Genome characterization and comparative genomics of <i>Limosilactobacillus reuteri</i> HDB isolated from the gut of an Indian infant

<i>Limosilactobacillus reuteri</i>, formerly <i>Lactobacillus reuteri</i>, is a rod-shaped, Gram-positive, facultative anaerobe that colonizes the gastrointestinal tract of most vertebrates, including humans. We report the first isolation of <i>L. reuteri</i> strain HDB from the stool of a healthy Indian infant. Species assignment using the Type (Strain) Genome Server (TYGS) placed HDB within the <i>L. reuteri</i> clade, showing closest affinity to <i>L. reuteri</i> subspecies <i>porcinus</i> (dDDH 69.7%) yet clustering phylogenomically with <i>L. reuteri</i> DSM 17938. Hybrid <i>de novo</i> 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 B₁₂ biosynthesis, reuterin production, and probiotic functions, along with enriched carbohydrate and cofactor metabolic pathways. Comparative analysis with 59 <i>L. reuteri</i> 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 <i>L. reuteri</i> 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.