Comparative genome analysis of dairy and non dairy isolated strains of Carnobacterium maltaromaticum

Abstract

Lactic acid bacteria (LAB) encompass several genera and numerous species that have been investigated extensively mainly due to their beneficial effect on human health. Carnobacterium maltaromaticum is a facultative anaerobic, gram-positive, rod-shaped lactic acid bacterium. It has been known to colonize range of habitats including dairy, meat and fish and has been isolated from vacuum-packed fish and meat products and live fish too. Studies have suggested that C. maltaromaticum strains can be applied as bio-preservative agents in food products due to its production of antimicrobial compounds, bacteriocins, which can inhibit foodborne pathogen Listeria monocytogenes. C. maltaromaticum strains can also be used as potential probiotic culture in aquaculture except for some, which have been identified as putative virulent strains. In present study, pan-genome approach was adopted to perform intraspecies genome analysis. Results suggested that dairy strains have larger genome size, higher percentage of pseudogenes and higher percentage of genomic islands that leads to a hypothesis that dairy strains may be acquiring genes beneficial for adaptation in dairy niche and shedding those genes that might be either virulent or not necessary for the bacterium. BRIG analysis revealed acquisition of three genomic islands common to dairy isolated strains only. Most of the acquired genes encodes for metabolic proteins, for instance, lactose and galactose metabolism genes, genes for hydrolytic activity and osmotic stress maintenance genes. Regarding safety aspect analysis, virulent factors were identified which proposed presence of ̴ 40 VFs not present in five established probiotic strains. Among those 40 VFs, dairy strains possess lowest and fish isolated strain ATCC35586 encodes highest. Antibiotic resistance genes were not identified in any strain while Bacteriocin prediction analysis showed presence of four bacteriocins in a meat-isolated strain DSM20722 and 3 bacteriocins in two dairy isolated strains LMA28 and DSM20342MX5.