Comparative Genomic Analysis of Vibrio cincinnatiensis Provides Insights into Genetic Diversity, Evolutionary Dynamics, and Pathogenic Traits of the Species

Abstract

Vibrio cincinnatiensis is a poorly understood pathogenic Vibrio species, and the underlying mechanisms of its genetic diversity, genomic plasticity, evolutionary dynamics, and pathogenicity have not yet been comprehensively investigated. Here, a comparative genomic analysis of V. cincinnatiensis was constructed. The open pan-genome with a flexible gene repertoire exhibited genetic diversity. The genomic plasticity and stability were characterized by the determinations of diverse mobile genetic elements (MGEs) and barriers to horizontal gene transfer (HGT), respectively. Evolutionary divergences were exhibited by the difference in functional enrichment and selective pressure between the different components of the pan-genome. The evolution on the Chr I and Chr II core genomes was mainly driven by purifying selection. Predicted essential genes in V. cincinnatiensis were mainly found in the core gene families on Chr I and were subject to stronger evolutionary constraints. We identified diverse virulence-related elements, including the gene clusters involved in encoding flagella, secretion systems, several pili, and scattered virulence genes. Our results indicated the pathogenic potential of V. cincinnatiensis and highlighted that HGT events from other Vibrio species promoted pathogenicity. This pan-genome study provides comprehensive insights into this poorly understood species from the genomic perspective.

Pan-Chromosome and Comparative Analysis of Agrobacterium fabrum Reveal Important Traits Concerning the Genetic Diversity, Evolutionary Dynamics, and Niche Adaptation of the Species

“…However, previous comparative genomic analysis of the C58 genome found that the linear chromosome exhibited higher plasticity and was much less conserved than the circular chromosome ( 12 , 18 ). Other bacteria with multi-chromosome genomes, such as Vibrio spp., have greater genetic diversity in the chromid than in Chr I ( 19 , 20 ). Thus, it is interesting that the Chr I and chromid pan-genomes of A. fabrum demonstrated similar genetic diversity.…”

“…6F ). Several studies have observed different evolutionary rates for each chromosome in a multipartite genome ( 19 ). The substitution rate of the secondary chromosome (chromid) of Burkholderia and Vibrio is higher than that of the chromosome, whereas purifying selection is weaker on the chromid ( 31 ).…”

Insights into Evolutionary, Genomic, and Biogeographic Characterizations of Chryseobacterium nepalense Represented by a Polyvinyl Alcohol-Degrading Bacterium, AC3

“…Horizontal gene transfer (HGT) mediated by MGEs is the major driver of bacterial genomic evolution and promotes the acquisition of new physiological functions, which is crucial for niche adaptation ( 34 , 35 ). A total of 236 potential horizontal genes were identified (Table S5).…”

Metagenomic Next-Generation Sequencing for the Diagnosis of Neonatal Infectious Diseases

“…Mupapillomavirus 2 and Dolosigranulum pigrum were classified as irrelevant pathogens ( 51 , 52 ). Vibrio cincinnatiensis and Wickerhamomyces anomalus are rarely pathogenic, but it was also reported that they can cause infections ( 53 – 56 ), and W. anomalus was also detected by culture. Associated with the clinical manifestations in the patients, these two pathogens were classified as causative pathogens.…”