Comparative Genome Analysis of Lactobacillus casei: Insights into Genomic Diversification for Niche Expansion

Abstract

Lactobacillus casei, as a probiotic, has to survive the industrial production processes and endure the harsh physical–chemical environment of the human gastrointestinal tract. To explore genetic variability supporting improved adaptation of these bacteria to their environments, we performed a comparative genome analysis of L. casei. A total of 806 novel regions ≥500 bp were also found, as compared to the 12 recently sequenced L. casei strains, constituting 2,976,837 bp of genomic DNA not present in the seven reference complete genomes of L. casei. The widespread distribution of phage-related proteins among these novel regions suggests the transduction could be an important mechanism for genomic evolution in this species. The core- and accessory-based MP trees of L. casei had identical topology compared with MLST-based MP tree. The orthologues and phylogeny between L. casei and 35 human gut bacterial strains was analyzed; and their shared genes were involved in coenzyme transport and metabolism, which contributed perhaps to the adaptation of the human gastrointestinal tract for L. casei. These findings will be certainly helpful for the design of physiological studies which in turn will lead to a better understanding of genomic diversification of L. casei for niche expansion.