Genome and pan-genome analysis to classify emerging bacteria

Aurélia Caputo (1) , Pierre-Edouard Fournier (2) , Didier Raoult (1)

1 MEPHI - Microbes évolution phylogénie et infections
2 VITROME - Vecteurs - Infections tropicales et méditerranéennes

Background In the recent years, genomic and pan-genomic studies have become increasingly important. Culturomics allows to study human microbiota through the use of different culture conditions, coupled with a method of rapid identification by MALDI-TOF, or 16S rRNA. Bacterial taxonomy is undergoing many changes as a consequence. With the help of pan-genomic analyses, species can be redefined, and new species definitions generated. Results Genomics, coupled with culturomics, has led to the discovery of many novel bacterial species or genera, including Akkermansia muciniphila and Microvirga massiliensis. Using the genome to define species has been applied within the genus Klebsiella. A discontinuity or an abrupt break in the core/pan-genome ratio can uncover novel species. Conclusions Applying genomic and pan-genomic analyses to the reclassification of other bacterial species or genera will be important in the future of medical microbiology. The pan-genome is one of many new innovative tools in bacterial taxonomy.

Mots clés: Genomic; Novel species; Pan-genome; Taxonomy

Domaines: Bactériologie; Génomique, Transcriptomique et Protéomique [q-bio.GN]; Maladies émergentes

Aurélia Caputo, Pierre-Edouard Fournier, Didier Raoult. Genome and pan-genome analysis to classify emerging bacteria. Biology Direct, 2019, 14 (1), ⟨10.1186/s13062-019-0234-0⟩. ⟨hal-02202166⟩