Human milk oligosaccharide mediated mutualism between Escherichia coli and Bifidobacterium bifidum

Infant gut microbiota development involves frequent colonization by Enterobacteriaceae, particularly Escherichia coli, yet their ecological role in healthy infants is unclear. We analysed longitudinal stool samples from healthy, term-born, breastfed infants (n=41) and related mothers (n=30) using shotgun metagenomics and novel computational approaches. Strain-resolved profiling indicates that Bifidobacterium spp. are frequently shared within families, whereas E. coli derives from external sources, but often persists within individuals. Despite differing ecological strategies, these genera co-exist and exhibit evolutionary adaptations related to utilizing human milk oligosaccharide (HMO)-degradation products. We demonstrate that E. coli depends on utilization of HMO-degradation products released during extracellular hydrolysis by primary degraders. Interactions between E. coli and Bifidobacterium bifidum are mutualistic in co-culture, where E. coli supplies cysteine to its auxotrophic partner, facilitating cooperative degradation of 2′-fucosyllactose (2′FL), the predominant HMO, and liberated monosaccharides supporting E. coli growth. These findings reveal fundamental cross-feeding interactions within the infant gut microbiota.