Longitudinal modelling of microbiome subcommunities reveals parity-dependent dynamics during pregnancy and postpartum.

BACKGROUND

Dysregulation of maternal adaptations to pregnancy due to high pre-pregnancy BMI (pBMI) is associated with worsened health outcomes for mothers and children. The role of the gut microbiome in these adaptations remains unclear.

METHODS

Stool samples were collected from pregnant participants (n = 52) enrolled in the Be Healthy in Pregnancy study (NCT01689961) during first, second, and third trimesters, and 6-months postpartum, along with samples from their infants at 6 months of age. Following 16S rRNA gene sequencing, we implemented time-aligned LDA (TALDA) using a time-weighted sampling strategy with exponentially decaying weights to construct time-proximal cohorts, applied LDA to each cohort independently, and aligned resulting topics using the alto R package. Infant samples were analyzed using standard LDA.

RESULTS

Seven distinct subcommunities were identified, one of which represented perineal contamination and was excluded from further analysis. Remaining subcommunities had distinct taxonomic definitions which remained stable throughout pregnancy (mean cross-cohort stability 0.899) while subcommunity proportions within individuals varied. Multiparous individuals showed greater shifts in subcommunity proportions during early pregnancy, while primiparous individuals displayed progressively increasing shifts with the largest changes during the transition from pregnancy to postpartum. High pBMI was associated with reduced microbiome remodelling, particularly among multiparous individuals. In exploratory analyses, maternal SCFA-producing subcommunity abundance at late pregnancy was positively associated with infant Bifidobacterium-dominated subcommunity proportions at 6 months, while pBMI > 25 was independently associated with lower infant Bifidobacterium.

CONCLUSION

TALDA effectively distinguished between stable subcommunity definitions and dynamic subcommunity proportions, revealing that the microbiome maintains functional organization while subcommunity proportional contributions shift over the course of pregnancy and postpartum. These maternal dynamics may have intergenerational consequences through their influence on infant gut colonization. This work demonstrates that maternal factors modify microbiome trajectories and supports the existence of an ecological memory of pregnancy history within the maternal gut microbiome.