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2019 Conference Publication Dietary fibre elevates SCFAS and protects against experimental COPDBudden, K., Shukla, S., Rehman, Firdous S., Donvan, C., Bowerman, K., Dennis, P., Hugenholtz, P. and Hansbro, P. (2019). Dietary fibre elevates SCFAS and protects against experimental COPD. TSANZSRS 2019 The Australia & New Zealand Society of Respiratory Science and The Thoracic Society of Australia and New Zealand (ANZSRS/TSANZ) Annual Scientific Meeting, Gold Coast, QLD, Australia, 29 March–2 April 2019. Richmond, VIC, Australia : Wiley-Blackwell Publishing Asia. doi: 10.1111/resp.13492 |
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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 |
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2018 Journal Article 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 |
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2018 Journal Article A natural history of actinic keratosis and cutaneous squamous cell carcinoma microbiomesWood, David L. A., Lachner, Nancy, Tan, Jean-Marie, Tang, Stephanie, Angel, Nicola, Laino, Antonia, Linedale, Richard, Lê Cao, Kim-Anh, Morrison, Mark, Frazer, Ian H., Soyer, H. Peter and Hugenholtz, Philip (2018). A natural history of actinic keratosis and cutaneous squamous cell carcinoma microbiomes. MBio, 9 (5) e01432-18. doi: 10.1128/mBio.01432-18 |
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2018 Journal Article A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of lifeParks, 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 |
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2018 Journal Article Culture- and metagenomics-enabled analyses of the Methanosphaera genus reveals their monophyletic origin and differentiation according to genome sizeHoedt, 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, 12 (12), 2942-2953. doi: 10.1038/s41396-018-0225-7 |
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2018 Journal Article 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. ... 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 |
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2018 Journal Article Network-guided genomic and metagenomic analysis of the faecal microbiota of the critically endangered kakapoWaite, David W., Dsouza, Melissa, Sekiguchi, Yuji, Hugenholtz, Philip and Taylor, Michael W. (2018). Network-guided genomic and metagenomic analysis of the faecal microbiota of the critically endangered kakapo. Scientific Reports, 8 (1) 8128, 8128. doi: 10.1038/s41598-018-26484-4 |
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2018 Journal Article American gut: an open platform for citizen science microbiome researchMcDonald, Daniel, Hyde, Embriette, Debelius, Justine W., Morton, James T., Gonzalez, Antonio, Ackermann, Gail, Aksenov, Alexander A., Behsaz, Bahar, Brennan, Caitriona, Chen, Yingfeng, DeRight Goldasich, Lindsay, Dorrestein, Pieter C., Dunn, Robert R., Fahimipour, Ashkaan K., Gaffney, James, Gilbert, Jack A., Gogul, Grant, Green, Jessica L, Hugenholtz, Philip, Humphrey, Greg, Huttenhower, Curtis, Jackson, Matthew A., Janssen, Stefan, Jeste, Dilip V., Jiang, Lingjing, Kelley, Scott T., Knights, Dan, Kosciolek, Tomasz, Ladau, Joshua ... Knight, Rob (2018). American gut: an open platform for citizen science microbiome research. mSystems, 3 (3) e00031-18. doi: 10.1128/mSystems.00031-18 |
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2018 Journal Article Mechanisms of persistence of the ammonia-oxidizing bacteria Nitrosomonas to the biocide free nitrous acidLaloo, Andrew E., Wei, Justin, Wang, Dongbo, Narayanasamy, Shaman, Vanwonterghem, Inka, Waite, David, Steen, Jason, Kaysen, Anne, Heintz-Buschart, Anna, Wang, Qilin, Schulz, Benjamin, Nouwens, Amanda, Wilmes, Paul, Hugenholtz, Philip, Yuan, Zhiguo and Bond, Philip L. (2018). Mechanisms of persistence of the ammonia-oxidizing bacteria Nitrosomonas to the biocide free nitrous acid. Environmental science & technology, 52 (9), 5386-5397. doi: 10.1021/acs.est.7b04273 |
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2018 Journal Article Addendum: Comparative genomic analysis of the class Epsilonproteobacteria and proposed reclassification to Epsilonbacteraeota (phyl. nov.) (vol 8, 682, 2017)Waite, David W., Vanwonterghem, Inka, Rinke, Christian, Parks, Donovan H., Zhang, Ying, Takai, Ken, Sievert, Stefan M., Simon, Jorg, Campbell, Barbara J., Hanson, Thomas E., Woyke, Tanja, Klotz, Martin G. and Hugenholtz, Philip (2018). Addendum: Comparative genomic analysis of the class Epsilonproteobacteria and proposed reclassification to Epsilonbacteraeota (phyl. nov.) (vol 8, 682, 2017). Frontiers in Microbiology, 9 (APR) 772, 772. doi: 10.3389/fmicb.2018.00772 |
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2018 Journal Article Recipient mucosal-associated invariant T cells control GVHD within the colonVarelias, Antiopi, Bunting, Mark D., Ormerod, Kate L., Koyama, Motoko, Olver, Stuart D., Straube, Jasmin, Kuns, Rachel D., Robb, Renee J., Henden, Andrea S., Cooper, Leanne, Lachner, Nancy, Gartlan, Kate H., Lantz, Olivier, Kjer-Nielsen, Lars, Mak, Jeffrey Y. W., Fairlie, David P., Clouston, Andrew D., McCluskey, James, Rossjohn, Jamie, Lane, Steven W., Hugenholtz, Philip and Hill, Geoffrey R. (2018). Recipient mucosal-associated invariant T cells control GVHD within the colon. Journal of Clinical Investigation, 128 (5), 1919-1936. doi: 10.1172/JCI91646 |
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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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2018 Book Chapter Design and evaluation of 16S rRNA-targeted oligonucleotide probes for fluorescence in situ hybridizationHugenholtz, Philip, Tyson, Gene W. and Blackall, Linda L. (2018). Design and evaluation of 16S rRNA-targeted oligonucleotide probes for fluorescence in situ hybridization. Gene probes: principles and protocols. (pp. 029-042) edited by Marilena Aquino de Muro and Ralph Rapley. New Jersey, United States: Humana Press. doi: 10.1385/1-59259-238-4:029 |
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2018 Conference Publication Recipient mucosal-associated invariant T cells control graft-versus-host-disease within the colonVarelias, Antiopi, Bunting, Mark, Ormerod, Kate, Koyama, Motoko, Olver, Stuart, Straube, Jasmin, Kuns, Rachel, Robb, Renee, Henden, Andrea, Cooper, Leanne, Lachner, Nancy, Gartlan, Kate, Lantz, Olivier J., Kjer-Nielsen, Lars, Mak, Jeffrey, Fairlie, David, Clouston, Andrew, McCluskey, James, Rossjohn, Jamie, Lane, Steven, Hugenholtz, Phil and Hill, Geoff (2018). Recipient mucosal-associated invariant T cells control graft-versus-host-disease within the colon. Immunology Meeting, Austin Tx, 4-8 May 2018. Bethesda, MD United States: American Association of Immunologists. |
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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 |
