Comparative genomics of Commensalibacter. Comparative genomics of insect associated Commensalibacter reveals host specific adaptations

Acetic acid bacteria are ubiquitous microbes in sugar-rich environments like fruits, flowers, and nectar. The family of acetic acid bacteria includes 19 different genera, of which Commensalibacter is the least studied. Commensalibacter has been associated with insects feeding on sugars, such as honeybees, bumble bees, and butterflies, in which it likely provides health benefits to the hosts. Nevertheless, little is known about Commensalibacter phylogeny and its role in insects. In this study, we performed comparative genomics on six Commensalibacter genomes obtained from isolates or metagenomes from the common fruit fly, honeybee, monarch butterfly, and the Southern green shield bug. Phylogenomic analyses revealed that the six Commensalibacter strains comprised four species with strains obtained from the same host clustering together. The six genomes differed in size and GC content. The genomes showed similar potential to generate energy, but differed in their ability to metabolize carbohydrates, amino acids, and vitamins. A core genome of 1227 genes was found for all strains with each strain containing numerous strain-specific genes. A detailed analysis of the accessory genome of a novel Commensalibacter strain (Nvir) originating from the Southern green shield, an agricultural important pest insect, revealed 319 unique protein-coding sequences involving carbohydrate, amino acid metabolism, and vitamin metabolism, in addition to potential detoxification of toxic secondary plant metabolites.. Altogether, we show a wide diversity within the genus Commensalibacter and reveal genomic specialisation towards a host-specific symbiotic lifestyle.