In Silico Analysis of CRISPR-Cas-mediated Bacteriophage Resistance in Lactobacilli

Abstract

Background and objectives: Recent advances in clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR associated sequences (Cas) technology has opened up immense possibilities for improving the gut health and overall immunity of the individual. In development of all these applications, lactic acid bacteria (LAB), which are already a part of human diet, are an attractive vehicle. The technology can utilize the evolutionary perspective of bacterial resistance to phages by this class of bacteria. Thus, the knowledge of CRISPR-based phage resistance in starter cultures is of interest to clinicians as well as food technologists. In the present study, an attempt has been made to explore the presence of CRISPR loci and cas gene clusters in the genomes of Lactobacilli strains available in public databases. A further analysis has been undertaken to identify the spacers left behind by the bacteriophages encountered by Lactobacilli during their evolution. Materials and methods: A total of 174 completed and draft genomes of Lactobacilli strains were analyzed by different online tools like CRISPR-Cas finder and CRISPR-Cas++. Results: Different types of the CRISPR-Cas system found in 58 genomes out of 174 genomes were analyzed. No CRISPR sequences were found in 109 genomes. The analysis yielded type I and type II CRISPR-Cas system in 14 genomes each and type III in 1 genome. The study found 32 bacteriophage spacers in different bacterial genomes that predict the identity of phages infecting the bacterium over its evolutionary history. Interpretation and conclusion:This study is an exploratory one that has predicted the presence of CRISPRs and their diversity across Lactobacillus species.