Metabolic diversity and competitive interactions of infant-derived bifidobacteria in human milk oligosaccharides and galacto-oligosaccharide utilization

Abstract

Human milk oligosaccharides (HMO) play a pivotal role in shaping the infant gut microbiome and immune system, primarily by selectively promoting Bifidobacterium species. Although the metabolic pathways of individual bifidobacterial strains for HMO are well-characterized, competitive interactions among multiple strains under single-HMO conditions remain poorly understood. Here, we evaluated metabolic capabilities of 15 infant-derived Bifidobacterium strains on 3 substrates: 2′-fucosyllactose (2′-FL), lacto-N-tetraose (LNT), and high-purity galacto-oligosaccharides (GOS-HP). Monoculture and mixed-culture analyses were conducted using growth kinetics, substrate consumption assays, and genomic profiling. Monoculture results demonstrated most strains exhibited robust growth on LNT and GOS-HP, whereas 2′-FL utilization varied. Genomic analysis indicated efficient HMO metabolism correlated with glycosyl hydrolase gene diversity and copy numbers. In mixed cultures, Bifidobacterium dentium initially dominated through monosaccharide consumption but was subsequently outcompeted by Bifidobacterium longum ssp. infantis and Bifidobacterium breve, highlighting oligosaccharide-driven competition. The LNT mixed culture resulted in a bifidobacterial community composition resembling that of breastfed infants. These findings guide oligosaccharide selection for infant formula design to better emulate human milk's microbiome-modulating benefits.