Dual human milk oligosaccharide-fibre utilisation drives gut microbiome selection during weaning

Gut microbiome (GM) maturation in early life follows organised taxonomic successions. How weaning impacts these trajectories remains underexplored. Here, we sampled faeces from seven mother-infant dyads at pre-, early and late weaning. Enrichment cultures (n=306) and metagenomic (n=108) analyses revealed an unexpected prevalence of fibre degradation genes and the growth of the pre-weaning infant GM on common dietary fibres. Utilisation of both human milk oligosaccharides (HMOs) and dietary fibres was revealed as a metabolic hallmark of the weaning GM. We showed that HMO-utilisation is retained beyond weaning, by analyses of maternal GM and HMO utilisation in 137 maternal isolates. Our findings highlight dual HMO-dietary fibre utilisation as a hitherto unrecognised driver that potentially orchestrates the selection of distinct adult GM species during weaning. This work outlines a plausible mechanism underlying the organised GM maturation in early life and highlights a previously overlooked role of HMOs during the weaning transition.