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2020 Journal Article A complete domain-to-species taxonomy for bacteria and archaeaParks, 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 |
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2020 Journal Article Draft genome sequence of Limisphaera ngatamarikiensis NGM72.4(T), a moderately alkaliphilic thermophile belonging to the class VerrucomicrobiaeCarere, 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 |
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2020 Journal Article GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy DatabaseChaumeil, 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 |
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2020 Journal Article 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 |
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2020 Journal Article Continuous pre- and post-transplant exposure to a disease-associated gut microbiome promotes hyper-acute graft-versus-host disease in wild-type miceBowerman, 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 |
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2020 Journal Article Roadmap for naming uncultivated Archaea and BacteriaMurray, 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 |
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2020 Journal Article Proposal to reclassify the proteobacterial classes Deltaproteobacteria and Oligoflexia, and the phylum Thermodesulfobacteria into four phyla reflecting major functional capabilitiesWaite, 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 |
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2019 Journal Article Functional effects of the microbiota in chronic respiratory diseaseBudden, 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 |
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2019 Journal Article Genomic Encyclopedia of Bacteria and Archaea (GEBA) VI: learning from type strainsWhitman, 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 |
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2019 Journal Article Faecal inoculations alter the gastrointestinal microbiome and allow dietary expansion in a wild specialist herbivore, the koalaBlyton, 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 |
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2019 Journal Article Defining the human gut host–phage network through single-cell viral taggingDžunková, 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 |
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2019 Journal Article Evaluation of a concatenated protein phylogeny for classification of tailed double-stranded DNA viruses belonging to the order CaudoviralesLow, 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 |
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2019 Journal Article Consent insufficient for data release ResponseAmann, 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 |
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2019 Journal Article Bacterial fermentation and respiration processes are uncoupled in anoxic permeable sedimentsKessler, 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 |
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2019 Journal Article IL-23 favours outgrowth of spondyloarthritis-associated pathobionts and suppresses host support for homeostatic microbiotaRehaume, 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 |
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2019 Journal Article Toward unrestricted use of public genomic dataAmann, 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 |
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2019 Journal Article An evolving view of methane metabolism in the ArchaeaEvans, 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 |
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2019 Journal Article The importance of designating type material for uncultured taxaChuvochina, 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 |
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2019 Journal Article Evolution of photosynthesis and aerobic respiration in the cyanobacteriaSoo, 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 |
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2018 Journal Article 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 |
