Jashbhai B. Prajapati and Suja Senan
In the field of functional genomics, the derivatives of gene transcription and translation are referred with the suffix ‘ome’. OMICS (comprehensive analysis of biochemical molecular species like the genes, transcripts, proteins and metabolites) have been applied to a great deal in probiotic studies. With the numerous records validating the health benefits of probiotics, sporadic cases of risk posed by such strains are also reported. Data mining of the complete genome sequences reveals the maximum potential risk of a probiotic organism and whole-genome sequencing of bacteria has recently emerged as a cost-effective and convenient approach for identifying virulent strains, testing resistance to antibiotics, and monitoring the spread of bacterial pathogens. Hence a study was undertaken in our lab on the established probiotic strain L. helveticus MTCC 5463 strain to re-assure its safety using metagenomic approaches. The genome does not pose the threat of transferability of such antibiotic resistance as it lacks the presence of a CRISPRs, plasmids and complete prophages, implying the mode as intrinsic resistance. Ten structural and regulatory genes associated with prophages and integrases, six uncategorised mobile genetic elements, 154 homologs of transposases and 13 genes related to R/M systems were established. For heavy metal effluxing MTCC 5463 carried total 16 genes involved in copper homeostasis, cobalt, cadmium, nickel and iron uptake system with 8 adverse metabolism genes associated with formation of putatively genotoxic metabolites. Falling into the category of host-interaction factors rather than virulence factors, the presence of 44 fitness related genes have been observed in the genome viz., adhesion, biofilm, surface proteins interacting with immunity, lipopolysaccharides formation and 15 stress related proteins that provide gastrointestinal robustness of the strain. Further, on the lines of EFSA proposed Quality Presumption of Safety guidelines, the above results provide safety assurance for the use of L. helveticus MTCC 5463.