicus and other Pathogenic Streptococci

Lars M. Blank, Philip Hugenholtz and Nielsen, Lars K. (2008). Evolution of Hyaluronic Acid Synthesis (has) Operon in Streptococcus zooepidemicus and other Pathogenic Streptococci. Journal of Molecular Evolution, 67 (1), 13-22. doi: 10.1007/s00239-008-9117-1

Millimeter-scale genetic gradients and community-level molecular convergence in a hypersaline microbial mat

Kunin, Victor, Raes, Jeroen, Harris, J. Kirk, Spear, John R., Walker, Jeffrey J., Ivanova, Natalia, Von Mering, Christian, Bebout, Brad M., Pace, Norman R., Bork, Peer and Hugenholtz, Philip (2008). Millimeter-scale genetic gradients and community-level molecular convergence in a hypersaline microbial mat. Molecular Systems Biology, 4 (1) 198, 198. doi: 10.1038/msb.2008.35

A korarchaeal genome reveals insights into the evolution of the Archaea

Elkins, James G., Podar, Mircea, Graham, David E., Makarova, Kira S., Wolf, Yuri, Randau, Lennart, Hedlund, Brian P., Brochier-Armanet, Celine, Kunin, Victor, Anderson, Iain, Lapidus, Alla, Goltsman, Eugene, Barry, Kerrie, Koonin, Eugene V., Hugenholtz, Philip, Kyrpides, Nikos, Wanner, Gerhard, Richardson, Paul, Keller, Martin and Stetter, Karl O. (2008). A korarchaeal genome reveals insights into the evolution of the Archaea. Proceedings of the National Academy of Sciences of the United States of America, 105 (23), 8102-8107. doi: 10.1073/pnas.0801980105

The minimum information about a genome sequence (MIGS) specification

Field, Dawn, Garrity, George, Gray, Tanya, Morrison, Norman, Selengut, Jeremy, Sterk, Peter, Tatusova, Tatiana, Thomson, Nicholas, Allen, Michael J., Angiuoli, Samuel V., Ashburner, Michael, Axelrod, Nelson, Baldauf, Sandra, Ballard, Stuart, Boore, Jeffrey, Cochrane, Guy, Cole, James, Dawyndt, Peter, De Vos, Paul, dePamphilis, Claude, Edwards, Robert, Faruque, Nadeem, Feldman, Robert, Gilbert, Jack, Gilna, Paul, Glockner, Frank Oliver, Goldstein, Philip, Guralnick, Robert, Haft, Dan ... Wipat, Anil (2008). The minimum information about a genome sequence (MIGS) specification. Nature Biotechnology, 26 (5), 541-547. doi: 10.1038/nbt1360

CRISPR - A widespread system that provides acquired resistance against phages in bacteria and archaea

Sorek, R, Kunin, V and Hugenholtz, P (2008). CRISPR - A widespread system that provides acquired resistance against phages in bacteria and archaea. Nature Reviews Microbiology, 6 (3), 181-186. doi: 10.1038/nrmicro1793

A bacterial metapopulation adapts locally to phage predation despite global dispersal

Kunin, V., He, S., Warnecke, F., Peterson, S. B., Martin, H. G., Haynes, M., Ivanova, N., Blackall, L. L., Breitbart, M., Rohwer, F., McMahon, K. D. and Hugenholtz, P. (2008). A bacterial metapopulation adapts locally to phage predation despite global dispersal. Genome Research, 18 (2), 293-297. doi: 10.1101/gr.6835308

IMG/M: A data management and analysis system for metagenomes

Markowitz, Victor M., Ivanova, Natalia N., Szeto, Ernest, Palaniappan, Krishna, Chu, Ken, Dalevi, Daniel, Chen, I-Min A., Grechkin, Yuri, Dubchak, Inna, Anderson, Iain, Lykidis, Athanasios, Mavromatis, Konstantinos, Hugenholtz, Philip and Kyrpides, Nikos C. (2008). IMG/M: A data management and analysis system for metagenomes. Nucleic Acids Research, 36 (Supp. 1), D534-D538. doi: 10.1093/nar/gkm869

Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite

Warnecke, Falk, Luginbuehl, Peter, Ivanova, Natalia, Ghassemian, Majid, Richardson, Toby H., Stege, Justin T., Cayouette, Michelle, McHardy, Alice C., Djordjevic, Gordana, Aboushadi, Nahla, Sorek, Rotem, Tringe, Susannah G., Podar, Mircea, Martin, Hector Garcia, Kunin, Victor, Dalevi, Daniel, Madejska, Julita, Kirton, Edward, Platt, Darren, Szeto, Ernest, Salamov, Asaf, Barry, Kerrie, Mikhailova, Natalia, Kyrpides, Nikos C., Matson, Eric G., Ottesen, Elizabeth A., Zhang, Xinning, Hernandez, Myriam, Murillo, Catalina ... Leadbetter, Jared R. (2007). Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite. Nature, 450 (7169), 560-565. doi: 10.1038/nature06269

Automated group assignment in large phylogenetic trees using GRUNT: GRouping, ungrouping, naming tool

Dalevi, Daniel, DeSantis, Todd Z., Fredslund, Jakob, Andersen, Gary L., Markowitz, Victor M. and Hugenholtz, Philip (2007). Automated group assignment in large phylogenetic trees using GRUNT: GRouping, ungrouping, naming tool. BMC Bioinformatics, 8 (1) 402. doi: 10.1186/1471-2105-8-402

Characterization of filamentous bacteria, belonging to candidate phylum KSB3, that are associated with bulking in methanogenic granular sludges

Yamada, Takeshi, Yamauchi, Toshihiro, Shiraishi, Koji, Hugenholtz, Philip, Ohashi, Akiyoshi, Harada, Hideki, Kamagata, Yoichi, Nakamura, Kazunori and Sekiguchi, Yuji (2007). Characterization of filamentous bacteria, belonging to candidate phylum KSB3, that are associated with bulking in methanogenic granular sludges. The ISME Journal, 1 (3), 246-255. doi: 10.1038/ismej.2007.28

Dissecting biological "dark matter" with single-cell genetic analysis of rare and uncultivated TM7 microbes from the human mouth

Marcy, Yann, Ouverney, Cleber, Bik, Elisabeth M., Losekann, Tina, Ivanova, Natalia, Martin, Hector Garcia, Szeto, Ernest, Platt, Darren, Hugenholtz, Philip, Relman, David A. and Quake, Stephen R. (2007). Dissecting biological "dark matter" with single-cell genetic analysis of rare and uncultivated TM7 microbes from the human mouth. Proceedings of the National Academy of Sciences of the United States of America, 104 (29), 11889-11894. doi: 10.1073/pnas.0704662104

CRISPR Recognition Tool (CRT) : A tool for automatic detection of clustered regularly interspaced palindromic repeats

Bland, Charles, Ramsey, Teresa L., Sabree, Fareedah, Lowe, Michael, Brown, Kyndall, Kyrpides, Nikos C. and Hugenholtz, Philip (2007). CRISPR Recognition Tool (CRT) : A tool for automatic detection of clustered regularly interspaced palindromic repeats. BMC Bioinformatics, 8 (1) 209, 209-1-209-8. doi: 10.1186/1471-2105-8-209

Increasing focus on environmental biotechnology in the face of pressing environmental challenges

Hugenholtz, Philip and Ron, Eliora Z. (2007). Increasing focus on environmental biotechnology in the face of pressing environmental challenges. Current Opinion in Biotechnology, 18 (3), 235-236. doi: 10.1016/j.copbio.2007.05.004

Integrating ecology into biotechnology

McMahon, KD, Martin, HG and Hugenholtz, P (2007). Integrating ecology into biotechnology. Current Opinion in Biotechnology, 18 (3), 287-292. doi: 10.1016/j.copbio.2007.04.007

Loss of bacterial diversity during antibiotic treatment of intubated patients colonized with Pseudomonas aeruginosa

Flanagan, J. L., Brodie, E. L., Weng, L., Lynch, S. V., Garcia, O., Brown, R., Hugenholtz, P., DeSantis, T. Z., Andersen, G. L., Wiener-Kronish, J. P. and Bristow, J. (2007). Loss of bacterial diversity during antibiotic treatment of intubated patients colonized with Pseudomonas aeruginosa. Journal of Clinical Microbiology, 45 (6), 1954-1962. doi: 10.1128/JCM.02187-06

Use of simulated data sets to evaluate the fidelity of metagenomic processing methods

Mavromatis, Konstantinos, Ivanova, Natalia, Barry, Kerry, Shapiro, Harris, Goltsman, Eugene, McHardy, Alice C., Rigoutsos, Isidore, Salamov, Asaf, Korzeniewski, Frank, Land, Miriam, Lapidus, Alla, Grigoriev, Igor, Richardson, Paul, Hugenholtz, Philip and Kyrpides, Nikos C. (2007). Use of simulated data sets to evaluate the fidelity of metagenomic processing methods. Nature Methods, 4 (6), 495-500. doi: 10.1038/nmeth1043

Quantitative phylogenetic assessment of microbial communities in diverse environments

von Mering, C., Hugenholtz, P., Raes, J., Tringe, S. G., Doerks, T., Jensen, L. J., Ward, N. and Bork, P. (2007). Quantitative phylogenetic assessment of microbial communities in diverse environments. Science, 315 (5815), 1126-1130. doi: 10.1126/science.1133420

Accurate phylogenetic classification of variable-length DNA fragments

McHardy, Alice Carolyn, Martin, Hector Garcia, Tsirigos, Aristotelis, Hugenholtz, Philip and Rigoutsos, Isidore (2007). Accurate phylogenetic classification of variable-length DNA fragments. Nature Methods, 4 (1), 63-72. doi: 10.1038/NMETH976

Building on basic metagenomics with complementary technologies

Warnecke, F and Hugenholtz, P (2007). Building on basic metagenomics with complementary technologies. Genome Biology, 8 (12) 231, 231.1-231.5. doi: 10.1186/gb-2007-8-12-231

Evolutionary conservation of sequence and secondary structures in CRISPR repeats

Kunin, Victor, Sorek, Rotem and Hugenholtz, Philip (2007). Evolutionary conservation of sequence and secondary structures in CRISPR repeats. Genome Biology, 8 (4 Article # R61) R61, R61-1-R61-3. doi: 10.1186/gb-2007-8-4-r61

Riding giants

Hugenholtz, Philip (2007). Riding giants. Environmental Microbiology, 9 (1), 5-5. doi: 10.1111/j.1462-2920.2006.01222_4.x

Lineages of acidophilic archaea revealed by community genomic analysis

Baker, Brett J., Tyson, Gene W., Webb, Richard I., Flanagan, Judith, Hugenholtz, Philip, Allen, Eric E. and Banfield, Jillian F. (2006). Lineages of acidophilic archaea revealed by community genomic analysis. Science, 314 (5807), 1933-1935. doi: 10.1126/science.1132690

An experimental metagenome data management and analysis system (vol 22, pg 359, 2006)

Markowitz, Victor M., Ivanova, Natalia, Palaniappan, Krishna, Szeto, Ernest, Korzeniewski, Frank, Lykidis, Athanasios, Anderson, Iain, Mavrommatis, Konstantinos, Kunin, Victor, Martin, Hector Garcia, Dubchak, Inna, Hugenholtz, Phil and Kyrpides, Nikos C. (2006). An experimental metagenome data management and analysis system (vol 22, pg 359, 2006). Bioinformatics, 22 (20), 2580-2580. doi: 10.1093/bioinformatics/btl436

NAST: A multiple sequence alignment server for comparative analysis of 16S rRNA genes

DeSantis, T. Z., Hugenholtz, P., Keller, K., Brodie, E. L., Larsen, N., Piceno, Y. M., Phan, R. and Andersen, G. L. (2006). NAST: A multiple sequence alignment server for comparative analysis of 16S rRNA genes. Nucleic Acids Research, 34 (suppl 2), W394-W399. doi: 10.1093/nar/gkl244

Numbers and locations of native bacteria on field-grown wheat roots quantified by fluorescence in situ hybridization (FISH)

Watt, Michelle, Hugenholtz, Philip, White, Rosemary and Vinall, Kerry (2006). Numbers and locations of native bacteria on field-grown wheat roots quantified by fluorescence in situ hybridization (FISH). Environmental Microbiology, 8 (5), 871-884. doi: 10.1111/j.1462-2920.2005.00973.x

Non-sulfate-reducing, syntrophic bacteria affiliated with Desulfotomaculum cluster I are widely distributed in methanogenic environments

Imachi, Hiroyuki, Sekiguchi, Yuji, Kamagata, Yoichi, Loy, Alexander, Qiu, Yan-Ling, Hugenholtz, Philip, Kimura, Nobutada, Wagner, Michael, Ohashi, Akiyoshi and Harada, Hideki (2006). Non-sulfate-reducing, syntrophic bacteria affiliated with Desulfotomaculum cluster I are widely distributed in methanogenic environments. Applied and Environmental Microbiology, 72 (3), 2080-2091. doi: 10.1128/AEM.72.3.2080-2091.2006

Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB

DeSantis, T. Z., Hugenholtz, P., Larsen, N., Rojas, M., Brodie, E. L., KELLER, K., Huber, T. L., Dalevi, D., Hu, P. and Andersen, G. L. (2006). Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Applied and Environmental Microbiology, 72 (7), 5069-5072. doi: 10.1128/AEM.03006-05

Metagenomic analysis of two enhanced biological phosphorus removal (EBPR) sludge communities

Martín, Hector Garcia, Ivanova, Natalia, Kunin, Victor, Warnecke, Falk, Barry, Kerrie W., McHardy, Alice C., Yeates, Christine, He, Shaomei, Salamov, Asaf A., Szeto, Ernest, Dalin, Eileen, Putnam, Nik H., Shapiro, Harris J., Pangilinan, Jasmyn L., Rigoutsos, Isidore, Kyrpides, Nikos C., Blackall, Linda Louise, McMahon, Katherine D. and Hugenholtz, Philip (2006). Metagenomic analysis of two enhanced biological phosphorus removal (EBPR) sludge communities. Nature Biotechnology, 24 (10), 1263-1269. doi: 10.1038/nbt1247

The Genomes On Line Database (GOLD) v.2: a monitor of genome projects worldwide

Liolios, Konstantinos, Tavernarakis, Nektarios, Hugenholtz, Philip and Kyrpides, Nikos C. (2006). The Genomes On Line Database (GOLD) v.2: a monitor of genome projects worldwide. Nucleic Acids Research, 34 (Supp. 1), D332-D334. doi: 10.1093/nar/gkj145

The integrated microbial genomes (IMG) system

Markowitz, Victor M., Korzeniewski, Frank, Palaniappan, Krishna, Szeto, Ernest, Werner, Greg, Padki, Anu, Zhao, Xueling, Dubchak, Inna, Hugenholtz, Philip, Anderson, Iain, Lykidis, Athanasios, Mavromatis, Konstantinos, Ivanova, Natalia and Kyrpides, Nikos C. (2006). The integrated microbial genomes (IMG) system. Nucleic Acids Research, 34 (Supp. 1), D344-D348. doi: 10.1093/nar/gkj024

SNP-VISTA: An interactive SNP visualization tool

Shah, Nameeta, Teplitsky, Michael V., Minovitsky, Simon, Pennacchio, Len A., Hugenholtz, Philip, Hamann, Bernd and Dubchak, Inna L. (2005). SNP-VISTA: An interactive SNP visualization tool. BMC Bioinformatics, 6 (1) 292. doi: 10.1186/1471-2105-6-292

Genome-Directed Isolation of the Key Nitrogen Fixer Leptospirillum ferrodiazotrophum sp. nov. from an Acidophilic Microbial Community

Tyson, Gene W., Lo, Ian, Baker, Brett J., Allen, Eric E., Hugenholtz, Philip and Banfield, Jillian F. (2005). Genome-Directed Isolation of the Key Nitrogen Fixer Leptospirillum ferrodiazotrophum sp. nov. from an Acidophilic Microbial Community. Applied and Environmental Microbiology, 71 (10), 6319-6324. doi: 10.1128/AEM.71.10.6319-6324.2005

Comparative metagenomics of microbial communities

Tringe, Susannah Green, von Mering, Christian, Kobayashi, Arthur, Salamov, Asaf A., Chen, Kevin, Chang, Hwai W., Podar, Mircea, Short, Jay M., Mathur, Eric J., Detter, John C., Bork, Peer, Hugenholtz, Philip and Rubin, Edward M. (2005). Comparative metagenomics of microbial communities. Science, 308 (5721), 554-557. doi: 10.1126/science.1107851

Reclassification of Sphaerobacter thermophilus from the subclass Sphaerobacteridae in the phylum Actinobacteria to the class Thermomicrobia (emended description) in the phylum Chloroflexi (emended description)

Hugenholtz, Philip and Stackebrandt, Erko (2004). Reclassification of Sphaerobacter thermophilus from the subclass Sphaerobacteridae in the phylum Actinobacteria to the class Thermomicrobia (emended description) in the phylum Chloroflexi (emended description). International Journal of Systematic and Evolutionary Microbiology, 54 (6), 2049-2051. doi: 10.1099/ijs.0.03028-0

Chthoniobacter flavus gen. nov., sp nov., the first pure-culture representative of subdivision two, Spartobacteria classis nov., of the phylum Verrucomicrobia

Sangwan, Parveen, Chen, Xiaolei, Hugenholtz, Philip and Janssen, Peter H. (2004). Chthoniobacter flavus gen. nov., sp nov., the first pure-culture representative of subdivision two, Spartobacteria classis nov., of the phylum Verrucomicrobia. Applied and Environmental Microbiology, 70 (10), 5875-5881. doi: 10.1128/AEM.70.10.5875-5881.2004

Liquid serial dilution is inferior to solid media for isolation of cultures representative of the phylum-level diversity of soil bacteria

Schoenborn, Liesbeth, Yates, Penelope S., Grinton, Bronwyn E., Hugenholtz, Philip and Janssen, Peter H. (2004). Liquid serial dilution is inferior to solid media for isolation of cultures representative of the phylum-level diversity of soil bacteria. Applied and Environmental Microbiology, 70 (7), 4363-4366. doi: 10.1128/AEM.70.7.4363-4366.2004

Bellerophon: a program to detect chimeric sequences in multiple sequence alignments

Huber, T, Faulkner, G and Hugenholtz, P (2004). Bellerophon: a program to detect chimeric sequences in multiple sequence alignments. Bioinformatics, 20 (14), 2317-2319. doi: 10.1093/bioinformatics/bth226

Community structure and metabolism through reconstruction of microbial genomes from the environment

Tyson, Gene W., Chapman, Jarrod, Hugenholtz, Philip, Allen, Eric E., Ram, Rachna J., Richardson, Paul M., Solovyev, Victor V., Rubin, Edward M., Rokhsar, Daniel S. and Banfield, Jillian F. (2004). Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature, 428 (6978), 37-43. doi: 10.1038/nature02340

Use of stable-isotope probing, full-cycle rRNA analysis, and fluorescence in situ hybridization-microautoradiography to study a methanol-fed denitrifying microbial community

Ginige, MP, Hugenholtz, P, Daims, H, Wagner, M, Keller, J and Blackall, LL (2004). Use of stable-isotope probing, full-cycle rRNA analysis, and fluorescence in situ hybridization-microautoradiography to study a methanol-fed denitrifying microbial community. Applied And Environmental Microbiology, 70 (1), 588-596. doi: 10.1128/AEM.70.1.588-596.2004

Laboratory cultivation of widespread and previously uncultured soil bacteria

Joseph, SJ, Hugenholtz, P, Sangwan, P, Osborne, CA and Janssen, PH (2003). Laboratory cultivation of widespread and previously uncultured soil bacteria. Applied and Environmental Microbiology, 69 (12), 7210-7215. doi: 10.1128/AEM.69.12.7210-7215.2003

Extremely acidophilic protists from acid mine drainage host Rickettsiales-lineage endosymbionts that have intervening sequences in their 16S rRNA genes

Baker, BJ, Hugenholtz, P, Dawson, SC and Banfield, JF (2003). Extremely acidophilic protists from acid mine drainage host Rickettsiales-lineage endosymbionts that have intervening sequences in their 16S rRNA genes. Applied and Environmental Microbiology, 69 (9), 5512-5518. doi: 10.1128/AEM.69.9.5512-5518.2003

Gemmatimonas aurantiaca gen. nov., sp nov., a gram-negative, aerobic, polyphosphate-accumulating micro-organism, the first cultured representative of the new bacterial phylum Gemmatimonadetes phyl. nov.

Zhang, H, Sekiguchi, Y, Hanada, S, Hugenholtz, P, Kim, H, Kamagata, Y and Nakamura, K (2003). Gemmatimonas aurantiaca gen. nov., sp nov., a gram-negative, aerobic, polyphosphate-accumulating micro-organism, the first cultured representative of the new bacterial phylum Gemmatimonadetes phyl. nov.. International Journal of Systematic and Evolutionary Microbiology, 53 (4), 1155-1163. doi: 10.1099/ijs.0.02520-0

Fermentation of glycolate by a pure culture of a strictly anaerobic gram-positive bacterium belonging to the family Lachnospiraceae

Janssen, PH and Hugenholtz, P (2003). Fermentation of glycolate by a pure culture of a strictly anaerobic gram-positive bacterium belonging to the family Lachnospiraceae. Archives of Microbiology, 179 (5), 321-328. doi: 10.1007/s00203-003-0528-5

PCR detection of Clostridium chauvoei in pure cultures and in formalin-fixed, paraffin-embedded tissues

Uzal, FA, Hugenholtz, P, Blackall, LL, Petray, S, Moss, S, Assis, RA, Miyakawa, MF and Carloni, G (2003). PCR detection of Clostridium chauvoei in pure cultures and in formalin-fixed, paraffin-embedded tissues. Veterinary Microbiology, 91 (2-3), 239-248. doi: 10.1016/S0378-1135(02)00291-2

Chimeric 16S rDNA sequences of diverse origin are accumulating in the public databases

Hugenholtz, P and Huber, T (2003). Chimeric 16S rDNA sequences of diverse origin are accumulating in the public databases. International Journal of Systematic And Evolutionary Microbiology, 53 (1), 289-293. doi: 10.1099/ijs.0.02441-0

Kinetic and phylogenetic characterization of an anaerobic dechlorinating microbial community

Rossetti, S, Blackall, LL, Majone, M, Hugenholtz, P, Plumb, JJ and Tandoi, V (2003). Kinetic and phylogenetic characterization of an anaerobic dechlorinating microbial community. Microbiology-sgm, 149 (2), 459-469. doi: 10.1099/mic.0.26018-0

Cultivation of globally distributed soil bacteria from phylogenetic lineages previously only detected in cultivation-independent surveys

Sait, M, Hugenholtz, P and Janssen, PH (2002). Cultivation of globally distributed soil bacteria from phylogenetic lineages previously only detected in cultivation-independent surveys. Environmental Microbiology, 4 (11), 654-666. doi: 10.1046/j.1462-2920.2002.00352.x

Filamentous Chloroflexi (green non-sulfur bacteria) are abundant in wastewater treatment processes with biological nutrient removal

Bjornsson, Lovisa, Hugenholtz, Philip, Tyson, Gene W. and Blackall, Linda L. (2002). Filamentous Chloroflexi (green non-sulfur bacteria) are abundant in wastewater treatment processes with biological nutrient removal. Microbiology, 148 (8), 2309-2318. doi: 10.1099/00221287-148-8-2309

In situ studies of the phylogeny and physiology of filamentous bacteria with attached growth

Thomsen, TR, Kjellerup, BV, Nielsen, JL, Hugenholtz, P and Nielsen, PH (2002). In situ studies of the phylogeny and physiology of filamentous bacteria with attached growth. Environmental Microbiology, 4 (7), 383-391. doi: 10.1046/j.1462-2920.2002.00316.x

Molecular analysis of dimethyl sulphide dehydrogenase from Rhodovulum sulfidophilum: its place in the dimethyl sulphoxide reductase family of microbial molybdopterin-containing enzymes

McDevitt, Christopher A., Hugenholtz, Philip, Hanson, Graeme R. and McEwan, Alastair G. (2002). Molecular analysis of dimethyl sulphide dehydrogenase from Rhodovulum sulfidophilum: its place in the dimethyl sulphoxide reductase family of microbial molybdopterin-containing enzymes. Molecular Microbiology, 44 (6), 1575-1587. doi: 10.1046/j.1365-2958.2002.02978.x

Design and evaluation of 16S rRNA-targeted oligonucleotide probes for fluorescence in situ hybridization

Hugenholtz, P., Tyson, G. W. and Blackall, L. L. (2002). Design and evaluation of 16S rRNA-targeted oligonucleotide probes for fluorescence in situ hybridization. Methods in molecular biology (Clifton, N.J.), 179, 29-42.

Exploring prokaryotic diversity in the genomic era

Hugenholtz, P (2002). Exploring prokaryotic diversity in the genomic era. Genome Biology, 3 (2) 0003, REVIEWS0003. doi: 10.1186/gb-2002-3-2-reviews0003

The DMSO reductase family of microbial molybdenum enzymes; Molecular properties and role in the dissimilatory reduction of toxic elements

McEwan, A. G., Ridge, J. P., McDevitt, C. A. and Hugenholtz, P. (2002). The DMSO reductase family of microbial molybdenum enzymes; Molecular properties and role in the dissimilatory reduction of toxic elements. Geomicrobiology Journal, 19 (1), 3-21. doi: 10.1080/014904502317246138

The development and use of real-time PCR for the quantification of nitrifiers in activated sludge

Hall, S. J., Hugenholtz, P., Siyambalapitiya, N., Keller, J. and Blackall, L. L. (2002). The development and use of real-time PCR for the quantification of nitrifiers in activated sludge. Water Science And Technology, 46 (1-2), 267-272. doi: 10.2166/wst.2002.0488

Multiple lateral transfers of dissimilatory sulfite reductase genes between major lineages of sulfate-reducing prokaryotes

Klein, M., Friedrich, M., Roger, A. J., Hugenholtz, P., Fishbain, S., Abicht, H., Blackall, L. L., Stahl, D. A. and Wagner, M. (2001). Multiple lateral transfers of dissimilatory sulfite reductase genes between major lineages of sulfate-reducing prokaryotes. Journal of Bacteriology, 183 (20), 6028-6035. doi: 10.1128/JB.183.20.6028-6035.2001

A multiple-outgroup approach to resolving division-level phylogenetic relationships using 16S rDNA data

Dalevi, D, Hugenholtz, P and Blackall, LL (2001). A multiple-outgroup approach to resolving division-level phylogenetic relationships using 16S rDNA data. International Journal of Systematic And Evolutionary Microbiology, 51 (2), 385-391. doi: 10.1099/00207713-51-2-385

Investigation of candidate division TM7, a recently recognized major lineage of the domain bacteria with no known pure-culture representatives

Hugenholtz, Philip, Tyson, Gene W., Webb, Richard I., Wagner, Ankia M. and Blackall, Linda L. (2001). Investigation of candidate division TM7, a recently recognized major lineage of the domain bacteria with no known pure-culture representatives. Applied And Environmental Microbiology, 67 (1), 411-419. doi: 10.1128/AEM.67.1.411-419.2001

Identification of polyphosphate-accumulating organisms and design of 16S rRNA-directed Probes for their detection and quantitation

Crocetti, GR, Hugenholtz, P, Bond, PL, Schuler, A, Keller, J, Jenkins, D and Blackall, LL (2000). Identification of polyphosphate-accumulating organisms and design of 16S rRNA-directed Probes for their detection and quantitation. Applied and Environmental Microbiology, 66 (3), 1175-1182. doi: 10.1128/AEM.66.3.1175-1182.2000

Microorganisms should be high on DNA preservation list

Fuerst, J. A. and Hugenholtz, P. (2000). Microorganisms should be high on DNA preservation list. Science, 290 (5496), 1503-1503. doi: 10.1126/science.290.5496.1503b

Diversity of radA genes from cultured and uncultured Archaea: Comparative analysis of putative RadA proteins and their use as a phylogenetic marker

Sandler, S. J., Hugenholtz, P., Schleper, C., DeLong, E. F., Pace, N. R. and Clark, A. J. (1999). Diversity of radA genes from cultured and uncultured Archaea: Comparative analysis of putative RadA proteins and their use as a phylogenetic marker. Journal of Bacteriology, 181 (3), 907-915.

Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity (vol 180, pg 4765, 1998)

Hugenholtz, P., Goebel, B. M. and Pace, N. R. (1998). Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity (vol 180, pg 4765, 1998). Journal of Bacteriology, 180 (24), 6793-6793. doi: 10.1128/jb.180.24.6793-6793.1998

Microbial diversity in a hydrocarbon- and chlorinated-solvent-contaminated aquifer undergoing intrinsic bioremediation

Dojka, M. A., Hugenholtz, P., Haack, S. K. and Pace, N. R. (1998). Microbial diversity in a hydrocarbon- and chlorinated-solvent-contaminated aquifer undergoing intrinsic bioremediation. Applied and Environmental Microbiology, 64 (10), 3869-3877.

Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity

Hugenholtz, P., Goebel, B. M. and Pace, N. R. (1998). Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity. Journal of Bacteriology, 180 (18), 4765-4774.

Novel division level bacterial diversity in a Yellowstone hot spring

Hugenholtz, P., Pitulle, C., Hershberger, K. L. and Pace, N. R. (1998). Novel division level bacterial diversity in a Yellowstone hot spring. Journal of Bacteriology, 180 (2), 366-376.

The characterization and description of representatives of 'G' bacteria from activated sludge plants

Blackall, LL, Rossetti, S, Christensson, C, Cunningham, M, Hartman, P, Hugenholtz, P and Tandoi, V (1997). The characterization and description of representatives of 'G' bacteria from activated sludge plants. Letters in Applied Microbiology, 25 (1), 63-69. doi: 10.1046/j.1472-765X.1997.00176.x

The filamentous morphotype Eikelboom Type 1863 is not a single genetic entity

Seviour, EM, Blackall, LL, Christensson, C, Hugenholtz, P, Cunningham, MA, Bradford, D, Stratton, HM and Seviour, RJ (1997). The filamentous morphotype Eikelboom Type 1863 is not a single genetic entity. Journal of Applied Microbiology, 82 (4), 411-421. doi: 10.1046/j.1365-2672.1997.00111.x

Isolation and molecular identification of planctomycete bacteria from postlarvae of the giant tiger prawn, Penaeus monodon

Fuerst, JA, Gwilliam, HG, Lindsay, M, Lichanska, A, Belcher, C, Vickers, JE and Hugenholtz, P (1997). Isolation and molecular identification of planctomycete bacteria from postlarvae of the giant tiger prawn, Penaeus monodon. Applied And Environmental Microbiology, 63 (1), 254-262. doi: 10.1128/aem.63.1.254-262.1997

16S rRNA analysis of isolates obtained from gram-negative, filamentous bacteria micromanipulated from activated sludge

Bradford, D, Hugenholtz, P, Seviour, EM, Cunningham, MA, Stratton, H, Seviour, RJ and Blackall, LL (1996). 16S rRNA analysis of isolates obtained from gram-negative, filamentous bacteria micromanipulated from activated sludge. Systematic and Applied Microbiology, 19 (3), 334-343. doi: 10.1016/S0723-2020(96)80060-9

Identifying microbial diversity in the natural environment: A molecular phylogenetic approach

Hugenholtz, P and Pace, NR (1996). Identifying microbial diversity in the natural environment: A molecular phylogenetic approach. Trends in Biotechnology, 14 (6), 190-197. doi: 10.1016/0167-7799(96)10025-1

Desiccation Resistance of Bacteria Isolated From An Air-Handling System Biofilm Determined Using a Simple Quantitative Membrane-Filter Method

Hugenholtz, P, Cunningham, MA, Hendrikz, JK and Fuerst, JA (1995). Desiccation Resistance of Bacteria Isolated From An Air-Handling System Biofilm Determined Using a Simple Quantitative Membrane-Filter Method. Letters in Applied Microbiology, 21 (1), 41-46. doi: 10.1111/j.1472-765X.1995.tb01003.x

Bacterial community structures of phosphate-removing and non-phosphate- removing activated sludges from sequencing batch reactors

Bond, P. L., Hugenholtz, P., Keller, J. and Blackall, L. L. (1995). Bacterial community structures of phosphate-removing and non-phosphate- removing activated sludges from sequencing batch reactors. Applied and Environmental Microbiology, 61 (5), 1910-1916. doi: 10.1128/aem.61.5.1910-1916.1995

Phylogenetic Analysis and Taxonomic History of Nocardia pinensis and Nocardia amarae

Blackall, Linda L., Barker, Stephen C. and Hugenholtz, Philip (1995). Phylogenetic Analysis and Taxonomic History of Nocardia pinensis and Nocardia amarae. Systematic and Applied Microbiology, 17 (4), 519-525. doi: 10.1016/S0723-2020(11)80071-8

“Microthrix parvicella” is a Novel, Deep Branching Member of the Actinomycetes Subphylum

Blackall, Linda L., Seviour, Elizabeth M., Cunningham, Mitchell A., Seviour, Robert J. and Hugenholtz, Philip (1995). “Microthrix parvicella” is a Novel, Deep Branching Member of the Actinomycetes Subphylum. Systematic and Applied Microbiology, 17 (4), 513-518. doi: 10.1016/S0723-2020(11)80070-6

Phylogenetic Positions of Novel Aerobic, Bacteriochlorophyll Alpha-Containing Bacteria and Description of Roseococcus-Thiosulfatophilus Gen-Nov, Sp-Nov, Erythromicrobium-Ramosum Gen-Nov, Sp-Nov, and Erythrobacter-Litoralis Sp-Nov

Yurkov, V, Stackebrandt, E, Holmes, A, Fuerst, JA, Hugenholtz, P, Golecki, J, Gadon, N, Gorlenko, VM, Kompantseva, EI and Drews, G (1994). Phylogenetic Positions of Novel Aerobic, Bacteriochlorophyll Alpha-Containing Bacteria and Description of Roseococcus-Thiosulfatophilus Gen-Nov, Sp-Nov, Erythromicrobium-Ramosum Gen-Nov, Sp-Nov, and Erythrobacter-Litoralis Sp-Nov. International Journal of Systematic Bacteriology, 44 (3), 427-434. doi: 10.1099/00207713-44-3-427

A Phylogenetic Analysis of the Genus Blastobacter with a View to its Future Reclassification

Hugenholtz, P, Stackebrandt, E and Fuerst, JA (1994). A Phylogenetic Analysis of the Genus Blastobacter with a View to its Future Reclassification. Systematic and Applied Microbiology, 17 (1), 51-57. doi: 10.1016/S0723-2020(11)80031-7

Heterotrophic Bacteria in An Air-Handling System

Hugenholtz, P and Fuerst, JA (1992). Heterotrophic Bacteria in An Air-Handling System. Applied and Environmental Microbiology, 58 (12), 3914-3920. doi: 10.1128/AEM.58.12.3914-3920.1992

Stimulation of Aldrin and Dieldrin Loss From Soils Treated with Carbon Amendments and Saturated-Ring Analogs

Hugenholtz, P and Macrae, IC (1990). Stimulation of Aldrin and Dieldrin Loss From Soils Treated with Carbon Amendments and Saturated-Ring Analogs. Bulletin of Environmental Contamination and Toxicology, 45 (2), 223-227. doi: 10.1007/BF01700187

Role of dietary lipids in chronic obstructive pulmonary disease

Rehman, S., Budden, K., Quaranta, A., Fuchs, D., Bowerman, K., Vaughan, A., Shukla, S., Brown, A., Alemao, C., Balachandra, L., Gomez, H., Kumar, , Idrees, S., Faiz, A., Hugenholtz, P., Wark, P., Horvat, J., Wood, L., Wheelock, C. and Hansbro, P. (2023). Role of dietary lipids in chronic obstructive pulmonary disease. HOBOKEN: WILEY.

Association between dietary fibre, microbial metabolites and airway obstruction in COPD patients and murine models

Budden, K., Rehman, S. F., Shukla, S., Bowerman, K., Donovan, C., Gomez, H., Alemao, C., Wood, L., Dennis, P., Hugenholtz, P., Wark, P. and Hansbro, P. (2022). Association between dietary fibre, microbial metabolites and airway obstruction in COPD patients and murine models. ERS International Congress 2022, Barcelona, Spain, 4-6 September 2022. Sheffield, United Kingdom: European Respiratory Society. doi: 10.1183/13993003.congress-2022.3289

Interferon Lambda Protects Gastrointestinal Stem Cells from Acute Gvhd

Henden, Andrea S., Robb, Renee, Forero, Adriana, Kuns, Rachel D., Ensbey, Kathleen S., Chang, Karshing, Varelias, Antiopi, Kazakoff, Stephen H., Waddell, Nic, Clouston, Andrew D., Giri, Rabina, Begun, Jakob, Blazar, Bruce R., Degli-Esposti, Mariapia A., Kotenko, Sergei V., Lane, Steven W., Bowerman, Kate L., Savan, Ram, Hugenholtz, Philip, Gartlan, Kate H. and Hill, Geoffrey (2021). Interferon Lambda Protects Gastrointestinal Stem Cells from Acute Gvhd. 2021 TCT Meetings of ASTCT and CIBMTR, Online, 8-12 February 2021. Amsterdam, Netherlands: Elsevier. doi: 10.1016/s2666-6367(21)00107-x

Changes in the Gut Microbiome in Chronic Obstructive Pulmonary Disease

Rehman, S.F., Bowerman, K.L., Lachner, N., Budden, K.F., Kim, R., Wood, D.L., Gellatly, S.L., Wark, P.A., Hugenholtz, P. and Hansbro, P.M. (2020). Changes in the Gut Microbiome in Chronic Obstructive Pulmonary Disease. American Thoracic Society International Conference 2020, Philadelphia, PA United States, 15-20 May 2020. New York, NY United States: American Thoracic Society. doi: 10.1164/ajrccm-conference.2020.201.1_meetingabstracts.a4473

Diet influences COPD pathogenesis by regulating microbial metabolism

Budden, K., Rehman, Firdous S., Shukla, S., Bowerman, K., Donovan, C., Gomez, H., Sahu, P., Alemao, C., Holmes, A., Dennis, P., Hugenholtz, P., Wark, P. and Hansbro, P. (2020). Diet influences COPD pathogenesis by regulating microbial metabolism. TSANZSRS 2020 The Australia & New Zealand Society of Respiratory Science and The Thoracic Society of Australia and New Zealand (ANZSRS/TSANZ) Annual Scientific Meeting for Leaders in Lung Health & Respiratory Science, Melbourne, VIC Australia, 27–31 March 2020. Richmond, VIC Australia: Wiley-Blackwell.

Fast forward bioprospecting of the gut microbiota for novel live biotherapeutics and anti-inflammatory bioactives

Cuiv, Paraic O., Krause, Lutz, Wood, David, Hugenholtz, Phil and Tyson, Gene (2020). Fast forward bioprospecting of the gut microbiota for novel live biotherapeutics and anti-inflammatory bioactives. FNM 2020 ‐ 4th Meeting of the Federation of Neurogastroenterology and Motility, Adelaide, SA Australia, 25 - 28 March 2020. Chichester, West Sussex United Kingdom: Wiley-Blackwell.

Variations of the mucosa associated microbiota along the human gastrointestinal tract in health and inflammatory bowel disease

Shah, Ayesha, Kang, Seungha, Tyson, Gene, Zaugg, Julian, Hugenholtz, Phil, Morrison, Mark and Holtmann, Gerald J. (2020). Variations of the mucosa associated microbiota along the human gastrointestinal tract in health and inflammatory bowel disease. Crohn's and Colitis Congress, Austin, TX, United States, 23-25 January 2020. Philadelphia, PA, United States: Elsevier . doi: 10.1016/s0016-5085(20)32052-7

2125. Staphylococcus Species Identification by Fourier Transform Infrared (FTIR) Spectroscopic Techniques: A Cross-Lab Study

Tsutsumi, Tamao, Shah, Alok, Lam, Lisa M T, Schlebusch, Sanmarie, Krueger, Annika, Frazer, Ian, Hugenholtz, Phil, Soyer, H Peter, Morrison, Mark, Hill, Michelle, Sedman, Jacqueline and Ismail, Ashraf (2019). 2125. Staphylococcus Species Identification by Fourier Transform Infrared (FTIR) Spectroscopic Techniques: A Cross-Lab Study. IDWeek 2019, Washington, DC, United States, 2-6 October 2019. Oxford, United Kingdom: Oxford University Press. doi: 10.1093/ofid/ofz360.1805

Dietary fibre elevates SCFAS and protects against experimental COPD

Budden, K., Shukla, S., Rehman, Firdous S., Donvan, C., Bowerman, K., Dennis, P., Hugenholtz, P. and Hansbro, P. (2019). Dietary fibre elevates SCFAS and protects against experimental COPD. TSANZSRS 2019 The Australia & New Zealand Society of Respiratory Science and The Thoracic Society of Australia and New Zealand (ANZSRS/TSANZ) Annual Scientific Meeting, Gold Coast, QLD, Australia, 29 March–2 April 2019. Richmond, VIC, Australia : Wiley-Blackwell Publishing Asia. doi: 10.1111/resp.13492

The Role of the Gastrointestinal Microbiome in Lung Cancer Pathogenesis

Budden, Kurtis, Shukla, Shakti, Rehman, Saima Firdous, Sahu, Priyanka, Donovan, Chantal, Bowerman, Kate L., Dennis, Paul G., Hugenholtz, Philip and Hansbro, Philip M. (2019). The Role of the Gastrointestinal Microbiome in Lung Cancer Pathogenesis. 2019 Hunter Cancer Research Symposium, Newcastle, NSW Australia, 8 November 2019. Chichester, West Sussex United Kingdom: Wiley-Blackwell.

Recipient mucosal-associated invariant T cells control graft-versus-host-disease within the colon

Varelias, Antiopi, Bunting, Mark, Ormerod, Kate, Koyama, Motoko, Olver, Stuart, Straube, Jasmin, Kuns, Rachel, Robb, Renee, Henden, Andrea, Cooper, Leanne, Lachner, Nancy, Gartlan, Kate, Lantz, Olivier J., Kjer-Nielsen, Lars, Mak, Jeffrey, Fairlie, David, Clouston, Andrew, McCluskey, James, Rossjohn, Jamie, Lane, Steven, Hugenholtz, Phil and Hill, Geoff (2018). Recipient mucosal-associated invariant T cells control graft-versus-host-disease within the colon. Immunology Meeting, Austin Tx, 4-8 May 2018. Bethesda, MD United States: American Association of Immunologists.

Acute graft-versus-host disease is regulated by an IL-17-sensitive microbiome

Varelias, Antiopi, Ormerod, Kate L., Bunting, Mark D., Koyama, Motoko, Gartlan, Kate H., Kuns, Rachel D., Lachner, Nancy, Locke, Kelly R., Lim, Chun Y., Henden, Andrea S., Zhang, Ping, Clouston, Andrew D., Hasnain, Sumaira Z., McGuckin, Michael A., Blazar, Bruce R., MacDonald, Kelli P. A., Hugenholtz, Philip and Hill, Geoff R. (2017). Acute graft-versus-host disease is regulated by an IL-17-sensitive microbiome. Immunology Meeting, Washington DC, 12-16 May 2017. Bethesda, MD United States: American Association of Immunologists.

Dietary fibre and microbial metabolites protect against cigarette smoke-induced lung pathology in mice

Budden, Kurtis, Gellatly, Shaan, Wood, David, Morrison, Mark, Cooper, Matthew, Dennis, Paul G., Hugenholtz, Philip and Hansbro, Philip (2017). Dietary fibre and microbial metabolites protect against cigarette smoke-induced lung pathology in mice. 22nd Congress of the Asian Pacific Society of Respirology, Sydney, Australia, 23–26 November 2017. Hoboken, NJ United States: Wiley.

IL-23 promotes fecal microbiota dysbiosis associated with susceptibility to spondyloarthritis and ileitis in ZAP-70 mutant SKG mice

Rehaume, Linda, Matigian, Nicholas, Ormerod, Kate, Kang, Alicia, Linedale, Richard, Zbarskaya, Olga, Kikly, Kristine, Daly, Joshua, Lachner, Nancy, Hugenholtz, Philip, Morrison, Mark, Le Cao, Kim-Anh and Thomas, Ranjeny (2017). IL-23 promotes fecal microbiota dysbiosis associated with susceptibility to spondyloarthritis and ileitis in ZAP-70 mutant SKG mice. ACR/ARHP Annual Meeting, San Diego, CA United States, 3-8 November 2017. Hoboken, NJ United States: John Wiley & Sons.

Streptococcus Species Enriched in the Oral Cavity of RA Patients: A Persistent Source of Peptidoglycan-Polysaccharide Polymers Which Drive Disseminated Synovial Inflammation

Moentadj, Rabia, Rehaume, Linda, Cuiv, Paraic O., Ormerod, Kate, Maradana, Muralidhara, Lakis, Vanessa Anne, Morrison, Mark, Hugenholtz, Philip, Benham, Helen, Le Cao, Kim-Anh and Thomas, Ranjeny (2017). Streptococcus Species Enriched in the Oral Cavity of RA Patients: A Persistent Source of Peptidoglycan-Polysaccharide Polymers Which Drive Disseminated Synovial Inflammation. 2017 ACR/ARHP Annual Meeting, San Diego CA, United States, 3–8 November 2017. Hoboken, NJ United States: John Wiley & Sons. doi: 10.1002/art.40321

Addressing the nitrogen problem in sugarcane production to reduce pollution of the Great Barrier Reef

Robinson, N., Brackin, R., Paungfoo-Lonhienne, C., Lonhienne, T., Westermann, M., Salazar, M., Yeoh, Y. K ., Hugenholtz, P., Ragan, M. A., Redding, M., Pratt, C., Wang, W. J., Royle, A., DiBella, L., Lakshmanan, P. and Schmidt, S. (2016). Addressing the nitrogen problem in sugarcane production to reduce pollution of the Great Barrier Reef. International Nitrogen Initiative Conference, Melbourne, Australia, 4-8 December 2016. Melbourne, Australia: International Nitrogen Initiative.

An Australian prospective cohort of rheumatoid arthritis patients and their first-degree relatives characterising environmental, genetic, microbial and immune factors

Benham, Helen, Wood, John, Nagl, Lisa, Maradana, Muralidhara, Daly, Joshua, Lachner, Nancy, Hugenholtz, Philip and Thomas, Ranjeny (2016). An Australian prospective cohort of rheumatoid arthritis patients and their first-degree relatives characterising environmental, genetic, microbial and immune factors. Australian Rheumatology Association in conjunction with Rheumatology Health Professionals Association, 57th Annual Scientific Meeting, Darwin, NT, Australia, 30 April–4 May 2016. Richmond, VIC, Australia: Wiley-Blackwell Publishing Asia. doi: 10.1111/imj.13052

Distinct Oral and Fecal Community Profiles Enriched in Opportunistic Pathogens in RA Patients and First Degree Relatives Are Influenced By Environmental Risk Factors, Including Smoking, Dental History and Lung Infection

Benham, Helen, Maradana, Muralidhara, Lakis, Vanessa Anne, Cuiv, Paraic O., Wood, John, Nagl, Lisa, Rammouth, Nishta, Owens, Clare, Daly, Joshua., Lachner, Nancy, Morrison, Mark, Hugenholtz, Philip, Le Cao, Kim-Anh and Thomas, Rarljeny (2016). Distinct Oral and Fecal Community Profiles Enriched in Opportunistic Pathogens in RA Patients and First Degree Relatives Are Influenced By Environmental Risk Factors, Including Smoking, Dental History and Lung Infection. 2016 ACR/ARHP Annual Meeting, Washington, DC, 11-16 November 2016. Hoboken, NJ, United States: John Wiley & Sons.

Healthy gut microbiota ameliorates experimental chronic obstructive pulmonary disease

Gellatly, S., Dennis, P., Jarnicki, A., Lachner, N., Wood, D., Fricker, M., Budden, K., Liu, G., Keely, S., Morrison, M., Willner, D., Cooper, M., Hugenholtz, P. and Hansbro, P. (2016). Healthy gut microbiota ameliorates experimental chronic obstructive pulmonary disease. Annual Scientific Meeting of the Thoracic Society of Australia and New Zealand and the Australian and New Zealand Society of Respiratory Science 2014, Perth, WA, Australia, 1–6 April 2016. Hoboken, NJ United States: Wiley. doi: 10.1111/resp.12754_22

Profiling immunogenic bacteria within the microbiota of SKG mice associated with spondyloarthritis and ileitis using IgA-SEQ

Rehaume, L. M., Kang, A., Zbarskaya, O., Mullaney, J. A., Kim, M., Cuiv, O. P., Angel, N., Lachner, N., Daly, J., Morrison, M., Hugenholtz, P. and Thomas, R. (2016). Profiling immunogenic bacteria within the microbiota of SKG mice associated with spondyloarthritis and ileitis using IgA-SEQ. International Congress of Immunology (ICI 2016), Melbourne, Australia, 21-26 August 2016. Weinheim, Germany: Wiley.

Treatment of ZAP-70 Mutant SKG Mice with Anti-IL-23 Antibody Alters Fecal Microbiota Composition and Prevents Outgrowth of Bacteria Associated with Susceptibility to Spondyloarthritis and Ileitis

Rehaume, Linda, Matigian, Nicholas, Kang, Alicia, Zbarskaya, Olga, Kikly, Kristine, Lachner, Nancy, Daly, Joshua, Hugenholtz, Philip, Morrison, Mark, Le Cao, Kim-Anh and Thomas, Ranjeny (2016). Treatment of ZAP-70 Mutant SKG Mice with Anti-IL-23 Antibody Alters Fecal Microbiota Composition and Prevents Outgrowth of Bacteria Associated with Susceptibility to Spondyloarthritis and Ileitis. 2016 ACR/ARHP Annual Meeting, Washington, DC United States, 11–16 November 2016 . Hoboken, NJ United States: Wiley.

Profiling Immunogenic Bacteria within the Microbiota of ZAP-70 Mutant SKG Mice Associated with Spondyloarthritis and Ileitis Using IgA-SEQ

Rehaume, Linda, Kang, Alicia, Zbarskaya, Olga, Mullaney, Jane, Kim, Matthew, Cuiv, Paraic O., Angel, Nicola, Hugenholtz, Philip, Morrison, Mark and Thomas, Ranjeny (2015). Profiling Immunogenic Bacteria within the Microbiota of ZAP-70 Mutant SKG Mice Associated with Spondyloarthritis and Ileitis Using IgA-SEQ. 2015 ACR/ARHP Annual Meeting, San Francisco, CA, United States, 6-11 November 2015. Hoboken, NJ, United States: John Wiley & Sons.

The microbial community of eutherian origin: Effects of maternal microbiota on the placental microbiome

Ragonesi, Leanne, Huygens, Flavia, Turner, Ross, Hugenholtz, Philip, Lourie, Rohan, Beagley, Ken and Pelzer, Elise (2015). The microbial community of eutherian origin: Effects of maternal microbiota on the placental microbiome. unknown, unknown, unknown. London, United Kingdom: Elsevier. doi: 10.1016/j.placenta.2015.07.308

The placental microbiome; microbial presence in nature’s transplant

Pelzer, Elise, Hugens, Flavia, Hugenholtz, Philip, Lourie, Rohan, Beagley, Kenneth and Turner, Ross (2015). The placental microbiome; microbial presence in nature’s transplant. unknown, unknown, unknown. London, United Kingdom: Elsevier. doi: 10.1016/j.placenta.2015.07.252

Embedding Undergraduate Research throughout Microbiology Majors

Wang, Jack T.H., Daly, Joshua N., Willner, Dana L., Patil, Jayee, Hall, Roy, Tyson, Gene W., Hugenholtz, Philip and Schembri, Mark A. (2014). Embedding Undergraduate Research throughout Microbiology Majors. ASM Conference for Undergraduate Educators, Danvers, MA United States, 15-18 May 2014.

Plant growth promoting rhizobacteria (PGPR) for use in horticulture.

Fangrath, S, Mudge, S., Deng, Y, Robinson, N, Schmidt, S, Hugenholtz, P, Ragan, M and Paungfoo-Lonhienne, C (2014). Plant growth promoting rhizobacteria (PGPR) for use in horticulture.. The 29th International Horticultural Congress, Brisbane Convention Centre, Brisbane Qld, Australia, 17 - 22 August 2014.

Granule shearing enables the high resolution microbial identity

Lu, Y., Slater, F., Bello Mendoza, R., Jensen, P., Hugenholtz, P. and Batstone, D. J. (2013). Granule shearing enables the high resolution microbial identity. 13th World Congress on Anaerobic Digestion (AD 13), Santiago de Compostela, Spain, 25-28 June, 2013. London, United Kingdom: International Water Association (IWA).

Longitudinal holistic profiling of the lung transplant microbiome

Willner, D., Ab-Ghani, N. A., Yerkovich, S., Tan, M. E., Hopkins, P. M., Chambers, D. C. and Hugenholtz, P. (2013). Longitudinal holistic profiling of the lung transplant microbiome. 33rd Annual Meeting and Scientific Sessions of the International Society for Heart and Lung Transplantation, Montreal, Canada, 24-27 April 2013. Philadelphia, PA, United States: Elsevier. doi: 10.1016/j.healun.2013.01.004

Distinct microbial signatures of healthy and failing lung allografts

Willner, D., Hugenholtz, P., Tan, M.E., Yerkovich, S.T., Hopkins, P.M. and Chambers, D.C. (2012). Distinct microbial signatures of healthy and failing lung allografts. 32nd Annual Meeting and Scientific Sessions of the International Society for Heart and Lung Transplantation/Meeting of the ISHLT Academy Core Competencies in Mechanical Circulatory Support, Prague, Czech Republic, 17-21 April 2012. Philadelphia, PA, United States: Elsevier. doi: 10.1016/j.healun.2012.01.072

Is the future of metagenomics, genomics?

Hugenholtz, Philip (2010). Is the future of metagenomics, genomics?. Experimental Biology 2010, Anaheim, CA, United States, 24-28 April 2010. Hoboken, NJ, United States: John Wiley & Sons.

Correlative TEM/FISH imaging of microbial communities

Knierim, Bernhard, Wilmes, Paul, Webb, Rick I., McDonald, Kent, Comolli, Luis, Luef, Birgit, Downing, Kenneth H., Banfield, Jill, Hugenholtz, Phil, Liphardt, Jan and Auer, Manfred (2010). Correlative TEM/FISH imaging of microbial communities. *, *, *. St. Louis, MO, United States: Cell Press. doi: 10.1016/j.bpj.2009.12.3157

ShotgunFunctionalizeR - an R-package for functional comparison of metagenomes

Kristiansson, E., Hugenholtz, P. and Dalevi, D. (2010). ShotgunFunctionalizeR - an R-package for functional comparison of metagenomes. 35th Congress of the Federation-of-European-Biochemical-Societies, Gothenburg Sweden, Jun 26-Jul 01, 2010. MALDEN: WILEY-BLACKWELL PUBLISHING, INC.

Characterization and development of a systems-level understanding of microbial metabolism in the foregut microbiome of the Tammar wallaby (Macropus eugenii).

Pope, P., Denman, S., Tringe, S., Hinds, L., Hugenholtz, P., McSweeney, C. and Morrison, M. (2009). Characterization and development of a systems-level understanding of microbial metabolism in the foregut microbiome of the Tammar wallaby (Macropus eugenii).. 2009 Conference on Gastrointestinal Function, Chicago, USA, 20-22 April, 2009. New York, NY, United States: Springer. doi: 10.1007/s00248-009-9496-x

Diversity of fiber-adherent bacteria on three potential bioenergy feedstocks during digestion in the cow rumen

Yannarell, A. C., Hess, M., Hugenholtz, P. and Mackie, R. I. (2009). Diversity of fiber-adherent bacteria on three potential bioenergy feedstocks during digestion in the cow rumen. Conference on Gastrointestinal Function, Chicago, USA, 20–22 April 2009. New York, NY United States: Springer. doi: 10.1007/s00248-009-9496-x

Annotation of metagenome short reads using proxygenes

Dalevi, Daneil, Ivanova, Natalia N., Mavromatis, Konstantinos, Hooper, Sean D., Szeto, Ernest, Hugenholtz, Philip, Kyrpides, Nikos C. and Markowitz, Victor M. (2008). Annotation of metagenome short reads using proxygenes. Joint Meeting of the 7th European Conference on Computational Biology and the 5th Meeting of the Bioinformatics Italian Society (ECCB 2008), Cagliari, Italy, 22-26 September 2008. Oxford, U.K.: Oxford University Press. doi: 10.1093/bioinformatics/btn276

An experimental metagenome data management and analysis system

Markowitz, Victor M., Ivanova, Natalia, Palaniappan, Krishna, Szeto, Ernest, Korzeniewski, Frank, Lykidis, Athanasios, Anderson, Iain, Mavrommatis, Konstantinos, Kunin, Victor, Martin, Hector Garcia, Dubchak, Inna, Hugenholtz, Phil and Kyrpides, Nikos C. (2006). An experimental metagenome data management and analysis system. 14th Conference on Intelligent Systems for Molecular Biology (ISMB 2006), Fortaleza, Brazil, 6-10 August 2006. Oxford, U.K.: Oxford University Press. doi: 10.1093/bioinformatics/btl217

Metagenomic analysis of phosphorus removing sludge communities

Martín, Héctor García, Kunin, Victor, Ivanova, Natalia, Warnecke, Falk, Peterson, S. B., Barry, Kerrie, McHardy, Alice C., Yeates, Christine, He, Shaomei, Salamov, Asaf, Szeto, Ernest, Dalin, Eileen, Putnam, Nik, Rigoutsos, Isidore, Kyrpides, Nikos C., Blackall, Linda Louise, McMahon, Katherine D. and Hugenholtz, Philip (2006). Metagenomic analysis of phosphorus removing sludge communities. ISME Vienna 2006: 11th International Symposium on Microbial Ecology. The hidden powers: Microbial communities in action, Vienna, Austria, 20-25 August 2006. Kenes International.

Magnetocardiography predicts coronary artery disease in patients presenting with acute chest pain

Park, JW, Hill, P, Hugenholtz, P, Chung, N and Jung, F (2004). Magnetocardiography predicts coronary artery disease in patients presenting with acute chest pain. In: ESC Congress 2004, Munich Germany, (303-304). Aug 28-Sep 01, 2004.

The tree of life - An overview

Baldauf, SL, Bhattacharya, D, Cockrill, J, Hugenholtz, P, Pawlowski, J and Simpson, AGB (2004). The tree of life - An overview. Conference on Assembling the Tree of Life, New York Ny, May 30-Jun 01, 2002. NEW YORK: OXFORD UNIV PRESS.

Diverted Cultivation of Phylogenetically Novell Bacteria

Hugenholtz, Phil (2000). Diverted Cultivation of Phylogenetically Novell Bacteria. ICCC9 9th International Congress for Culture Collections, Brisbane, Australia, 23-28 July, 2000. Australia: UQ Press/World Federation for Culture Studies.

Real-Time PCR: Can it accurately assess specific members in a mixed microbial community

Blackall, L. L., Hall, S. J., Hugenholtz, P., Keller, J. and Siyambalapitiya, N. (2000). Real-Time PCR: Can it accurately assess specific members in a mixed microbial community. 4th Annual Australian Environmental Engineering Research Event, Victor Harbor, South Australia, Australia, 21-24 November, 2000. Australia: EERE Organising Committee.

The determination of the bacteria involved in biological phosphorus removal from wastewater

Blackall, L. L., Bond, P. L., Crocetti, G., Hugenholtz, P., Jenkins, D., Keller, J. and Schuler, A. (1999). The determination of the bacteria involved in biological phosphorus removal from wastewater. IXth International Congress of Bacteriology and Applied Microbiology, Sydney, August 2-6, 1999.

The microbiology of biological nutrient removal - latest discoveries and developments

Blackall, L. L., Bond, P. L., Burrell, P. C., Crocetti, G. and Hugenholtz, P. (1999). The microbiology of biological nutrient removal - latest discoveries and developments. IBC Conference on Advanced Wastewater and Sludge Treatment, Sydney, Australia, 27-28 Jan 1999. not available: not available.

New foam-forming nocardioforms found in activated sludge

Soddell, JA, Seviour, RJ, Blackall, LL and Hugenholtz, P (1998). New foam-forming nocardioforms found in activated sludge. 2nd International Conference on Microorganisms in Activated Sludge and Biofilm Processes, Berkeley California, Jul 21-23, 1997. OXFORD: PERGAMON-ELSEVIER SCIENCE LTD. doi: 10.1016/S0273-1223(98)00151-6

The use of 16S rDNA clone libraries to describe the microbial diversity of activated sludge communities

Blackall, L. L., Burrell, P. C., Gwilliam, H., Bradford, D., Bond, P. L. and Hugenholtz, P. (1998). The use of 16S rDNA clone libraries to describe the microbial diversity of activated sludge communities. In: 2nd International Conference on Microorganisms in Activated Sludge and Biofilm Processes, Berkeley, CA, United States, (451-454). 21-23 July 1997. doi:10.2166/wst.1998.0691

Towards understanding the taxonomy of some of the filamentous bacteria causing bulking and foaming in activated sludge plants

Blackall, LL, Seviour, EM, Bradford, D, Stratton, HM, Cunningham, MA, Hugenholtz, P and Seviour, RJ (1996). Towards understanding the taxonomy of some of the filamentous bacteria causing bulking and foaming in activated sludge plants. 18th Biennial Conference of the International-Association-on-Water-Quality, Singapore Singapore, Jun 23-28, 1996. OXFORD: PERGAMON-ELSEVIER SCIENCE LTD. doi: 10.1016/0273-1223(96)00639-7

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes: supplemental material

Parks, Donovan H., Imelfort, Michael, Skennerton, Connor T., Hugenholtz, Philip and Tyson, Gene W. (2015). CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes: supplemental material. Cold Spring Harbor Laboratory Press. (Dataset) doi: 10.14264/uql.2016.841

Bringing large-scale multiple genome analysis one step closer: ScalaBLAST and beyond

Oehmen, Christopher S., Sofia, Heidi J., Baxter, Douglas, Szeto, Ernest, Hugenholtz, Philip, Kyrpides, Nikos, Markowitz, Victor and Straatsma, Tjerk P. (2007). Bringing large-scale multiple genome analysis one step closer: ScalaBLAST and beyond. Oak Ridge, TN, United States: Office of Scientific and Technical Information (OSTI). doi: 10.2172/960403

An ecological and phylogenetic investigation of a bacterial biofilm growing on the cooling coils in an air-handling system

Hugenholtz, Philip (1994). An ecological and phylogenetic investigation of a bacterial biofilm growing on the cooling coils in an air-handling system. PhD Thesis, School of Molecular and Microbial Sciences. doi: 10.14264/uql.2015.257