Perioperative Antibiotic Prophylaxis in Cesarean Section and the Maternal Gut Microbiome: Protocol for a Remote Observational Cohort Study

Background: Cesarean section (CS) requires perioperative antibiotic prophylaxis (PAP) for the prevention of surgical site infections. However, systemic antibiotics during the peripartum period may induce compositional perturbations of the maternal gut microbiome, a system already characterized by reduced resilience. Data on maternal gut microbiome dynamics after CS with PAP are scarce, largely due to logistical and feasibility barriers that limit the participation of pregnant women and new mothers in conventional clinical studies. Objective: This protocol primarily aims to evaluate the feasibility of a fully decentralized, remote study design for longitudinal gut microbiome research in the peripartum period. Secondary exploratory objectives include the comparative analyses of microbiome composition between CS with PAP and vaginal delivery (VD) without antibiotic exposure to inform future adequately powered studies. Methods: The MAMA (Microbiome Changes Due to Antibiotic Prophylaxis in Mothers at Birth) study is a prospective, 2-arm observational cohort study conducted entirely off-site. Women in the third trimester of pregnancy were recruited at 2 German level-1 perinatal centers and affiliated outpatient facilities. Participants underwent either CS with PAP (single dose cefuroxime 1.5 g intravenously) or VD without antibiotics. Stool samples were self-collected at home and returned by mail at 3 predefined time points: late pregnancy (T0), 2 to 3 days post partum (T1), and 90±10 days post partum (T2). Primary outcomes are feasibility indicators, including recruitment rate, sample and questionnaire return rates at each time point, adherence to sampling windows, and participant retention across follow-up. Secondary outcomes are exploratory microbiome measures based on 16S rRNA gene sequencing (V3-V4), including alpha diversity indices, beta diversity metrics, and relative taxonomic abundances. Microbiome analyses are explicitly compositional and hypothesis-generating. Group comparisons and longitudinal within-individual changes will be assessed using nonparametric diversity metrics and multivariate distance-based methods. No confirmatory hypothesis testing is planned. Results: Recruitment occurred between May 2022 and October 2023, with 37 women enrolled (25 CSs and 12 VDs). Follow-up was completed with receipt of the final stool sample in March 2024. DNA extraction and sequencing were completed in a single batch in October 2024. Bioinformatic processing and statistical analyses were initiated in June 2025 and are ongoing as of December 2025. Results from the exploratory microbiome analyses are expected to be published in 2026. Conclusions: This protocol demonstrates the feasibility of conducting fully decentralized, longitudinal microbiome research in a peripartum population without requiring on-site visits. By integrating study procedures into maternal realities, the remote design reduces participation barriers and addresses a clinically relevant research gap that has remained largely unexamined despite routine use of PAP. While microbiome-related outcomes are exploratory, the methodological framework established here provides a scalable model for future maternal and postpartum research, supporting ethically grounded, participant-centered study designs and evidence-informed care strategies.