| Summary: | <i>Lactobacillus acidophilus</i> is a common kind of lactic acid bacteria usually found in the human gastrointestinal tract, oral cavity, vagina, and various fermented foods. At present, many studies have focused on the probiotic function and industrial application of <i>L. acidophilus</i>. Additionally, dozens of <i>L. acidophilus</i> strains have been genome sequenced, but there has been no research to compare them at the genomic level. In this study, 46 strains of <i>L. acidophilus</i> were performed comparative analyses to explore their genetic diversity. The results showed that all the <i>L. acidophilus</i> strains were divided into two clusters based on ANI values, phylogenetic analysis and whole genome comparison, due to the difference of their predicted gene composition of bacteriocin operon, CRISPR-Cas systems and prophages mainly. Additionally, <i>L. acidophilus</i> was a pan-genome open species with a difference in carbohydrates utilization, antibiotic resistance, EPS operon, surface layer protein operon and other functional gene composition. This work provides a better understanding of <i>L. acidophilus</i> from a genetic perspective, and offers a frame for the biotechnological potentiality of this species.
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