Comparative genomic analysis of 455 Lactiplantibacillus plantarum isolates: Habitat-specific genomes shaped by frequent recombination

A large-scale comparative genomic analysis together with genome-wide association study of 455 Lactiplantibacillus (L.) plantarum genomes was performed. Firstly, the study generated phylogenic tree using core-genome of L. plantarum, and the phylogenetic tree comprised two major clades. The isolates in clade B were genetically more diverse than those of clade A. Furthermore, a mono-clade (clade B1) of 12 isolates was identified within clade B in L. plantarum. It is interesting to note that these 12 isolates were originated from diverse niches and wide geographic regions. Plant-associated isolates were distributed evenly across the phylogenetic tree. In contrast, more dairy product-originated isolates were distributed in clade B, while the animal- and meat product-originated isolates located mainly in clade A. The overall r/m ratio (ratio of recombination and mutation events) of all 455 L. plantarum isolates (1.181) was a lot lower than that of clade B1 (5.510), and there was a seven-fold difference in the r/m ratio between animal-originated isolates distributed to clade A (0.607) and clade B (4.373). The dairy and animal-originated isolates possessed multiple environment-specific genes. Our findings deepen the understanding of the niche-specific genome diversity of L. plantarum. •A large-scale genomic analysis to identify habitat-specific genomic signatures.•Isolates from animal and dairy showed significant biases in phylogenic distribution.•The dairy and animal-originated isolates had multiple environment-specific genes.