title: The impact of culturomics on taxonomy in clinical microbiology.
abstract: Over the past decade, new culture methods coupled to genome and metagenome sequencing have enabled the number of isolated bacterial species with standing in nomenclature to rise to more than 15,000 whereas it was only 1791 in 1980. 'Culturomics', a new approach based on the diversification of culture conditions, has enabled the isolation of more than 1000 distinct human-associated bacterial species since 2012, including 247 new species. This strategy was demonstrated to be complementary to metagenome sequencing for the exhaustive study of the human microbiota and its roles in health and diseases. However, by identifying a large number of new bacterial species in a short time, culturomics has highlighted a need for taxonomic approaches adapted to clinical microbiology that would include the use of modern and reproducible tools, including high throughput genomic and proteomic analyses. Herein, we review the development of culturomics and genomics in the clinical microbiology field and their impact on bacterial taxonomy.
authors.affiliation: Unité de recherche sur les maladies infectieuses et tropicales émergentes (URMITE), UM 63CNRS 7278IRD 198Inserm 1095IHU Méditerranée Infection, Faculté de Médecine, Aix-Marseille Université, 27 Bd Jean Moulin, 13385, Marseille Cedex5, France.
authors.forename: Rita Abou
authors.initials: RA
authors.lastname: Abdallah
authors.affiliation: Unité de recherche sur les maladies infectieuses et tropicales émergentes (URMITE), UM 63CNRS 7278IRD 198Inserm 1095IHU Méditerranée Infection, Faculté de Médecine, Aix-Marseille Université, 27 Bd Jean Moulin, 13385, Marseille Cedex5, France.
authors.forename: Mamadou
authors.initials: M
authors.lastname: Beye
authors.affiliation: Unité de recherche sur les maladies infectieuses et tropicales émergentes (URMITE), UM 63CNRS 7278IRD 198Inserm 1095IHU Méditerranée Infection, Faculté de Médecine, Aix-Marseille Université, 27 Bd Jean Moulin, 13385, Marseille Cedex5, France.
authors.forename: Awa
authors.initials: A
authors.lastname: Diop
authors.affiliation: Unité de recherche sur les maladies infectieuses et tropicales émergentes (URMITE), UM 63CNRS 7278IRD 198Inserm 1095IHU Méditerranée Infection, Faculté de Médecine, Aix-Marseille Université, 27 Bd Jean Moulin, 13385, Marseille Cedex5, France.
authors.forename: Sofiane
authors.initials: S
authors.lastname: Bakour
authors.affiliation: Unité de recherche sur les maladies infectieuses et tropicales émergentes (URMITE), UM 63CNRS 7278IRD 198Inserm 1095IHU Méditerranée Infection, Faculté de Médecine, Aix-Marseille Université, 27 Bd Jean Moulin, 13385, Marseille Cedex5, France.
authors.forename: Didier
authors.initials: D
authors.lastname: Raoult
authors.affiliation: Unité de recherche sur les maladies infectieuses et tropicales émergentes (URMITE), UM 63CNRS 7278IRD 198Inserm 1095IHU Méditerranée Infection, Faculté de Médecine, Aix-Marseille Université, 27 Bd Jean Moulin, 13385, Marseille Cedex5, France. pierre-edouard.fournier@univ-amu.fr.
authors.forename: Pierre-Edouard
authors.initials: PE
authors.lastname: Fournier
mesh_terms: D001419:Bacteria / Q000145:classification* / Q000235:genetics / Q000254:growth & development* / Q000302:isolation & purification; D001424:Bacterial Infections / Q000382:microbiology*; D015373:Bacterial Typing Techniques; D046508:Culture Techniques; D041981:Gastrointestinal Tract / Q000382:microbiology; D006801:Humans; D054892:Metagenome; D064307:Microbiota; D010802:Phylogeny; D020543:Proteome
chemical_list: D020543:Proteome
keywords: Bacteria; Culturomics; Genome; Human microbiota; Taxonomy