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2023 Journal Article Draft genome sequence of two “Candidatus Intestinicoccus colisanans” strains isolated from faeces of healthy humansZhou, Joyce, Boyd, Joel A., Nyeverecz, Bozica, Vivian, Charlotte, Angel, Nicola, Wood, David L. A., Hugenholtz, Philip, Tyson, Gene W., Krause, Lutz and Ó Cuív, Páraic (2023). Draft genome sequence of two “Candidatus Intestinicoccus colisanans” strains isolated from faeces of healthy humans. BMC Research Notes, 16 (1) 174, 1-4. doi: 10.1186/s13104-023-06447-3 |
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2023 Journal Article Corrigendum: 'A comparative genome analysis of the Bacillota (Firmicutes) class Dehalobacteriia'Song, Young C., Holland, Sophie I., Lee, Matthew, Chen, Gao, Zaugg, Julian, Löffler, Frank E., Manefield, Michael J., Hugenholtz, Philip and Kappler, Ulrike (2023). Corrigendum: 'A comparative genome analysis of the Bacillota (Firmicutes) class Dehalobacteriia'. Microbial Genomics, 9 (8) 001092. doi: 10.1099/mgen.0.001092 |
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2023 Journal Article Greengenes2 unifies microbial data in a single reference treeMcDonald, Daniel, Jiang, Yueyu, Balaban, Metin, Cantrell, Kalen, Zhu, Qiyun, Gonzalez, Antonio, Morton, James T., Nicolaou, Giorgia, Parks, Donovan H., Karst, Søren M., Albertsen, Mads, Hugenholtz, Philip, DeSantis, Todd, Song, Se Jin, Bartko, Andrew, Havulinna, Aki S., Jousilahti, Pekka, Cheng, Susan, Inouye, Michael, Niiranen, Teemu, Jain, Mohit, Salomaa, Veikko, Lahti, Leo, Mirarab, Siavash and Knight, Rob (2023). Greengenes2 unifies microbial data in a single reference tree. Nature Biotechnology, 42 (5), 715-718. doi: 10.1038/s41587-023-01845-1 |
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2023 Journal Article Proposal of names for 329 higher rank taxa defined in the Genome Taxonomy Database under two prokaryotic codesChuvochina, Maria, Mussig, Aaron J., Chaumeil, Pierre-Alain, Skarshewski, Adam, Rinke, Christian, Parks, Donovan H. and Hugenholtz, Philip (2023). Proposal of names for 329 higher rank taxa defined in the Genome Taxonomy Database under two prokaryotic codes. FEMS Microbiology Letters, 370 fnad071, 1-33. doi: 10.1093/femsle/fnad071 |
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2023 Journal Article Parameter estimation and species tree rooting using ALE and GeneRaxWilliams, Tom A., Davín, Adrián A., Morel, Benoit, Szánthó, Lénárd L., Spang, Anja, Stamatakis, Alexandros, Hugenholtz, Philip and Szöllősi, Gergely J. (2023). Parameter estimation and species tree rooting using ALE and GeneRax. Genome Biology and Evolution, 15 (7) evad134. doi: 10.1093/gbe/evad134 |
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2023 Journal Article Structure, function, and evolution of metallo-β-lactamases from the B3 subgroup—emerging targets to combat antibiotic resistanceKrco, Stefan, Davis, Samuel J., Joshi, Pallav, Wilson, Liam A., Monteiro Pedroso, Marcelo, Douw, Andrew, Schofield, Christopher J., Hugenholtz, Philip, Schenk, Gerhard and Morris, Marc T. (2023). Structure, function, and evolution of metallo-β-lactamases from the B3 subgroup—emerging targets to combat antibiotic resistance. Frontiers in Chemistry, 11 1196073, 1196073. doi: 10.3389/fchem.2023.1196073 |
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2023 Journal Article A comparative genome analysis of the Bacillota (Firmicutes) class DehalobacteriiaSong, Young C., Holland, Sophie I., Lee, Matthew, Chen, Gao, Löffler, Frank E., Manefield, Michael J., Hugenholtz, Philip and Kappler, Ulrike (2023). A comparative genome analysis of the Bacillota (Firmicutes) class Dehalobacteriia. Microbial Genomics, 9 (6) 001039, 1-15. doi: 10.1099/mgen.0.001039 |
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2023 Journal Article Isolation and characterisation of novel Methanocorpusculum species indicates the genus is ancestrally host-associatedVolmer, James G., Soo, Rochelle M., Evans, Paul N., Hoedt, Emily C., Astorga Alsina, Ana L., Woodcroft, Benjamin J., Tyson, Gene W., Hugenholtz, Philip and Morrison, Mark (2023). Isolation and characterisation of novel Methanocorpusculum species indicates the genus is ancestrally host-associated. BMC Biology, 21 (1) 59, 1-17. doi: 10.1186/s12915-023-01524-2 |
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2023 Journal Article The koala gut microbiome is largely unaffected by host translocation but rather influences host dietBlyton, Michaela D. J., Pascoe, Jack, Hynes, Emily, Soo, Rochelle M., Hugenholtz, Philip and Moore, Ben D. (2023). The koala gut microbiome is largely unaffected by host translocation but rather influences host diet. Frontiers in Microbiology, 14 1085090, 1-13. doi: 10.3389/fmicb.2023.1085090 |
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2023 Conference Publication Role of dietary lipids in chronic obstructive pulmonary diseaseRehman, S., Budden, K., Quaranta, A., Fuchs, D., Bowerman, K., Vaughan, A., Shukla, S., Brown, A., Alemao, C., Balachandra, L., Gomez, H., Kumar, , Idrees, S., Faiz, A., Hugenholtz, P., Wark, P., Horvat, J., Wood, L., Wheelock, C. and Hansbro, P. (2023). Role of dietary lipids in chronic obstructive pulmonary disease. HOBOKEN: WILEY. |
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2023 Journal Article Targeting Staphylococcus aureus dominated skin dysbiosis in actinic keratosis to prevent the onset of cutaneous squamous cell carcinoma: Outlook for future therapies?Bromfield, Jacoba Isobella, Hugenholtz, Philip, Frazer, Ian Hector, Khosrotehrani, Kiarash and Chandra, Janin (2023). Targeting Staphylococcus aureus dominated skin dysbiosis in actinic keratosis to prevent the onset of cutaneous squamous cell carcinoma: Outlook for future therapies?. Frontiers in Oncology, 13 1091379, 1091379. doi: 10.3389/fonc.2023.1091379 |
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2023 Journal Article Toward a universal unit for quantification of antibiotic resistance genes in environmental samplesYin, Xiaole, Chen, Xi, Jiang, Xiao-Tao, Yang, Ying, Li, Bing, Shum, Marcus Ho-Hin, Lam, Tommy T. Y., Leung, Gabriel M., Rose, Joan, Sanchez-Cid, Concepcion, Vogel, Timothy M., Walsh, Fiona, Berendonk, Thomas U., Midega, Janet, Uchea, Chibuzor, Frigon, Dominic, Wright, Gerard D., Bezuidenhout, Carlos, Picão, Renata C., Ahammad, Shaikh Z., Nielsen, Per Halkjær, Hugenholtz, Philip, Ashbolt, Nicholas J., Corno, Gianluca, Fatta-Kassinos, Despo, Bürgmann, Helmut, Schmitt, Heike, Cha, Chang-Jun, Pruden, Amy ... Zhang, Tong (2023). Toward a universal unit for quantification of antibiotic resistance genes in environmental samples. Environmental Science and Technology, 57 (26), 9713-9721. doi: 10.1021/acs.est.3c00159 |
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2023 Journal Article Author Correction: Greengenes2 unifies microbial data in a single reference tree (Nature Biotechnology, (2023), 10.1038/s41587-023-01845-1)McDonald, Daniel, Jiang, Yueyu, Balaban, Metin, Cantrell, Kalen, Zhu, Qiyun, Gonzalez, Antonio, Morton, James T., Nicolaou, Giorgia, Parks, Donovan H., Karst, Søren M., Albertsen, Mads, Hugenholtz, Philip, DeSantis, Todd, Song, Se Jin, Bartko, Andrew, Havulinna, Aki S., Jousilahti, Pekka, Cheng, Susan, Inouye, Michael, Niiranen, Teemu, Jain, Mohit, Salomaa, Veikko, Lahti, Leo, Mirarab, Siavash and Knight, Rob (2023). Author Correction: Greengenes2 unifies microbial data in a single reference tree (Nature Biotechnology, (2023), 10.1038/s41587-023-01845-1). Nature Biotechnology, 42 (5), 813-813. doi: 10.1038/s41587-023-02026-w |
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2022 Journal Article Probiotic Bifidobacterium longum subsp. longum protects against cigarette smoke-induced inflammation in miceBudden, Kurtis F., Gellatly, Shaan L., Vaughan, Annalicia, Amorim, Nadia, Horvat, Jay C., Hansbro, Nicole G., Wood, David L. A., Hugenholtz, Philip, Dennis, Paul G., Wark, Peter A. B. and Hansbro, Philip M. (2022). Probiotic Bifidobacterium longum subsp. longum protects against cigarette smoke-induced inflammation in mice. International Journal of Molecular Sciences, 24 (1) 252, 1-12. doi: 10.3390/ijms24010252 |
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2022 Journal Article GTDB-Tk v2: memory friendly classification with the genome taxonomy databaseChaumeil, Pierre-Alain, Mussig, Aaron J., Hugenholtz, Philip and Parks, Donovan H. (2022). GTDB-Tk v2: memory friendly classification with the genome taxonomy database. Bioinformatics, 38 (23), 5315-5316. doi: 10.1093/bioinformatics/btac672 |
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2022 Journal Article SeqCode: a nomenclatural code for prokaryotes described from sequence dataHedlund, Brian P., Chuvochina, Maria, Hugenholtz, Philip, Konstantinidis, Konstantinos T., Murray, Alison E., Palmer, Marike, Parks, Donovan H., Probst, Alexander J., Reysenbach, Anna-Louise, Rodriguez-R, Luis M., Rossello-Mora, Ramon, Sutcliffe, Iain C., Venter, Stephanus N. and Whitman, William B. (2022). SeqCode: a nomenclatural code for prokaryotes described from sequence data. Nature Microbiology, 7 (10), 1702-1708. doi: 10.1038/s41564-022-01214-9 |
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2022 Book Chapter Relative time inference using lateral gene transfersDavín, Adrián A., Schrempf, Dominik, Williams, Tom A., Hugenholtz, Philip and Szöllősi, Gergely J. (2022). Relative time inference using lateral gene transfers. Environmental microbial evolution: methods and protocols. (pp. 75-94) edited by Haiwei Luo. New York, United States: Humana Press. doi: 10.1007/978-1-0716-2691-7_4 |
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2022 Conference Publication Association between dietary fibre, microbial metabolites and airway obstruction in COPD patients and murine modelsBudden, K., Rehman, S. F., Shukla, S., Bowerman, K., Donovan, C., Gomez, H., Alemao, C., Wood, L., Dennis, P., Hugenholtz, P., Wark, P. and Hansbro, P. (2022). Association between dietary fibre, microbial metabolites and airway obstruction in COPD patients and murine models. ERS International Congress 2022, Barcelona, Spain, 4-6 September 2022. Sheffield, United Kingdom: European Respiratory Society. doi: 10.1183/13993003.congress-2022.3289 |
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2022 Journal Article Development of the SeqCode: A proposed nomenclatural code for uncultivated prokaryotes with DNA sequences as typeWhitman, William B., Chuvochina, Maria, Hedlund, Brian P., Hugenholtz, Philip, Konstantinidis, Konstantinos T., Murray, Alison E., Palmer, Marike, Parks, Donovan H., Probst, Alexander J., Reysenbach, Anna-Louise, Rodriguez-R, Luis M., Rossello-Mora, Ramon, Sutcliffe, Iain and Venter, Stephanus N. (2022). Development of the SeqCode: A proposed nomenclatural code for uncultivated prokaryotes with DNA sequences as type. Systematic and Applied Microbiology, 45 (5) 126305, 1-8. doi: 10.1016/j.syapm.2022.126305 |
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2022 Journal Article Persistence and resistance: survival mechanisms of Candidatus Dormibacterota from nutrient‐poor Antarctic soilsMontgomery, Kate, Williams, Timothy J., Brettle, Merryn, Berengut, Jonathan F., Ray, Angelique E. , Zhang, Eden, Zaugg, Julian, Hugenholtz, Philip and Ferrari, Belinda C. (2022). Persistence and resistance: survival mechanisms of Candidatus Dormibacterota from nutrient‐poor Antarctic soils. Environmental Microbiology, 24 (9), 4491-4491. doi: 10.1111/1462-2920.16191 |
