In-silico analysis of Bifidobacterium bifidum strain 900791 genome in the context of the B. bifidum pangenome.

INTRODUCTION

Bifidobacterium bifidum is a key member of the human gut microbiota with well-recognised roles in intestinal homeostasis, glycan metabolism, and immunomodulation. Strain 900791, isolated from the meconium of a Siberian infant, has been used as a commercial probiotic ingredient for decades and has demonstrated, in previously published clinical trials, an ability to improve lactose tolerance and reduce gastrointestinal symptoms in both children and adults; however, the genomic basis for these properties has not been characterised.

METHODS

We present the complete genome sequence and comprehensive in silico genomic and pangenomic analysis of B. bifidum strain 900791. Hybrid sequencing was used for genome assembly. Phylogenomic analysis, including core genome MLST (cgMLST), integrated 229 high-quality B. bifidum genomes, representing the largest dataset for this species to date. Functional annotation and carbohydrate-active enzyme (CAZyme) profiling, antimicrobial resistance prediction, and bioinformatic screening for probiotic-associated genomic features were also performed.

RESULTS

Hybrid sequencing yielded a single circular chromosome of 2,280,092 bp, comprising 1,852 protein-coding sequences. Phylogenomic analysis revealed that strain 900791 belongs to a clonal subgroup of nine closely related strains (>99% cgMLST identity), consistent with a geographically structured lineage. The species pangenome comprised 4,152 orthogroups and a core of 1,450 gene families; 23 orthogroups were exclusive to the 900791 clonal subgroup, including a predicted lantibiotic biosynthetic cluster. CAZyme profiling identified glycoside hydrolase families associated with human milk oligosaccharide degradation (GH2, GH20, GH33, GH84), mucin glycan cleavage (including ten GH families), and lactose metabolism (GH2, GH42). Safety assessment identified only species-typical resistance to mupirocin and rifampicin, with no acquired resistance markers. Bioinformatic screening of the clonal subgroup detected the presence of adhesion-associated proteins, acid resistance systems, bile salt tolerance determinants, oxidative stress response proteins, and two putative bacteriocin gene clusters.

DISCUSSION

These findings provide a genomic framework consistent with the documented clinical role of strain 900791 in lactose tolerance and support its further investigation as a candidate probiotic. The probiotic-associated features identified here may help explain its observed properties and represent priority targets for experimental validation in future in vitro and in vivo studies.

Copyright © 2026 Cárdenas, Vidal-Veuthey, Meza, Almonacid and Gutkevich.