Nutrition-dependent development of the Oral Microbiome in Early Pregnancy
Discuss this preprint
Start a discussion What are Sciety discussions?Listed in
This article is not in any list yet, why not save it to one of your lists.Abstract
Background
Most studies of the oral microbiome during pregnancy have focused on the second and third trimesters. Findings remain inconsistent-some report shifts in specific taxa, whereas others observe little change in diversity. To date, no large-scale longitudinal study has examined oral microbiome development across all three trimesters, leaving the early gestational dynamics largely unexplored.
Methods
We conducted a longitudinal analysis of the oral microbiome in 346 pregnant women from Israel and validated key findings in an independent cohort of 154 pregnant women from Russia. In Israel, Saliva samples were collected during the first (T1, 11-14 weeks), second (T2, 24-28 weeks), and third (T3, 32-38 weeks) trimesters; in Russia, samples were collected during the second and third trimesters at the same time points. Alongside sample collection, participants completed comprehensive dietary and health questionnaires to assess maternal factors that could influence microbial composition. Microbial profiles were analyzed to test for (i) differential abundance across trimesters, (ii) the influence of maternal nutrition and lifestyle factors.
Results
Significant shifts in oral microbial composition were observed as early as the transition from T1 to T2. Alpha diversity decreased progressively from T1 (Shannon’s diversity index: 3.261) to T2 (3.173) and T3 (3.109; Kruskal-Wallis test, p = 0.0023) in the Israeli cohort. Notable taxonomic changes included significant decreases in Verrucomicro-biota and Euryarchaeota from T1 to T2, with Akkermansia muciniphila showing a particular reduction. Conversely, Synergistota increased significantly during this transition. Gammaproteobacteria increased while Erysipelotrichia decreased between T1 and T2, suggesting an ecological shift from commensal, barrier-supporting taxa toward communities associated with dysbiosis and inflammation. Despite these systematic changes, individual microbial signatures-measured as pairwise distances between trimesters-remained relatively conserved across trimesters. Maternal factors that significantly modulated oral microbiome composition included adherence to gluten-free diets (the most robust association across all trimesters in Israeli women), smoking history, and conception method, with gluten-free diet showing consistent associations with taxa in the Lachnospiraceae and Ruminococcaceae families.
Conclusions
This study provides the first large-scale evidence of significant oral microbiome changes beginning in early pregnancy, characterized by reduced diversity and a directional shift toward potentially pro-inflammatory communities. The strong associations with gluten consumption and smoking suggest that early pregnancy represents a critical window for microbiome modulation through dietary interventions. The alteration in the microbial composition highlights the oral microbiome as a sensitive marker of gestational physiology.
