Work

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

Year: 2026

Type: article

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.

Source: Frontiers in Microbiology

DOI: 10.3389/fmicb.2026.1780782

Authors: Hemang D. Brahmbhatt, Priyank Chavda, Dhruvinkumar Vadee, Amrutlal K. Patel, Snehal Bagatharia

Institutions: Government of Gujarat, Gujarat Biotechnology Research Centre

Language: English

Topic: Probiotics and Fermented Foods

Subfield: Food Science

Field: Agricultural and Biological Sciences

Domain: Life Sciences

SDG: Good health and well-being

Open Access status: gold

Estimated APC paid: $3,801