Early pregnancy is characterized by a significant decrease in the diversity of the oral microbiome and strong associations with lifestyle and conception method.

Background: Most studies of the oral microbiome during pregnancy have focused on the second and third trimesters (T2, T3, respectively). To date, no large-scale longitudinal study has examined oral microbiome development across all three trimesters, leaving early gestational dynamics largely unexplored. Methods: We conducted a longitudinal analysis of 346 pregnant Israeli women, validated in an independent cohort of 154 Russian women. In Israel, saliva samples were collected during T1 (11-14 weeks), T2 (24-28 weeks), and T3 (32-38 weeks); in Russia, samples were collected during T2 and T3 at similar gestational ages. Microbial profiles were analyzed for differential abundance and associations with maternal nutrition and lifestyle. Results: Significant shifts in oral microbial composition were observed as early as the transition from T1 to T2. Alpha diversity decreased progressively across pregnancy. Taxonomic changes included a reduction in Verrucomicrobiota and an increase in Synergistota. Gluten-free diet showed the strongest associations with microbiome composition across all trimesters, followed by smoking history and conception method. Conclusions: This study provides the first large-scale evidence of significant oral microbiome changes beginning in early-mid pregnancy, characterized by reduced diversity and a directional shift toward inflammation-associated communities. Strong associations between gluten consumption and smoking suggest a lifestyle effect on the oral microbiome.