Comparative genomics of canineLactobacillus reuterireveals adaptation to a shared environment with humans

Background Lactobacillus reuteriis a gram-positive, non-motile bacterial species that has been used as a representative microorganism model to describe the ecology and evolution of vertebrate gut symbionts. Objective Because the genetic features and evolutionary strategies ofL. reuterifrom the gastrointestinal tract of canines remain unknown, we tried to construct draft genome canineL. reuteriand investigate modified, acquired, or lost genetic features that have facilitated the evolution and adaptation of strains to specific environmental niches by this study. Methods To examine canineL. reuteri, we sequenced anL. reuteristrain isolated from a dog in Korea. A comparative genomic approach was used to assess genetic diversity and gain insight into the distinguishing features related to different hosts based on 27 published genomic sequences. Results The pan-genome of 28L. reuteristrains contained 7,369 gene families, and the core genome contained 1070 gene families. The ANI tree based on the core genes in the canineL. reuteristrain (C1) was very close to those for three strains (IRT, DSM20016, JCM1112) from humans. Evolutionarily, these four strains formed one clade, which we regarded as C1-clade in this study. We could investigate a total of 32,050 amino acid substitutions among the 28L. reuteristrain genomes. In this comparison, 283 amino acid substitutions were specific to strain C1 and four strains in C1-clade shared most of these 283 C1-strain specific amino acid substitutions, suggesting strongly similar selective pressure. In accessory genes, we could identify 127 C1-clade host-specific genes and found that several genes were closely related to replication, recombination, and repair. Conclusion This study provides new insights into the adaptation ofL. reuterito the canine intestinal habitat, and suggests that the genome ofL. reuterifrom canines is closely associated with their living and shared environment with humans.