Genomic diversity and taxonomic marker for Arcobacter species

Guilan Zhou; Yixin Gu; Hairui Wang; Xiaoli Chen; Xin Zhang; Zhujun Shao; Xiaomei Yan; Jianzhong Zhang; Maojun Zhang

doi:10.3389/fmicb.2023.1278268

Genomic diversity and taxonomic marker for Arcobacter species

Front Microbiol. 2023 Oct 10:14:1278268. doi: 10.3389/fmicb.2023.1278268. eCollection 2023.

Authors

Guilan Zhou¹, Yixin Gu¹, Hairui Wang¹, Xiaoli Chen¹, Xin Zhang¹, Zhujun Shao¹, Xiaomei Yan¹, Jianzhong Zhang¹, Maojun Zhang¹

Affiliation

¹ State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.

Abstract

Arcobacter was recognized as an emerging enteropathogen and controversies regarding its classification persisted. This study aimed to reevaluate the taxonomy of Arcobacter utilizing the 16S rRNA gene, 23S rRNA gene, single-copy orthologous genes, as well as genomic indices such as Average Nucleotide Identity (ANI) and in silico DNA-DNA hybridization (isDDH). The taxonomy of this genus was reevaluated in this study using multiple indices with a dataset of 371 genomes comprising 34 known species and 14 potentially new species. Good discrimination could be achieved only in some species but not for the species with higher sequence similarity using the comparisons of the 16S rRNA gene and 23S rRNA gene sequences. A high-accuracy phylogenomic approach for Arcobacter was established using 84 single-copy orthologous genes obtained through various bioinformatics methods. One marker gene (gene711), which was found to possess the same distinguishing ability as ANI, isDDH, and single-copy orthologous methods, was identified as a reliable locus for inferring the phylogeny of the genus. The effective species classification was achieved by employing gene711 with a sequence similarity exceeding 96%, even for species like A. cloacae, A. lanthieri, and A. skirrowii, which exhibited ambiguous classification using ANI and isDDH. Additionally, excellent subspecies categorizing among A. cryaerophilus could be distinguished using gene711. In conclusion, this framework strategy had the potential advantage of developing rapid species identification, particularly for highly variable species, providing a novel insight into the behavior and characteristics of Arcobacter.

Keywords: ANI; Arcobacter; genome sequencing; isDDH; reliable marker gene; taxonomy.

Grants and funding

The author(s) declare financial support was received for the research, authorship, and/or publication of this article. This work was supported by the National Key Research and Development Program of China under Grant 2021YFC2301000; the Project for Novel Detection Techniques of Bacterial Pathogens under Grant 32073; Prevention and Intervention of Bacterial and Fungal Infectious Diseases under Grant 102393220020020000031; and Enhancement of Comprehensive Monitoring, Prevention, and Control Capabilities for Traditional Infectious Diseases Such as Plague, Cholera, and Brucellosis under Grant 102393230020020000002.