Lactobacillus plantarum colonizes a range of natural habitat. A phylogenomic analysis showed little association between the range of habitats and diversity in the core-genome. However, the functional genetic features and evolutionary strategies used by L. plantarum to adapt to its niches have not been well investigated using statistical methods. In this study, 140 genomes of L. plantarum recorded in the NCBI database were subjected to comparative genomic analysis to evaluate the genetic diversity and elucidate the distinguishing features associated with the occupation of different niches, including humans, dairy products, Drosophila melanogaster and vegetables. Notably, the genome sizes and GC contents of strains isolated from D. melanogaster were markedly different. By aligning the genomes against the Clusters of Orthologous Groups of Proteins database, the Carbohydrate-Active Enzyme database, the Virulence Factor database and the Comprehensive Antibiotic Resistance database, statistically different functional genome profiles in strains from those 4 niches were determined, as well as correlations of some functional genes with the ability to adapt to a habitat. Based on these results, 20 strains of L. plantarum from human feces and Chinese pickles were isolated and their genomic features were analyzed. Subsequently, a machine learning model confirmed the consistency of functional features of L. plantarum in different niches. This study showed that although most L. plantarum strains were not native to their habitats and had distinct genetic backgrounds, this organism could undergo genomic variation in response to ecological constraints. Moreover, strains within the same niche tended to harbor similar functional genome profiles.

植物乳杆菌在许多自然栖息地定居。系统进化分析表明，生境范围与核心基因组多样性之间没有关联。然而，尚未使用统计方法很好地研究植物乳杆菌适应其生态位的功能遗传特征和进化策略。在这项研究中，对NCBI数据库中记录的140个植物乳杆菌基因组进行了比较基因组分析，以评估遗传多样性并阐明与占领不同生态位（包括人类，乳制品，果蝇和蔬菜）有关的区别特征。值得注意的是，从中分离的菌株的基因组大小和GC含量D. melanogaster明显不同。通过将基因组与直系同源蛋白质簇数据库，碳水化合物-活性酶数据库，毒力因子数据库和综合抗生素抗性数据库比对，确定了这4个生态位菌株的统计上不同的功能基因组谱，以及相关性一些具有适应栖息地能力的功能基因。根据这些结果，从人粪便和泡菜中分离出20株植物乳杆菌，并对其基因组特征进行了分析。随后，机器学习模型证实了植物乳杆菌在不同生态位中功能特征的一致性。这项研究表明，尽管大多数植物乳杆菌由于这些菌株不是其栖息地的原生物种，并且具有独特的遗传背景，这种生物体可能会因生态限制而发生基因组变异。此外，在同一位置上的菌株往往具有相似的功能基因组图谱。