A critical rebuttal of the proposed division of the genus Arcobacter into six genera using comparative genomic, phylogenetic, and phenotypic criteria

Authors: ON, STEPHEN - Lincoln University - New Zealand; Miller, William - Bill; BIGGS, PATRICK - Massey University; CORNELIUS, ANGELA - Institute Of Environmental Science And Research; VANDAMME, PETER - Ghent University

Submitted to: Systematic and Applied Microbiology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/23/2020
Publication Date: 7/30/2020
Citation: On, S.L., Miller, W.G., Biggs, P., Cornelius, A., Vandamme, P. 2020. A critical rebuttal of the proposed division of the genus Arcobacter into six genera using comparative genomic, phylogenetic, and phenotypic criteria. Systematic and Applied Microbiology. 43(5):126108. https://doi.org/10.1016/j.syapm.2020.126108.
DOI: https://doi.org/10.1016/j.syapm.2020.126108

Interpretive Summary: A proposal was recently published that outlined a reorganization of the genus Arcobacter, whose member species have been recovered from food, food animals, water and environmental sources and have been implicated in human gastroenteritis. This study refutes that proposal on the basis of genetic and biochemical analyses and demonstrates that division of Arcobacter into six new groups is not warranted, was based on faulty analyses, and causes unnecessary confusion in the placement of new organisms (due to characteristics that overlap between the six proposed groups) into the proposed framework. This study recommends that the existing classification of arcobacters should stand as is. New bacterial species can have either (or sometimes both) agricultural or clinical importance. Thus, it is vitally necessary for such species to be unambiguously defined, with a clearly-delineated set of phenotypic characteristics (for example: tolerance to air, resistance to certain antibiotics, growth on different substrates) that can be used to construct typing methods for both field and clinical use. Moreover, each new species must be clearly separated phenotypically and genotypically (that is, at the DNA sequence level) from related species, to prevent confusion in veterinary and clinical diagnoses.

Technical Abstract: The proposal to restructure the genus Arcobacter (Vandamme et al. 1991) into six distinct genera (Pérez-Cataluña et al. 2018) was critically examined using: comparative analyses of complete genome sequences of 82 Epsilonproteobacteria (including 26 arcobacters); phylogenetic analyses of three housekeeping genes and also 342 core genes; and phenotypic criteria. Genome sequences were analysed with tools to calculate average nucleotide identity, in silico DNA-DNA hybridisation values and G+C ratios. Genome analyses revealed Arcobacter sensu strictu to be relatively homogenous and phylogenetic analyses clearly distinguished the group from other Epsilonproteobacteria: distinction of the groups proposed by Pérez-Cataluña et al. (2018) was questionable. Similarly, phenotypic analyses supported the delineation of Arcobacter sensu strictu but did not justify the position of the proposed genera. This polyphasic taxonomic study supports the continuance of the previous classification of “aerotolerant campylobacters” as Arcobacter and refutes the proposed subdivision of Pérez-Cataluña et al. (2018). Emendments to descriptions of the genus Arcobacter and to A. anaerophilus are made on the basis of our findings.