Infant gut microbiota in multi-child families converges with adults without a sibling-specific signature

Abstract The human gut microbiota undergoes rapid development during early life. Sibling presence has been associated with altered infant microbiota composition and accelerated maturation, but distinguishing direct microbial transmission between siblings from confounding by maternal reproductive history (parity) remains challenging. We analysed >5,000 faecal samples from >800 mother-father-infant triads in the Finnish HELMi birth cohort to characterise microbiota patterns that could inform underlying mechanisms. While sibling presence was associated with accelerated microbiota maturation and modest compositional differences, infants who both had siblings (or both lacked siblings) were no more similar to each other than mixed pairs. Instead, infants with siblings exhibited non-specific convergence with adult microbiota profiles and contributed fewer unique genera to their family metacommunities (infant–mother–father triads). Multi-child families harboured smaller but compositionally distinct metacommunities. These patterns challenge simple models of direct sibling transmission and suggest that multiple factors associated with family structure may jointly influence infant microbiota development, though specific mechanisms remain unclear. Competing Interest Statement The authors have declared no competing interest. Footnotes List of references added, no other changes. Data availability The 16S rRNA amplicon sequencing data from the HELMi birth cohort is publicly available at https://www.ebi.ac.uk/ena/browser/view/PRJEB55243. Metadata, aerotolerance data, taxonomy table, ASV relative abundance table as well as R code used in this study will be made publicly available on GitHub upon publication.