Comparative genomics of Lactobacillus johnsonii reveals extensive intraspecific genetic variation

Lactobacillus johnsonii, as a microorganism widely presenting in the intestinal tract of mammals, dairy products, and poultry, possesses various probiotic characteristics. Currently, many research focused on the probiotic functions and industrial applications of L. johnsonii. In this study, 98 strains of L. johnsonii were subjected to comparative genomic analyses to explore its genetic diversity. The results indicated that based on ANI values, d-DDH values, phylogenetic analysis, and whole-genome comparison, the 98 strains of L. johnsonii were classified into two phylogenetic clusters. The carbohydrate utilization genes, bacteriocin operon, extracellular polysaccharide gene cluster, and bile salt hydrolase encoding genes in L. johnsonii shared common features and exhibited systematic differences based on phylogenetic clustering. The main reason for the high intra-species gene diversity of L. johnsonii might be differences in phages and other mobile genetic elements. This study provides new insights into the genomic features and functional genes of L. johnsonii.