The University of Queensland

Journal Article

• Genome Taxonomy Database and SeqCode: Microbial taxonomy and nomenclature in the age of big sequence data

  Chuvochina, Maria, Rinke, Christian, Mussig, Aaron, Chaumeil, Pierre-Alain, Parks, Donovan and Hugenholtz, Philip (2023). Genome Taxonomy Database and SeqCode: Microbial taxonomy and nomenclature in the age of big sequence data. Biodiversity Information Science and Standards, 7. doi: 10.3897/biss.7.111135

• 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. doi: 10.1093/femsle/fnad071

• Naming genera after geographical locations. Proposal to emend Appendix 9 of the International Code of Nomenclature of Prokaryotes

  Oren, Aharon and Chuvochina, Maria (2023). Naming genera after geographical locations. Proposal to emend Appendix 9 of the International Code of Nomenclature of Prokaryotes. International Journal of Systematic and Evolutionary Microbiology, 73 (5) 005873. doi: 10.1099/ijsem.0.005873

• Hyperactive nanobacteria with host-dependent traits pervade Omnitrophota

  Seymour, Cale O., Palmer, Marike, Becraft, Eric D., Stepanauskas, Ramunas, Friel, Ariel D., Schulz, Frederik, Woyke, Tanja, Eloe-Fadrosh, Emiley, Lai, Dengxun, Jiao, Jian-Yu, Hua, Zheng-Shuang, Liu, Lan, Lian, Zheng-Han, Li, Wen-Jun, Chuvochina, Maria, Finley, Brianna K., Koch, Benjamin J., Schwartz, Egbert, Dijkstra, Paul, Moser, Duane P., Hungate, Bruce A. and Hedlund, Brian P. (2023). Hyperactive nanobacteria with host-dependent traits pervade Omnitrophota. Nature Microbiology, 8 (4), 727-744. doi: 10.1038/s41564-022-01319-1

• Guidelines for interpreting the International Code of Nomenclature of Prokaryotes and for preparing a Request for an Opinion

  Arahal, David R., Bull, Carolee T., Busse, Hans-Jürgen, Christensen, Henrik, Chuvochina, Maria, Dedysh, Svetlana N., Fournier, Pierre-Edouard, Konstantinidis, Konstantinos T., Parker, Charles T., Rossello-Mora, Ramon, Ventosa, Antonio and Göker, Markus (2023). Guidelines for interpreting the International Code of Nomenclature of Prokaryotes and for preparing a Request for an Opinion. International Journal of Systematic and Evolutionary Microbiology, 73 (3) 005782, 1-20. doi: 10.1099/ijsem.0.005782

• Judicial Opinion 128

  Arahal, David R., Bull, Carolee T., Christensen, Henrik, Chuvochina, Maria, Dedysh, Svetlana N., Fournier, Pierre-Edouard, Konstantinidis, Konstantinos T., Parker, Charles T., Rossello-Mora, Ramon, Ventosa, Antonio and Göker, Markus (2023). Judicial Opinion 128. International Journal of Systematic and Evolutionary Microbiology, 73 (3) 005797. doi: 10.1099/ijsem.0.005797

• 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

• Judicial Opinions 103–111

  Arahal, David R., Busse, Hans-Jürgen, Bull, Carolee T., Christensen, Henrik, Chuvochina, Maria, Dedysh, Svetlana N., Fournier, Pierre-Edouard, Konstantinidis, Konstantinos T., Parker, Charles T., Rosselló-Móra, Ramon, Ventosa, Antonio and Göker, Markus (2022). Judicial Opinions 103–111. International Journal of Systematic and Evolutionary Microbiology, 72 (1) 005197. doi: 10.1099/ijsem.0.005197

• 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

• 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

• 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

• Drivers of bacterial diversity along a natural transect from freshwater to saline subtropical wetlands

  Chuvochina, Maria, Adame, Maria Fernanda, Guyot, Adrien, Lovelock, Catherine, Lockington, David, Gamboa-Cutz, Julieta N. and Dennis, Paul G. (2021). Drivers of bacterial diversity along a natural transect from freshwater to saline subtropical wetlands. Science of the Total Environment, 759 143455, 1-8. doi: 10.1016/j.scitotenv.2020.143455

• 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

• 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

• Lists of names of prokaryotic Candidatus taxa

  Oren, Aharon, Garrity, George M., Parker, Charles T., Chuvochina, Maria and Trujillo, Martha E. (2020). Lists of names of prokaryotic Candidatus taxa. International Journal of Systematic and Evolutionary Microbiology, 70 (7) 003789, 3956-4042. doi: 10.1099/ijsem.0.003789

• 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

• 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

• 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

• The use of Greek and Latin prepositions and prefixes in compound names: proposed emendation of Appendix 9 of the International Code of Nomenclature of Prokaryotes

  Oren, Aharon, Chuvochina, Maria and Schink, Bernhard (2019). The use of Greek and Latin prepositions and prefixes in compound names: proposed emendation of Appendix 9 of the International Code of Nomenclature of Prokaryotes. International Journal of Systematic and Evolutionary Microbiology, 69 (6), 1831-1832. doi: 10.1099/ijsem.0.003389

• Naming classes of prokaryotes based on the rules of Latin grammar

  Oren, Aharon, Chuvochina, Maria, Schink, Bernhard and Ventura, Stefano (2019). Naming classes of prokaryotes based on the rules of Latin grammar. International Journal of Systematic and Evolutionary Microbiology, 69 (5) 003311, 1526-1527. doi: 10.1099/ijsem.0.003311

• Metabolic potential of uncultured bacteria and archaea associated with petroleum seepage in deep-sea sediments

  Dong, Xiyang, Greening, Chris, Rattray, Jayne E., Chakraborty, Anirban, Chuvochina, Maria, Mayumi, Daisuke, Dolfing, Jan, Li, Carmen, Brooks, James M., Bernard, Bernie B., Groves, Ryan A., Lewis, Ian A. and Hubert, Casey R. J. (2019). Metabolic potential of uncultured bacteria and archaea associated with petroleum seepage in deep-sea sediments. Nature Communications, 10 (1) 1816, 1-12. doi: 10.1038/s41467-019-09747-0

• Formation of compound generic names based on personal names: a proposal for emendation of Appendix 9 of the International Code of Nomenclature of Prokaryotes

  Oren, Aharon, Chuvochina, Maria and Ventura, Stefano (2019). Formation of compound generic names based on personal names: a proposal for emendation of Appendix 9 of the International Code of Nomenclature of Prokaryotes. International Journal of Systematic and Evolutionary Microbiology, 69 (2) 003192, 594-596. doi: 10.1099/ijsem.0.003192

• 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

• 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 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

• Proposal of the suffix -ota to denote phyla. Addendum to 'Proposal to include the rank of phylum in the International Code of Nomenclature of Prokaryotes'

  Whitman, William B, Oren, Aharon, Chuvochina, Maria, da Costa, Milton S, Garrity, George M, Rainey, Fred A, Rossello-Mora, Ramon, Schink, Bernhard, Sutcliffe, Iain, Trujillo, Martha E and Ventura, Stefano (2018). Proposal of the suffix -ota to denote phyla. Addendum to 'Proposal to include the rank of phylum in the International Code of Nomenclature of Prokaryotes'. International Journal of Systematic and Evolutionary Microbiology, 68 (3) 002593, 967-969. doi: 10.1099/ijsem.0.002593

• 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

• 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

• Microbial communities within the water column of freshwater Lake Radok, East Antarctica: predominant 16S rDNA phylotypes and bacterial cultures

  Karlov, Denis S., Marie, Dominique, Sumbatyan, Danil A., Chuvochina, Maria S., Kulichevskaya, Irina S., Alekhina, Irina A. and Bulat, Sergey A. (2016). Microbial communities within the water column of freshwater Lake Radok, East Antarctica: predominant 16S rDNA phylotypes and bacterial cultures. Polar Biology, 40 (4), 1-14. doi: 10.1007/s00300-016-2008-9

• Community variability of bacteria in alpine snow (Mont Blanc) containing Saharan dust deposition and their snow colonisation potential

  Chuvochina, Maria S., Marie, Dominique, Chevaillier, Servanne, Petit, Jean-Robert, Normand, Philippe, Alekhina, Irina A. and Bulat, Sergey A. (2011). Community variability of bacteria in alpine snow (Mont Blanc) containing Saharan dust deposition and their snow colonisation potential. Microbes and Environments, 26 (3), 237-247. doi: 10.1264/jsme2.ME11116

• Microbial communities of water column of Lake Radok, East Antarctica, dominated by abundant actinobacterium "Candidatus Planktophila limnetica"

  Karlov, D. S., Marie, D., Chuvochina, M. S., Alekhina, I. A. and Bulat, S. A. (2011). Microbial communities of water column of Lake Radok, East Antarctica, dominated by abundant actinobacterium "Candidatus Planktophila limnetica". Microbiology, 80 (4), 576-579. doi: 10.1134/S0026261711040084

• Three events of Saharan dust deposition on the Mont Blanc glacier associated with different snow-colonizing bacterial phylotypes

  Chuvochina, M. S., Alekhina, I. A., Normand, P., Petit, J. R. and Bulat, S. A. (2011). Three events of Saharan dust deposition on the Mont Blanc glacier associated with different snow-colonizing bacterial phylotypes. Microbiology, 80 (1), 125-131. doi: 10.1134/S0026261711010061

• Microbial communities of water column of Lake Radok, East Antarctica, dominated by abundant actinobacterium “Candidatus Planktophila limnetica”

  Karlov, D S, Marie, D, Chuvochina, M S, Alekhina, I A and Bulat, S A (2011). Microbial communities of water column of Lake Radok, East Antarctica, dominated by abundant actinobacterium “Candidatus Planktophila limnetica”. Mikrobiologiia, 80 (4), 571-4. doi: 10.1134/S0026261711040084

• Cytochromes c of the anaerobic methacrylate reducer Geobacter sulfurreducens AM-1

  Arkhipova, O. V., Chuvochina, M. S. and Trutko, S. M. (2009). Cytochromes c of the anaerobic methacrylate reducer Geobacter sulfurreducens AM-1. Microbiology, 78 (3), 296-303. doi: 10.1134/S0026261709030060

• Cytochromes c of anaerobic methacrylate-reducing Geobacter sulfurreducens AM-1

  Arkhipova, O V, Chuvochina, M S and Trutko, S M (2009). Cytochromes c of anaerobic methacrylate-reducing Geobacter sulfurreducens AM-1. Mikrobiologiia, 78 (3), 334-41.