Comprehensive Genomic Characterization of <i>Campylobacter</i> Genus Reveals Some Underlying Mechanisms for its Genomic Diversification

<div><p><i>Campylobacter species.</i>are phenotypically diverse in many aspects including host habitats and pathogenicities, which demands comprehensive characterization of the entire <i>Campylobacter</i> genus to study their underlying genetic diversification. Up to now, 34 <i>Campylobacter</i> 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 <i>Campylobacter</i> 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 <i>Campylobacter jejuni</i> strains. Combined with the phylogeny of all the collected <i>Campylobacter</i> species based on genome-wide core gene information, comprehensive phylogenetic inference of all 34 <i>Campylobacter</i> organisms was determined. It was found that <i>C. jejuni</i> harbors a high fraction of ACFs possibly through intraspecies recombination, whereas other <i>Campylobacter</i> members possess numerous ACFs possibly via intragenus recombination. Furthermore, some <i>Campylobacter</i> 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 <i>Campylobacter</i> genus.</p>