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