PRJNA866315
Comparative de novo genomic analysis of indigenous probiotic Enterococcus faecium LR13 reveals cholesterol-assimilation as an intrinsic strain specific trait
AbstractProbiotics are live microbes associated with several health benefits. In an earlier study we had reported a rhizospheric isolate Enterococcus faecium LR13 which exhibited probiotic and hypo-cholesterolemic potential in vitro. In the present study we have conducted its de novo genome analysis to unravel the genes and pathways associated with probiotic traits. Also, the pan-genome sequence of LR13 was compared with the pan-genome sequences of other E. faecium probiotic strains T110, 170M39, SP15 and WEFA23 and, with pathogenic and non-pathogenic non-probiotic strains to determine genomic relatedness and differences among such E. faecium strains. Our results revealed that LR13 was genetically distinct from pathogenic strains but closely related to food-grade enterococci and did not harbour virulence or antimicrobial resistance genes. Besides the probiotic benefits, consumption of LR13 can bestow additional metabolic benefits since its genome encoded genes for biosynthesis of essential amino acids, carbohydrate metabolism, iron acquisition and, production of bacteriocins and antimicrobial peptides. Among all the probiotic strains tested, LR13 was genetically more related to E. faecium WEFA23 another cholesterol assimilating probiotic. Interestingly, both LR13 and WEFA23 harboured 21 unique proteins which were absent in other probiotic strains. Of these, three proteins were indirectly related to cholesterol-assimilation while 14 proteins might directly help in cholesterol-assimilation by, production of short chain fatty acids, lipid like sterol transport and membrane stabilization, and bile salt hydrolase activity. This suggests that cholesterol assimilation might be an intrinsic, strain specific trait exhibited by probiotics with a specific genetic constitution. This study might serve as a useful basis for discerning/characterizing more cholesterol assimilating probiotics as novel biotherapeutics for treating cardiovascular diseases.