Comparative Genome Analysis of Lactiplantibacillus paraplantarum

Abstract

Lactiplantibacillus paraplantarum is a lactic acid bacteria species that is associated with food microbiomes and has been found to be either detrimental or beneficial to specific food processes. In this study, an in-silico genomic approach was applied using JGI’s IMG/MER and PATRIC to compare the genomes of the L. paraplantarum DSM10667, L-ZS9, and AS-7 strains to uncover metabolic differences and lifestyle adaptations between these isolates, and better utilizing these species in food bioprocesses. Bacteriocin and prophage screenings were performed using Bagel4 and PHASTER software, respectively. BRIG was used to identify alignments of strains with each other for visual inspection of each genome. KEGG was used to predict putative carbohydrate, pyruvate, and aminoacid metabolisms. Genome sizes of DSM10667, L-ZS9, and AS-7 were 3.36, 3.14, and 3.01 Mbp, respectively. Unique genes were found to predict the evolutionary adaptation of strains against their corresponding microniche. For example, the gene encoding arginase was only found in sausage isolate L-ZS9, while the dextran-sucraseencoding gene was unique to beer contaminant DSM10667. Three strains were predicted to carry the plnAEFJ operon for plantaricin biosynthesis, and the AS-7 genome contains leucocin K. Although DSM 10667 harbors four intact prophages, both L-ZS9 and AS-7 carried one prophage region, still showing the plasticity of the genome. Genome analysis predicted that isolation sources might potentially affect the metabolic capabilities of strains as part of the adaptation of the strains to their habitats.