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2016 Journal Article Near complete genome sequence of the animal feed probiotic, Bacillus amyloliquefaciens H57Schofield, Benjamin J., Skarshewski, Adam, Lachner, Nancy, Ouwerkerk, Diane, Klieve, Athol V., Dart, Peter and Hugenholtz, Philip (2016). Near complete genome sequence of the animal feed probiotic, Bacillus amyloliquefaciens H57. Standards in Genomic Sciences, 11 (1) 60, 60. doi: 10.1186/s40793-016-0189-z |
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2016 Journal Article 'Candidatus Adiutrix intracellularis', an endosymbiont of termite gut flagellates, is the first representative of a deep-branching clade of Deltaproteobacteria and a putative homoacetogenIkeda-Ohtsubo, Wakako, Strassert, Juergen F. H., Kohler, Tim, Mikaelyan, Aram, Gregor, Ivan, Mchardy, Alice C., Tringe, Susannah Green, Hugenholtz, Phil, Radek, Renate and Brune, Andreas (2016). 'Candidatus Adiutrix intracellularis', an endosymbiont of termite gut flagellates, is the first representative of a deep-branching clade of Deltaproteobacteria and a putative homoacetogen. Environmental Microbiology, 18 (8), 2548-2564. doi: 10.1111/1462-2920.13234 |
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2016 Journal Article Genomic characterization of the uncultured Bacteroidales family S24-7 inhabiting the guts of homeothermic animalsOrmerod, Kate L., Wood, David L. A., Lachner, Nancy, Gellatly, Shaan L., Daly, Joshua N., Parsons, Jeremy D., Dal’Molin, Cristiana G. O., Palfreyman, Robin W., Nielsen, Lars K., Cooper, Matthew A., Morrison, Mark, Hansbro, Philip M. and Hugenholtz, Philip (2016). Genomic characterization of the uncultured Bacteroidales family S24-7 inhabiting the guts of homeothermic animals. Microbiome, 4 (1) 36, 36.1-36.17. doi: 10.1186/s40168-016-0181-2 |
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2016 Journal Article A catalogue of 136 microbial draft genomes from Red Sea metagenomesHaroon, Mohamed F., Thompson, Luke R., Parks, Donovan H., Hugenholtz, Philip and Stingl, Ulrich (2016). A catalogue of 136 microbial draft genomes from Red Sea metagenomes. Scientific Data, 3 (1) 160050, 160050.1-160050.6. doi: 10.1038/sdata.2016.50 |
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2016 Journal Article Introducing BASE: the Biomes of Australian Soil Environments soil microbial diversity databaseBissett, Andrew, Fitzgerald, Anna, 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., Paungfoo-Lonhienne, Chanyarat ... Young, Andrew (2016). Introducing BASE: the Biomes of Australian Soil Environments soil microbial diversity database. Gigascience, 5 (1) 21, 21.1-21.11. doi: 10.1186/s13742-016-0126-5 |
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2016 Journal Article Genome-based microbial taxonomy coming of ageHugenholtz, Philip, Skarshewski, Adam and Parks, Donovan H. (2016). Genome-based microbial taxonomy coming of age. Cold Spring Harbor Perspectives in Biology, 8 (6) a018085, a018085. doi: 10.1101/cshperspect.a018085 |
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2016 Journal Article Airway dysbiosis: Haemophilus influenzae and Tropheryma in poorly controlled asthmaSimpson, Jodie L., Daly, Joshua, Baines, Katherine J., Yang, Ian A., Upham, John W., Reynolds, Paul N., Hodge, Sandra, James, Alan L., Hugenholtz, Philip, Willner, Dana and Gibson, Peter G. (2016). Airway dysbiosis: Haemophilus influenzae and Tropheryma in poorly controlled asthma. European Respiratory Journal, 47 (3), 792-800. doi: 10.1183/13993003.00405-2015 |
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2016 Journal Article Metagenomic insights into the uncultured diversity and physiology of microbes in four hypersaline soda lake brinesVavourakis, Charlotte D., Ghai, Rohit, Rodriguez-Valera, Francisco, Sorokin, Dimitry Y., Tringe, Susannah G., Hugenholtz, Philip and Muyzer, Gerard (2016). Metagenomic insights into the uncultured diversity and physiology of microbes in four hypersaline soda lake brines. Frontiers in Microbiology, 7 (FEB) 211, 211.1-211.18. doi: 10.3389/fmicb.2016.00211 |
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2016 Journal Article High-resolution phylogenetic microbial community profilingSinger, Esther, Bushnell, Brian, Coleman-Derr, Devin, Bowman, Brett, Bowers, Robert M., Levy, Asaf, Gies, Esther A., Cheng, Jan-Fang, Copeland, Alex, Klenk, Hans-Peter, Hallam, Steven J., Hugenholtz, Philip, Tringe, Susannah G. and Woyke, Tanja (2016). High-resolution phylogenetic microbial community profiling. ISME Journal, 10 (8), 2020-2032. doi: 10.1038/ismej.2015.249 |
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2016 Journal Article A phylogenomic analysis of the bacterial phylum fibrobacteresAbdul Rahman, Nurdyana, Parks, Donovan H., Vanwonterghem, Inka, Morrison, Mark, Tyson, Gene W. and Hugenholtz, Philip (2016). A phylogenomic analysis of the bacterial phylum fibrobacteres. Frontiers in Microbiology, 6 (JAN) 1469, 1469.1-1469.15. doi: 10.3389/fmicb.2015.01469 |
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2016 Conference Publication Treatment of ZAP-70 Mutant SKG Mice with Anti-IL-23 Antibody Alters Fecal Microbiota Composition and Prevents Outgrowth of Bacteria Associated with Susceptibility to Spondyloarthritis and IleitisRehaume, Linda, Matigian, Nicholas, Kang, Alicia, Zbarskaya, Olga, Kikly, Kristine, Lachner, Nancy, Daly, Joshua, Hugenholtz, Philip, Morrison, Mark, Le Cao, Kim-Anh and Thomas, Ranjeny (2016). Treatment of ZAP-70 Mutant SKG Mice with Anti-IL-23 Antibody Alters Fecal Microbiota Composition and Prevents Outgrowth of Bacteria Associated with Susceptibility to Spondyloarthritis and Ileitis. 2016 ACR/ARHP Annual Meeting, Washington, DC United States, 11–16 November 2016 . Hoboken, NJ United States: Wiley. |
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2016 Conference Publication Healthy gut microbiota ameliorates experimental chronic obstructive pulmonary diseaseGellatly, S., Dennis, P., Jarnicki, A., Lachner, N., Wood, D., Fricker, M., Budden, K., Liu, G., Keely, S., Morrison, M., Willner, D., Cooper, M., Hugenholtz, P. and Hansbro, P. (2016). Healthy gut microbiota ameliorates experimental chronic obstructive pulmonary disease. Annual Scientific Meeting of the Thoracic Society of Australia and New Zealand and the Australian and New Zealand Society of Respiratory Science 2014, Perth, WA, Australia, 1–6 April 2016. Hoboken, NJ United States: Wiley. doi: 10.1111/resp.12754_22 |
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2016 Conference Publication An Australian prospective cohort of rheumatoid arthritis patients and their first-degree relatives characterising environmental, genetic, microbial and immune factorsBenham, Helen, Wood, John, Nagl, Lisa, Maradana, Muralidhara, Daly, Joshua, Lachner, Nancy, Hugenholtz, Philip and Thomas, Ranjeny (2016). An Australian prospective cohort of rheumatoid arthritis patients and their first-degree relatives characterising environmental, genetic, microbial and immune factors. Australian Rheumatology Association in conjunction with Rheumatology Health Professionals Association, 57th Annual Scientific Meeting, Darwin, NT, Australia, 30 April–4 May 2016. Richmond, VIC, Australia: Wiley-Blackwell Publishing Asia. doi: 10.1111/imj.13052 |
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2016 Conference Publication Distinct Oral and Fecal Community Profiles Enriched in Opportunistic Pathogens in RA Patients and First Degree Relatives Are Influenced By Environmental Risk Factors, Including Smoking, Dental History and Lung InfectionBenham, Helen, Maradana, Muralidhara, Lakis, Vanessa Anne, Cuiv, Paraic O., Wood, John, Nagl, Lisa, Rammouth, Nishta, Owens, Clare, Daly, Joshua., Lachner, Nancy, Morrison, Mark, Hugenholtz, Philip, Le Cao, Kim-Anh and Thomas, Rarljeny (2016). Distinct Oral and Fecal Community Profiles Enriched in Opportunistic Pathogens in RA Patients and First Degree Relatives Are Influenced By Environmental Risk Factors, Including Smoking, Dental History and Lung Infection. 2016 ACR/ARHP Annual Meeting, Washington, DC, 11-16 November 2016. Hoboken, NJ, United States: John Wiley & Sons. |
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2016 Conference Publication Addressing the nitrogen problem in sugarcane production to reduce pollution of the Great Barrier ReefRobinson, N., Brackin, R., Paungfoo-Lonhienne, C., Lonhienne, T., Westermann, M., Salazar, M., Yeoh, Y. K ., Hugenholtz, P., Ragan, M. A., Redding, M., Pratt, C., Wang, W. J., Royle, A., DiBella, L., Lakshmanan, P. and Schmidt, S. (2016). Addressing the nitrogen problem in sugarcane production to reduce pollution of the Great Barrier Reef. International Nitrogen Initiative Conference, Melbourne, Australia, 4-8 December 2016. Melbourne, Australia: International Nitrogen Initiative. |
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2016 Conference Publication Profiling immunogenic bacteria within the microbiota of SKG mice associated with spondyloarthritis and ileitis using IgA-SEQRehaume, L. M., Kang, A., Zbarskaya, O., Mullaney, J. A., Kim, M., Cuiv, O. P., Angel, N., Lachner, N., Daly, J., Morrison, M., Hugenholtz, P. and Thomas, R. (2016). Profiling immunogenic bacteria within the microbiota of SKG mice associated with spondyloarthritis and ileitis using IgA-SEQ. International Congress of Immunology (ICI 2016), Melbourne, Australia, 21-26 August 2016. Weinheim, Germany: Wiley. |
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2015 Journal Article Comparative genomics of candidate phylum TM6 suggests that parasitism is widespread and ancestral in this lineageYeoh, Yun Kit, Sekiguchi, Yuji, Parks, Donovan H. and Hugenholtz, Philip (2015). Comparative genomics of candidate phylum TM6 suggests that parasitism is widespread and ancestral in this lineage. Molecular Biology and Evolution, 33 (4), 915-927. doi: 10.1093/molbev/msv281 |
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2015 Journal Article Evaluating DNA Extraction Methods for Community Profiling of Pig Hindgut Microbial CommunityLu, Yang, Hugenholtz, Phillip and Batstone, Damien John (2015). Evaluating DNA Extraction Methods for Community Profiling of Pig Hindgut Microbial Community. PLoS One, 10 (11) e0142720, e0142720.1-e0142720.10. doi: 10.1371/journal.pone.0142720 |
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2015 Journal Article Draft genome sequences of Anaerolinea thermolimosa IMO-1, Bellilinea caldifistulae GOMI-1, Leptolinea tardivitalis YMTK-2, Levilinea saccharolytica KIBI-1, Longilinea arvoryzae KOME-1, previously described as members of the class Anaerolineae (ChloroflexiMatsuura, Norihisa, Tourlousse, Dieter M., Ohashi, Akiko, Hugenholtz, Philip and Sekiguchia, Yuji (2015). Draft genome sequences of Anaerolinea thermolimosa IMO-1, Bellilinea caldifistulae GOMI-1, Leptolinea tardivitalis YMTK-2, Levilinea saccharolytica KIBI-1, Longilinea arvoryzae KOME-1, previously described as members of the class Anaerolineae (Chloroflexi. Genome Announcements, 3 (5) e00975-15. doi: 10.1128/genomeA.00975-15 |
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2015 Journal Article Comparative genomics of non-pseudomonal bacterial species colonising paediatric cystic fibrosis patientsOrmerod, Kate L., George, Narelle M., Fraser, James A., Wainwright, Claire and Hugenholtz, Philip (2015). Comparative genomics of non-pseudomonal bacterial species colonising paediatric cystic fibrosis patients. PeerJ, 3 (9) e1223, e1223.1-e1223.27. doi: 10.7717/peerj.1223 |
