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Genome and pan-genome analysis to classify emerging bacteria

Authors
  • Caputo, Aurélia1
  • Fournier, Pierre-Edouard2
  • Raoult, Didier1
  • 1 Aix Marseille Univ, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Marseille, France , Marseille (France)
  • 2 Aix Marseille Univ, IRD, APHM, SSA, VITROME, IHU-Méditerranée Infection, Marseille, France , Marseille (France)
Type
Published Article
Journal
Biology Direct
Publisher
Springer (Biomed Central Ltd.)
Publication Date
Feb 26, 2019
Volume
14
Issue
1
Identifiers
DOI: 10.1186/s13062-019-0234-0
Source
Springer Nature
Keywords
License
Green

Abstract

BackgroundIn 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.ResultsGenomics, 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.ConclusionsApplying 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.ReviewersThis article was reviewed by William Martin, Eric Bapteste and James Mcinerney.Open peer reviewReviewed by William Martin, Eric Bapteste and James Mcinerney.

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