Comprehensive genomic analyses revealed the adaptation strategies of Exiguobacterium and its phage genomic diversity.

Exiguobacterium exhibits high species diversity and complex evolutionary patterns, with members widely distributed across diverse habitats. To elucidate the mechanisms enabling its high adaptability to various environments, 187 genomes of Exiguobacterium strains were analyzed using the phylogenomic and comparative genomics methods. Our analysis revealed that nearly all Exiguobacterium strains harbor genes encoding the utilization of diverse complex polysaccharides and proteinaceous, as well as intact glycolysis and tricarboxylic acid cycle pathways. These abilities suggest that the strains of this genus can easily obtain carbon and nitrogen from the environment. Furthermore, Exiguobacterium strains encode heat- and cold-shock proteins for temperature adaptation, accumulate potassium and compatible solutes such as mannitol, betaine, glutamate, and proline for osmotic balance, and synthesize antioxidant enzymes including superoxide dismutase, catalase, peroxidase, disulfide isomerase, and methionine sulfoxide reductase to mitigate oxidative stress. Each Exiguobacterium strain also contains many genes for resistance to antibiotics and heavy metals, many of which are identified within genomic islands, indicating that horizontal gene transfer has substantially contributed to the rapid acquisition and spread of these adaptive traits. In addition, the presence of diverse phages further enhances genomic variability, and the identification of three auxiliary metabolic genes indicates a potential role for these phages in modulating specific host metabolic processes during infection. This study enhances our understanding of the adaptive mechanisms and key genomic traits of Exiguobacterium that enable its cosmopolitan distribution.