Comparative genomics shows niche-specific variations of Lactobacillus plantarum strains isolated from human, Drosophila melanogaster, vegetable and dairy sources

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.