The University of Queensland

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. In Marilena Aquino de Muro and Ralph Rapley (Ed.), Gene probes: principles and protocols (pp. 029-042) New Jersey, United States: Humana Press. doi:10.1385/1-59259-238-4:029

Metagenomics using next-generation sequencing

Bragg,Lauren and Tyson, Gene W. (2014). Metagenomics using next-generation sequencing. In Ian T. Paulsen and Andrew J. Holmes (Ed.), Environmental Microbiology: Methods and Protocols (pp. 183-201) New York, NY United States: Humana Press Inc.. doi:10.1007/978-1-62703-712-9_15

Rhizosphere Metatranscriptomics: Challenges and Opportunities

Carvalhais, Lilia C., Dennis, Paul G., Tyson, Gene W. and Schenk, Peer M. (2013). Rhizosphere Metatranscriptomics: Challenges and Opportunities. In Frans J. de Bruijn (Ed.), Molecular Microbial Ecology of the Rhizosphere (pp. 1137-1144) Hoboken, NJ United States: Wiley-Blackwell. doi:10.1002/9781118297674.ch109

Environmental shotgun sequencing

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

The search for a molecular-level understanding of the processes that underpin the Earth's biogeochemical cycles

Banfield, Jillian, F., Tyson, Gene W., Allen, E. E. and Whitaker, B. J. (2005). The search for a molecular-level understanding of the processes that underpin the Earth's biogeochemical cycles. In Banfield, Jillian F., Cervini-Silva, Javiera and Nealson, Kenneth M. (Ed.), Molecular geomicrobiology (pp. 1-7) Chantilly, U.S.: Mineralogical Society of America, Geochemical Society.

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). In Aquino de Muro. M and Rapley. R (Ed.), Gene Probes - Principles and Protocols (pp. 1-17) London: Humana Press.

Goethite Reduction by a Neutrophilic Member of the Alphaproteobacterial Genus Telmatospirillum

Gagen, Emma J., Zaugg, Julian, Tyson, Gene W. and Southam, Gordon (2019) Goethite Reduction by a Neutrophilic Member of the Alphaproteobacterial Genus Telmatospirillum. Frontiers in Microbiology, 10 . doi:10.3389/fmicb.2019.02938

The effect of methane and odd-chain fatty acids on 3-hydroxybutyrate (3HB) and 3-hydroxyvalerate (3HV) synthesis by a Methylosinus-dominated mixed culture

Luangthongkam, Pawarisa, Strong, Peter James, Syed Mahamud, Syarifah Nuraqmar, Evans, Paul, Jensen, Paul, Tyson, Gene, Laycock, Bronwyn, Lant, Paul Andrew and Pratt, Steven (2019) The effect of methane and odd-chain fatty acids on 3-hydroxybutyrate (3HB) and 3-hydroxyvalerate (3HV) synthesis by a Methylosinus-dominated mixed culture. Bioresources and Bioprocessing, 6 1: . doi:10.1186/s40643-019-0285-1

A genomic view of the reef-building coral Porites lutea and its microbial symbionts

Robbins, Steven J., Singleton, Caitlin M., Chan, Cheong Xin, Messer, Lauren F., Geers, Aileen U., Ying, Hua, Baker, Alexander, Bell, Sara C., Morrow, Kathleen M., Ragan, Mark A., Miller, David J., Forêt, Sylvain, Voolstra, Christian R., Tyson, Gene W. and Bourne, David G. (2019) A genomic view of the reef-building coral Porites lutea and its microbial symbionts. Nature Microbiology, 4 12: 2090-2100. doi:10.1038/s41564-019-0532-4

Insights into the ecological roles and evolution of methyl-coenzyme M reductase-containing hot spring Archaea

Hua, Zheng-Shuang, Wang, Yu-Lin, Evans, Paul N., Qu, Yan-Ni, Goh, Kian Mau, Rao, Yang-Zhi, Qi, Yan-Ling, Li, Yu-Xian, Huang, Min-Jun, Jiao, Jian-Yu, Chen, Ya-Ting, Mao, Yan-Ping, Shu, Wen-Sheng, Hozzein, Wael, Hedlund, Brian P., Tyson, Gene W., Zhang, Tong and Li, Wen-Jun (2019) Insights into the ecological roles and evolution of methyl-coenzyme M reductase-containing hot spring Archaea. Nature Communications, 10 1: 4574. doi:10.1038/s41467-019-12574-y

Acetate production from anaerobic oxidation of methane via intracellular storage compounds

Cai, Chen, Shi, Ying, Guo, Jianhua, Tyson, Gene W., Hu, Shihu and Yuan, Zhiguo (2019) Acetate production from anaerobic oxidation of methane via intracellular storage compounds. Environmental Science & Technology, 53 13: 7371-7379. doi:10.1021/acs.est.9b00077

Biochar-mediated anaerobic oxidation of methane

Zhang, Xueqin, Xia, Jun, Pu, Jiaoyang, Cai, Chen, Tyson, Gene W., Yuan, Zhiguo and Hu, Shihu (2019) Biochar-mediated anaerobic oxidation of methane. Environmental Science and Technology, 53 12: 6660-6668. doi:10.1021/acs.est.9b01345

Microbial community analyses inform geochemical reaction network models for predicting pathways of greenhouse gas production

Wilson, Rachel M., Neumann, Rebecca B., Crossen, Kelsey B., Raab, Nicole M., Hodgkins, Suzanne B., Saleska, Scott R., Bolduc, Ben, Woodcroft, Ben J., Tyson, Gene W., Chanton, Jeffrey P. and Rich, Virginia (2019) Microbial community analyses inform geochemical reaction network models for predicting pathways of greenhouse gas production. Frontiers in Earth Science, 7 . doi:10.3389/feart.2019.00059

Using machine learning to predict antimicrobial MICs and associated genomic features for nontyphoidal Salmonella

Nguyen, Marcus, Long, S. Wesley, McDermott, Patrick F., Olsen, Randall J., Olson, Robert, Stevens, Rick L., Tyson, Gregory H., Zhao, Shaohua and Davis, James J. (2019) Using machine learning to predict antimicrobial MICs and associated genomic features for nontyphoidal Salmonella. Journal of Clinical Microbiology, 57 2: . doi:10.1128/JCM.01260-18

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., Patrinos, Aristides A. N., Podar, Mircea, Pollard, Katherine S., Ravel, Jacques, Munoz, Alejandro Reyes, Roberts, Richard J., Rossello-Mora, Ramon, Sansone, Susanna-Assunta, Schloss, Patrick D., Schriml, Lynn M., Setubal, Jogo C., Sorek, Rotem, Stevens, Rick L., Tiedje, James M., Turjanski, Adrian, Tyson, Gene W., Ussery, David W., Weinstock, George M., White, Owen, Whitman, William B. and 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, . doi:10.1038/s41579-018-0136-7

Divergent methyl-coenzyme M reductase genes in a deep-subseafloor Archaeoglobi

Boyd, Joel A., Jungbluth, Sean P., Leu, Andy O., Evans, Paul N., Woodcroft, Ben J., Chadwick, Grayson L., Orphan, Victoria J., Amend, Jan P., Rappé, Michael S. and Tyson, Gene W. (2019) Divergent methyl-coenzyme M reductase genes in a deep-subseafloor Archaeoglobi. The ISME Journal, 13 5: 1269-1279. doi:10.1038/s41396-018-0343-2

Discovery and ecogenomic context of a global Caldiserica-related phylum active in thawing permafrost, Candidatus Cryosericota phylum nov., Ca. Cryosericia class nov., Ca. Cryosericales ord. nov., Ca. Cryosericaceae fam. nov., comprising the four species Cryosericum septentrionale gen. nov. sp. nov., Ca. C. hinesii sp. nov., Ca. C. odellii sp. nov., Ca. C. terrychapinii sp. nov

Martinez, Miguel A., Woodcroft, Ben J., Ignacio Espinoza, Julio C., Zayed, Ahmed A., Singleton, Caitlin M., Boyd, Joel A., Li, Yueh-Fen, Purvine, Samuel, Maughan, Heather, Hodgkins, Suzanne B., Anderson, Darya, Sederholm, Maya, Temperton, Ben, Bolduc, Benjamin, Saleska, Scott R., Tyson, Gene W. and Rich, Virginia I. (2019) Discovery and ecogenomic context of a global Caldiserica-related phylum active in thawing permafrost, Candidatus Cryosericota phylum nov., Ca. Cryosericia class nov., Ca. Cryosericales ord. nov., Ca. Cryosericaceae fam. nov., comprising the four species Cryosericum septentrionale gen. nov. sp. nov., Ca. C. hinesii sp. nov., Ca. C. odellii sp. nov., Ca. C. terrychapinii sp. nov. Systematic and Applied Microbiology, . doi:10.1016/j.syapm.2018.12.003

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, . doi:10.1038/s41396-018-0282-y

Soil viruses are underexplored players in ecosystem carbon processing

Trubl, Gareth, Jang, Ho Bin, Roux, Simon, Emerson, Joanne B., Solonenko, Natalie, Vik, Dean R., Solden, Lindsey, Ellenbogen, Jared, Runyon, Alexander T., Bolduc, Benjamin, Woodcroft, Ben J., Saleska, Scott R., Tyson, Gene W., Wrighton, Kelly C., Sullivan, Matthew B. and Rich, Virginia I. (2018) Soil viruses are underexplored players in ecosystem carbon processing. mSystems, 3 5: . doi:10.1128/mSystems.00076-18

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, . doi:10.1038/s41396-018-0225-7

Genome-centric view of carbon processing in thawing permafrost

Woodcroft, Ben J., Singleton, Caitlin M., Boyd, Joel A., Evans, Paul N., Emerson, Joanne B., Zayed, Ahmed A. F., Hoelzle, Robert D., Lamberton, Timothy O., McCalley, Carmody K., Hodgkins, Suzanne B., Wilson, Rachel M., Purvine, Samuel O., Nicora, Carrie D., Li, Changsheng, Frolking, Steve, Chanton, Jeffrey P., Crill, Patrick M., Saleska, Scott R., Rich, Virginia I. and Tyson, Gene W. (2018) Genome-centric view of carbon processing in thawing permafrost. Nature, 560 7716: 49-54. doi:10.1038/s41586-018-0338-1

Host-linked soil viral ecology along a permafrost thaw gradient

Emerson, Joanne B., Roux, Simon, Brum, Jennifer R., Bolduc, Benjamin, Woodcroft, Ben J., Jang, Ho Bin, Singleton, Caitlin M., Solden, Lindsey M., Naas, Adrian E., Boyd, Joel A., Hodgkins, Suzanne B., Wilson, Rachel M., Trubl, Gareth, Li, Changsheng, Frolking, Steve, Pope, Phillip B., Wrighton, Kelly C., Crill, Patrick M., Chanton, Jeffrey P., Saleska, Scott R., Tyson, Gene W., Rich, Virginia I. and Sullivan, Matthew B. (2018) Host-linked soil viral ecology along a permafrost thaw gradient. Nature Microbiology, 3 8: 870-880. doi:10.1038/s41564-018-0190-y

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., Ettema, Thijs J.G., Tighe, Scott, Konstantinidis, Konstantinos T., Liu, Wen-Tso, Baker, Brett J., Rattei, Thomas, Eisen, Jonathan A., Hedlund, Brian, Mcmahon, Katherine D., Fierer, Noah, Knight, Rob, Finn, Rob, Cochrane, Guy, Karsch-Mizrachi, Ilene, Tyson, Gene W, Rinke, Christian, Lapidus, Alla, Meyer, Folker, Yilmaz, Pelin, Parks, Donovan H., Eren, A. M., Schriml, Lynn, Banfield, Jillian F., Hugenholtz, Philip and 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

Biogenic methane cycling in a laboratory model of an abandoned bituminous coal mine

Raudsepp, Maija J., Fluggen, Markus, Shypanski, Adam H., Tyson, Gene W., Golding, Suzanne D. and Southam, Gordon (2018) Biogenic methane cycling in a laboratory model of an abandoned bituminous coal mine. Geomicrobiology Journal, 35 6: 491-502. doi:10.1080/01490451.2017.1392652

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 (2018) The importance of designating type material for uncultured taxa. Systematic and Applied Microbiology, . doi:10.1016/j.syapm.2018.07.003

Methanotrophy across a natural permafrost thaw environment

Singleton, Caitlin M., McCalley, Carmody K., Woodcroft, Ben J., Boyd, Joel A., Evans, Paul N., Hodgkins, Suzanne B., Chanton, Jeffrey P., Frolking, Steve, Crill, Patrick M., Saleska, Scott R., Rich, Virginia I. and Tyson, Gene W. (2018) Methanotrophy across a natural permafrost thaw environment. The ISME journal, 12 10: 2544-2558. doi:10.1038/s41396-018-0065-5

A methanotrophic archaeon couples anaerobic oxidation of methane to Fe(III) reduction

Cai, Chen, Leu, Andy O., Xie, Guo-Jun, Guo, Jianhua, Feng, Yuexing, Zhao, Jian-Xin, Tyson, Gene W., Yuan, Zhiguo and Hu, Shihu (2018) A methanotrophic archaeon couples anaerobic oxidation of methane to Fe(III) reduction. The ISME Journal, 12 8: 1929-1939. doi:10.1038/s41396-018-0109-x

GraftM: a tool for scalable, phylogenetically informed classification of genes within metagenomes

Boyd, Joel A., Woodcroft, Ben J. and Tyson, Gene W. (2018) GraftM: a tool for scalable, phylogenetically informed classification of genes within metagenomes. Nucleic Acids Research, 46 10: e59-e59. doi:10.1093/nar/gky174

Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea (vol 35, pg 725, 2017)

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, Glockner, Frank O., Gilbert, Jack A., Nelson, William C., Hallam, Steven J., Jungbluth, Sean P., Ettema, Thijs J. G., Tighe, Scott, Konstantinidis, Konstantinos T., Liu, Wen-Tso, Baker, Brett J., Rattei, Thomas, Eisen, Jonathan A., Hedlund, Brian, McMahon, Katherine D., Fierer, Noah, Knight, Rob, Finn, Rob, Cochrane, Guy, Karsch-Mizrachi, Ilene, Tyson, Gene W., Rinke, Christian, Lapidus, Alla, Meyer, Folker, Yilmaz, Pelin, Parks, Donovan H., Eren, A. Murat, Schriml, Lynn, Banfield, Jillian F., Hugenholtz, Philip and Woyke, Tanja (2018) Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea (vol 35, pg 725, 2017). Nature Biotechnology, 36 2: 196-196. doi:10.1038/nbt0218-196a

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, 3 253: 253-253. doi:10.1038/s41564-017-0083-5

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

Redefining the sponge-symbiont acquisition paradigm: sponge microbes exhibit chemotaxis towards host-derived compounds

Tout, Jessica, Astudillo-García, Carmen, Taylor, Michael W., Tyson, Gene W., Stocker, Roman, Ralph, Peter J., Seymour, Justin R. and Webster, Nicole S. (2017) Redefining the sponge-symbiont acquisition paradigm: sponge microbes exhibit chemotaxis towards host-derived compounds. Environmental Microbiology Reports, 9 6: 750-755. doi:10.1111/1758-2229.12591

Methane-Fueled Syntrophy through Extracellular Electron Transfer: Uncovering the Genomic Traits Conserved within Diverse Bacterial Partners of Anaerobic Methanotrophic Archaea (vol 8, e00530-17, 2017)

Skennerton, Connor T., Chourey, Karuna, Iyer, Ramsunder, Hettich, Robert L., Tyson, Gene W. and Orphan, Victoria J. (2017) Methane-Fueled Syntrophy through Extracellular Electron Transfer: Uncovering the Genomic Traits Conserved within Diverse Bacterial Partners of Anaerobic Methanotrophic Archaea (vol 8, e00530-17, 2017). Mbio, 8 5: 1-2. doi:10.1128/mBio.01561-17

The effect of bituminous coal on methanogenic mixed cultures and pure cultures of Methanococcus and Methanosarcina

Raudsepp, Maija J., Gagen, Emma J., Golding, Suzanne D., Tyson, Gene W. and Southam, Gordon (2017) The effect of bituminous coal on methanogenic mixed cultures and pure cultures of Methanococcus and Methanosarcina. Fuel, 205 60-70. doi:10.1016/j.fuel.2017.05.059

Comparison of microbial communities across sections of a corroding sewer pipe and the effects of wastewater flooding

Cayford, Barry I., Jiang, Guangming, Keller, Jurg, Tyson, Gene and Bond, Philip L. (2017) Comparison of microbial communities across sections of a corroding sewer pipe and the effects of wastewater flooding. Biofouling, 33 9: 780-792. doi:10.1080/08927014.2017.1369050

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., Ettema, Thijs J. G., Tighe, Scott, Konstantinidis, Konstantinos T., Liu, Wen-Tso, Baker, Brett J., Rattei, Thomas, Eisen, Jonathan A., Hedlund, Brian, McMahon, Katherine D., Fierer, Noah, Knight, Rob, Finn, Rob, Cochrane, Guy, Karsch-Mizrachi, Ilene, Tyson, Gene W., Rinke, Christian, Lapidus, Alla, Meyer, Folker, Yilmaz, Pelin, Parks, Donovan H., Eren, A. M., Schriml, Lynn, Banfield, Jillian F., Hugenholtz, Philip and 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

Safety and outcomes in 100 consecutive donation after circulatory death liver transplants using a protocol that includes thrombolytic therapy

Bohorquez, H., Seal, J.B., Cohen, A.J., Kressel, A., Bugeaud, E., Bruce, D.S., Carmody, I.C., Reichman, T.W., Battula, N., Alsaggaf, M., Therapondos, G., Bzowej, N., Tyson, G., Joshi, S., Nicolau-Raducu, R., Girgrah, N. and Loss, G.E. (2017) Safety and outcomes in 100 consecutive donation after circulatory death liver transplants using a protocol that includes thrombolytic therapy. American Journal of Transplantation, 17 8: 2155-2164. doi:10.1111/ajt.14261

Methane-fueled syntrophy through extracellular electron transfer: uncovering the genomic traits conserved within diverse bacterial partners of anaerobic methanotrophic archaea

Skennerton, Connor T., Chourey, Karuna, Iyer, Ramsunder, Hettich, Robert L., Tyson, Gene W. and Orphan, Victoria J. (2017) Methane-fueled syntrophy through extracellular electron transfer: uncovering the genomic traits conserved within diverse bacterial partners of anaerobic methanotrophic archaea. MBio, 8 4: e00530-17. doi:10.1128/mBio.00530-17

Adding stable carbon isotopes improves model representation of the role of microbial communities in peatland methane cycling

Deng, Jia, McCalley, Carmody K., Frolking, Steve, Chanton, Jeff, Crill, Patrick, Varner, Ruth, Tyson, Gene, Rich, Virginia, Hines, Mark, Saleska, Scott R. and Li, Changsheng (2017) Adding stable carbon isotopes improves model representation of the role of microbial communities in peatland methane cycling. Journal of Advances in Modeling Earth Systems, 9 2: 1412-1430. doi:10.1002/2016MS000817

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 39114. doi:10.1038/srep39114

PH and organic carbon dose rates control microbially driven bioremediation efficacy in alkaline bauxite residue

Santini, Talitha C., Malcolm, Laura I., Tyson, Gene W. and Warren, Lesley A. (2016) PH and organic carbon dose rates control microbially driven bioremediation efficacy in alkaline bauxite residue. Environmental Science and Technology, 50 20: 11164-11173. doi:10.1021/acs.est.6b01973

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. 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: 1-28. doi:10.7717/peerj.2486

Genome-centric resolution of microbial diversity, metabolism and interactions in anaerobic digestion

Vanwonterghem, Inka, Jensen, Paul D., Rabaey, Korneel and Tyson, Gene W. (2016) Genome-centric resolution of microbial diversity, metabolism and interactions in anaerobic digestion. Environmental Microbiology, 18 9: 3144-3158. doi:10.1111/1462-2920.13382

Genome-centric analysis of microbial populations enriched by hydraulic fracture fluid additives in a coal bed methane production well

Robbins, Steven J., Evans, Paul N., Parks, Donovan H., Golding, Suzanne D. and Tyson, Gene W. (2016) Genome-centric analysis of microbial populations enriched by hydraulic fracture fluid additives in a coal bed methane production well. Frontiers in Microbiology, 7 731: 1-15. doi:10.3389/fmicb.2016.00731

Phylogenomic analysis of Candidatus 'Izimaplasma' species: free-living representatives from a Tenericutes clade found in methane seeps

Skennerton, Connor T., Haroon, Mohamed F., Briegel, Ariane, Shi, Jian, Jensen, Grant J., Tyson, Gene W. and Orphan, Victoria J. (2016) Phylogenomic analysis of Candidatus 'Izimaplasma' species: free-living representatives from a Tenericutes clade found in methane seeps. ISME Journal, 10 11: 2679-2692. doi:10.1038/ismej.2016.55

Diuron tolerance and potential degradation by pelagic microbiomes in the Great Barrier Reef lagoon

Angly, Florent E., Pantos, Olga, Morgan, Thomas C., Rich, Virginia, Tonin, Hemerson, Bourne, David G., Mercurio, Philip, Negri, Andrew P. and Tyson, Gene W. (2016) Diuron tolerance and potential degradation by pelagic microbiomes in the Great Barrier Reef lagoon. PeerJ, 4 3: e1758. doi:10.7717/peerj.1758

The influence of hydrogeological disturbance and mining on coal seam microbial communities

Raudsepp, M. J., Gagen, E. J., Evans, P., Tyson, G. W., Golding, S. D. and Southam, G. (2016) The influence of hydrogeological disturbance and mining on coal seam microbial communities. Geobiology, 14 2: 163-175. doi:10.1111/gbi.12166

The opportunity for high-performance biomaterials from methane

Strong, Peter James, Laycock, Bronwyn, Syed Mahamud, Syarifah, Jensen, Paul, Lant, Paul A., Gene Tyson and Pratt, Steven (2016) The opportunity for high-performance biomaterials from methane. Microorganisms, 4 1: 11. doi:10.3390/microorganisms4010011

The effect of coal rank on biogenic methane potential and microbial composition

Robbins, Steven J., Evans, Paul N., Esterle, Joan S., Golding, Suzanne D. and Tyson, Gene W. (2016) The effect of coal rank on biogenic methane potential and microbial composition. International Journal of Coal Geology, 154 205-212. doi:10.1016/j.coal.2016.01.001

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: 1469.1-1469.15. doi:10.3389/fmicb.2015.01469

Marine microbial communities of the Great Barrier Reef lagoon are influenced by riverine floodwaters and seasonal weather events

Angly, Florent E., Heath, Candice, Morgan, Thomas C., Tonin, Hemerson, Rich, Virginia, Schaffelke, Britta, Bourne, David G. and Tyson, Gene W. (2016) Marine microbial communities of the Great Barrier Reef lagoon are influenced by riverine floodwaters and seasonal weather events. PeerJ, 4 1: 1-24. doi:10.7717/peerj.1511

Archaeal and bacterial communities across a chronosequence of drained lake basins in arctic Alaska

Kao-Kniffin, J., Woodcroft, B.J., Carver, S.M., Bockheim J.G., Handelsman, J., Tyson, G.W., Hinkel, K.M. and Mueller, C.W. (2015) Archaeal and bacterial communities across a chronosequence of drained lake basins in arctic Alaska. Scientific Reports, 5 . doi:10.1038/srep18165

Methane metabolism in the archaeal phylum Bathyarchaeota revealed by genome-centric metagenomics.

Evans, Paul N., Parks, Donovan H., Chadwick, Grayson L., Robbins, Steven J., Orphan, Victoria J., Golding, Suzanne D. and Tyson, Gene W. (2015) Methane metabolism in the archaeal phylum Bathyarchaeota revealed by genome-centric metagenomics.. Science, 350 6259: 434-438. doi:10.1126/science.aac7745

The ReFuGe 2020 Consortium—using “omics” approaches to explore the adaptability and resilience of coral holobionts to environmental change

ReFuGe 2020 Consortium, Voolstra, Christian R, Miller, David J., Ragan, Mark A., Hoffmann, Ary A., Hoegh-Guldberg, Ove, Bourne, David G., Ball, Eldon E., Ying, Hua, Forêt, Sylvain, Takahashi, Shunichi, Weynberg, Karen D., van Oppen, Madeleine J. H., Morrow, Kathleen, Chan, Cheong Xin, Rosic, Nedeljka, Leggat, William, Sprungala, Susanne, Imelfort, Michael, Tyson, Gene W., Kassahn, Karin S., Lundgren, Petra B., Beeden, Roger J., Ravasi, Timothy, Berumen, Michael L., Abal, Eva and Fyffe, Theresa (2015) The ReFuGe 2020 Consortium—using “omics” approaches to explore the adaptability and resilience of coral holobionts to environmental change. Frontiers in Marine Science, 2 Art No.: 68: . doi:10.3389/fmars.2015.00068

Selective enrichment establishes a stable performing community for microbial electrosynthesis of acetate from CO2

Patil, Sunil A., Arends, Jan B. A., Vanwonterghem, Inka, Van Meerbergen, Jarne, Guo, Kun, Tyson, Gene W. and Rabaey, Korneel (2015) Selective enrichment establishes a stable performing community for microbial electrosynthesis of acetate from CO2. Environmental Science and Technology, 49 14: 8833-8843. doi:10.1021/es506149d

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

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: Art. No.: e968-Art. No.: e968. doi:10.7717/peerj.968

Effects of nitrate dosing on sulfidogenic and methanogenic activities in sewer sediment

Liu, Yiwen, Sharma, Keshab R., Ni, Bing-Jie, Fan, Lu, Murthy, Sudhir, Tyson, Gene Q. and Yuan, Zhiguo (2015) Effects of nitrate dosing on sulfidogenic and methanogenic activities in sewer sediment. Water Research, 74 155-165. doi:10.1016/j.watres.2015.02.017

A laboratory investigation of interactions between denitrifying anaerobic methane oxidation (DAMO) and anammox processes in anoxic environments

Hu, Shihu, Zeng, Raymond J., Haroon, Mohamed F., Keller, Jurg, Lant, Paul A., Tyson, Gene W. and Yuan, Zhiguo (2015) A laboratory investigation of interactions between denitrifying anaerobic methane oxidation (DAMO) and anammox processes in anoxic environments. Scientific Reports, 5 8706: 1-9. doi:10.1038/srep08706

Temperature and solids retention time control microbial population dynamics and volatile fatty acid production in replicated anaerobic digesters.

Vanwonterghem, Inka, Jensen, Paul D., Rabaey, Korneel and Tyson, Gene W. (2015) Temperature and solids retention time control microbial population dynamics and volatile fatty acid production in replicated anaerobic digesters.. Scientific Reports, 5 . doi:10.1038/srep08496

Habitat-specific environmental conditions primarily control the microbiomes of the coral Seriatopora hystrix

Pantos, Olga, Bongaerts, Pim, Dennis, Paul G., Tyson, Gene W. and Hoegh-Guldberg, OVe (2015) Habitat-specific environmental conditions primarily control the microbiomes of the coral Seriatopora hystrix. The ISME Journal, 9 9: 1916-1927. doi:10.1038/ismej.2015.3

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: 1-24. doi:10.7717/peerj.740

Where next for microbiome research?

Waldor, Matthew K., Tyson, Gene, Borenstein, Elhanan, Ochman, Howard, Moeller, Andrew, Finlay, Brett B., Kong, Hedi H., Gordon, Jeffrey I., Nelson, Karen E., Dabbagh, Karim and Smith, Hamilton (2015) Where next for microbiome research?. PLoS Biology, 13 1: 1-9. doi:10.1371/journal.pbio.1002050

Chemotaxis by natural populations of coral reef bacteria.

Tout, Jessica, Jeffries, Thomas C., Petrou, Katherina, Tyson, Gene W., Webster, Nicole S., Garren, Melissa, Stocker, Roman, Ralph, Peter J. and Seymour, Justin R. (2015) Chemotaxis by natural populations of coral reef bacteria.. ISME Journal, 9 8: 1764-1777. doi:10.1038/ismej.2014.261

Metagenomic and metaproteomic analyses of Accumulibacter phosphatis enriched floccular and granular biofilm

Barr, Jeremy J., Dutilh, Bas E., Skennerton, Connor T., Fukushima, Toshikazu, Hastie, Marcus L., Gorman, Jeffrey J., Tyson, Gene W. and Bond, Philip L. (2015) Metagenomic and metaproteomic analyses of Accumulibacter phosphatis enriched floccular and granular biofilm. Environmental Microbiology, 18 1: 273-287. doi:10.1111/1462-2920.13019

Temporal changes in microbial community composition during culture enrichment experiments with Indonesian coals

Susilawati, Rita, Evans, Paul N., Esterle, Joan S., Robbins, Steven J., Tyson, Gene W., Golding, Suzanne D. and Mares, Tennille E. (2015) Temporal changes in microbial community composition during culture enrichment experiments with Indonesian coals. International Journal of Coal Geology, 137 66-76. doi:10.1016/j.coal.2014.10.015

Methane dynamics regulated by microbial community response to permafrost thaw

McCalley, Carmody K., Woodcroft, Ben J., Hodgkins, Suzanne B., Wehr, Richard A., Kim, Eun-Hae, Mondav, Rhiannon, Crill, Patrick M., Chanton, Jeffrey P., Rich, Virginia I., Tyson, Gene W. and Saleska, Scott R. (2014) Methane dynamics regulated by microbial community response to permafrost thaw. Nature, 514 7523: 478-481. doi:10.1038/nature13798

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: 1-16. doi:10.7717/peerj.603

Expanding our view of genomic diversity in Candidatus Accumulibacter clades

Skennerton, Connor T., Barr, Jeremy J., Slater, Frances R., Bond, Philip L. and Tyson, Gene W. (2014) Expanding our view of genomic diversity in Candidatus Accumulibacter clades. Environmental Microbiology, 17 5: 1574-1585. doi:10.1111/1462-2920.12582

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

The Bio-Community Perl toolkit for microbial ecology

Angly, Florent E., Fields, Christopher J. and Tyson, Gene W. (2014) The Bio-Community Perl toolkit for microbial ecology. Bioinformatics, 30 13: 1926-1927. doi:10.1093/bioinformatics/btu130

Linking microbial community structure, interactions and function in anaerobic digesters using new molecular techniques

Vanwonterghem, Inka, Jensen, Paul D., Ho, Dang P., Batstone Damien J. and Tyson, Gene W. (2014) Linking microbial community structure, interactions and function in anaerobic digesters using new molecular techniques. Current Opinion in Biotechnology, 27 55-64. doi:10.1016/j.copbio.2013.11.004

Biomass retention on electrodes rather than electrical current enhances stability in anaerobic digestion

De Vrieze, Jo, Gildemyn, Sylvia, Arends, Jan B. A., Vanwonterghem, Inka, Verbeken, Kim, Boon, Nico, Verstraete, Willy, Tyson, Gene W., Hennebel, Tom and Rabaey, Korneel (2014) Biomass retention on electrodes rather than electrical current enhances stability in anaerobic digestion. Water Research, 54 211-221. doi:10.1016/j.watres.2014.01.044

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. doi:10.1186/2049-2618-2-11

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: 3212.1-3212.7. doi:10.1038/ncomms4212

Drivers of microbial community composition in mesophilic and thermophilic temperature-phased anaerobic digestion pre-treatment reactors

Pervin, Hasina M., Dennis, Paul G., Lim, Hui J., Tyson, Gene W., Batstone, Damien J. and Bond, Philip L. (2013) Drivers of microbial community composition in mesophilic and thermophilic temperature-phased anaerobic digestion pre-treatment reactors. Water Research, 47 19: 7098-7108. doi:10.1016/j.watres.2013.07.053

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

Future reef decalcification under a business-as-usual CO2 emission scenario

Dove, Sophie G., Kline, David I., Pantos, Olga, Angly, Florent E., Tyson, Gene W. and Hoegh-Guldberg, Ove (2013) Future reef decalcification under a business-as-usual CO2 emission scenario. Proceedings of the National Academy of Sciences of the United States of America, 110 38: 15342-15347. doi:10.1073/pnas.1302701110

Coral reef invertebrate microbiomes correlate with the presence of photosymbionts

Bourne, David G., Dennis, Paul G., Uthicke, Sven, Soo, Rochelle M., Tyson, Gene W. and Webster, Nicole (2013) Coral reef invertebrate microbiomes correlate with the presence of photosymbionts. Isme Journal, 7 7: 1452-1458. doi:10.1038/ismej.2012.172

Coral reef invertebrate microbiomes correlate with the presence of photosymbionts

Bourne, David G, Dennis, Paul G., Uthicke, Sven, Soo, Rochelle M., Tyson, Gene W. and Webster, Nicole (2013) Coral reef invertebrate microbiomes correlate with the presence of photosymbionts. Isme Journal, 7 7: 1459-1459. doi:10.1038/ismej.2013.71

Dynamics of cathode-associated microbial communities and metabolite profiles in a glycerol-fed bioelectrochemical system

Dennis, Paul G., Harnisch, Falk, Yeoh, Yun Kit, Tyson, Gene W. and Rabaey, Korneel (2013) Dynamics of cathode-associated microbial communities and metabolite profiles in a glycerol-fed bioelectrochemical system. Applied and Environmental Microbiology, 79 13: 4008-4014. doi:10.1128/AEM.00569-13

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

Sequencing platform and library preparation choices impact viral metagenomes

Solonenko, Sergei A., Ignacio-Espinoza, J. Cesar, Alberti, Adriana, Cruaud, Corinne, Hallam, Steven, Konstantinidis, Kostas, Tyson, Gene, Wincker, Patrick and Sullivan, Matthew B. (2013) Sequencing platform and library preparation choices impact viral metagenomes. Bmc Genomics, 14 1: 320.1-320.12. doi:10.1186/1471-2164-14-320

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: e1003031.1-e1003031.18. doi:10.1371/journal.pcbi.1003031

Diverse populations of lake water bacteria exhibit chemotaxis towards inorganic nutrients

Dennis, Paul G., Seymour, Justin, Kumbun, Kimber and Tyson, Gene W. (2013) Diverse populations of lake water bacteria exhibit chemotaxis towards inorganic nutrients. ISME Journal, 7 8: 1661-1664. doi:10.1038/ismej.2013.47

Crass: identification and reconstruction of CRISPR from unassembled metagenomic data

Skennerton, Connor T., Imelfort, Michael and Tyson, Gene W. (2013) Crass: identification and reconstruction of CRISPR from unassembled metagenomic data. Nucleic Acids Research, 41 10: e105.1-e105.10. doi:10.1093/nar/gkt183

Activation of the jasmonic acid plant defence pathway alters the composition of rhizosphere bacterial communities

Carvalhais, Lilia C., Dennis, Paul G., Badri, Dayakar V., Tyson, Gene W., Vivanco, Jorge M. and Schenk, Peer M. (2013) Activation of the jasmonic acid plant defence pathway alters the composition of rhizosphere bacterial communities. PLoS ONE, 8 2: e56457. doi:10.1371/journal.pone.0056457

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

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

Spatial uniformity of microbial diversity in a continuous bioelectrochemical system

Dennis, Paul G., Guo, Kun, Imelfort, Michael, Jensen, Paul, Tyson, Gene W. and Rabaey, Korneel (2012) Spatial uniformity of microbial diversity in a continuous bioelectrochemical system. Bioresource Technology, 129 10: 599-605. doi:10.1016/j.biortech.2012.11.098

Application of metatranscriptomics to soil environments

Carvalhais, Lilia C., Dennis, Paul G., Tyson, Gene W. and Schenk, Peer M. (2012) Application of metatranscriptomics to soil environments. Journal of Microbiological Methods, 91 2: 246-251. doi:10.1016/j.mimet.2012.08.011

High-throughput amplicon sequencing reveals distinct communities within a corroding concrete sewer system

Cayford, Barry I., Dennis, Paul G., Keller, Jurg, Tyson, Gene W. and Bond, Philip L. (2012) High-throughput amplicon sequencing reveals distinct communities within a corroding concrete sewer system. Applied and Environmental Microbiology, 78 19: 7160-7162. doi:10.1128/AEM.01582-12

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

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

Integrated metatranscriptomic and metagenomic analyses of stratified microbial assemblages in the open ocean

Shi, Yanmei, Tyson, Gene, Eppley, John M. and DeLong, Edward F. (2011) Integrated metatranscriptomic and metagenomic analyses of stratified microbial assemblages in the open ocean. The ISME Journal, 5 6: 999-1013. doi:10.1038/ismej.2010.189

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: e20095-1-e20095-7. doi:10.1371/journal.pone.0020095

Are divergent viral communities controlling individual gut microbiota?

Angly, Florent and Tyson, Gene (2011) Are divergent viral communities controlling individual gut microbiota?. Medecine Sciences, 27 3: 229-231. doi:10.1051/medsci/2011273229

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

Metatranscriptomics reveals unique microbial small RNAs in the ocean's water column

Shi, Yanmei, Tyson, Gene W. and DeLong, Edward F. (2009) Metatranscriptomics reveals unique microbial small RNAs in the ocean's water column. Nature, 459 7244: 266-269. doi:10.1038/nature08055

Insights into the Diversity of Eukaryotes in Acid Mine Drainage Biofilm Communities

Baker, Brett J., Tyson, Gene W., Goosherst, Lindsey and Banfield, Jillian F. (2009) Insights into the Diversity of Eukaryotes in Acid Mine Drainage Biofilm Communities. Applied and Environmental Microbiology, 75 7: 2192-2199. doi:10.1128/AEM.02500-08

Widespread known and novel phosphonate utilization pathways in marine bacteria revealed by functional screening and metagenomic analyses

Martinex, Asuncion, Tyson, Gene W. and DeLong, Edward F. (2009) Widespread known and novel phosphonate utilization pathways in marine bacteria revealed by functional screening and metagenomic analyses. Environmental Microbiology, 12 1: 222-238. doi:10.1111/j.1462-2920.2009.02062.x

Microbiology: Metagenomics

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

Microbial community gene expression in ocean surface waters

Frias-Lopez, Jorge, Shi,Yanmei, Tyson, Gene, Coleman, Maureen, Schuster, Stephan, Chisholm, Sallie and DeLong, Edward (2008) Microbial community gene expression in ocean surface waters. Proceedings of the National Academy of Sciences of the United States of America, 105 10: 3805-3810. doi:10.1073/pnas.0708897105

Rapidly evolving CRISPRs implicated in acquired resistance of microorganisms to viruses

Tyson, Gene W. and Banfield, Jillian F. (2008) Rapidly evolving CRISPRs implicated in acquired resistance of microorganisms to viruses. Environmental Microbiology, 10 1: 200-207. doi:10.1111/j.1462-2920.2007.01444.x

Strainer: Software for analysis of population variation in community genomic datasets

Eppley John M., Tyson Gene W., Getz Wayne M. and Banfield Jillian F. (2007) Strainer: Software for analysis of population variation in community genomic datasets. BMC Bioinformatics, 8 398: 1-11. doi:10.1186/1471-2105-8-398

Genetic exchange across a species boundary in the Archaeal genus Ferroplasma

Eppley, John M., Tyson, Gene W., Getz, Wayne M. and Banfield, Jillian F. (2007) Genetic exchange across a species boundary in the Archaeal genus Ferroplasma. Genetics, 177 1: 407-416. doi:10.1534/genetics.107.072892

Strain-resolved community proteomics reveals recombining genomes of acidophilic bacteria

Lo, Ian, Denef, Vincent J., VerBerkmoes, Nathan C., Shah, Manesh B., Goltsman, Daniela, DiBartolo, Genevieve, Tyson, Gene W., Allen, Eric E., Ram, Rachna J., Detter, J. Chris, Richardson, Paul, Thelen, Michael P., Hettich, Robert L. and Banfield, Jillian F. (2007) Strain-resolved community proteomics reveals recombining genomes of acidophilic bacteria. Nature, 446 7135: 537-541. doi:10.1038/nature05624

Genome dynamics in a natural archaeal population

Allen, Eric E., Tyson, Gene W., Whitaker, Rachel J., Detter, John C., Richardson, Paul M. and Banfield, Jillian F. (2007) Genome dynamics in a natural archaeal population. Proceedings of the National Academy of Sciences of the United States of America, 104 6: 1883-1888. doi:10.1073/pnas.0604851104

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

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

Cultivating the uncultivated: A community genomics perspective

Tyson, Gene W. and Banfield, Jillian F. (2005) Cultivating the uncultivated: A community genomics perspective. Trends in Microbiology, 13 9: 411-415. doi:10.1016/j.tim.2005.07.003

Community proteomics of a natural microbial biofilm

Ram, Rachna J., VerBerkmoes, Nathan C., Thelen, Michael P., Tyson, Gene W., Baker, Brett J., Blake, Robert C., Shah, Manesh, Hettich, Robert L. and Banfield, Jillian F. (2005) Community proteomics of a natural microbial biofilm. Science, 308 5730: 1915-1920. doi:10.1126/science.1109070

The search for a molecular-level understanding of the processes that underpin the earth's biogeochemical cycles

Banfield, , Tyson, GW, Allen, EE and Whitaker, RJ (2005) The search for a molecular-level understanding of the processes that underpin the earth's biogeochemical cycles. Molecular Geomicrobiology, 59 1: 1-7. doi:10.2138/rmg.2005.59.1

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

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.

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.

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

Accelerating bauxite residue remediation with microbial biotechnology

Santini, T. C., Warren, K., Raudsepp, M., Carter, N., Hamley, D., McCosker, C., Couperthwaite, S., Southam, G., Tyson, G. W. and Warren, L. A. (2019). Accelerating bauxite residue remediation with microbial biotechnology. In: Light Metals 2019. Light Metals Symposium held at the TMS Annual Meeting and Exhibition, 2019, San Antonio, TX United States, (69-77). 10-14 March 2019. doi:10.1007/978-3-030-05864-7_10

OrfM: a fast open reading frame predictor for metagenomic data

Woodcroft, Ben J., Boyd, Joel A. and Tyson, Gene W. (2016) OrfM: a fast open reading frame predictor for metagenomic data. Bioinformatics, 32 17: 2702-2703. doi:10.1093/bioinformatics/btw241

Future gas through bioconversion of waster coal

Golding, S. D., Hamilton, S. K., Baublys, K. A., Esterle, J. S., Tyson, G., Robbins, S., Rudolph, V., Zheng, H., Gilcrease, P. C. and Papendick, S. L. (2013). Future gas through bioconversion of waster coal. In: Goldschmidt Conference Abstracts 2013. Goldschmidt Conference 2013, Florence, Italy, (1187-1187). 25-30 August 2013. doi:10.1180/minmag.2013.077.5.7

Microbial community composition and function associated with enhanced anaerobic digestion of organic biosolids.

Pervin, H.P., Hastie, M., Dennis, P.G., Jensen, P., Gorman, J., Tyson, G.W., Batstone, D. and Bond, P.L. (2013). Microbial community composition and function associated with enhanced anaerobic digestion of organic biosolids.. In: 2nd Water Research Conference, Singapore EXPO, Singapore, (). 20-23 January, 2013.

Microbial community dynamics correlate to reactor parameters and performance in a pre-treatment stage of temperature–phased anaerobic digestion.

Pervin, H.P., Dennis, P.G., Lim, H.J., Tyson, G.W., Batstone, D. and Bond, P.L. (2013). Microbial community dynamics correlate to reactor parameters and performance in a pre-treatment stage of temperature–phased anaerobic digestion.. In: 2nd Water Research Conference, Singapore International Convention and Exhibition Centre, (). 20-23 January 2013.

Determining ecosystem community and function important for enhanced anaerobic digestion of organic biosolids

Pervin, H. P., Hastie, M., Dennis, P. G., Gorman, J., Tyson, G. W., Batstone, D. and Bond, P. L. (2012). Determining ecosystem community and function important for enhanced anaerobic digestion of organic biosolids. In: Australian Society for Microbiology Annual Scientific Meeting (ASM2012), Brisbane, Australia, (). 1-4 July 2012.

Metaproteomic and metagenomic characterisation of floccular and granular phosphorus removal biofilms

Barr, Jeremy, Dutilh, Bas, Cook, Andrew, Fukushima, Toshikazu, Hastie, Marcus, Gorman, Jeffery, Pan, Chongle, Hettich, Rorbert, Tyson, Gene and Bond, Philip (2012). Metaproteomic and metagenomic characterisation of floccular and granular phosphorus removal biofilms. In: 14th International Symposium on Microbial Ecology (ISME14), Copenhagan, Denmark, (). 19-24 August 2012.

Microbial communities involved in the corrosion of concrete sewer infrastructure

Cayford, Barry I., Dennis, Paul G., Tyson, Gene W. and Bond, Philip L. (2012). Microbial communities involved in the corrosion of concrete sewer infrastructure. In: 14th International Symposium on Microbial Ecology (ISME14), Copenhagan, Denmark, (). 19-24 August 2012.

Microbial corrosion of concrete sewer pipes

Cayford, B. I., Tyson, G. W., Dennis, P. G., Keller, J. and Bond, P .L. (2012). Microbial corrosion of concrete sewer pipes. In: Australian Society for Microbiology Annual Scientific Meeting (ASM2012), Brisbane, Australia, (). 1-4 July 2012.

Coal-to-biomethane potential of microbial consortia native to coal seam formation waters

Papendick, Samuel, Tyson, Gene, Esterle, Joan, Golding, Suzanne D., Rudolph, Victor and Gilcrease, Patrick C. (2011). Coal-to-biomethane potential of microbial consortia native to coal seam formation waters. In: Sustainable Engineering Forum: Core Programming Topic at the 2011 AIChE Annual Meeting. Sustainable Engineering Forum: Core Programming Topic at the 2011 AIChE Annual Meeting, Minneapolis, MN, (1302-1303). October 16, 2011-October 21, 2011.

Coal-to-biomethane potential of microbial consortia native to coal seam formation waters

Papendick, Samuel, Tyson, Gene, Esterle, Joan, Golding, Suzanne D., Rudolph, Victor and Gilcrease, Patrick C. (2011). Coal-to-biomethane potential of microbial consortia native to coal seam formation waters. In: Catalysis and Reaction Engineering Division - Core Programming Topic at the 2011 AIChE Annual Meeting. Catalysis and Reaction Engineering Division - Core Programming Topic at the 2011 AIChE Annual Meeting, Minneapolis, MN, (1110-1110). October 16, 2011-October 21, 2011.

Microbial community composition associated with sewer corrosion

Cayford, B. I., Tyson, G. W., Keller, J and Bond, P. L. (2011). Microbial community composition associated with sewer corrosion. In: Engineers Australia Queensland Water Panel's Post-Graduate Presentation Evening, Engineers Australia Queensland Branch, (). 18 May 2011.

Bridges cnd Chasms: Summary of the IMAGE 2 meeting in Montreal, Canada, 30 April to 3 May 2007

Bender, Robert A., Downs, Diana, Kiley, Patricia, LaRossa, Robert A., Sonenshein, Abraham L., Storz, Gisela, Bender, Robert, Roth, John, Schilling, Christoff, Rine's, Jasper, Merrick, Mike, Tyson, Gene, Skovran, Elizabeth, Liao, J., Stephanopolous', Greg, Anesiades, Nikolas, San, Kai-Yu, Durot, Maxim, Reich, Claudia, De Crecy-Legard, Valerie, Dean's, Dennis, Barras, Frederic, Dwyer, Daniel, De Reuse, Hilde, Massé, Eric, Hwa, Terrance, Vanderpool, Carin, Henkin's, Tina, Warner, Digby, Ron, Eliora, Gourse, Rick, Wang, Jade, Nicholson, Wayne, Burkholder, Bill, Gon, Stephanie, Ellison, Michael, Savchenko, Alexei, Pichersky, Eran, Wanner, Barry, Mori, Hirotada, LaRossa, Bob and Straight, Paul (2008). Bridges cnd Chasms: Summary of the IMAGE 2 meeting in Montreal, Canada, 30 April to 3 May 2007. In: , , (792-797). . doi:10.1128/JB.01097-07

Population dynamics in acid mine drainage biofilms from the Richmond Mine at Iron Mountain, California

Whitaker, R, Allen, E, Tyson, G and Banfield, J (2005). Population dynamics in acid mine drainage biofilms from the Richmond Mine at Iron Mountain, California. In: 15th Annual V M Goldschmidt Conference, Moscow Id, (A222-A222). May, 2005.

Challenges of life in an extremely acidic environment

Ram, RJ, VerBerkmoes, N, Tyson, GW, Baker, BJ, Thelen, MP, Hettich, RL and Banfield, JF (2005). Challenges of life in an extremely acidic environment. In: 229th National Meeting of the American-Chemical-Society, San Diego Ca, (U889-U889). Mar 13-17, 2005.

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

Microscale Experiments to Understand a Microscale World

Tyson, Gene and Rinke, Christian (2015): Microscale Experiments to Understand a Microscale World. The University of Queensland. Collection. doi:10.14264/uql.2017.105