Comprehensive Genomic Characterization of Campylobacter Genus Reveals Some Underlying Mechanisms for its Genomic Diversification

Yizhuang Zhou,Jie Liu,Liyu Chen,Yongdong Wang,Chengran Zhou,Min Guo,Lijing Bu,Mikael Skurnik

doi:10.1371/journal.pone.0070241

Abstract

Campylobacter species.are phenotypically diverse in many aspects including host habitats and pathogenicities, which demands comprehensive characterization of the entire Campylobacter genus to study their underlying genetic diversification. Up to now, 34 Campylobacter strains have been sequenced and published in public databases, providing good opportunity to systemically analyze their genomic diversities. In this study, we first conducted genomic characterization, which includes genome-wide alignments, pan-genome analysis, and phylogenetic identification, to depict the genetic diversity of Campylobacter genus. Afterward, we improved the tetranucleotide usage pattern-based naïve Bayesian classifier to identify the abnormal composition fragments (ACFs, fragments with significantly different tetranucleotide frequency profiles from its genomic tetranucleotide frequency profiles) including horizontal gene transfers (HGTs) to explore the mechanisms for the genetic diversity of this organism. Finally, we analyzed the HGTs transferred via bacteriophage transductions. To our knowledge, this study is the first to use single nucleotide polymorphism information to construct liable microevolution phylogeny of 21 Campylobacter jejuni strains. Combined with the phylogeny of all the collected Campylobacter species based on genome-wide core gene information, comprehensive phylogenetic inference of all 34 Campylobacter organisms was determined. It was found that C. jejuni harbors a high fraction of ACFs possibly through intraspecies recombination, whereas other Campylobacter members possess numerous ACFs possibly via intragenus recombination. Furthermore, some Campylobacter strains have undergone significant ancient viral integration during their evolution process. The improved method is a powerful tool for bacterial genomic analysis. Moreover, the findings would provide useful information for future research on Campylobacter genus.

Highlights

Campylobacter is a genus of Gram-negative bacteria that are spiral-shaped microaerophilic and motile [1]
23 species are recorded in the National Center for Biotechnology Information (NCBI) Taxonomy Division
Other Campylobacter species are related to severe animal diseases; for instance, Campylobacter fetus can cause abortion in animals [20,21,22] and bovine genital campylobacteriosis [23,24]

Summary

Introduction

Campylobacter is a genus of Gram-negative bacteria that are spiral-shaped microaerophilic and motile [1]. Protein Family Construction and Pan-genome Analysis All protein coding gene sequences were translated into protein sequences according to Codon Table 11 from NCBI. The protein sequences of the repeat genes of an organism and the core genes of Campylobacter genus plus the total representative protein sequences were extracted to conduct alignments against the Cluster of Orthologous Groups (COG) database [39] using the local alignment tool BLASTP.

Results

Conclusion