{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,11,4]],"date-time":"2026-11-04T07:06:11Z","timestamp":1793775971864,"version":"4.6.1"},"reference-count":49,"publisher":"Springer Science and Business Media LLC","issue":"6","license":[{"start":{"date-parts":[[2023,4,8]],"date-time":"2023-04-08T00:00:00Z","timestamp":1680912000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"},{"start":{"date-parts":[[2023,4,8]],"date-time":"2023-04-08T00:00:00Z","timestamp":1680912000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"}],"funder":[{"DOI":"10.13039\/501100001665","name":"Agence Nationale de la Recherche","doi-asserted-by":"crossref","award":["10-IAHU-03"],"award-info":[{"award-number":["10-IAHU-03"]}],"id":[{"id":"10.13039\/501100001665","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100001665","name":"Agence Nationale de la Recherche","doi-asserted-by":"crossref","award":["10-IAHU-03"],"award-info":[{"award-number":["10-IAHU-03"]}],"id":[{"id":"10.13039\/501100001665","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100001665","name":"Agence Nationale de la Recherche","doi-asserted-by":"crossref","award":["10-IAHU-03"],"award-info":[{"award-number":["10-IAHU-03"]}],"id":[{"id":"10.13039\/501100001665","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100001665","name":"Agence Nationale de la Recherche","doi-asserted-by":"crossref","award":["10-IAHU-03"],"award-info":[{"award-number":["10-IAHU-03"]}],"id":[{"id":"10.13039\/501100001665","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100001665","name":"Agence Nationale de la Recherche","doi-asserted-by":"crossref","award":["10-IAHU-03"],"award-info":[{"award-number":["10-IAHU-03"]}],"id":[{"id":"10.13039\/501100001665","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100001665","name":"Agence Nationale de la Recherche","doi-asserted-by":"crossref","award":["10-IAHU-03"],"award-info":[{"award-number":["10-IAHU-03"]}],"id":[{"id":"10.13039\/501100001665","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100001665","name":"Agence Nationale de la Recherche","doi-asserted-by":"crossref","award":["10-IAHU-03"],"award-info":[{"award-number":["10-IAHU-03"]}],"id":[{"id":"10.13039\/501100001665","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100001665","name":"Agence Nationale de la Recherche","doi-asserted-by":"crossref","award":["10-IAHU-03"],"award-info":[{"award-number":["10-IAHU-03"]}],"id":[{"id":"10.13039\/501100001665","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100001665","name":"Agence Nationale de la Recherche","doi-asserted-by":"crossref","award":["10-IAHU-03"],"award-info":[{"award-number":["10-IAHU-03"]}],"id":[{"id":"10.13039\/501100001665","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100001665","name":"Agence Nationale de la Recherche","doi-asserted-by":"crossref","award":["10-IAHU-03"],"award-info":[{"award-number":["10-IAHU-03"]}],"id":[{"id":"10.13039\/501100001665","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100001665","name":"Agence Nationale de la Recherche","doi-asserted-by":"crossref","award":["10-IAHU-03"],"award-info":[{"award-number":["10-IAHU-03"]}],"id":[{"id":"10.13039\/501100001665","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100001665","name":"Agence Nationale de la Recherche","doi-asserted-by":"crossref","award":["10-IAHU-03"],"award-info":[{"award-number":["10-IAHU-03"]}],"id":[{"id":"10.13039\/501100001665","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Antonie van Leeuwenhoek"],"published-print":{"date-parts":[[2023,6]]},"DOI":"10.1007\/s10482-023-01824-1","type":"journal-article","created":{"date-parts":[[2023,4,8]],"date-time":"2023-04-08T15:02:26Z","timestamp":1680966146000},"page":"541-555","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":5,"title":["Description of Agathobaculum massiliense sp. nov., a new bacterial species prevalent in the human gut and predicted to produce indole and tryptophan based on genomic analysis"],"prefix":"10.1007","volume":"116","author":[{"given":"Reham","family":"Magdy Wasfy","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Malak","family":"Zoaiter","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Melhem","family":"Bilen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maryam","family":"Tidjani Alou","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Cheikh Ibrahima","family":"Lo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sara","family":"Bellali","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Aurelia","family":"Caputo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"St\u00e9phane","family":"Alibar","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Claudia","family":"Andrieu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Didier","family":"Raoult","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pierre Edouard","family":"Fournier","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Matthieu","family":"Million","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2023,4,8]]},"reference":[{"issue":"9","key":"1824_CR1","doi-asserted-by":"publisher","first-page":"3656","DOI":"10.1099\/ijsem.0.001195","volume":"66","author":"S Ahn","year":"2016","unstructured":"Ahn S, Jin TE, Chang DH, Rhee MS, Kim HJ, Lee SJ, Park DS, Kim BC (2016) Agathobaculum butyriciproducens gen. nov.; sp nov., a strict anaerobic, butyrate-producing gut bacterium isolated from human faeces and reclassification of Eubacterium desmolans as Agathobaculum desmolans comb. Nov. Int J Syst Evolut Microbiol 66(9):3656\u20133661. https:\/\/doi.org\/10.1099\/ijsem.0.001195","journal-title":"Int J Syst Evolut Microbiol"},{"issue":"10","key":"1824_CR2","doi-asserted-by":"publisher","first-page":"1038","DOI":"10.1039\/C2NP20016C","volume":"29","author":"DL Akey","year":"2012","unstructured":"Akey DL, Gehret JJ, Khare D, Smith JL (2012) Insights from the sea: structural biology of marine polyketide synthases. Nat Prod Rep 29(10):1038. https:\/\/doi.org\/10.1039\/C2NP20016C","journal-title":"Nat Prod Rep"},{"issue":"D1","key":"1824_CR3","doi-asserted-by":"publisher","first-page":"D517","DOI":"10.1093\/nar\/gkz935","volume":"48","author":"BP Alcock","year":"2020","unstructured":"Alcock BP, Raphenya AR, Lau TTY, Tsang KK, Bouchard M, Edalatmand A, Huynh W, Nguyen AV, Cheng AA, Liu S, Min SY, Miroshnichenko A, Tran HK, Werfalli RE, Nasir JA, Oloni M, Speicher DJ, Florescu A, Singh B, Faltyn M, Hernandez-Koutoucheva A, Sharma AN, Bordeleau E, Pawlowski AC, Zubyk HL, Dooley D, Griffiths E, Maguire F, Winsor GL, Beiko RG, Brinkman FSL, Hsiao WWL, Domselaar GV, McArthur AG, CARD (2020) Antibiotic resistome surveillance with the comprehensive antibiotic resistance database. Nucleic Acids Res 48(D1):D517\u2013D525. https:\/\/doi.org\/10.1093\/nar\/gkz935","journal-title":"Nucleic Acids Res"},{"key":"1824_CR4","doi-asserted-by":"publisher","first-page":"420","DOI":"10.1038\/s41587-019-0036-z","volume":"37","author":"JJ Almagro Armenteros","year":"2019","unstructured":"Almagro Armenteros JJ, Tsirigos KD, Sonderby CK et al (2019) SignalP 5.0 improves signal peptide predictions using deep neural networks. Nat Biotechnol 37:420\u2013423. https:\/\/doi.org\/10.1038\/s41587-019-0036-z","journal-title":"Nat Biotechnol"},{"issue":"1","key":"1824_CR5","doi-asserted-by":"publisher","first-page":"17199","DOI":"10.1038\/s41598-019-53791-1","volume":"9","author":"H Anani","year":"2019","unstructured":"Anani H, Abdallah RA, Khoder M, Fontanini A, Mailhe M, Ricaboni D, Raoult D, Fournier PE (2019) Colibacter massiliensis gen. nov. sp. Nov., a novel gram-stain-positive anaerobic diplococcal bacterium, isolated from the human left colon. Sci Rep 9(1):17199. https:\/\/doi.org\/10.1038\/s41598-019-53791-1","journal-title":"Sci Rep"},{"key":"1824_CR6","doi-asserted-by":"publisher","first-page":"117","DOI":"10.4056\/sigs.531120","volume":"2","author":"AF Auch","year":"2010","unstructured":"Auch AF, von Jan M, Klenk H-P, G\u00f6ker M (2010) Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison. Stand Genom Sci 2:117\u2013134. https:\/\/doi.org\/10.4056\/sigs.531120","journal-title":"Stand Genom Sci"},{"key":"1824_CR7","doi-asserted-by":"publisher","DOI":"10.1007\/s10482-022-01777-x","author":"S Bellali","year":"2022","unstructured":"Bellali S, Haddad G, Pham TPT, Iwaza R, Ibrahim A, Armstrong N, Fadlane A, Couderc C, Diallo A, Sokhna C, Million M, Raoult D, Tidjani Alou M (2022) Draft genomes and descriptions of Urmitella timonensis gen. nov., sp. nov. and Marasmitruncus massiliensis gen. nov., sp. Nov., isolated from severely malnourished African children using culturomics. Antonie Van Leeuwenhoek. https:\/\/doi.org\/10.1007\/s10482-022-01777-x","journal-title":"Antonie Van Leeuwenhoek"},{"key":"1824_CR8","unstructured":"BioM\u00e9rieux France\u2014diagnostic microbiologique clinique ou industriel Available online: https:\/\/www.biomerieux.fr\/ (accessed on June 8, 2022)"},{"issue":"12","key":"1824_CR9","doi-asserted-by":"publisher","first-page":"3491","DOI":"10.1093\/jac\/dkaa345","volume":"75","author":"V Bortolaia","year":"2020","unstructured":"Bortolaia V, Kaas RF, Ruppe E et al (2020) ResFinder 4.0 for predictions of phenotypes from genotypes. J Antimicrob Chemother 75(12):3491\u20133500. https:\/\/doi.org\/10.1093\/jac\/dkaa345","journal-title":"J Antimicrob Chemother"},{"issue":"8","key":"1824_CR10","doi-asserted-by":"publisher","first-page":"1621","DOI":"10.1038\/ismej.2012.8","volume":"6","author":"JG Caporaso","year":"2012","unstructured":"Caporaso JG, Lauber CL, Walters WA, Berg-Lyons D, Huntley J, Fierer N, Owens SM, Betley J, Fraser L, Bauer M, Gormley N, Gilbert JA, Smith G, Knight R (2012) Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms. ISME J 6(8):1621\u20131624. https:\/\/doi.org\/10.1038\/ismej.2012.8","journal-title":"ISME J"},{"issue":"10","key":"1824_CR11","doi-asserted-by":"publisher","first-page":"e2000136","DOI":"10.1002\/biot.202000136","volume":"15","author":"Y Chen","year":"2020","unstructured":"Chen Y, Yang Y, Ji X, Zhao R, Li G, Gu Y, Shi A, Jiang W, Zhang Q (2020) The SCIFF-derived ranthipeptides participate in quorum sensing in solventogenic clostridia. Biotechnol J 15(10):e2000136. https:\/\/doi.org\/10.1002\/biot.202000136","journal-title":"Biotechnol J"},{"key":"1824_CR12","doi-asserted-by":"publisher","first-page":"2325","DOI":"10.1194\/jlr.R036012","volume":"54","author":"G Den Besten","year":"2013","unstructured":"Den Besten G, van Eunen K, Groen AK, Venema K, Reijngoud DJ, Bakker BM (2013) The role of short-chain fatty acids in the interplay between diet, gut microbiota, and host energy metabolism. J Lipid Res 54:2325\u20132340","journal-title":"J Lipid Res"},{"issue":"10","key":"1824_CR13","doi-asserted-by":"publisher","first-page":"e0223543","DOI":"10.1371\/journal.pone.0223543","volume":"14","author":"A Diakite","year":"2019","unstructured":"Diakite A, Dubourg G, Dione N, Afouda P, Bellali S, Ngom II, Valles C, Million M, Levasseur A, Cadoret F, Lagier JC, Raoult D (2019) Extensive culturomics of 8 healthy samples enhances metagenomics efficiency. PLoS ONE 14(10):e0223543. https:\/\/doi.org\/10.1371\/journal.pone.0223543","journal-title":"PLoS ONE"},{"key":"1824_CR14","doi-asserted-by":"publisher","first-page":"104698","DOI":"10.1016\/j.micpath.2020.104698","volume":"150","author":"A Diakite","year":"2021","unstructured":"Diakite A, Dubourg G, Raoult D (2021) Updating the repertoire of cultured bacteria from the human being. Microbial Pathog 150:104698. https:\/\/doi.org\/10.1016\/j.micpath.2020.104698","journal-title":"Microbial Pathog"},{"issue":"12","key":"1824_CR15","doi-asserted-by":"publisher","first-page":"2799","DOI":"10.1099\/ijs.0.65730-0","volume":"58","author":"V Eeckhaut","year":"2008","unstructured":"Eeckhaut V, Van Immerseel F, Teirlynck E, Pasmans F, Fievez V, Snauwaert C, Haesebrouck F, Ducatelle R, Louis P, Vandamme P (2008) Butyricicoccus pullicaecorum gen. nov., sp. Nov., an anaerobic, butyrate-producing bacterium isolated from the caecal content of a broiler chicken. Int J Syst Evolut Microbiol 58(12):2799\u20132802. https:\/\/doi.org\/10.1099\/ijs.0.65730-0","journal-title":"Int J Syst Evolut Microbiol"},{"issue":"22","key":"1824_CR16","doi-asserted-by":"publisher","first-page":"R943","DOI":"10.1016\/j.cub.2012.10.029","volume":"22","author":"B Fontaine","year":"2012","unstructured":"Fontaine B, Perrard A, Bouchet P (2012) 21 years of shelf life between discovery and description of new species. Curr Biology CB 22(22):R943-944. https:\/\/doi.org\/10.1016\/j.cub.2012.10.029","journal-title":"Curr Biology CB"},{"issue":"1","key":"1824_CR17","doi-asserted-by":"publisher","first-page":"16","DOI":"10.1038\/s43705-021-00017-z","volume":"1","author":"TCA Hitch","year":"2021","unstructured":"Hitch TCA, Riedel T, Oren A, Overmann J, Lawley TD, Clavel T (2021) Automated analysis of genomic sequences facilitates high-throughput and comprehensive description of bacteria. ISME Commun 1(1):16. https:\/\/doi.org\/10.1038\/s43705-021-00017-z","journal-title":"ISME Commun"},{"key":"1824_CR18","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1016\/j.phrs.2018.03.020","volume":"132","author":"N Israelyan","year":"2018","unstructured":"Israelyan N, Margolis KG (2018) Serotonin as a link between the gut-brain-microbiome axis in autism spectrum disorders. Pharmacol Res 132:1\u20136","journal-title":"Pharmacol Res"},{"key":"1824_CR19","doi-asserted-by":"publisher","first-page":"726","DOI":"10.1016\/j.jmb.2015.11.006","volume":"428","author":"M Kanehisa","year":"2016","unstructured":"Kanehisa M, Sato Y, Morishima K (2016) BlastKOALA and GhostKOALA: KEGG tools for functional characterization of genome and Metagenome sequences. J Mol Biol 428:726\u2013731. https:\/\/doi.org\/10.1016\/j.jmb.2015.11.006","journal-title":"J Mol Biol"},{"issue":"6","key":"1824_CR20","doi-asserted-by":"publisher","first-page":"1012","DOI":"10.1101\/gr.171322.113","volume":"24","author":"S Kim","year":"2014","unstructured":"Kim S, Kim D, Cho SW, Kim J, Kim JS (2014) Highly efficient RNA-guided genome editing in human cells via delivery of purified Cas9 ribonucleoproteins. Genome Res 24(6):1012\u20131019. https:\/\/doi.org\/10.1101\/gr.171322.113","journal-title":"Genome Res"},{"key":"1824_CR21","doi-asserted-by":"publisher","first-page":"1332","DOI":"10.1016\/j.cell.2016.05.041","volume":"165","author":"A Koh","year":"2016","unstructured":"Koh A, De Vadder F, Kovatcheva-Datchary P, B\u00e4ckhed F (2016) From dietary fiber to host physiology: short-chain fatty acids as key bacterial metabolites. Cell 165:1332\u20131345","journal-title":"Cell"},{"issue":"6","key":"1824_CR22","doi-asserted-by":"publisher","first-page":"1547","DOI":"10.1093\/molbev\/msy096","volume":"35","author":"S Kumar","year":"2018","unstructured":"Kumar S, Stecher G, Li M, Knyaz C, Tamura K (2018) MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol 35(6):1547\u20131549. https:\/\/doi.org\/10.1093\/molbev\/msy096","journal-title":"Mol Biol Evol"},{"issue":"12","key":"1824_CR23","doi-asserted-by":"publisher","first-page":"1185","DOI":"10.1111\/1469-0691.12023","volume":"18","author":"JC Lagier","year":"2012","unstructured":"Lagier JC, Armougom F, Million M, Hugon P, Pagnier I, Robert C, Bittar F, Fournous G, Gimenez G, Maraninchi M, Trape JF, Koonin EV, La Scola B, Raoult D (2012) Microbial culturomics: paradigm shift in the human gut microbiome study. Clin Microbiol Infect 18(12):1185\u20131193. https:\/\/doi.org\/10.1111\/1469-0691.12023","journal-title":"Clin Microbiol Infect"},{"issue":"1","key":"1824_CR24","doi-asserted-by":"publisher","first-page":"208","DOI":"10.1128\/CMR.00110-14","volume":"28","author":"JC Lagier","year":"2015","unstructured":"Lagier JC, Edouard S, Pagnier I, Mediannikov O, Drancourt M, Raoult D (2015) Current and past strategies for bacterial culture in clinical microbiology. Clin Microbiol Rev 28(1):208\u2013236. https:\/\/doi.org\/10.1128\/CMR.00110-14","journal-title":"Clin Microbiol Rev"},{"key":"1824_CR25","doi-asserted-by":"publisher","first-page":"16203","DOI":"10.1038\/nmicrobiol.2016.203","volume":"1","author":"JC Lagier","year":"2016","unstructured":"Lagier JC, Khelaifia S, Alou MT, Ndongo S, Dione N, Hugon P, Caputo A, Cadoret F, Traore SI, Seck EH, Dubourg G, Durand G, Mourembou G, Guilhot E, Togo A, Bellali S, Bachar D, Cassir N, Bittar F, Raoult D (2016) Culture of previously uncultured members of the human gut microbiota by culturomics. Nat Microbiol 1:16203. https:\/\/doi.org\/10.1038\/nmicrobiol.2016.203","journal-title":"Nat Microbiol"},{"key":"1824_CR26","doi-asserted-by":"publisher","first-page":"33721","DOI":"10.1038\/srep33721","volume":"6","author":"I Lagkouvardos","year":"2016","unstructured":"Lagkouvardos I, Joseph D, Kapfhammer M et al (2016) IMNGS: a comprehensive open resource of processed 16S rRNA microbial profiles for ecology and diversity studies. Sci Rep 6:33721. https:\/\/doi.org\/10.1038\/srep33721","journal-title":"Sci Rep"},{"key":"1824_CR27","doi-asserted-by":"publisher","first-page":"416","DOI":"10.1038\/nchembio.1535","volume":"10","author":"WJ Lee","year":"2014","unstructured":"Lee WJ, Hase K (2014) Gut microbiota-generated metabolites in animal health and disease. Nat Chem Biol 10:416\u2013424","journal-title":"Nat Chem Biol"},{"key":"1824_CR28","doi-asserted-by":"publisher","first-page":"426","DOI":"10.1111\/j.1574-6976.2009.00204.x","volume":"34","author":"JH Lee","year":"2010","unstructured":"Lee JH, Lee J (2010) Indole as an intercellular signal in microbial communities. FEMS Microbiol Rev 34:426\u2013444. https:\/\/doi.org\/10.1111\/j.1574-6976.2009.00204.x","journal-title":"FEMS Microbiol Rev"},{"key":"1824_CR29","doi-asserted-by":"publisher","first-page":"1100","DOI":"10.1099\/ijsem.0.000760","volume":"66","author":"I Lee","year":"2016","unstructured":"Lee I, Ouk Kim Y, Park S-C, Chun J (2016) OrthoANI: an improved algorithm and software for calculating average nucleotide identity. Int J Syst Evol Microbiol 66:1100\u20131103. https:\/\/doi.org\/10.1099\/ijsem.0.000760","journal-title":"Int J Syst Evol Microbiol"},{"issue":"4","key":"1824_CR30","doi-asserted-by":"publisher","first-page":"126218","DOI":"10.1016\/j.syapm.2021.126218","volume":"44","author":"W Ludwig","year":"2021","unstructured":"Ludwig W, Viver T, Westram R, Francisco Gago J, Bustos-Caparros E, Knittel K, Amann R, Rossello-Mora R (2021) Release LTP_12_2020, featuring a new ARB alignment and improved 16S rRNA tree for prokaryotic type strains. Syst Appl Microbiol 44(4):126218. https:\/\/doi.org\/10.1016\/j.syapm.2021.126218","journal-title":"Syst Appl Microbiol"},{"issue":"4","key":"1824_CR31","doi-asserted-by":"publisher","first-page":"O255","DOI":"10.1111\/1469-0691.12373","volume":"20","author":"E Matuschek","year":"2014","unstructured":"Matuschek E, Brown DFJ, Kahlmeter G (2014) Development of the EUCAST disk diffusion antimicrobial susceptibility testing method and its implementation in routine microbiology laboratories. Clin Microbiol Infect 20(4):O255\u2013O266. https:\/\/doi.org\/10.1111\/1469-0691.12373","journal-title":"Clin Microbiol Infect"},{"key":"1824_CR32","doi-asserted-by":"publisher","first-page":"W479","DOI":"10.1093\/nar\/gky359","volume":"46","author":"AJ Medlar","year":"2018","unstructured":"Medlar AJ, T\u00f6r\u00f6nen P, Holm L (2018) AAI-profiler: fast proteome- wide exploratory analysis reveals taxonomic identity, misclassification and contamination. Nucleic Acids Res 46:W479\u2013W485. https:\/\/doi.org\/10.1093\/nar\/gky359","journal-title":"Nucleic Acids Res"},{"issue":"1","key":"1824_CR33","doi-asserted-by":"publisher","first-page":"2182","DOI":"10.1038\/s41467-019-10210-3","volume":"10","author":"JP Meier-Kolthoff","year":"2019","unstructured":"Meier-Kolthoff JP, G\u00f6ker M (2019) TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy. Nat Commun 10(1):2182. https:\/\/doi.org\/10.1038\/s41467-019-10210-3","journal-title":"Nat Commun"},{"key":"1824_CR34","doi-asserted-by":"publisher","first-page":"127","DOI":"10.1016\/j.micpath.2016.02.003","volume":"106","author":"M Million","year":"2017","unstructured":"Million M, Diallo A, Raoult D (2017) Gut microbiota and malnutrition. Microb Pathog 106:127\u2013138. https:\/\/doi.org\/10.1016\/j.micpath.2016.02.003","journal-title":"Microb Pathog"},{"issue":"2","key":"1824_CR35","doi-asserted-by":"publisher","first-page":"183","DOI":"10.1099\/00207713-36-2-183","volume":"36","author":"GN Morris","year":"1986","unstructured":"Morris GN, Winter J, Cato EP, Ritchie AE, Bokkenheuser VDY (1986) Eubacterium desmolans sp. Nov., a steroid desmolase-producing species from cat fecal flora. Int J Syst Evol Microbiol 36(2):183\u2013186. https:\/\/doi.org\/10.1099\/00207713-36-2-183","journal-title":"Int J Syst Evol Microbiol"},{"issue":"22","key":"1824_CR36","doi-asserted-by":"publisher","first-page":"3691","DOI":"10.1093\/bioinformatics\/btv421","volume":"31","author":"AJ Page","year":"2015","unstructured":"Page AJ et al (2015) Roary: rapid large-scale prokaryote pan genome analysis. Bioinformatics 31(22):3691\u20133693. https:\/\/doi.org\/10.1093\/bioinformatics\/btv421","journal-title":"Bioinformatics"},{"issue":"11","key":"1824_CR37","doi-asserted-by":"publisher","first-page":"5607","DOI":"10.1099\/ijsem.0.004332","volume":"70","author":"AC Parte","year":"2020","unstructured":"Parte AC, Sard\u00e0 Carbasse J, Meier-Kolthoff JP, Reimer LC, G\u00f6ker M (2020) List of prokaryotic names with standing in nomenclature (LPSN) moves to the DSMZ. Int J Syst Evol Microbiol 70(11):5607\u20135612. https:\/\/doi.org\/10.1099\/ijsem.0.004332","journal-title":"Int J Syst Evol Microbiol"},{"key":"1824_CR38","doi-asserted-by":"publisher","first-page":"3125","DOI":"10.1093\/bioinformatics\/btq588","volume":"26","author":"A Petkau","year":"2010","unstructured":"Petkau A, Stuart-Edwards M, Stothard P, Van Domselaar G (2010) Interactive microbial genome visualization with GView. Bioinformatics 26:3125\u20133126. https:\/\/doi.org\/10.1093\/bioinformatics\/btq588","journal-title":"Bioinformatics"},{"issue":"1","key":"1824_CR39","doi-asserted-by":"publisher","first-page":"102","DOI":"10.1002\/cpbi.102","volume":"70","author":"A Prjibelski","year":"2020","unstructured":"Prjibelski A, Antipov D, Meleshko D, Lapidus A, Korobeynikov A (2020) Using SPAdes De Novo assembler. Curr Protoc Bioinform 70(1):102. https:\/\/doi.org\/10.1002\/cpbi.102","journal-title":"Curr Protoc Bioinform"},{"issue":"Pt_2","key":"1824_CR40","doi-asserted-by":"publisher","first-page":"384","DOI":"10.1099\/ijs.0.057091-0","volume":"64","author":"D Ramasamy","year":"2014","unstructured":"Ramasamy D, Mishra AK, Lagier JC, Padhmanabhan R, Rossi M, Sentausa E, Raoult D, Fournier PE (2014) A polyphasic strategy incorporating genomic data for the taxonomic description of novel bacterial species. Int J Syst Evolut Microbiol 64(Pt_2):384\u2013391. https:\/\/doi.org\/10.1099\/ijs.0.057091-0","journal-title":"Int J Syst Evolut Microbiol"},{"key":"1824_CR100","unstructured":"ResFinder 4.1 (2022) https:\/\/cge.food.dtu.dk\/services\/ResFinder\/. Accessed 26 Nov 2022"},{"key":"1824_CR41","doi-asserted-by":"publisher","first-page":"18","DOI":"10.1016\/j.nmni.2016.12.008","volume":"17","author":"D Ricaboni","year":"2017","unstructured":"Ricaboni D, Mailhe M, Vitton V, Cadoret F, Fournier PE, Raoult D (2017) Intestinibacillus massiliensis\u2019 gen. nov., sp. nov., isolated from human left colon. New Microbes and New Infections 17:18\u201320. https:\/\/doi.org\/10.1016\/j.nmni.2016.12.008","journal-title":"New Microbes and New Infections"},{"key":"1824_CR42","unstructured":"Sasser, M (2006) Bacterial identification by gas chromatographic analysis of fatty acids methyl esters (GC-FAME). Newark, NY: Microbial ID."},{"key":"1824_CR43","doi-asserted-by":"publisher","first-page":"671","DOI":"10.1038\/nmeth.2089","volume":"9","author":"CA Schneider","year":"2012","unstructured":"Schneider CA, Rasband WS, Eliceiri KW (2012) NIH image to imageJ: 25 years of image analysis. Nat Methods 9:671\u2013675","journal-title":"Nat Methods"},{"issue":"14","key":"1824_CR44","doi-asserted-by":"publisher","first-page":"2068","DOI":"10.1093\/bioinformatics\/btu153","volume":"30","author":"T Seemann","year":"2014","unstructured":"Seemann T (2014) Prokka: rapid prokaryotic genome annotation. Bioinformatics 30(14):2068\u20132069. https:\/\/doi.org\/10.1093\/bioinformatics\/btu153","journal-title":"Bioinformatics"},{"issue":"4","key":"1824_CR45","doi-asserted-by":"publisher","first-page":"543","DOI":"10.1086\/600885","volume":"49","author":"P Seng","year":"2009","unstructured":"Seng P, Drancourt M, Gouriet F, La Scola B, Fournier PE, Rolain JM, Raoult D (2009) Ongoing revolution in bacteriology: Routine identification of bacteria by matrix-assisted laser desorption ionization time-of-flight mass spectrometry. Clin Infect Dis 49(4):543\u2013551. https:\/\/doi.org\/10.1086\/600885","journal-title":"Clin Infect Dis"},{"issue":"10","key":"1824_CR46","doi-asserted-by":"publisher","first-page":"4125","DOI":"10.1099\/ijsem.0.001323","volume":"66","author":"T Takada","year":"2016","unstructured":"Takada T, Watanabe K, Makino H, Kushiro A (2016) Reclassification of Eubacterium desmolans as Butyricicoccus desmolans comb. Nov., and description of Butyricicoccus faecihominis sp. nov., a butyrate-producing bacterium from human faeces. Int J Syst Evolut Microbiol 66(10):4125\u20134131. https:\/\/doi.org\/10.1099\/ijsem.0.001323","journal-title":"Int J Syst Evolut Microbiol"},{"key":"1824_CR47","doi-asserted-by":"publisher","first-page":"913","DOI":"10.1186\/1471-2164-14-913","volume":"14","author":"CC Thompson","year":"2013","unstructured":"Thompson CC, Chimetto L, Edwards RA, Swings J, Stackebrandt E et al (2013) Microbial genomic taxonomy. BMC Genom 14:913","journal-title":"BMC Genom"},{"issue":"20","key":"1824_CR48","doi-asserted-by":"publisher","first-page":"2191","DOI":"10.1001\/jama.2013.281053","volume":"310","author":"World Medical Association","year":"2013","unstructured":"World Medical Association (2013) World medical association declaration of helsinki: ethical principles for medical research involving human subjects. JAMA 310(20):2191\u20132194. https:\/\/doi.org\/10.1001\/jama.2013.281053","journal-title":"JAMA"}],"container-title":["Antonie van Leeuwenhoek"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s10482-023-01824-1.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1007\/s10482-023-01824-1\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s10482-023-01824-1.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,5,20]],"date-time":"2023-05-20T09:20:13Z","timestamp":1684574413000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1007\/s10482-023-01824-1"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,4,8]]},"references-count":49,"journal-issue":{"issue":"6","published-print":{"date-parts":[[2023,6]]}},"alternative-id":["1824"],"URL":"https:\/\/doi.org\/10.1007\/s10482-023-01824-1","relation":{},"ISSN":["0003-6072","1572-9699"],"issn-type":[{"value":"0003-6072","type":"print"},{"value":"1572-9699","type":"electronic"}],"subject":[],"published":{"date-parts":[[2023,4,8]]},"assertion":[{"value":"28 November 2022","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"16 March 2023","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"8 April 2023","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"The authors would like to declare that Didier Raoult is a consultant in microbiology for the Hitachi High-Tech Corporation from March 2018 until March 2020. Otherwise, the authors declare no other conflict of interest.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Conflict of interest"}}]}}