Abstract
Since the description of the genus Arcobacter in 1991, a total of 27 species have been 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 genus Arcobacter using information derived from the core genome (286 genes), a Multilocus Sequence Analysis (MLSA) with 13 housekeeping genes, as well as different genomic indexes like Average Nucleotide Identity (ANI), in silico DNA–DNA hybridization (isDDH), Average Amino-acid Identity (AAI), Percentage of Conserved Proteins (POCPs), and Relative Synonymous Codon Usage (RSCU). The study included a total of 39 strains that represent all the 27 species included in the genus Arcobacter together with 13 strains that are potentially new species, and the analysis of 57 genomes. The different phylogenetic analyses showed that the Arcobacter species grouped into four clusters. In addition, A. lekithochrous and the candidatus species ‘A. aquaticus’ appeared, as did A. nitrofigilis, the type species of the genus, in separate branches. Furthermore, the genomic indices ANI and isDDH not only confirmed that all the species were well-defined, but also the coherence of the clusters. The AAI and POCP values showed intra-cluster ranges above the respective cut-off values of 60% and 50% described for species belonging to the same genus. Phenotypic analysis showed that certain test combinations could allow the differentiation of the four clusters and the three orphan species established by the phylogenetic and genomic analyses. The origin of the strains showed that each of the clusters embraced species recovered from a common or related environment. The results obtained enable the division of the current genus Arcobacter in at least seven different genera, for which the names Arcobacter, Aliiarcobacter gen. nov., Pseudoarcobacter gen. nov., Haloarcobacter gen. nov., Malacobacter gen. nov., Poseidonibacter gen. nov., and Candidate ‘Arcomarinus’ gen. nov. are proposed.
Highlights
The genus Arcobacter was created by Vandamme et al (1991) to accommodate Gram-negative, curved-shaped bacteria belonging to two species Campylobacter cryaerophila ( Arcobacter cryaerophilus) and Campylobacter nitrofigilis ( A. nitrofigilis), considered atypical campylobacters due to their ability to grow at lower temperatures (15◦C–30◦C) and without microaerophilic conditions (Vandamme et al, 1991)
One year later the genus was enlarged with the addition of two new species, A. skirrowii with an animal origin being isolated from aborted ovine, porcine and bovine fetuses, and from lambs with diarrhea, and A. butzleri, which was recovered from cases of human and animal diarrhea (Vandamme et al, 1992)
All the 27 species currently included in the genus Arcobacter and 13 candidate species have been investigated in the present study, which has analyzed 55 genomes, 16 of them from the public databases and 39 sequenced in this study (Tables 1, 2)
Summary
The genus Arcobacter was created by Vandamme et al (1991) to accommodate Gram-negative, curved-shaped bacteria belonging to two species Campylobacter cryaerophila ( Arcobacter cryaerophilus) and Campylobacter nitrofigilis ( A. nitrofigilis), considered atypical campylobacters due to their ability to grow at lower temperatures (15◦C–30◦C) and without microaerophilic conditions (Vandamme et al, 1991). One year later the genus was enlarged with the addition of two new species, A. skirrowii with an animal origin being isolated from aborted ovine, porcine and bovine fetuses, and from lambs with diarrhea, and A. butzleri, which was recovered from cases of human and animal diarrhea (Vandamme et al, 1992). A. halophilus was isolated from water from a hypersaline lagoon in Hawaii (Donachie et al, 2005), and A. cibarius was isolated from broiled carcasses in Belgium (Houf et al, 2005) These species were assigned to the genus Arcobacter on the basis of the 16S rRNA gene similarity (94% and 95% for A. nitrofigilis with A. halophilus and A. cibarius, respectively). These values are equal, or even below, the cut-off of 95% for genus definition (Rosselló-Mora and Amann, 2001; Yarza et al, 2008, 2014; Tindall et al, 2010)
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