Comprehensive pan-genome analysis of Lactiplantibacillus plantarum complete genomes.

Aims The aim of this work was to refine the taxonomy and the functional characterization of publicly available Lactiplantibacillus plantarum complete genomes through a pan-genome analysis. Particular attention was paid in depicting the probiotic potential of each strain. Methods and results Complete genome sequence of 127 L. plantarum strains, without detected anomalies, was downloaded from NCBI. Roary analysis of L. plantarum pan-genome identified 1,436 core, 414 soft core, 1,858 shell and 13,203 cloud genes, highlighting the "open" nature of L. plantarum pan-genome. Identification and characterization of plasmid content, mobile genetic elements, adaptative immune system and probiotic marker genes (PMGs) revealed unique features across all the L. plantarum strains included in the present study. Considering our updated list of PMGs, we determined that approximatively 70% of the PMGs belongs to the core/soft-core genome. Conclusions The comparative genomic analysis conducted in this study provide new insights into the genomic content and variability of L. plantarum. Significance and impact of study This study provides a comprehensive pan-genome analysis of L. plantarum, including the largest number (N=127) of complete L. plantarum genomes retrieved from publicly available repositories. Our effort aimed to determine a solid reference panel for the future characterization of newly sequenced L. plantarum strains useful as probiotic supplements.