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2018 Journal Article 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life (vol 35, pg 676, 2017)Mukherjee, Supratim, Seshadri, Rekha, Varghese, Neha J., Eloe-Fadrosh, Emiley A., Meier-Kolthoff, Jan P., Goeker, Markus, Coates, R. Cameron, Hadjithomas, Michalis, Pavlopoulos, Georgios A., Paez-Espino, David, Yoshikuni, Yasuo, Visel, Axel, Whitman, William B., Garrity, George M., Eisen, Jonathan A., Hugenholtz, Philip, Pati, Amrita, Ivanova, Natalia N., Woyke, Tanja, Klenk, Hans-Peter and Kyrpides, Nikos C. (2018). 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life (vol 35, pg 676, 2017). Nature Biotechnology, 36 (4), 368-368. doi: 10.1038/nbt0418-368c |
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2018 Journal Article Beneficial changes in rumen bacterial community profile in sheep and dairy calves as a result of feeding the probiotic Bacillus amyloliquefaciens H57Schofield, Benjamin J., Lachner, Nancy, Le, Oanh T., McNeill, David M., Dart, Peter, Ouwerkerk, Diane, Hugenholtz, Philip and Klieve, Athol V. (2018). Beneficial changes in rumen bacterial community profile in sheep and dairy calves as a result of feeding the probiotic Bacillus amyloliquefaciens H57. Journal of Applied Microbiology, 124 (3), 855-866. doi: 10.1111/jam.13688 |
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2017 Journal Article Author correction: recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of lifeParks, 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 |
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2017 Journal Article Atmospheric trace gases support primary production in Antarctic desert surface soilJi, Mukan, Greening, Chris, Vanwonterghem, Inka, Carere, Carlo R., Bay, Sean K., Steen, Jason A., Montgomery, Kate, Lines, Thomas, Beardall, John, van Dorst, Josie, Snape, Ian, Stott, Matthew B., Hugenholtz, Philip and Ferrari, Belinda C. (2017). Atmospheric trace gases support primary production in Antarctic desert surface soil. Nature, 552 (7685), 400-403. doi: 10.1038/nature25014 |
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2017 Journal Article Evolutionary conservation of a core root microbiome across plant phyla along a tropical soil chronosequenceYeoh, Yun Kit, Dennis, Paul G., Paungfoo-Lonhienne, Chanyarat, Weber, Lui, Brackin, Richard, Ragan, Mark A., Schmidt, Susanne and Hugenholtz, Philip (2017). Evolutionary conservation of a core root microbiome across plant phyla along a tropical soil chronosequence. Nature Communications, 8 (1) 002628, 215. doi: 10.1038/s41467-017-00262-8 |
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2017 Journal Article Gene and genome-centric analyses of koala and wombat fecal microbiomes point to metabolic specialization for Eucalyptus digestionShiffman, 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 |
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2017 Journal Article Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of lifeParks, 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 |
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2017 Journal Article A microfluidics-based in situ chemotaxis assay to study the behaviour of aquatic microbial communitiesLambert, 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 |
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2017 Journal Article Characterization of a highly efficient antibiotic-degrading metallo-β-lactamase obtained from an uncultured member of a permafrost communityPedroso, 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 |
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2017 Journal Article Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaeaBowers, Robert M., Kyrpides, Nikos C., Stepanauskas, Ramunas, Harmon-Smith, Miranda, Doud, Devin, Reddy, T. B. K., Schulz, Frederik, Jarett, Jessica, Rivers, Adam R., Eloe-Fadrosh, Emiley A., Tringe, Susannah G., Ivanova, Natalia N., Copeland, Alex, Clum, Alicia, Becraft, Eric D., Malmstrom, Rex R., Birren, Bruce, Podar, Mircea, Bork, Peer, Weinstock, George M., Garrity, George M., Dodsworth, Jeremy A., Yooseph, Shibu, Sutton, Granger, Gloeckner, Frank O., Gilbert, Jack A., Nelson, William C., Hallam, Steven J., Jungbluth, Sean P. ... Woyke, Tanja (2017). Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea. Nature Biotechnology, 35 (8), 725-731. doi: 10.1038/nbt.3893 |
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2017 Journal Article 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life.Mukherjee, Supratim, Seshadri, Rekha, Varghese, Neha J., Eloe-Fadrosh, Emiley A., Meier-Kolthoff, Jan P., Göker, Markus, Coates, R Cameron, Hadjithomas, Michalis, Pavlopoulos, Georgios A., Paez-Espino, David, Yoshikuni, Yasuo, Visel, Axel, Whitman, William B., Garrity, George M., Eisen, Jonathan A., Hugenholtz, Philip, Pati, Amrita, Ivanova, Natalia N., Woyke, Tanja, Klenk, Hans-Peter and Kyrpides, Nikos C. (2017). 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life.. Nature Biotechnology, 35 (7), 676-683. doi: 10.1038/nbt.3886 |
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2017 Journal Article Introducing BASE: the Biomes of Australian Soil Environments soil microbial diversity database (vol 5, 1, 2016)Bissett, Andrew, Fitzgerald, Anna, Court, Leon, Meintjes, Thys, Mele, Pauline M., Reith, Frank, Dennis, Paul G., Breed, Martin F., Brown, Belinda, Brown, Mark V., Brugger, Joel, Byrne, Margaret, Caddy-Retalic, Stefan, Carmody, Bernie, Coates, David J., Correa, Carolina, Ferrari, Belinda C., Gupta, Vadakattu V. S. R., Hamonts, Kelly, Haslem, Asha, Hugenholtz, Philip, Karan, Mirko, Koval, Jason, Lowe, Andrew J., Macdonald, Stuart, McGrath, Leanne, Martin, David, Morgan, Matt, North, Kristin I. ... Young, Andrew (2017). Introducing BASE: the Biomes of Australian Soil Environments soil microbial diversity database (vol 5, 1, 2016). Gigascience, 6 (5) gix021, 1-1. doi: 10.1093/gigascience/gix021 |
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2017 Journal Article Comparative genomic analysis of the class Epsilonproteobacteria and proposed reclassification to Epsilonbacteraeota (phyl. nov.)Waite, David W., Vanwonterghem, Inka, Rinke, Christian, Parks, Donovan H. , Zhang, Ying, Takai, Ken, Sievert, Stefan M. , Simon, Joerg, Campbell, Barbara J. , Hanson, Thomas E. , Woyke, Tanja, Klotz, Martin G. and Hugenholtz, Philip (2017). Comparative genomic analysis of the class Epsilonproteobacteria and proposed reclassification to Epsilonbacteraeota (phyl. nov.). Frontiers in Microbiology, 8 (APR) 682 doi: 10.3389/fmicb.2017.00682. |
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2017 Journal Article On the origins of oxygenic photosynthesis and aerobic respiration in CyanobacteriaSoo, Rochelle M. , Hemp, James, Parks, Donovan H. , Fischer, Woodward W. and Hugenholtz, Philip (2017). On the origins of oxygenic photosynthesis and aerobic respiration in Cyanobacteria. Science, 355 (6332), 1436-1440. doi: 10.1126/science.aal3794 |
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2017 Journal Article Microbiomes in respiratory health and disease: an Asia-Pacific perspectiveChotirmall, Sanjay H., Gellatly, Shaan L., Budden, Kurtis F., Mac Aogain, Micheál, Shukla, Shakti D., Wood, David L. A., Hugenholtz, Philip, Pethe, Kevin and Hansbro, Philip M. (2017). Microbiomes in respiratory health and disease: an Asia-Pacific perspective. Respirology, 22 (2), 240-250. doi: 10.1111/resp.12971 |
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2017 Journal Article Acute graft-versus-host disease is regulated by an IL-17-sensitive microbiomeVarelias, Antiopi, Ormerod, Kate L., Bunting, Mark D., Koyama, Motoko, Gartlan, Kate H., Kuns, Rachel D., Lachner, Nancy, Locke, Kelly R., Lim, Chun Y., Henden, Andrea S., Zhang, Ping, Clouston, Andrew D., Hasnain, Sumaira Z., McGuckin, Michael A., Blazar, Bruce R., MacDonald, Kelli P. A ., Hugenholtz, Philip and Hill, Geoffrey R. (2017). Acute graft-versus-host disease is regulated by an IL-17-sensitive microbiome. Blood, 129 (15), 2172-2185. doi: 10.1182/blood-2016-08-732628 |
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2016 Journal Article Anode potential influences the structure and function of anodic electrode and electrolyte-associated microbiomesDennis, Paul G., Virdis, Bernardino, Vanwonterghem, Inka, Hassan, Alif, Hugenholtz, Phil, Tyson, Gene W. and Rabaey, Korneel (2016). Anode potential influences the structure and function of anodic electrode and electrolyte-associated microbiomes. Scientific Reports, 6 (1) 39114, 39114. doi: 10.1038/srep39114 |
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2016 Journal Article Crosstalk between sugarcane and a plant-growth promoting Burkholderia speciesPaungfoo-Lonhienne, Chanyarat, Lonhienne, Thierry G. A., Yeoh, Yun Kit, Donose, Bogdan C., Webb, Richard I., Parsons, Jeremy, Liao, Webber, Sagulenko, Evgeny, Lakshmanan, Prakash, Hugenholtz, Philip, Schmidt, Susanne and Ragan, Mark A. (2016). Crosstalk between sugarcane and a plant-growth promoting Burkholderia species. Scientific Reports, 6 (1) 37389, 37389. doi: 10.1038/srep37389 |
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2016 Journal Article Methylotrophic methanogenesis discovered in the archaeal phylum VerstraetearchaeotaVanwonterghem, Inka, Evans, Paul N., Parks, Donovan H., Jensen, Paul D., Woodcroft, Ben J., Hugenholtz, Philip and Tyson, Gene W. (2016). Methylotrophic methanogenesis discovered in the archaeal phylum Verstraetearchaeota. Nature Microbiology, 1 (16170) 16170, 16170. doi: 10.1038/nmicrobiol.2016.170 |
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2016 Journal Article Emerging pathogenic links between microbiota and the gut-lung axis.Budden, Kurtis F. , Gellatly, Shaan L. , Wood, David L., Cooper, Matthew A. , Morrison, Mark, Hugenholtz, Philip and Hansbro, Philip M. (2016). Emerging pathogenic links between microbiota and the gut-lung axis.. Nature Reviews Microbiology, 15 (1), 55-63. doi: 10.1038/nrmicro.2016.142 |
