Abstract
Limosilactobacillus reuteri, formerly Lactobacillus reuteri, is a rod-shaped, Gram-positive, facultative anaerobe that colonizes the gastrointestinal tract of most vertebrates, including humans. We report the first isolation of L. reuteri strain HDB from the stool of a healthy Indian infant. Species assignment using the Type (Strain) Genome Server (TYGS) placed HDB within the L. reuteri clade, showing closest affinity to L. reuteri subspecies porcinus (dDDH 69.7%) yet clustering phylogenomically with L. reuteri DSM 17938. Hybrid de novo assembly (Illumina + Oxford Nanopore GridION MK1) generated a single circular 2,226,956 bp chromosome (GC 39.04%) encoding 2,160 CDS. Functional annotation identified genes involved in vitamin B(12) biosynthesis, reuterin production, and probiotic functions, along with enriched carbohydrate and cofactor metabolic pathways. Comparative analysis with 59 L. reuteri genomes revealed a pangenome of 11,725 gene families, including 944 core gene families, 171 soft-core gene families, 1912 shell gene families, and 8698 cloud gene families, highlighting notable diversity. Core-genome phylogeny aligns HDB closely with the reference strain DSM 17938, confirming its identity as a human-associated lineage. dN/dS analysis indicated strong purifying selection across host niches, with no evidence of widespread positive selection. Genome-scale modeling predicts expanded carbohydrate flux in HDB against global references. The genetic background, along with its conserved metabolic features, suggests that HDB carries genomic characteristics commonly associated with human-derived L. reuteri strains. These observations support its consideration for further evaluation as a regionally sourced probiotic candidate. These conclusions are based on genomic and computational predictions and require experimental validation through adhesion, colonization, and safety studies.