Fetal sex is associated with maternal gut microbiota composition and predicted metabolic potential in healthy pregnant women

Pregnancy affects almost every organ and system, including the microorganisms that reside in the gastrointestinal tract, the gut microbiota. Pregnancy hormones, such as progesterone and estradiol, alter the composition of the maternal gut microbiota, both directly and indirectly; in turn, gastrointestinal microorganisms can produce and modulate the activity of reproductive hormones. While the levels of pregnancy hormones depend on the fetal sex, there is limited research on the role of fetal sex in the maternal gut microbiota composition and function. Using publicly available microbial sequencing data from a cohort of 485 pregnant women in Guangzhou, China, we identified taxonomical and predicted metabolic signatures associated with fetal sex and gestational age using zero-inflated negative binomial models and linear models, respectively, correcting for pre-pregnancy BMI, maternal age, parity, and residency status. We trained and tested three different machine learning models, XGBoost, Random Forest, and Elastic Net-Logistic Regression, to predict fetal sex based on maternal microbial characteristics. Further, we generated sex-specific microbial co-abundance networks using SPIEC-EASI. We identified multiple microbial species and predicted microbial enzymes that were significantly differentially abundant between the fetal sex groups, including increased levels of Bifidobacterium breve and the predicted microbial enzyme β-glucuronidase in female pregnancies, but these sex-associated microbial features represented only a weak signal to predict fetal sex (AUC < 0.6 for all explored machine learning models). Maternal microbial co-abundance networks from pregnancies carrying male or female fetuses exhibited a similar core community, yet those from female pregnancies were more densely connected than those from male pregnancies. Several of the highly connected species of the maternal microbiota from individuals carrying female pregnancies were microorganisms with previously reported β-glucuronidase activity. Our study demonstrated that the maternal gut microbiota differs between female and male pregnancies and that these differences depend on gestational age. Our results not only point to the need to include fetal sex when studying the perinatal period but also suggest a novel, data-driven mechanistic hypothesis whereby fetal sex-specific maternal-placental-fetal interactions influence hormonal regulation, which may in turn, interact bidirectionally with maternal gut microbiota composition. Given the essential role of the gut microbiota in maternal health and infant development, a better understanding of how maternal microbial communities vary in response to fetal sex during pregnancy may provide important insights into maternal health and fetal outcomes.