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Multiple techniques have been used to identify isolates of this genus, such as phenotyping, polymerase chain reaction genotyping, and in silico whole-genome taxonomy. In this study, we demonstrate that whole-genome-based taxonomy, using average nucleotide identity and molecular phylogeny, is the most accurate approach for Flavobacterium species. We obtained various isolated strains from official collections; these strains had been previously characterized by a third party using various identification methodologies. We analyzed isolates by PCR genotyping using previously published primers targeting gyrB and gyrA genes, which are supposedly specific to the genus Flavobacterium and Flavobacterium psychrophilum, respectively. After genomic analysis, nearly half of the isolates had their identities re-evaluated: around a quarter of them were re-assigned to other genera and two isolates are new species of flavobacteria. In retrospect, the phenotyping method was the least accurate. While gyrB genotyping was accurate with the isolates included in this study, bioinformatics analysis suggests that only 70% of the Flavobacterium species could be appropriately identified using this approach. We propose that whole-genome taxonomy should be used for accurate Flavobacterium identification, and we encourage bacterial collections to review the identification of isolates identified by phenotyping.<\/jats:p>","DOI":"10.1093\/femsle\/fnae089","type":"journal-article","created":{"date-parts":[[2024,10,23]],"date-time":"2024-10-23T06:04:05Z","timestamp":1729663445000},"source":"Crossref","is-referenced-by-count":3,"title":["Whole-genome-based taxonomy as the most accurate approach to identify <i>Flavobacterium<\/i> species"],"prefix":"10.1093","volume":"371","author":[{"given":"Vincent","family":"G\u00e9linas","sequence":"first","affiliation":[{"name":"Institut de Biologie Int\u00e9grative et des Syst\u00e8mes (IBIS), Universit\u00e9 Laval , Qu\u00e9bec City, QC G1V 0A6 ,","place":["Canada"]},{"name":"D\u00e9partement de Biochimie, de Microbiologie et de Bio-Informatique, Facult\u00e9 des Sciences et de G\u00e9nie, Universit\u00e9 Laval , Qu\u00e9bec City, QC G1V 0A6 ,","place":["Canada"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Val\u00e9rie E","family":"Paquet","sequence":"additional","affiliation":[{"name":"Institut de Biologie Int\u00e9grative et des Syst\u00e8mes (IBIS), Universit\u00e9 Laval , Qu\u00e9bec City, QC G1V 0A6 ,","place":["Canada"]},{"name":"D\u00e9partement de Biochimie, de Microbiologie et de Bio-Informatique, Facult\u00e9 des Sciences et de G\u00e9nie, Universit\u00e9 Laval , Qu\u00e9bec City, QC G1V 0A6 ,","place":["Canada"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Maude F","family":"Paquet","sequence":"additional","affiliation":[{"name":"Institut de Biologie Int\u00e9grative et des Syst\u00e8mes (IBIS), Universit\u00e9 Laval , Qu\u00e9bec City, QC G1V 0A6 ,","place":["Canada"]},{"name":"D\u00e9partement de Biochimie, de Microbiologie et de Bio-Informatique, Facult\u00e9 des Sciences et de G\u00e9nie, Universit\u00e9 Laval , Qu\u00e9bec City, QC G1V 0A6 ,","place":["Canada"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Antony T","family":"Vincent","sequence":"additional","affiliation":[{"name":"Institut de Biologie Int\u00e9grative et des Syst\u00e8mes (IBIS), Universit\u00e9 Laval , Qu\u00e9bec City, QC G1V 0A6 ,","place":["Canada"]},{"name":"D\u00e9partement des Sciences Animales, Facult\u00e9 des Sciences de l'Agriculture et de l'Alimentation, Universit\u00e9 Laval , Qu\u00e9bec City, QC G1V 0A6 ,","place":["Canada"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0199-2852","authenticated-orcid":false,"given":"Steve J","family":"Charette","sequence":"additional","affiliation":[{"name":"Institut de Biologie Int\u00e9grative et des Syst\u00e8mes (IBIS), Universit\u00e9 Laval , Qu\u00e9bec City, QC G1V 0A6 ,","place":["Canada"]},{"name":"D\u00e9partement de Biochimie, de Microbiologie et de Bio-Informatique, Facult\u00e9 des Sciences et de G\u00e9nie, Universit\u00e9 Laval , Qu\u00e9bec City, QC G1V 0A6 ,","place":["Canada"]}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2024,10,22]]},"reference":[{"key":"2024111416050233600_bib1","doi-asserted-by":"publisher","first-page":"7","DOI":"10.1093\/nar\/gkq291","article-title":"TranslatorX: multiple alignment of nucleotide sequences guided by amino acid translations","volume":"38","author":"Abascal","year":"2010","journal-title":"Nucleic Acids Res"},{"key":"2024111416050233600_bib2","first-page":"481","article-title":"The prokaryotes: a handbook on the biology of bacteria. 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