AUTHOR=Gauthier Jeff , Vincent Antony T. , Charette Steve J. , Derome Nicolas 

TITLE=Strong Genomic and Phenotypic Heterogeneity in the Aeromonas sobria Species Complex

JOURNAL=Frontiers in Microbiology

VOLUME=8

YEAR=2017

URL=https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2017.02434

DOI=10.3389/fmicb.2017.02434

ISSN=1664-302X

ABSTRACT=<p><italic>Aeromonas sobria</italic> is a mesophilic motile aeromonad currently depicted as an opportunistic pathogen, despite increasing evidence of mutualistic interactions in salmonid fish. However, the determinants of its host-microbe associations, either mutualistic or pathogenic, remain less understood than for other aeromonad species. On one side, there is an over-representation of pathogenic interactions in the <italic>A. sobria</italic> literature, of which only three articles to date report mutualistic interactions; on the other side, genomic characterization of this species is still fairly incomplete as only two draft genomes were published prior to the present work. Consequently, no study specifically investigated the biodiversity of <italic>A. sobria</italic>. In fact, the investigation of <italic>A. sobria</italic> as a species complex may have been clouded by: (i) confusion with <italic>A. veronii</italic> biovar <italic>sobria</italic> because of their similar biochemical profiles, and (ii) the intrinsic low resolution of previous studies based on 16S rRNA gene sequences and multilocus sequence typing. So far, the only high-resolution, phylogenomic studies of the genus <italic>Aeromonas</italic> included one <italic>A. sobria</italic> strain (CECT 4245 / Popoff 208), making it impossible to robustly conclude on the phylogenetic intra-species diversity and the positioning among other <italic>Aeromonas</italic> species. To further understand the biodiversity and the spectrum of host-microbe interactions in <italic>A. sobria</italic> as well as its potential genomic diversity, we assessed the genomic and phenotypic heterogeneity among five <italic>A. sobria</italic> strains: two clinical isolates recovered from infected fish (JF2635 and CECT 4245), one from an infected amphibian (08005) and two recently isolated brook charr probionts (TM12 and TM18) which inhibit <italic>in vitro</italic> growth of <italic>A. salmonicida</italic> subsp. <italic>salmonicida</italic> (a salmonid fish pathogen). A phylogenomic assessment including 2,154 softcore genes corresponding to 946,687 variable sites from 33 <italic>Aeromonas</italic> genomes confirms the status of <italic>A. sobria</italic> as a distinct species divided in two subclades, with 100% bootstrap support. The phylogenomic split of <italic>A. sobria</italic> in two subclades is corroborated by a deep dichotomy between all five <italic>A. sobria</italic> strains in terms of inhibitory effect against <italic>A. salmonicida</italic> subsp. <italic>salmonicida</italic>, gene contents and codon usage. Finally, the antagonistic effect of <italic>A. sobria</italic> strains TM12 and TM18 suggests novel control methods against <italic>A. salmonicida</italic> subsp. <italic>salmonicida</italic>.</p>