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2024 Journal Article Phage Anti-Pycsar Proteins Efficiently Degrade β-Lactam AntibioticsJoshi, Pallav, Krco, Stefan, Davis, Samuel J., Asser, Lachlan, Brück, Thomas, Soo, Rochelle M., Bodén, Mikael, Hugenholtz, Philip, Wilson, Liam A., Schenk, Gerhard and Morris, Marc T. (2024). Phage Anti-Pycsar Proteins Efficiently Degrade β-Lactam Antibiotics. Applied Biosciences, 3 (4), 438-449. doi: 10.3390/applbiosci3040028 |
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2024 Journal Article Microbial Solutions for Climate ChangePeixoto, R., Voolstra, C. R., Stein, L. Y., Hugenholtz, P., Salles, Falcao J., Amin, S. A., Häggblom, M., Gregory, A., Makhalanyane, T. P., Wang, F., Agbodjato, N. A., Wang, Y., Jiao, N., Lennon, J. T., Ventosa, A., Bavoil, P. M., Miller, V., Gilbert, J. A. and Zambrano, María Mercedes (2024). Microbial Solutions for Climate Change. Revista de la Academia Colombiana de Ciencias Exactas, Fisicas y Naturales, 48 (189), 977-981. doi: 10.18257/raccefyn.3134 |
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2024 Journal Article Phylogenetic reconciliation: making the most of genomes to understand microbial ecology and evolutionWilliams, Tom A., Davin, Adrian A., Szánthó, Lénárd L., Stamatakis, Alexandros, Wahl, Noah A., Woodcroft, Ben J., Soo, Rochelle M., Eme, Laura, Sheridan, Paul O., Gubry-Rangin, Cecile, Spang, Anja, Hugenholtz, Philip and Szöllősi, Gergely J. (2024). Phylogenetic reconciliation: making the most of genomes to understand microbial ecology and evolution. The ISME Journal, 18 (1) wrae129. doi: 10.1093/ismejo/wrae129 |
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2024 Journal Article Putative genome contamination has minimal impact on the GTDB taxonomyMussig, Aaron J., Chaumeil, Pierre-Alain, Chuvochina, Maria, Rinke, Christian, Parks, Donovan H. and Hugenholtz, Philip (2024). Putative genome contamination has minimal impact on the GTDB taxonomy. Microbial Genomics, 10 (5) 001256. doi: 10.1099/mgen.0.001256 |
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2024 Journal Article Advancements in prokaryotic systematics and the role of Bergey's International Society for Microbial Systematics (BISMiS) in addressing challenges in the meta-data eraYu Jiao, Jian-, Abdugheni, Rashidin, Zhang, Dao-Feng, Ahmed, Iftikhar, Ali, Mukhtiar, Chuvochina, Maria, Dedysh, Svetlana N., Dong, Xiuzhu, Göker, Markus, Hedlund, Brian P., Hugenholtz, Philip, Jangid, Kamlesh, Liu, Shuang-Jiang, Moore, Edward R. B., Rao, Manik Prabhu Narsing, Oren, Aharon, Rossello-Mora, Ramon, Rekadwad, Bhagwan Narayan, Salam, Nimaichand, Shu, Wensheng, Sutcliffe, Iain C., Teo, Wee Fei Aaron, Trujillo, Martha E., Venter, Stephanus N., Whitman, William B., Zhao, Guoping and Li, Wen-Jun (2024). Advancements in prokaryotic systematics and the role of Bergey's International Society for Microbial Systematics (BISMiS) in addressing challenges in the meta-data era. National Science Review, 11 (7) nwae168. doi: 10.1093/nsr/nwae168 |
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2024 Journal Article Characterization of the skin microbiome in normal and cutaneous squamous cell carcinoma affected cats and dogsBromfield, Jacoba I., Zaugg, Julian, Straw, Rodney C., Cathie, Julia, Krueger, Annika, Sinha, Debottam, Chandra, Janin, Hugenholtz, Philip and Frazer, Ian H. (2024). Characterization of the skin microbiome in normal and cutaneous squamous cell carcinoma affected cats and dogs. mSphere, 9 (4) e0055523, e0055523. doi: 10.1128/msphere.00555-23 |
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2024 Journal Article Novel spore-forming species exhibiting intrinsic resistance to third- and fourth-generation cephalosporins and description of Tigheibacillus jepli gen. nov., sp. novMiliotis, Georgios, Sengupta, Pratyay, Hameed, Asif, Chuvochina, Maria, McDonagh, Francesca, Simpson, Anna C., Parker, Ceth W., Singh, Nitin K., Rekha, Punchappady D., Morris, Dearbháile, Raman, Karthik, Kyrpides, Nikos C., Hugenholtz, Philip and Venkateswaran, Kasthuri (2024). Novel spore-forming species exhibiting intrinsic resistance to third- and fourth-generation cephalosporins and description of Tigheibacillus jepli gen. nov., sp. nov. mBio, 15 (4) e0018124, e0018124. doi: 10.1128/mbio.00181-24 |
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2024 Journal Article Faecal microbial transfer and complex carbohydrates mediate protection against COPDBudden, Kurtis F, Shukla, Shakti D, Bowerman, Kate L, Vaughan, Annalicia, Gellatly, Shaan L, Wood, David L A, Lachner, Nancy, Idrees, Sobia, Rehman, Saima Firdous, Faiz, Alen, Patel, Vyoma K, Donovan, Chantal, Alemao, Charlotte A, Shen, Sj, Amorim, Nadia, Majumder, Rajib, Vanka, Kanth S, Mason, Jazz, Haw, Tatt Jhong, Tillet, Bree, Fricker, Michael, Keely, Simon, Hansbro, Nicole, Belz, Gabrielle T, Horvat, Jay, Ashhurst, Thomas, van Vreden, Caryn, McGuire, Helen, Fazekas de St Groth, Barbara ... Hansbro, Philip M (2024). Faecal microbial transfer and complex carbohydrates mediate protection against COPD. Gut, 73 (5), 751-769. doi: 10.1136/gutjnl-2023-330521 |
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2024 Journal Article Anaerobic gut fungal communities in marsupial hostsJones, Adrienne L., Pratt, Carrie J., Meili, Casey H., Soo, Rochelle M., Hugenholtz, Philip, Elshahed, Mostafa S. and Youssef, Noha H. (2024). Anaerobic gut fungal communities in marsupial hosts. Mbio, 15 (2) e0337023. doi: 10.1128/mbio.03370-23 |
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2024 Journal Article Multiple independent losses of sporulation and peptidoglycan in the Mycoplasmatales and related orders of the class BacilliField, Christian J., Bowerman, Kate L. and Hugenholtz, Philip (2024). Multiple independent losses of sporulation and peptidoglycan in the Mycoplasmatales and related orders of the class Bacilli. Microbial Genomics, 10 (1) 001176. doi: 10.1099/mgen.0.001176 |
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2024 Journal Article Identification of the mechanism for dehalorespiration of monofluoroacetate in the phylum SynergistotaLeong, Lex E. X., Denman, Stuart E., Kang, Seungha, Mondot, Stanislas, Hugenholtz, Philip and McSweeney, Chris S. (2024). Identification of the mechanism for dehalorespiration of monofluoroacetate in the phylum Synergistota. Animal Bioscience, 37 (2), 396-403. doi: 10.5713/ab.23.0351 |
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2024 Journal Article Microbial solutions must be deployed against climate catastrophePeixoto, Raquel, Voolstra, Christian R., Stein, Lisa Y., Hugenholtz, Philip, Salles, Joana Falcao, Amin, Shady A., Häggblom, Max, Gregory, Ann, Makhalanyane, Thulani P., Wang, Fengping, Agbodjato, Nadège Adoukè, Wang, Yinzhao, Jiao, Nianzhi, Lennon, Jay T., Ventosa, Antonio, Bavoil, Patrik M., Miller, Virginia and Gilbert, Jack A. (2024). Microbial solutions must be deployed against climate catastrophe. Sustainable Microbiology, 1 (1) qvae029, 1-3. doi: 10.1093/sumbio/qvae029 |
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2023 Journal Article A long-awaited taxogenomic investigation of the family Halomonadaceaede la Haba, Rafael R., Arahal, David R., Sánchez-Porro, Cristina, Chuvochina, Maria, Wittouck, Stijn, Hugenholtz, Philip and Ventosa, Antonio (2023). A long-awaited taxogenomic investigation of the family Halomonadaceae. Frontiers in Microbiology, 14 1293707, 1-28. doi: 10.3389/fmicb.2023.1293707 |
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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 |
