The Menstrual Cycle Reshapes Your Gut Microbiome, But Hormones Aren’t the Whole Story

For years, researchers have known that men and women tend to harbor different gut microbial communities, and that sex hormones are a plausible reason. What they haven't known is how much the hormonal swings within a single woman's cycle actually move the needle on her microbiome. A new preprint from the Women4Health cohort offers the most detailed look yet at that question, and the answer is more nuanced than most researchers expected.

Microbial alpha and beta diversity shift across the follicular and luteal phases

The study, led by S. Sanna and colleagues and published on Research Square in June 2026, followed 160 healthy Italian women aged 18 to 45 with regular menstrual cycles. Each participant provided stool samples at enrollment and four follow-up visits timed to distinct menstrual phases: follicular, ovulatory, early luteal, and late luteal. Crucially, the team defined those phases using directly measured LH concentrations rather than counting days from the last period, a methodological refinement that makes the hormone-microbiome comparisons considerably more trustworthy.

From 542 fecal samples processed with shotgun metagenomic sequencing, two clear patterns emerged. Microbial alpha diversity, a measure of species richness within a sample, was significantly lower in the follicular phase than in the ovulatory phase (p = 0.03). Beta diversity, which captures how different communities are from each other, increased significantly from the follicular to the late luteal phase (p = 8.7 x 10^-6). In plain terms: the gut microbial landscape is most uniform early in the cycle and most variable by its end.

Gonadotropins, not estrogen, show the strongest hormone-microbiome links

Twenty-eight bacterial species and twenty-two metabolic pathways showed statistically significant associations with reproductive hormones, but the surprising result was which hormones mattered most. The majority of hormone-microbiome associations were tied to gonadotropins, specifically FSH and LH, rather than to the gonadal steroids estradiol and progesterone that most people assume are the dominant drivers.

FSH and LH were both positively associated with Phocaeicola vulgatus (formerly Bacteroides vulgatus), a species already linked to polycystic ovary syndrome-like phenotypes in mouse models. Meanwhile, 17-beta-estradiol showed a negative association with Akkermansia muciniphila, a bacterium widely regarded as a marker of gut health. These associations suggest that the pituitary hormones governing the cycle, not just the ovarian hormones they regulate, may matter for gut ecology. Given the emerging evidence that gut microbiota interact with a broad range of women's health conditions, including PCOS and cardiovascular disease, identifying which hormones are doing the driving has real clinical relevance.

Diet explained more microbial variation than hormones did

The study collected dietary data two ways: food frequency questionnaires (FFQs) and daily diary entries logged via MyFitnessPal. The two methods told somewhat different stories about absolute intake, with daily diaries recording higher total energy, carbohydrates, fats, proteins, and sugars, while FFQs estimated higher cholesterol and fiber. Despite those discrepancies, both tools captured dietary-microbiome relationships that held up in multivariable models.

Higher fiber intake was associated with increased abundance of Roseburia hominis, an important short-chain fatty acid producer. Sugar intake was negatively associated with Clostridium sp. AM22_11AC. Coffee consumption showed a strong positive association with Lawsonibacter asaccharolyticus, replicating findings from prior studies, and yogurt consumption independently predicted higher levels of the same species. Olive oil consumption correlated with the superpathway of beta-D-glucuronosides degradation. Altogether, hormonal fluctuations across the menstrual cycle contributed to microbial shifts, but fiber intake and stool consistency (Bristol Stool Scale score) remained significant independent predictors of beta diversity in multivariable models that explained 7.6% of total variance.

Critically, mediation analysis found no evidence that hormones mediate the effect of diet on the gut microbiome. Diet and hormones appear to act on the microbiome through separate mechanisms.

Estrobolome enzymes shift across phases but don't track estradiol levels

The team also quantified the estrobolome, the set of microbial enzymes that process circulating estrogens and return them to active form in the gut. Six enzyme families were measured: beta-glucuronidase, beta-galactosidase, beta-glucosidase, 6-phospho-beta-glucosidase, arylsulfatase type 1, and aryl-sulfate sulfotransferase. Beta-galactosidase was the most prevalent; aryl-sulfate sulfotransferase had the lowest abundance across samples.

Four of those enzymes, including beta-galactosidase, beta-glucosidase, arylsulfatase, and beta-glucuronidase, were significantly lower in the follicular phase compared to the early luteal phase. That cycle-dependent shift is intriguing, but the punchline is that none of the estrobolome enzymes showed a significant association with circulating 17-beta-estradiol or progesterone levels. The enzymes change across the cycle, but whether they are influencing or responding to hormone levels remains unresolved.

What this study can and can't settle

The Women4Health cohort is a genuine methodological advance: longitudinal design, LH-timed phase assignments, shotgun sequencing, and dual dietary assessment tools all in one study. But 160 participants from a relatively homogeneous Italian population, all healthy and with regular cycles, limits how far the findings can travel. The authors note that the sample may be underpowered to detect subtler hormone effects, and that unmeasured variables like sleep quality and stress could be shifting the microbiome independently.

The restriction to total circulating hormones, without separating conjugated from unconjugated forms, also leaves mechanistic questions open. Twenty-one of the thirty hormone- and diet-associated species identified are short-chain fatty acid producers, including Akkermansia muciniphila and Faecalibacterium prausnitzii, suggesting the downstream metabolic consequences of these shifts could be real, but tracing cause and effect will require larger and more diverse cohorts. For now, the clearest takeaway is that the menstrual cycle shapes gut ecology in measurable ways, that pituitary hormones deserve more attention than they typically receive in this context, and that what a woman eats may matter as much as, or more than, where she is in her cycle.

Evidence rating

EMERGING — 80/100

Caveats:

• Longitudinal observational study — shows associations, not causation.
• Sample limited to 160 healthy Italian women; findings may not generalize to other populations or women with hormonal conditions.
• Study is a preprint and has not yet completed peer review.
• Only 7.6% of total microbiome variation was explained by all measured factors combined, suggesting many influences remain uncharacterized.
• No significant mediation by hormones on dietary microbiome effects was found, so the biological mechanism linking hormones to microbiome shifts remains unclear.

Longitudinal observational cohort (n=160) using shotgun metagenomics across four hormonally confirmed menstrual phases. Identifies associations between reproductive hormones and specific microbial species and pathways, but cannot establish causation. Findings are consistent with prior diet-microbiome literature and partially replicated (e.g., Lawsonibacter-coffee link), though the hormone-specific associations have not yet been independently replicated. Currently available as a preprint pending peer review.

References

1. Serena Sanna, Valeria Lo Faro, Paola Forabosco, et al. (2026). Gut Microbiome Variation Across Menstrual Phases: Distinct Roles of Diet and Physiological Hormonal Fluctuations in Healthy Women. https://doi.org/10.21203/rs.3.rs-9888793/v1
2. The Gut Microbiome and Female Health – PMC. NIH. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8900146/
3. Gut Microbiota and Women's Health: Insights from Basic Research to Clinical Applications. frontiersin.org. https://www.frontiersin.org/research-topics/50950/gut-microbiota-and-womens-health-insights-from-basic-research-to-clinical-applications
4. Muriel Tahtouh Zaatar, Rima Othman, Mohammed Abushawish, et al. (2026). The Women’s Microbiome: Molecular Insights, Clinical Gaps, and Future Frontiers in Precision Health with Implications for Gulf Cooperation Council Populations. International Journal of Molecular Sciences. https://doi.org/10.3390/ijms27062521