Food Science and Technology Department, Federal University of Santa Catarina, Florianópolis, SC, Brazil.
Department of Soil Science, Luiz de Queiroz College of Agriculture, Piracicaba, SP, Brazil.
Probiotics Antimicrob Proteins. 2023 Jun;15(3):548-557. doi: 10.1007/s12602-021-09868-3. Epub 2021 Oct 26.
The Gram-positive Lacticaseibacillus rhamnosus has been broadly reported as capable of exerting beneficial health effects. Bacterial genomic diversity may promote niche specialization, thus creating subpatterns within populations. As L. rhamnosus advantageous effects have been widely reported at strain level and few is known regarding the distribution of beneficial genes among L. rhamnosus strains, we investigated all publicly available genomes of Lactobacillus and Lacticaseibacillus genera to study the pangenome and general population structure of L. rhamnosus. Core genome multilocus sequence typing detected eight L. rhamnosus phylogroups (PG1 to PG8). L. rhamnosus harbors an open pangenome; PG1, PG3, PG4, and PG5 exhibited highly conserved gene distribution patterns. Genes significantly associated to the PG1, which comprises L. rhamnosus GG, are mainly phage-related. The adhesion operon spaCBA-srtC1 was found in 44 (24.7%) genomes; however, considering only the PG1, the prevalence was of 65%. In PG2 the spaCBA-srtC1 prevalence was of 43%. Nevertheless, both human and milk-derived strains harbored this operon. Further, two main types of bacteriocin clusters were found (Bact1 and Bact2). Bact1 predictions indicate the presence of garQ, encoding the class II bacteriocin garvieacin Q, that is mainly present in the closely related PG8A and a PG2 subcluster. PG2 harbors two distinct subclusters, harboring either spaCBA-srtC1 or Bact1. Our findings provide novel insights on the distribution of biotechnological relevant genes across L. rhamnosus population, uncovering intra-species patterns that may bring forth the development of more efficient probiotic products.
被广泛报道的革兰氏阳性鼠李糖乳杆菌能够发挥有益的健康作用。细菌基因组多样性可能促进生态位特化，从而在种群中创造亚模式。由于鼠李糖乳杆菌的有利影响已在菌株水平上广泛报道，而关于鼠李糖乳杆菌菌株中有益基因的分布知之甚少，我们研究了乳杆菌属和乳酸乳球菌属的所有公开基因组，以研究鼠李糖乳杆菌的泛基因组和总体种群结构。核心基因组多位点序列分型检测到 8 个鼠李糖乳杆菌进化枝（PG1 到 PG8）。鼠李糖乳杆菌拥有一个开放的泛基因组；PG1、PG3、PG4 和 PG5 表现出高度保守的基因分布模式。与 PG1 相关的基因显著相关，PG1 主要由鼠李糖乳杆菌 GG 组成，主要与噬菌体有关。在 44 个（24.7%）基因组中发现了粘附操纵子 spaCBA-srtC1；然而，仅考虑 PG1，流行率为 65%。PG2 中的 spaCBA-srtC1 流行率为 43%。然而，人类和牛奶来源的菌株都携带该操纵子。此外，发现了两种主要的细菌素簇（Bact1 和 Bact2）。Bact1 的预测表明存在 garQ，编码 II 型细菌素 garvieacin Q，主要存在于密切相关的 PG8A 和 PG2 亚群中。PG2 含有两个不同的亚群，分别携带 spaCBA-srtC1 或 Bact1。我们的研究结果提供了关于鼠李糖乳杆菌种群中生物技术相关基因分布的新见解，揭示了种内模式，可能为开发更有效的益生菌产品提供依据。
