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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 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 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 |
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2022 Journal Article Atmospheric chemosynthesis is phylogenetically and geographically widespread and contributes significantly to carbon fixation throughout cold desertsRay, Angelique E., Zaugg, Julian, Benaud, Nicole, Chelliah, Devan S., Bay, Sean, Wong, Hon Lun, Leung, Pok Man, Ji, Mukan, Terauds, Aleks, Montgomery, Kate, Greening, Chris, Cowan, Don A., Kong, Weidong, Williams, Timothy J., Hugenholtz, Philip and Ferrari, Belinda C. (2022). Atmospheric chemosynthesis is phylogenetically and geographically widespread and contributes significantly to carbon fixation throughout cold deserts. The ISME Journal, 16 (11), 1-14. doi: 10.1038/s41396-022-01298-5 |
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2022 Journal Article Chemotaxis may assist marine heterotrophic bacterial diazotrophs to find microzones suitable for N2 fixation in the pelagic oceanHallstrøm, Søren, Raina, Jean-Baptiste, Ostrowski, Martin, Parks, Donovan H., Tyson, Gene W., Hugenholtz, Philip, Stocker, Roman, Seymour, Justin R. and Riemann, Lasse (2022). Chemotaxis may assist marine heterotrophic bacterial diazotrophs to find microzones suitable for N2 fixation in the pelagic ocean. The ISME Journal, 16 (11), 2525-2534. doi: 10.1038/s41396-022-01299-4 |
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2022 Journal Article A genome and gene catalog of glacier microbiomesLiu, Yongqin, Ji, Mukan, Yu, Tao, Zaugg, Julian, Anesio, Alexandre M., Zhang, Zhihao, Hu, Songnian, Hugenholtz, Philip, Liu, Keshao, Liu, Pengfei, Chen, Yuying, Luo, Yingfeng and Yao, Tandong (2022). A genome and gene catalog of glacier microbiomes. Nature Biotechnology, 40 (9), 1341-1348. doi: 10.1038/s41587-022-01367-2 |
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2022 Journal Article Skin cancer-associated S. aureus strains can induce DNA damage in human keratinocytes by downregulating DNA repair and promoting oxidative stressKrueger, Annika, Mohamed, Ahmed, Kolka, Cathryn M., Stoll, Thomas, Zaugg, Julian, Linedale, Richard, Morrison, Mark, Soyer, H. Peter, Hugenholtz, Philip, Frazer, Ian H. and Hill, Michelle M. (2022). Skin cancer-associated S. aureus strains can induce DNA damage in human keratinocytes by downregulating DNA repair and promoting oxidative stress. Cancers, 14 (9) 2143, 2143. doi: 10.3390/cancers14092143 |
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2022 Journal Article Chemotaxis shapes the microscale organization of the ocean’s microbiomeRaina, Jean-Baptiste, Lambert, Bennett S., Parks, Donovan H., Rinke, Christian, Siboni, Nachshon, Bramucci, Anna, Ostrowski, Martin, Signal, Brandon, Lutz, Adrian, Mendis, Himasha, Rubino, Francesco, Fernandez, Vicente I., Stocker, Roman, Hugenholtz, Philip, Tyson, Gene W. and Seymour, Justin R. (2022). Chemotaxis shapes the microscale organization of the ocean’s microbiome. Nature, 605 (7908), 132-138. doi: 10.1038/s41586-022-04614-3 |
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2022 Journal Article Changes in the skin microbiome associated with squamous cell carcinoma in transplant recipientsKrueger, Annika, Zaugg, Julian, Lachner, Nancy, Bialasiewicz, Seweryn, Lin, Lynlee L., Gabizon, Sharon, Sobarun, Priyamvada, Morrison, Mark, Soyer, H. Peter, Hugenholtz, Philip and Frazer, Ian H. (2022). Changes in the skin microbiome associated with squamous cell carcinoma in transplant recipients. ISME Communications, 2 (1) 13, 13. doi: 10.1038/s43705-022-00095-7 |
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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 |
