Revisiting the Taxonomy of the Genus Arcobacter: Getting Order From the Chaos

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, Aliarcobacter gen. nov., Pseudoarcobacter gen. nov., Haloarcobacter gen. nov., Malacobacter gen. nov., Poseidonibacter gen. nov., and Candidate ‘Arcomarinus’ gen. nov. are proposed.

Dynamics of the Pacific oyster pathobiota during mortality episodes in Europe assessed by 16S rRNA gene profiling and a new target enrichment next‐generation sequencing strategy

“…The species Arcobacter haliotis was isolated from the gut of an abalone of the species Haliotis gigantea collected in Japan (Tanaka et al, 2017), however, taxonomy of the Arcobacter sp. strain found in this study and its potential role as an opportunistic pathogen for C. gigas deserve further investigations (Pérez-Cataluña et al, 2018).…”

“…strain found in this study and its potential role as an opportunistic pathogen for C . gigas deserve further investigations (Pérez‐Cataluña et al ., ).…”

Virulence and antibiotic resistance plasticity ofArcobacter butzleri: insights on the genomic diversity of an emerging human pathogen

“…The characterization of new species pointed to the need of a clarification of the genus' taxonomy, and recently, a genomic comparative analysis of the class Epsilonproteobacteria suggested a reclassification of Arcobacter genus as a new family Arcobacteraceae [3]. Furthermore, a taxonomic and phylogenetic analyses of the 29 recognized species and 11 candidate species led Pérez-Cataluña et al (2018) [4] to propose a division of the current genus Arcobacter in seven different genera: Arcobacter, Aliarcobacter gen. nov., Pseudarcobacter gen. nov., Halarcobacter gen. nov., Malaciobacter gen. nov., Poseidonibacter gen. nov., and Candidate 'Arcomarinus' gen. nov., of which four genera have already be validated [4,5]. The species A. butzleri, A. cryaerophilus, A. skirrowii and A. thereius, all considered human pathogens, will be included in Aliarcobacter genus [4].…”

“…Furthermore, a taxonomic and phylogenetic analyses of the 29 recognized species and 11 candidate species led Pérez-Cataluña et al (2018) [4] to propose a division of the current genus Arcobacter in seven different genera: Arcobacter, Aliarcobacter gen. nov., Pseudarcobacter gen. nov., Halarcobacter gen. nov., Malaciobacter gen. nov., Poseidonibacter gen. nov., and Candidate 'Arcomarinus' gen. nov., of which four genera have already be validated [4,5]. The species A. butzleri, A. cryaerophilus, A. skirrowii and A. thereius, all considered human pathogens, will be included in Aliarcobacter genus [4]. Amongst these species, the International Commission on Microbiological Specifications for Foods included A. butzleri and A. cryaerophilus in the list of microbes considered a serious hazard to human health [6].…”

Occurrence, virulence gene and antimicrobial susceptibility profiles of Arcobacter sp . isolated from catla ( Catla catla ) in India

“…Members of the genus arcobacters are Gram-negative, motile, non-spore forming, spiral-shaped bacteria belonging to the family Campylobacteriaceae (Vandamme et al 1991). Currently, this genus comprises 27 recognized species isolated from different environments and hosts (Levican et al 2015;Whiteduck-L eveill ee et al 2015;P erez-Cataluña et al 2018), of which Arcobacter butzleri, A. cryaerophilus, A. cibarus, A. skirrowii and A. mytili are considered as potential human pathogens (Ho et al 2006;Collado and Figueras 2011;Levican et al 2015). Pathogenic arcobacters have been associated with gastrointestinal and extra-gastrointestinal diseases ranging from diarrhoea to bacteraemia (Figueras et al 2014) and hence are increasingly being recognized as emerging sea foodand water-borne human pathogens (Fera et al 2004;Collado and Figueras, 2011;Patyal et al 2011;Rathlavath et al 2016).…”