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  • Comparative Genomics of Nov...
    Singh, Nitin K; Lavire, Céline; Nesme, Joseph; Vial, Ludovic; Nesme, Xavier; Mason, Christopher E; Lassalle, Florent; Venkateswaran, Kasthuri

    Frontiers in microbiology, 12/2021, Letnik: 12
    Journal Article

    Strains of genomospecies 3 (i.e., genomovar G3 of the species complex) have been previously isolated from diverse environments, including in association with plant roots, with algae, as part of a lignocellulose degrading community, from a hospital environment, as a human opportunistic pathogen, or as reported in this study, from a surface within the International Space Station. Polyphasic taxonomic methods revealed the relationship of G3 strains to other spp., which supports the description of a novel species. The G3 strains tested ( = 9) were phenotypically distinguishable among the strains from other genomospecies of the genus Phylogenetic analyses of the 16S rRNA gene, B gene, multi-locus sequence analysis, and 1,089-gene core-genome gene concatenate concur that tested G3 strains belong to the genus and they form a clade distinct from other validly described species. The distinctiveness of this clade was confirmed by average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) comparisons between the G3 tested strains and all known species type strains, since obtained values were considerably below the 95% (ANI) and 70% (dDDH) thresholds used for the species delineation. According to the core-genome phylogeny and ANI comparisons, the closest relatives of G3 strains were sp. strains UGM030330-04 and K599, members of a novel genomospecies we propose to call genomovar G21. Using this polyphasic approach, we characterized the phenotypic and genotypic synapomorphies of G3, showing it is a bacterial species, well separated from previously named species or other recognized genomic species. We thus propose the name for this species previously referred to as genomospecies 3. The type strain of is IIF1SW-B1 (= LMG 32164 = NRRL B-65602). Comparative genomic analysis show strains have species-specific genes associated with secretion of secondary metabolites, including an exopolysaccharide and putative adhesins and resistance to copper. specific gene functions notably relate to surface adhesion and could be involved to colonize nutrient-poor and harsh habitats. The strains from the ISS showed presence of a 40-kbp plasmid and several other potential mobile genetic elements detected that could also be part of conjugative elements or integrated prophages.