Revisiting the taxonomy of the genus Arcobacter: Getting order from the chaos

Abstract

Since the description of the genusArcobacterin 1991, a total of 27 species havebeen described, although some species have shown 16S rRNA similarities below 95%,which is the cut-off that usually separates species that belong to different genera.The objective of the present study was to reassess the taxonomy of the genusArcobacterusing information derived from the core genome (286 genes), a MultilocusSequence Analysis (MLSA) with 13 housekeeping genes, as well as different genomicindexes like Average Nucleotide Identity (ANI),in silicoDNA–DNA hybridization (isDDH),Average Amino-acid Identity (AAI), Percentage of Conserved Proteins (POCPs), andRelative Synonymous Codon Usage (RSCU). The study included a total of 39 strainsthat represent all the 27 species included in the genusArcobactertogether with 13strains that are potentially new species, and the analysis of 57 genomes. The differentphylogenetic analyses showed that theArcobacterspecies grouped into four clusters.In addition,A. lekithochrousand the candidatus species ‘A. aquaticus’ appeared, asdidA. nitrofigilis,the type species of the genus, in separate branches. Furthermore,the genomic indices ANI andisDDH not only confirmed that all the species were well-defined, but also the coherence of the clusters. The AAI and POCP values showedintra-cluster ranges above the respective cut-off values of 60% and 50% describedfor species belonging to the same genus. Phenotypic analysis showed that certaintest combinations could allow the differentiation of the four clusters and the threeorphan species established by the phylogenetic and genomic analyses. The originof the strains showed that each of the clusters embraced species recovered froma common or related environment. The results obtained enable the division of thecurrent genusArcobacterin at least seven different genera, for which the namesArcobacter,Aliiarcobactergen. nov.,Pseudoarcobactergen. nov.,Haloarcobactergen.nov.,Malacobactergen. nov.,Poseidonibactergen. nov., and Candidate ‘Arcomarinus’gen. nov. are proposed