Phenotypic Characterization and Genomic Profiling of Prebiotic Utilization in Human-Derived Indonesian Bifidobacterium Isolates

Bifidobacterium species are recognized for their beneficial roles in gut health, while prebiotics serve as selective substrates that support the growth of beneficial microorganisms. This study evaluated the responses of human-derived Indonesian Bifidobacterium isolates to different prebiotic substrates and explored their genomic potential for carbohydrate utilization. Four strains—B. animalis BR2-5, B. breve BS2-PS1, BS2-PS2, and BS2-PB3—were assessed using fructo-oligosaccharide (FOS), galacto-oligosaccharide (GOS), xylo-oligosaccharide (XOS), inulin, maltodextrin, and L-arabinose. In vitro fermentation assays were conducted to evaluate growth responses and pH changes, while genome annotation was performed to identify putative genes related to carbohydrate utilization. B. animalis BR2-5 exhibited growth in all tested substrates, whereas B. breve strains grew primarily in maltodextrin, FOS, GOS, and inulin. GOS supported the highest growth response across all strains. Genome annotation revealed putative carbohydrate-active enzyme genes potentially associated with carbohydrate utilization pathways. These findings provide baseline information for the development of locally sourced synbiotic formulations and future investigations of Indonesian Bifidobacterium isolates.