The Core- and Pan-Genomic Analyses of the Genus Comamonas: From Environmental Adaptation to Potential Virulence

Abstract

<i>Comamonas</i> is often reported to be one of the major members of microbial communities in various natural and engineered environments. Versatile catabolic capabilities of <i>Comamonas</i> have been studied extensively in the last decade. In contrast, little is known about the ecological roles and adaptation of <i>Comamonas</i> to different environments as well as the virulence of potentially pathogenic <i>Comamonas</i> strains. In this study, we provide genomic insights into the potential ecological roles and virulence of <i>Comamonas</i> by analysing the entire gene set (pangenome) and the genes present in all genomes (core genome) using 34 genomes of 11 different <i>Comamonas</i> species. The analyses revealed that the metabolic pathways enabling <i>Comamonas</i> to acquire energy from various nutrient sources are well conserved. Genes for denitrification and ammonification are abundant in <i>Comamonas</i>, suggesting that <i>Comamonas</i> plays an important role in the nitrogen biogeochemical cycle. They also encode sophisticated redox sensory systems and diverse c-di-GMP controlling systems, allowing them to be able to effectively adjust their biofilm lifestyle to changing environments. The virulence factors in <i>Comamonas</i> were found to be highly species-specific. The conserved strategies used by potentially pathogenic <i>Comamonas</i> for surface adherence, motility control, nutrient acquisition and stress tolerance were also revealed.