Non-redundant nature of Lactiplantibacillus plantarum plasmidome revealed by comparative genomic analysis of 105 strains.

ABSTRACT

Lactiplantibacillus plantarum is a homofermentative lactic acid bacterium (LAB) most often found in fermented foods with many strains displaying probiotic properties. Strains belonging to L. plantarum are more stress tolerant and metabolically flexible than other lactobacilli and display larger genomes and higher plasmid abundance. This study aimed at understanding whether plasmids play a particular role in L. plantarum as compared to chromosomes by comparative genomic analysis. Assessment of chromosomes and 395 plasmids of 105 strains with publicly available complete genome sequences revealed that the majority of the plasmids encoded protein families (PFs) (57.6%) were not encoded by the chromosomes. The most abundant PFs unique to plasmids contained hypothetical proteins while others were involved in exopolysaccharides biosynthesis, biofilm formation, stress tolerance, and carbohydrate metabolism. The sequences of common plasmid-encoded and chromosome-encoded PFs differed from each other, suggesting that they might exhibit different biochemical properties. Common PF genes were predominantly present on larger plasmids pointing to another possible way to reduce redundancy by encoding shared PFs by low copy number plasmids. Overall, this study demonstrates the unique contributions of the plasmids to the versatility, survival, and evolutionary success of L. plantarum while also highlighting a need to functionally characterize hypothetical proteins encoded by them.