Lactobacillus plantarum, a widely used probiotic in the food industry, exists in diverse habitats, which has led to its niche-specific genetic evolution. However, the relationship between this type of genetic evolution and the bacterial phenotype remains unclear. Here, six L. plantarum strains derived from paocai and human feces were analyzed at the genomic and phenotypic levels to investigate the features of adaptive evolution in different habitats. A comparative genomic analysis showed that 93 metabolism-related genes underwent structural variations (SVs) during adaptive evolution, including genes responsible for carbohydrate, lipid, amino acid, inorganic ion and coenzyme transport and metabolism, and energy production and conversion. Notably, seven virulence factor-related genes in strains from both habitats showed SVs — similar to the pattern found in the orthologous virulence genes of pathogenic bacteria shared similar niches, suggesting the possibility of horizontal gene transfer. These genomic variations further influenced the metabolic abilities of strains and their interactions with the commensal microbiota in the host intestine. Compared with the strains from feces, those from paocai exhibited a shorter stagnation period and a higher growth rate in a diluted paocai solution because of variations in functional genes. In addition, opposite correlations were identified between the relative abundances of L. plantarum strains and the genus Bifidobacterium in two media inoculated with strains from the two habitats. Overall, our findings revealed that the niche-specific genetic evolution of L. plantarum strains is associated with their fermentation abilities and physiological functions in host gut health. This knowledge can help guiding the exploration and application of probiotics from the specific niches-based probiotic exploitation.

植物乳杆菌是食品工业中广泛使用的益生菌，存在于不同的生境中，这导致了其利基特有的遗传进化。但是，这种类型的遗传进化和细菌表型之间的关系仍然不清楚。来六个植物乳杆菌在基因组和表型水平上分析了来自paocai和人类粪便的菌株，以研究不同生境中适应性进化的特征。比较基因组分析表明，在适应性进化过程中，有93个与代谢相关的基因经历了结构变异（SV），包括负责碳水化合物，脂质，氨基酸，无机离子和辅酶运输和代谢以及能量产生和转化的基因。值得注意的是，两个生境中的菌株中有七个与毒力因子相关的基因均显示出SV-与致病细菌直系同源性毒力基因的模式相似，具有相似的生态位，这表明水平基因转移的可能性。这些基因组变异进一步影响了菌株的代谢能力以及它们与宿主肠道中共生微生物的相互作用。与粪便菌株相比，由于功能基因的差异，来自粪便的菌株在稀释的粪便溶液中表现出更短的停滞期和更高的生长速率。此外，在相对丰度之间确定了相反的相关性。植物乳杆菌 菌株和属 双歧杆菌在两种培养基中接种了来自两个栖息地的菌株。总的来说，我们的研究结果表明，植物乳杆菌菌株与其在宿主肠道健康中的发酵能力和生理功能有关。这些知识可以帮助指导基于特定生态位的益生菌开发中益生菌的探索和应用。