Son Seungwoo, Oh Jae-Don, Lee Sung Ho, Shin Donghyun, Kim Yangseon
The Animal Molecular Genetics and Breeding Center, Jeonbuk National University, Jeollabuk-do, Jeonju-si, 54896, Republic of Korea.
Woogene B&G Co., Ltd., Gyeonggi-do, Hwaseong-si, 18630, Republic of Korea.
Genes Genomics. 2020 Sep;42(9):1107-1116. doi: 10.1007/s13258-020-00978-w. Epub 2020 Aug 6.
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.
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.
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.
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.
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.
罗伊氏乳杆菌是一种革兰氏阳性、不运动的细菌物种，已被用作描述脊椎动物肠道共生体生态和进化的代表性微生物模型。
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尚不清楚，我们试图构建犬罗伊氏乳杆菌的基因组草图，并通过本研究调查促进菌株进化和适应特定环境生态位的修饰、获得或丢失的遗传特征。
为了检测犬罗伊氏乳杆菌，我们对从韩国一只狗身上分离出的一株罗伊氏乳杆菌进行了测序。基于27个已发表的基因组序列，采用比较基因组学方法评估遗传多样性，并深入了解与不同宿主相关的独特特征。
28株罗伊氏乳杆菌的泛基因组包含7369个基因家族，核心基因组包含1070个基因家族。基于犬罗伊氏乳杆菌菌株（C1）核心基因的ANI树与来自人类的三株菌株（IRT、DSM20016、JCM1112）的ANI树非常接近。在进化上，这四株菌株形成一个分支，在本研究中我们将其视为C1分支。我们总共可以研究28株罗伊氏乳杆菌菌株基因组中的32050个氨基酸替换。在这次比较中，283个氨基酸替换是菌株C1特有的，C1分支中的四株菌株共享了这283个C1菌株特有的氨基酸替换中的大部分，这表明它们具有非常相似的选择压力。在辅助基因中，我们可以鉴定出127个C1分支宿主特异性基因，并发现几个基因与复制、重组和修复密切相关。
本研究为罗伊氏乳杆菌对犬肠道栖息地的适应性提供了新的见解，并表明犬源罗伊氏乳杆菌的基因组与其与人类的生活和共享环境密切相关。
