Dual Human Milk Oligosaccharide-Fibre Utilisation Is a Selection Cue for the Weaning Gut Microbiome
A 2026 study published in Nature Communications used an infant cohort to examine how the gut microbiome shifts during the transition from breast milk to solid food. Researchers collected stool samples from 7 vaginally delivered, exclusively breastfed mother-infant pairs at three weaning stages: pre-weaning (100% breast milk), early weaning (70% breast milk), and late weaning (30% breast milk). Fecal samples were cultured on human milk oligosaccharides (HMOs), dietary fibers found in solid foods (arabinoxylan, pectin, xyloglucan, galactomannan, and Arabic gum), and mucin. The team mapped which bacteria were present and which carbohydrate-digesting enzymes they carried, using whole-genome sequencing of the gut community. Findings were validated in a Swedish cohort of 98 additional infants and against 137 maternal isolates.
The study produced two findings that hadn’t been shown before. Fiber-eating bacteria are already present before solid food is introduced: all pre-weaning fecal samples carried the genetic machinery to break down plant fiber, and all 7 pre-weaning consortia actually grew on arabinoxylan in culture. At pre-weaning, the HMO specialist Bifidobacterium infantis is dominant, present in 6 of 7 infants. As solid food increases, certain Clostridia begin outcompeting HMO-focused bifidobacteria, using HMO and fiber utilization pathways simultaneously. Their advantage comes from targeting the HMO type 1 backbone, a structural component of HMOs that B. infantis largely passes over in favor of another component, fucosylated fractions. Maternal stool samples and isolates showed HMO utilization capacity still active in adult gut communities, suggesting the dual-use trait is selected for during weaning and carried forward into adulthood.
The core finding is that the weaning diet (the mix of HMOs and dietary fibers in the 6 month-2 year window) acts as a selection pressure on which bacteria persist into adulthood. Bacteria capable of using both substrates outcompete specialists, and those species appear to form the foundation of the adult gut microbiome. The cohort is small (7 pairs), and the authors call for larger, more geographically diverse studies with detailed diet tracking to confirm these trajectories. For the prebiotic field, and larger pediatric research areas, this study raises an intriguing question: if HMOs select and retain core adult microbiome species during weaning, what happens to that process when breastfeeding is cut short or weaning-period diets are low in fiber?
