{"response":{"status":"ok","message_type":"publication"},"id":3724,"citation":"Jiao et al., 2024, Microbiome","doi":"10.1186/s40168-024-01836-7","url":"https://api.seqco.de/v1/publications/3724.json","link_ext":"https://doi.org/10.1186/s40168-024-01836-7","title":"Cultivation of novel Atribacterota from oil well provides new insight into their diversity, ecology, and evolution in anoxic, carbon-rich environments","journal":"Microbiome","journal_loc":"12 (1)","journal_date":"2024-07-06","pub_type":"journal-article","abstract":"\u003cjats:title\u003eAbstract\u003c/jats:title\u003e\u003cjats:sec\u003e\n                \u003cjats:title\u003eBackground\u003c/jats:title\u003e\n                \u003cjats:p\u003eThe \u003cjats:italic\u003eAtribacterota\u003c/jats:italic\u003e are widely distributed in the subsurface biosphere. Recently, the first \u003cjats:italic\u003eAtribacterota\u003c/jats:italic\u003e isolate was described and the number of \u003cjats:italic\u003eAtribacterota\u003c/jats:italic\u003e genome sequences retrieved from environmental samples has increased significantly; however, their diversity, physiology, ecology, and evolution remain poorly understood.\u003c/jats:p\u003e\n              \u003c/jats:sec\u003e\u003cjats:sec\u003e\n                \u003cjats:title\u003eResults\u003c/jats:title\u003e\n                \u003cjats:p\u003eWe report the isolation of the second member of \u003cjats:italic\u003eAtribacterota\u003c/jats:italic\u003e, \u003cjats:italic\u003eThermatribacter velox\u003c/jats:italic\u003e gen. nov., sp. nov., within a new family \u003cjats:italic\u003eThermatribacteraceae\u003c/jats:italic\u003e fam. nov., and the short-term laboratory cultivation of a member of the JS1 lineage, \u003cjats:italic\u003ePhoenicimicrobium oleiphilum\u003c/jats:italic\u003e HX-OS.bin.34\u003cjats:sup\u003eTS\u003c/jats:sup\u003e, both from a terrestrial oil reservoir. Physiological and metatranscriptomics analyses showed that \u003cjats:italic\u003eThermatribacter velox\u003c/jats:italic\u003e B11\u003cjats:sup\u003eT\u003c/jats:sup\u003e and \u003cjats:italic\u003ePhoenicimicrobium oleiphilum\u003c/jats:italic\u003e HX-OS.bin.34\u003cjats:sup\u003eTS\u003c/jats:sup\u003e ferment sugars and \u003cjats:italic\u003en\u003c/jats:italic\u003e-alkanes, respectively, producing H\u003cjats:sub\u003e2\u003c/jats:sub\u003e, CO\u003cjats:sub\u003e2,\u003c/jats:sub\u003e and acetate as common products. Comparative genomics showed that all members of the \u003cjats:italic\u003eAtribacterota\u003c/jats:italic\u003e lack a complete Wood-Ljungdahl Pathway (WLP), but that the Reductive Glycine Pathway (RGP) is widespread, indicating that the RGP, rather than WLP, is a central hub in \u003cjats:italic\u003eAtribacterota\u003c/jats:italic\u003e metabolism. Ancestral character state reconstructions and phylogenetic analyses showed that key genes encoding the RGP (\u003cjats:italic\u003efdhA\u003c/jats:italic\u003e, \u003cjats:italic\u003efhs\u003c/jats:italic\u003e, \u003cjats:italic\u003efolD\u003c/jats:italic\u003e, \u003cjats:italic\u003eglyA\u003c/jats:italic\u003e, \u003cjats:italic\u003egcvT\u003c/jats:italic\u003e, \u003cjats:italic\u003egcvPAB\u003c/jats:italic\u003e, \u003cjats:italic\u003epdhD\u003c/jats:italic\u003e) and other central functions were gained independently in the two classes, \u003cjats:italic\u003eAtribacteria\u003c/jats:italic\u003e (OP9) and \u003cjats:italic\u003ePhoenicimicrobiia\u003c/jats:italic\u003e (JS1), after which they were inherited vertically; these genes included fumarate-adding enzymes (\u003cjats:italic\u003efaeA\u003c/jats:italic\u003e; \u003cjats:italic\u003ePhoenicimicrobiia\u003c/jats:italic\u003e only), the CODH/ACS complex (\u003cjats:italic\u003eacsABCDE\u003c/jats:italic\u003e), and diverse hydrogenases (NiFe group 3b, 4b and FeFe group A3, C). Finally, we present genome-resolved community metabolic models showing the central roles of \u003cjats:italic\u003eAtribacteria\u003c/jats:italic\u003e (OP9) and \u003cjats:italic\u003ePhoenicimicrobiia\u003c/jats:italic\u003e (JS1) in acetate- and hydrocarbon-rich environments.\u003c/jats:p\u003e\n              \u003c/jats:sec\u003e\u003cjats:sec\u003e\n                \u003cjats:title\u003eConclusion\u003c/jats:title\u003e\n                \u003cjats:p\u003eOur findings expand the knowledge of the diversity, physiology, ecology, and evolution of the phylum \u003cjats:italic\u003eAtribacterota\u003c/jats:italic\u003e. This study is a starting point for promoting more incisive studies of their syntrophic biology and may guide the rational design of strategies to cultivate them in the laboratory.\u003c/jats:p\u003e\n                \n              \u003c/jats:sec\u003e","long_citation_html":"Jiao et al. (2024). Cultivation of novel Atribacterota from oil well provides new insight into their diversity, ecology, and evolution in anoxic, carbon-rich environments. \n\u003ci\u003eMicrobiome\u003c/i\u003e. \u003ca href=\"https://doi.org/10.1186/s40168-024-01836-7\" target=\"_blank\"\u003eDOI:10.1186/s40168-024-01836-7\u003c/a\u003e\n","created_at":"2024-07-19T10:31:18.226Z","updated_at":"2025-11-06T14:41:07.716Z","authors":[{"id":7321,"given":"Jian-Yu","family":"Jiao","created_at":"2020-03-29T06:30:52.866Z","updated_at":"2020-03-29T06:30:52.866Z","url":"https://api.seqco.de/v1/authors/7321.json"},{"id":14572,"given":"Shi-Chun","family":"Ma","created_at":"2024-07-19T10:31:18.255Z","updated_at":"2024-07-19T10:31:18.255Z","url":"https://api.seqco.de/v1/authors/14572.json"},{"id":10194,"given":"Nimaichand","family":"Salam","created_at":"2022-04-04T08:10:05.901Z","updated_at":"2022-04-04T08:10:05.901Z","url":"https://api.seqco.de/v1/authors/10194.json"},{"id":12092,"given":"Zhuo","family":"Zhou","created_at":"2023-07-24T19:43:25.749Z","updated_at":"2023-07-24T19:43:25.749Z","url":"https://api.seqco.de/v1/authors/12092.json"},{"id":6404,"given":"Zheng-Han","family":"Lian","created_at":"2019-04-15T19:30:27.423Z","updated_at":"2019-04-15T19:30:27.423Z","url":"https://api.seqco.de/v1/authors/6404.json"},{"id":14573,"given":"Li","family":"Fu","created_at":"2024-07-19T10:31:18.288Z","updated_at":"2024-07-19T10:31:18.288Z","url":"https://api.seqco.de/v1/authors/14573.json"},{"id":14574,"given":"Ying","family":"Chen","created_at":"2024-07-19T10:31:18.299Z","updated_at":"2024-07-19T10:31:18.299Z","url":"https://api.seqco.de/v1/authors/14574.json"},{"id":14575,"given":"Cheng-Hui","family":"Peng","created_at":"2024-07-19T10:31:18.310Z","updated_at":"2024-07-19T10:31:18.310Z","url":"https://api.seqco.de/v1/authors/14575.json"},{"id":14576,"given":"Yu-Ting","family":"OuYang","created_at":"2024-07-19T10:31:18.321Z","updated_at":"2024-07-19T10:31:18.321Z","url":"https://api.seqco.de/v1/authors/14576.json"},{"id":13479,"given":"Hui","family":"Fan","created_at":"2024-01-24T20:08:35.988Z","updated_at":"2024-01-24T20:08:35.988Z","url":"https://api.seqco.de/v1/authors/13479.json"},{"id":11158,"given":"Ling","family":"Li","created_at":"2022-12-24T23:01:00.453Z","updated_at":"2022-12-24T23:01:00.453Z","url":"https://api.seqco.de/v1/authors/11158.json"},{"id":14577,"given":"Yue","family":"Yi","created_at":"2024-07-19T10:31:18.347Z","updated_at":"2024-07-19T10:31:18.347Z","url":"https://api.seqco.de/v1/authors/14577.json"},{"id":14578,"given":"Jing-Yi","family":"Zhang","created_at":"2024-07-19T10:31:18.357Z","updated_at":"2024-07-19T10:31:18.357Z","url":"https://api.seqco.de/v1/authors/14578.json"},{"id":14579,"given":"Jing-Yuan","family":"Wang","created_at":"2024-07-19T10:31:18.366Z","updated_at":"2024-07-19T10:31:18.366Z","url":"https://api.seqco.de/v1/authors/14579.json"},{"id":13446,"given":"Lan","family":"Liu","created_at":"2024-01-16T18:04:31.536Z","updated_at":"2024-01-16T18:04:31.536Z","url":"https://api.seqco.de/v1/authors/13446.json"},{"id":14580,"given":"Lei","family":"Gao","created_at":"2024-07-19T10:31:18.384Z","updated_at":"2024-07-19T10:31:18.384Z","url":"https://api.seqco.de/v1/authors/14580.json"},{"id":4832,"given":"Aharon","family":"Oren","created_at":"2019-04-15T19:27:56.944Z","updated_at":"2019-04-15T19:27:56.944Z","url":"https://api.seqco.de/v1/authors/4832.json"},{"id":3528,"given":"Tanja","family":"Woyke","created_at":"2019-04-15T18:48:02.299Z","updated_at":"2019-04-15T18:48:02.299Z","url":"https://api.seqco.de/v1/authors/3528.json"},{"id":9965,"given":"Jeremy 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