Abstract：
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.
摘要：
鼠李糖乳杆菌（L.鼠李糖）被广泛认为是一种益生菌，它存在于各种环境中，包括宿主肠道和乳制品。这项工作旨在对384个鼠李糖乳杆菌基因组进行大规模比较基因组学分析（来自肠道相关分离株的257个全序列或宏基因组组装的基因组[122和135从UHGG和NCBI数据库检索，分别]和127个来自乳制品分离株的基因组[34个来自NCBI数据库；93个从奶酪样品中分离并在此处测序]）。我们的结果表明，鼠李糖乳杆菌具有大而开放的泛基因组（从所有384个基因组中鉴定出15,253个泛基因；如果排除了93个奶酪来源的分离株，则为15,028个泛基因）。由384个鼠李糖乳杆菌基因组构建的核心基因系统发育树包括五个系统发育分支，乳制品和肠道相关分离株/基因组在整个树上随机分布。在乳制品和肠道相关基因组之间的代谢相关基因的总体概况中没有发现显着差异；但是，特别是,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-生物糖苷酶（EC3.2.1.140；GT20）和乳-N-二糖磷酸化酶/半乳糖-N-二糖磷酸化酶（EC2.4.1.211；GH112）。Further,我们发现93个奶酪来源的鼠李糖乳杆菌分离株具有明显的种内多样性，形成三个进化枝(进化枝A，B,和C)在重建的核心基因系统发育树中。在这三个进化枝上有许多单核苷酸变异(超过10,000)。此外，不同进化枝的代谢相关基因含量差异显著(p<0.05,Adonis检验),其特征在于在进化枝C中富含糖苷水解酶并且在每个进化枝中拥有独特的代谢途径。这些结果涉及鼠李糖乳杆菌在单一食物基质中的基因组学/功能多样化，以及来自乳制品和宿主肠道相关来源的分离物的生态位驱动的适应性进化。我们的研究为食品工业应用的候选菌株的选择提供了见解。
