Genome Characterization of Indigenous Probiotic Lacticaseibacillus rhamnosus Y59 Isolated From Artisanal Curd (Dahi)

Abstract

Probiotic strain Lacticaseibacillus rhamnosus Y59 was isolated from artisanal curd and is considered to have health-improving qualities. Whole genome sequencing and comparative genome analysis L. rhamnosus Y59 with 35 complete genomes of other L.rahmnosus strains were carried out to identify the molecular mechanism of Y59's probiotic potential and the genes present in it. A 2.9 Mb circular genome with a 46.7% guanine-cytosine (GC) content and 53 transfer RNA (tRNA) genes were present in the Y59 genome. There were 2967 protein coding sequences (CDSs). In silico analysis helped to identify genes that played a vital role in carbohydrate metabolism, defense and regulating the stress response of the probiotic strain Y59. The comparative genomic analysis of L. rhamnosus strains, showed 657 pan-genome orthologous gene clusters and 1,936 core-genome orthologous gene clusters. Core phylogenetic tree showed that L. rhamnosus Y59 had a closer relationship with the L. rhamnosus CAU 1365 which was isolated from Kimchi. The analysis revealed unique genes which were strain-specific. The number of these genes ranged from 0 to 91. Our strain L. rhamnosus Y59 had 29 unique genes which encoded hypothetical proteins. The findings of our study provided us with significant data highlighting the genes and pathways that were a critical part of the general probiotic properties and health benefits