AUTHOR=Talagrand-Reboul Emilie , Roger Frédéric , Kimper Jean-Luc , Colston Sophie M. , Graf Joerg , Latif-Eugenín Fadua , Figueras Maria José , Petit Fabienne , Marchandin Hélène , Jumas-Bilak Estelle , Lamy Brigitte 

TITLE=Delineation of Taxonomic Species within Complex of Species: Aeromonas media and Related Species as a Test Case

JOURNAL=Frontiers in Microbiology

VOLUME=8

YEAR=2017

URL=https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2017.00621

DOI=10.3389/fmicb.2017.00621

ISSN=1664-302X

ABSTRACT=<p><italic>Aeromonas media</italic> is an opportunistic pathogen for human and animals mainly found in aquatic habitats and which has been noted for significant genomic and phenotypic heterogeneities. We aimed to better understand the population structure and diversity of strains currently affiliated to <italic>A. media</italic> and the related species <italic>A. rivipollensis</italic>. Forty-one strains were included in a population study integrating, multilocus genetics, phylogenetics, comparative genomics, as well as phenotypics, lifestyle, and evolutionary features. Sixteen gene-based multilocus phylogeny delineated three clades. Clades corresponded to different genomic groups or genomospecies defined by phylogenomic metrics ANI (average nucleotide identity) and <italic>is</italic>DDH (<italic>in silico</italic> DNA-DNA hybridization) on 14 whole genome sequences. DL-lactate utilization, cefoxitin susceptibility, nucleotide signatures, ribosomal multi-operon diversity, and differences in relative effect of recombination and mutation (i.e., in evolution mode) distinguished the two species <italic>Aeromonas media</italic> and <italic>Aeromonas rivipollensis</italic>. The description of these two species was emended accordingly. The genome metrics and comparative genomics suggested that a third clade is a distinct genomospecies. Beside the species delineation, genetic and genomic data analysis provided a more comprehensive knowledge of the cladogenesis determinants at the root and inside <italic>A. media</italic> species complex among aeromonads. Particular lifestyles and phenotypes as well as major differences in evolution modes may represent putative factors associated with lineage emergence and speciation within the <italic>A. media</italic> complex. Finally, the integrative and populational approach presented in this study is considered broadly in order to conciliate the delineation of taxonomic species and the population structure in bacterial genera organized in species complexes.</p>