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.

中文翻译：

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犬路氏乳杆菌的比较基因组学揭示了对人类共享环境的适应性。

背景

罗伊氏乳杆菌是革兰氏阳性，非运动性细菌，已被用作代表微生物模型来描述脊椎动物肠道共生体的生态和进化。

目的

由于来自犬胃肠道的罗伊氏乳杆菌的遗传特征和进化策略仍然未知，因此我们试图构建基因组草案的罗伊氏乳杆菌并研究修饰，获得或丢失的遗传特征，这些特征有助于菌株的进化和适应这项研究的具体环境。

方法

为了检查路氏乳杆菌，我们对从韩国的狗中分离出的路氏乳杆菌进行了测序。比较基因组学方法用于评估遗传多样性，并基于已发布的27个基因组序列深入了解与不同宿主相关的区别特征。

结果

28个罗伊氏乳杆菌菌株的全基因组包含7,369个基因家族，核心基因组包含1070个基因家族。基于犬路氏乳杆菌菌株（C1）核心基因的ANI树与人类的三种菌株（IRT，DSM20016，JCM1112）的树非常接近。从进化上讲，这四个菌株形成一个进化枝，在本研究中我们将其视为C1进化枝。我们可以调查28个罗伊氏乳杆菌中总共32,050个氨基酸取代菌株基因组。在该比较中，C1菌株特异地有283个氨基酸取代，而C1包层中的四个菌株共享了这283个C1菌株特异的氨基酸取代中的大部分，表明选择性压力非常相似。在辅助基因中，我们可以鉴定出127个C1-clade宿主特异性基因，并发现几个基因与复制，重组和修复密切相关。

结论

这项研究为罗伊氏乳杆菌对犬肠道栖息地的适应提供了新的见解，并表明来自犬的罗伊氏乳杆菌的基因组与其生活和与人类共享的环境密切相关。