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2020 Journal Article COVID-19 pandemic reveals the peril of ignoring metadata standardsSchriml, 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 |
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2020 Journal Article Fluconazole resistance in Candida albicans is induced by Pseudomonas aeruginosa quorum sensingBandara, 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 |
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2020 Journal Article Disease-associated gut microbiome and metabolome changes in patients with chronic obstructive pulmonary diseaseBowerman, 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 |
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2020 Journal Article Author Correction: 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). Author Correction: Roadmap for naming uncultivated Archaea and Bacteria. Nature Microbiology, 6 (1), 136-136. doi: 10.1038/s41564-020-00827-2 |
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2020 Journal Article 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 |
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2020 Journal Article 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 communityAhmed, 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 |
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2020 Journal Article A unified catalog of 204,938 reference genomes from the human gut microbiomeAlmeida, 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 |
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2020 Journal Article 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 travelersAhmed, 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) taaa116, 1-11. doi: 10.1093/jtm/taaa116 |
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2020 Journal Article Broad spectrum antibiotic-degrading metallo-β-lactamases are phylogenetically diversePedroso, 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 |
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2020 Conference Publication Changes in the Gut Microbiome in Chronic Obstructive Pulmonary DiseaseRehman, 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 |
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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 Conference Publication Fast forward bioprospecting of the gut microbiota for novel live biotherapeutics and anti-inflammatory bioactivesCuiv, 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. |
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2020 Conference Publication Variations of the mucosa associated microbiota along the human gastrointestinal tract in health and inflammatory bowel diseaseShah, 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 |
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2020 Conference Publication Diet influences COPD pathogenesis by regulating microbial metabolismBudden, 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. |
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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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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 |
