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2022 Journal Article Secreted toxins from Staphylococcus aureus strains isolated from keratinocyte skin cancers mediate pro-tumorigenic inflammatory responses in the skinKrueger, Annika, Zaugg, Julian, Chisholm, Sarah, Linedale, Richard, Lachner, Nancy, Teoh, Siok Min, Tuong, Zewen K., Lukowski, Samuel W., Morrison, Mark, Soyer, H. Peter, Hugenholtz, Philip, Hill, Michelle M. and Frazer, Ian H. (2022). Secreted toxins from Staphylococcus aureus strains isolated from keratinocyte skin cancers mediate pro-tumorigenic inflammatory responses in the skin. Frontiers in Microbiology, 12 789042, 789042. doi: 10.3389/fmicb.2021.789042 |
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2022 Journal Article Correction: Recoding of stop codons expands the metabolic potential of two novel AsgardarchaeotaSun, Jiarui, Evans, Paul N., Gagen, Emma J., Woodcroft, Ben J., Hedlund, Brian P., Woyke, Tanja, Hugenholtz, Philip and Rinke, Christian (2022). Correction: Recoding of stop codons expands the metabolic potential of two novel Asgardarchaeota. ISME Communications, 2 (1) 6, 6. doi: 10.1038/s43705-021-00048-6 |
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2022 Journal Article Characterization of the juvenile koala gut microbiome across wild populationsBlyton, Michaela D. J., Soo, Rochelle M., Hugenholtz, Philip and Moore, Ben D. (2022). Characterization of the juvenile koala gut microbiome across wild populations. Environmental Microbiology, 24 (9), 4209-4219. doi: 10.1111/1462-2920.15884 |
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2022 Journal Article GTDB: an ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalized and complete genome-based taxonomyParks, Donovan H., Chuvochina, Maria, Rinke, Christian, Mussig, Aaron J., Chaumeil, Pierre-Alain and Hugenholtz, Philip (2022). GTDB: an ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalized and complete genome-based taxonomy. Nucleic Acids Research, 50 (D1), D785-D794. doi: 10.1093/nar/gkab776 |
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2022 Journal Article Maternal inheritance of the koala gut microbiome and its compositional and functional maturation during juvenile developmentBlyton, Michaela D.J, Soo, Rochelle M., Hugenholtz, Philip and Moore, Ben D. (2022). Maternal inheritance of the koala gut microbiome and its compositional and functional maturation during juvenile development. Environmental Microbiology, 24 (1), 475-493. doi: 10.1111/1462-2920.15858 |
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2021 Journal Article Microvolume DNA extraction methods for microscale amplicon and metagenomic studiesBramucci, Anna R., Focardi, Amaranta, Rinke, Christian, Hugenholtz, Philip, Tyson, Gene W., Seymour, Justin R. and Raina, Jean-Baptiste (2021). Microvolume DNA extraction methods for microscale amplicon and metagenomic studies. ISME Communications, 1 (1) 79. doi: 10.1038/s43705-021-00079-z |
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2021 Journal Article Successional dynamics and alternative stable states in a saline activated sludge microbial community over 9 yearsWang, Yulin, Ye, Jun, Ju, Feng, Liu, Lei, Boyd, Joel A., Deng, Yu, Parks, Donovan H., Jiang, Xiaotao, Yin, Xiaole, Woodcroft, Ben J., Tyson, Gene W., Hugenholtz, Philip, Polz, Martin F. and Zhang, Tong (2021). Successional dynamics and alternative stable states in a saline activated sludge microbial community over 9 years. Microbiome, 9 (1) 199, 199. doi: 10.1186/s40168-021-01151-5 |
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2021 Journal Article Kinetic and structural characterization of the first B3 metallo-β-lactamase with an active site glutamic acidWilson, Liam A., Knaven, Esmée G., Morris, Marc T., Monteiro Pedroso, Marcelo, Schofield, Christopher J., Brück, Thomas, Boden, Mikael, Waite, David W., Hugenholtz, Philip, Guddat, Luke and Schenk, Gerhard (2021). Kinetic and structural characterization of the first B3 metallo-β-lactamase with an active site glutamic acid. Antimicrobial Agents and Chemotherapy, 65 (10) e00936-21, e0093621. doi: 10.1128/aac.00936-21 |
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2021 Journal Article Effects of laboratory domestication on the rodent gut microbiomeBowerman, Kate L., Knowles, Sarah C. L., Bradley, Janette E., Baltrūnaitė, Laima, Lynch, Michael D. J., Jones, Kathryn M. and Hugenholtz, Philip (2021). Effects of laboratory domestication on the rodent gut microbiome. ISME Communications, 1 (1) 49, 49. doi: 10.1038/s43705-021-00053-9 |
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2021 Journal Article Persistence and resistance: survival mechanisms of Candidatus Dormibacterota from nutrient-poor Antarctic soilsMontgomery, Kate, Williams, Timothy J., Brettle, Merryn, Berengut, Jonathan F., Zhang, Eden, Zaugg, Julian, Hugenholtz, Philip and Ferrari, Belinda C. (2021). Persistence and resistance: survival mechanisms of Candidatus Dormibacterota from nutrient-poor Antarctic soils. Environmental Microbiology, 23 (8), 4276-4294. doi: 10.1111/1462-2920.15610 |
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2021 Journal Article Termite gas emissions select for hydrogenotrophic microbial communities in termite moundsChiri, Eleonora, Nauer, Philipp A., Lappan, Rachael, Jirapanjawat, Thanavit, Waite, David W., Handley, Kim M., Hugenholtz, Philip, Cook, Perran L.M., Arndt, Stefan K. and Greening, Chris (2021). Termite gas emissions select for hydrogenotrophic microbial communities in termite mounds. Proceedings of the National Academy of Sciences of the United States of America, 118 (30) e2102625118, 1-8. doi: 10.1073/pnas.2102625118 |
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2021 Journal Article Recoding of stop codons expands the metabolic potential of two novel Asgardarchaeota lineagesSun, Jiarui, Evans, Paul N., Gagen, Emma J., Woodcroft, Ben J., Hedlund, Brian P., Woyke, Tanja, Hugenholtz, Philip and Rinke, Christian (2021). Recoding of stop codons expands the metabolic potential of two novel Asgardarchaeota lineages. ISME Communications, 1 (1) 30, 1-14. doi: 10.1038/s43705-021-00032-0 |
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2021 Journal Article A standardized archaeal taxonomy for the Genome Taxonomy DatabaseRinke, Christian, Chuvochina, Maria, Mussig, Aaron J., Chaumeil, Pierre-Alain, Davín, Adrián A., Waite, David W., Whitman, William B., Parks, Donovan H. and Hugenholtz, Philip (2021). A standardized archaeal taxonomy for the Genome Taxonomy Database. Nature Microbiology, 6 (7), 946-959. doi: 10.1038/s41564-021-00918-8 |
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2021 Journal Article Metagenomic compendium of 189,680 DNA viruses from the human gut microbiomeNayfach, Stephen, Páez-Espino, David, Call, Lee, Low, Soo Jen, Sberro, Hila, Ivanova, Natalia N., Proal, Amy D., Fischbach, Michael A., Bhatt, Ami S., Hugenholtz, Philip and Kyrpides, Nikos C. (2021). Metagenomic compendium of 189,680 DNA viruses from the human gut microbiome. Nature Microbiology, 6 (7), 960-970. doi: 10.1038/s41564-021-00928-6 |
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2021 Journal Article Chemosynthetic and photosynthetic bacteria contribute differentially to primary production across a steep desert aridity gradientBay, Sean K., Waite, David W., Dong, Xiyang, Gillor, Osnat, Chown, Steven L., Hugenholtz, Philip and Greening, Chris (2021). Chemosynthetic and photosynthetic bacteria contribute differentially to primary production across a steep desert aridity gradient. The ISME Journal, 15 (11), 3339-3356. doi: 10.1038/s41396-021-01001-0 |
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2021 Journal Article A rooted phylogeny resolves early bacterial evolutionColeman, Gareth A., Davín, Adrián A., Mahendrarajah, Tara A., Szánthó, Lénárd L., Spang, Anja, Hugenholtz, Philip, Szöllősi, Gergely J. and Williams, Tom A. (2021). A rooted phylogeny resolves early bacterial evolution. Science, 372 (6542) eabe0511, eabe0511-+. doi: 10.1126/science.abe0511 |
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2021 Journal Article IFN-λ therapy prevents severe gastrointestinal graft-versus-host diseaseHenden, Andrea S., Koyama, Motoko, Robb, Renee J., Forero, Adriana, Kuns, Rachel D., Chang, Karshing, Ensbey, Kathleen S., Varelias, Antiopi, Kazakoff, Stephen H., Waddell, Nicole, Clouston, Andrew D., Giri, Rabina, Begun, Jakob, Blazar, Bruce R., Degli-Esposti, Mariapia A., Kotenko, Sergei V., Lane, Steven W., Bowerman, Kate L., Savan, Ram, Hugenholtz, Philip, Gartlan, Kate H. and Hill, Geoffrey R. (2021). IFN-λ therapy prevents severe gastrointestinal graft-versus-host disease. Blood, 138 (8), 722-737. doi: 10.1182/blood.2020006375 |
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2021 Journal Article Critical evaluation of faecal microbiome preservation using metagenomic analysisPribyl, Alena L., Parks, Donovan H., Angel, Nicola Z., Boyd, Joel A., Hasson, Alexander G., Fang, Liang, MacDonald, Samantha L., Wills, Blake A., Wood, David L. A., Krause, Lutz, Tyson, Gene W. and Hugenholtz, Philip (2021). Critical evaluation of faecal microbiome preservation using metagenomic analysis. ISME Communications, 1 (1) 14, 14. doi: 10.1038/s43705-021-00014-2 |
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2021 Journal Article Metabolic flexibility allows bacterial habitat generalists to become dominant in a frequently disturbed ecosystemChen, Ya-Jou, Leung, Pok Man, Wood, Jennifer L., Bay, Sean K., Hugenholtz, Philip, Kessler, Adam J., Shelley, Guy, Waite, David W., Franks, Ashley E., Cook, Perran L. M. and Greening, Chris (2021). Metabolic flexibility allows bacterial habitat generalists to become dominant in a frequently disturbed ecosystem. The ISME Journal, 15 (10), 2986-3004. doi: 10.1038/s41396-021-00988-w |
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2021 Journal Article Evaluation of the microba community profiler for taxonomic profiling of metagenomic datasets from the human gut microbiomeParks, Donovan H., Rigato, Fabio, Vera-Wolf, Patricia, Krause, Lutz, Hugenholtz, Philip, Tyson, Gene W. and Wood, David L. A. (2021). Evaluation of the microba community profiler for taxonomic profiling of metagenomic datasets from the human gut microbiome. Frontiers in Microbiology, 12 643682, 1-15. doi: 10.3389/fmicb.2021.643682 |
