一项大规模的比较基因组学研究揭示了鼠李糖乳杆菌中与小生境相关的和样本内种内功能多样化。
A large-scale comparative genomics study reveals niche-driven and within-sample intra-species functional diversification in Lacticaseibacillus rhamnosus.
机构信息
Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China; Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China; Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China.
Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China; Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China; Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China.
出版信息
Food Res Int. 2023 Nov;173(Pt 2):113446. doi: 10.1016/j.foodres.2023.113446. Epub 2023 Sep 10.
Lacticaseibacillus rhamnosus (L. rhamnosus) is widely recognized as a probiotic species, and it exists in a variety of environments including host gut and dairy products. This work aimed at conducting a large-scale comparative genomics analysis of 384 L. rhamnosus genomes (257 whole-sequence or metagenomic-assembled genomes from gut-associated isolates [122 and 135 retrieved from the UHGG and NCBI databases, respectively] and 127 genomes from dairy isolates [34 from the NCBI database; 93 isolated from a cheese sample and sequenced here]). Our results showed that L. rhamnosus had a large and open pan-genome (15,253 pan-genes identified from all 384 genomes; 15,028 pan-genes if the 93 cheese-originated isolates were excluded). The core-gene phylogenetic tree constructed from the 384 L. rhamnosus genomes comprised five phylogenetic branches, with a random distribution of dairy and gut-associated isolates/genomes across the tree. No significant difference was identified in the overall profile of metabolism-related genes between dairy and gut-associated genomes; however, notably, the gut-associated strains/isolates contained more genes coding for specific metabolic pathways and carbohydrate-active enzymes, e.g., lacto-N-biosidase (EC 3.2.1.140; GT20) and lacto-N-biose phosphorylase/galacto-N-biose phosphorylase (EC 2.4.1.211; GH112). Further, we found that there was obvious intra-species diversification of the 93 cheese-originated L. rhamnosus isolates, forming three clades (Clades A, B, and C) in the reconstructed core-gene phylogenetic tree. There were numerous single nucleotide variations (over 10,000) across the three clades. Moreover, significant differences were observed in the content of metabolism-related genes across clades (p < 0.05, Adonis test), characterized by the enrichment in glycoside hydrolases in Clade C and the possession of unique metabolic pathways in each clade. These results implicated genomics/functional diversification of L. rhamnosus in a single food matrix and niche-driven adaptive evolution of isolates from dairy and host gut-associated origins. Our study shed insights into the selection of candidate strains for food industry applications.
鼠李糖乳杆菌（Lactobacillus rhamnosus）被广泛认为是一种益生菌，存在于宿主肠道和乳制品等多种环境中。本研究旨在对 384 株鼠李糖乳杆菌基因组进行大规模比较基因组学分析（257 株全序列或宏基因组组装基因组来自肠道相关分离株[分别从 UHGG 和 NCBI 数据库中获得 122 株和 135 株]，127 株来自乳制品分离株[34 株来自 NCBI 数据库；93 株从奶酪样本中分离并在此处测序]）。结果表明，鼠李糖乳杆菌具有一个较大的、开放的泛基因组（从所有 384 株基因组中鉴定出 15253 个泛基因；如果排除 93 株奶酪来源的分离株，则有 15028 个泛基因）。从 384 株鼠李糖乳杆菌基因组构建的核心基因系统发育树包含五个系统发育分支，树中随机分布有乳制品和肠道相关的分离株/基因组。乳制品和肠道相关基因组的代谢相关基因总体特征无显著差异；然而，值得注意的是，肠道相关菌株/分离株含有更多编码特定代谢途径和碳水化合物活性酶的基因，例如乳-N-酰基-β-氨基葡萄糖苷酶（EC 3.2.1.140；GT20）和乳-N-酰基-β-氨基葡萄糖苷磷酸酶/半乳糖-N-酰基-β-氨基葡萄糖苷磷酸酶（EC 2.4.1.211；GH112）。此外，我们发现，93 株奶酪来源的鼠李糖乳杆菌分离株在种内存在明显的多样化，在重建的核心基因系统发育树中形成了三个分支（分支 A、B 和 C）。三个分支之间存在大量的单核苷酸变异（超过 10000 个）。此外，在分支之间观察到代谢相关基因的含量存在显著差异（p<0.05，Adonis 检验），表现为分支 C 中糖苷水解酶的富集和每个分支中独特代谢途径的存在。这些结果表明，在单一食品基质中，鼠李糖乳杆菌的基因组/功能多样化以及乳制品和宿主肠道相关来源的分离株的适应进化是由生态位驱动的。本研究为食品工业应用中候选菌株的选择提供了思路。
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