Extended Data Fig. 6: Strain-level dynamics and stability across NGM species.

(a) Frequency of study participants detected with the same strains (in grey, otherwise in white) from their mother's faecal samples across NGM community states. To delineate transmission trends, the chart is categorized by birth mode and the three NGM driver species. Frequency of strain-sharing event (for example, maternal transmission in mother-baby pair or strain persistence within-individual longitudinal samples) is presented as raw counts of detectable strain sharing events normalized by the total number of subjects per birth mode and NGM community state (week 1). (b) Bar plots counting strain-sharing events across three settings: (Left) Maternal transmission in mother-infant dyads (183 subjects; 167 transmissions from 213 evaluated species-sample pairs). (Middle) Neonatal persistence via neonatal longitudinal sampling (359 subjects; 700 transmissions from 938 evaluated pairs). (Right) Infancy persistence from neonatal into infancy period (302 subjects; 464 transmissions from 920 evaluated pairs). When longitudinal samples were considered, strain sharing events were considered only once per subject per setting, using the time point with highest counts. Only species with ≥20 strain-sharing events detected across three settings are shown. Three community state driver species are highlighted in boxes. Transmission patterns often align with phylogeny: Actinomycetota/Actinobacteria (pink) and Bacteroidota/Bacteroidetes (green) typically transmit maternally during vaginal birth and persist into infancy. Conversely, Bacillota/Firmicutes (purple) and Pseudomonadota/Proteobacteria (orange) show lower maternal transmission rates and reduced neonatal persistence. Notable outliers include E. coli and B. breve. The size of bubbles represents the transmissibility of each species, which is its ratio of detected to potential strain-sharing events, as determined by StrainPhlAn4. Only subject pairs with sequencing depth sufficient for StrainPhlAn strain-level analyses are displayed; data points not shown are non-evaluable.