摘要

在禁止家畜使用抗生素促生长剂（AGPs）后，饲养环境，包括动物肠道微生物群的组成，发生了迅速变化。我们假设微生物基因组也受到这种法律禁止的影响，并且采用全基因组方法研究了猪肠道微生物群的一个重要成员 - 唾液乳杆菌（Lactobacillus salivarius）。在这里，我们分离了21个唾液乳杆菌菌株，它们由在AGP禁止之前分离的6个菌株（SBP）和在AGP禁止之后分离的15个菌株（SAPs）以10年的间隔组成，并且从头生成基因组草图。虽然抗生素抗性基因的数量和功能没有不同，但SBP和SAPs之间的几个基因组差异被确定。SBPs和SAPs在基因组上存在差异，但耐药基因的数量和功能没有差异。SBP具有与利用L-鼠李糖和D-塔格糖进行能量生产相关的基因。由于这些糖也用于胞外多糖（EPS）合成，我们试图鉴定生物膜形成相关基因的差异。用于产生EPS和胞外蛋白的基因在氨基酸序列上存在差异。实际上，SAPs在猪肠道环境中形成致密的生物膜并且比SBPs存活得更好。这些结果表明，SAPs已经发展并适应于通过形成致密的生物膜，采用不同的抗生素抗性策略,进化适应来保护自己免受猪肠道微环境的新选择压力。这一发现对于了解宿主 - 微生物相互作用的进化变化特别重要，并为开发有效的家畜益生菌提供了详细的见解。

After the introduction of a ban on the use of antibiotic growth promoters (AGPs) for livestock, the feeding environment, including the composition of animal intestinal microbiota, has changed rapidly. We hypothesized that the microbial genomes have also been affected by this legal prohibition, and investigated an important member of the swine gut microbiota,Lactobacillus salivarius, with a pan-genomic approach. Here, we isolated 21 L. salivariusstrains composed of 6 strains isolated before the AGP prohibition (SBPs) and 15 strains isolated after the AGP prohibition (SAPs) at an interval of a decade, and the draft genomes were generated de novo. Several genomic differences between SBPs and SAPs were identified, although the number and function of antibiotic resistance genes were not different. SBPs showed larger genome size and a higher number of orthologs, as well as lower genetic diversity, than SAPs. SBPs had genes associated with the utilization of L-rhamnose and D-tagatose for energy production. Because these sugars are also used in exopolysaccharide (EPS) synthesis, we tried to identify differences in biofilm formation-associated genes. The genes for the production of EPSs and extracellular proteins were different in terms of amino acid sequences. Indeed, SAPs formed dense biofilm and survived better than SBPs in the swine intestinal environment. These results suggest that SAPs have evolved and adapted to protect themselves from new selection pressure of the swine intestinal microenvironment by forming dense biofilms, adopting a distinct antibiotic resistance strategy. This finding is particularly important to understand the evolutionary changes in host-microbe interaction and provide detailed insight for the development of effective probiotics for livestock.

http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0186671