Comparative genomics of canine Lactobacillus reuteri reveals adaptation to a shared environment with humans
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Genes & Genomics https://doi.org/10.1007/s13258-020-00978-w
RESEARCH ARTICLE
Comparative genomics of canine Lactobacillus reuteri reveals adaptation to a shared environment with humans Seungwoo Son1 · Jae‑Don Oh1 · Sung Ho Lee2 · Donghyun Shin1 · Yangseon Kim3 Received: 8 January 2020 / Accepted: 23 July 2020 © The Genetics Society of Korea 2020
Abstract Background Lactobacillus reuteri is 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 of L. reuteri from the gastrointestinal tract of canines remain unknown, we tried to construct draft genome canine L. reuteri and 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 canine L. reuteri, we sequenced an L. reuteri strain 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 28 L. reuteri strains contained 7,369 gene families, and the core genome contained 1070 gene families. The ANI tree based on the core genes in the canine L. reuteri strain (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 28 L. reuteri strain 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 of L. reuteri to the canine intestinal habitat, and suggests that the genome of L. reuteri from canines is closely associated with their living and shared environment with humans. Keywords Lactobacillus reuteri · Comparative genomics · Pan-genome analysis · Host adaptation · Dog
Introduction Seungwoo Son and Jae-Don Oh authors equally contributed to this work. Electronic supplementary material The online version of this article (https://doi.org/10.1007/s13258-020-00978-w) contains supplementary material, which is available to authorized users.
Lactobacillus reuteri persisting in the intestinal microbiota of vertebrate animals (Walter 2008), is a gram-positive, non-motile, obligately heterofermentative bacterial species 1
* Yangseon Kim [email protected]
The Animal Molecular Genetics and Breeding Center, Jeonbuk National University, Jeollabuk‑do, Jeonju‑si 54896, Republic of Kore
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