Pregnancy involves hormonal, immunological and metabolic adaptations that may influence the composition and function of the maternal gut microbiota. However, findings across gestation are mixed, with some studies reporting compositional shifts across trimesters and others reporting stability. Gestational diabetes mellitus (GDM) is a common pregnancy complication associated with adverse maternal and child outcomes (1), and has been linked to differences in gut microbiota composition, including changes detectable before diagnosis. However, evidence remains inconsistent, and most studies rely on 16S rRNA sequencing, which offers limited taxonomic and functional resolution (2). Diet is a key modifiable factor shaping the gut microbiota outside pregnancy, but evidence in pregnancy remains limited, inconsistent, and largely confined to single time point assessments. No studies have examined fermented or prebiotic food intake in relation to the gut microbiota during pregnancy. Accurate dietary assessment also remains challenging, given recall bias, misreporting and under-reporting of energy intake, which can obscure true diet-microbiota associations (3).
This secondary analysis of the Healthy Gut Diet Study examined longitudinal associations between dietary intake, pregnancy stage and GDM with the antenatal gut microbiota using a consensus dietary assessment approach combining food frequency questionnaires and 24-hour recall data. Participants were women with dietary data and matched stool samples collected in early and/or late pregnancy (n = 66), characterised using shotgun metagenomic sequencing. Linear mixed-effects models and MaAsLin2 assessed associations between dietary variables and microbial diversity, taxonomic composition, and functional pathways, adjusting for potential confounders, including maternal age, pre-pregnancy BMI, and antibiotic use.
No differences in microbial composition or function were observed across pregnancy or by GDM status. Higher fibre intake was positively associated with alpha diversity (Shannon diversity, β = 0.06, p = 0.03; Evenness, β = 0.01, p = 0.03; but not Richness, β = 5.11, p = 0.17). Higher prebiotic-rich food intake (fibre-rich plant-based foods) was associated with taxonomic and functional pathways, including the nitrobenzene degradation pathway (PWY.5637)(β = 0.68, q = 0.002) and a higher abundance of butyrate-producing members of the Oscillospiraceae family, including Dysosmobacter sp900544615 (β = 0.47, q < 0.001). Higher protein intake (% energy) was associated with increased abundance of proteolytic and lipolytic taxa and reduced abundance of taxa involved in complex carbohydrate fermentation. It was also associated with reduced functional capacity for amino acid biosynthesis, nitrogen assimilation, and carbohydrate degradation and storage pathways (all p < 0.001).
These findings suggest that diet, rather than pregnancy stage or GDM status, is a key factor shaping the antenatal gut microbiota. These results support further investigation of dietary protein and fibre quality as targets for microbiota-informed dietary strategies during pregnancy.