Menopause is one of the most significant physiological transitions in a woman's life, and yet its effects on the gut have received surprisingly little attention until recently. Most clinical conversations about menopause center on hot flashes, bone density, cardiovascular risk, and mood. The digestive system rarely comes up, even though many women going through perimenopause and early postmenopause report new or worsening GI symptoms: bloating that appears out of nowhere, changes in bowel habits, increased gas, and a general sense that their gut is behaving differently than it used to. A 2025 study by the ZOE research group, analyzing gut microbiome data from 70,399 women, has brought the menopause-gut connection into sharper focus. The findings confirm that menopause reshapes the gut microbiome in ways that go beyond normal aging, and they raise important questions about whether supporting gut health during this transition could make a meaningful difference.
What the ZOE study of 70,399 women found
The 2025 ZOE study, led by Bermingham et al. and published in a peer-reviewed journal, is the largest analysis to date of gut microbiome differences across menopausal status. The researchers analyzed shotgun metagenomic sequencing data from stool samples provided by women participating in the ZOE PREDICT study and its associated community science program. Participants were categorized as premenopausal, perimenopausal, or postmenopausal based on self-reported menstrual status, and analyses controlled for age, BMI, diet quality, and medication use.
The headline finding was that menopausal status was independently associated with significant differences in gut microbiome composition. Postmenopausal women showed lower overall microbial diversity compared to premenopausal women of similar age. Specific species associated with short-chain fatty acid (SCFA) production, including several Faecalibacterium and Roseburia species, were reduced in postmenopausal participants. Conversely, species associated with metabolic inflammation and less favorable metabolic profiles were more abundant in the postmenopausal group.
Critically, these differences persisted after adjusting for age, which means they were not simply an artifact of getting older. Menopause itself, or more precisely the hormonal shifts associated with it, appears to independently reshape the gut microbial community. The effect sizes were modest but consistent across multiple analytical approaches, and the sample size provides statistical power that smaller studies could not achieve.
The estrobolome: where gut bacteria meet estrogen metabolism
To understand why menopause affects the gut microbiome, it helps to understand the estrobolome. This term, coined by Plottel and Blaser in 2011, refers to the collection of gut bacterial genes and species capable of metabolizing estrogen. Certain gut bacteria produce an enzyme called beta-glucuronidase, which deconjugates estrogen in the gut, allowing it to be reabsorbed into circulation rather than excreted. In this way, the estrobolome acts as a secondary regulator of circulating estrogen levels, working alongside ovarian production.
In premenopausal women, this system operates as part of a feedback loop. The ovaries produce estrogen, the liver conjugates and excretes it into bile, and gut bacteria partially deconjugate it, allowing some to recirculate. When ovarian estrogen production declines during menopause, the estrobolome's contribution to circulating estrogen becomes proportionally more important, even as the estrobolome itself appears to be disrupted by the very hormonal changes it is trying to compensate for (Baker et al., 2017).
âšī¸The estrobolome is not a single species or strain. It is a functional group of bacteria defined by their ability to metabolize estrogen through beta-glucuronidase activity. Members include species within Bacteroides, Bifidobacterium, Clostridium, Escherichia, and Lactobacillus, among others. Disruption of the estrobolome can shift estrogen metabolism in either direction: too much beta-glucuronidase activity can increase estrogen recirculation, while too little can accelerate estrogen depletion.
This bidirectional relationship has implications beyond menopause. An overactive estrobolome has been linked to estrogen-driven conditions like endometriosis and certain breast cancers, while an underactive estrobolome during menopause may worsen estrogen depletion symptoms. The ZOE data suggests that menopausal changes in estrobolome composition could compound the effects of declining ovarian function, creating a feedback loop where hormonal changes alter the gut microbiome, which in turn affects hormone metabolism (Plottel and Blaser, 2011).
Why GI symptoms spike during perimenopause
If you are going through perimenopause and your gut feels different, you are not imagining it. Surveys consistently find that 40 to 60 percent of perimenopausal and early postmenopausal women report new or worsening GI symptoms, including bloating, abdominal discomfort, constipation, and changes in stool consistency. These symptoms are frequently dismissed as stress-related or coincidental, but there are clear biological reasons for them.
Estrogen receptors are expressed throughout the gastrointestinal tract, including in the esophagus, stomach, small intestine, and colon. Estrogen influences gut motility (the speed at which food moves through the digestive system), visceral sensitivity (how much you feel sensations in the gut), mucosal blood flow, and the secretion of protective mucus. Declining estrogen levels during menopause affect all of these functions. Studies have shown that gut transit time tends to slow in postmenopausal women, which can contribute to constipation and bloating (Heitkemper and Chang, 2009). The gut barrier may also become more permeable, allowing more bacterial products to interact with the immune system.
On top of these direct effects, progesterone fluctuations during perimenopause can further alter motility. The hormonal volatility of perimenopause, where estrogen and progesterone levels swing unpredictably before settling into their postmenopausal baseline, may explain why GI symptoms are often most pronounced during the transition itself rather than after it.
HRT and the microbiome: what the data shows
One of the more intriguing findings from the ZOE study was that postmenopausal women using hormone replacement therapy (HRT) had gut microbiome profiles that more closely resembled those of premenopausal women compared to postmenopausal women not using HRT. The HRT group showed higher microbial diversity, greater abundance of SCFA-producing species, and lower levels of species associated with metabolic inflammation.
This finding is observational and carries important caveats. Women who use HRT may differ from non-users in ways that independently affect the microbiome, including socioeconomic status, healthcare access, diet quality, and exercise habits. The ZOE study controlled for several of these variables, but residual confounding cannot be ruled out. It is also unclear whether HRT directly affects the gut microbiome through estrogenic activity on gut tissue and bacteria, or whether the effect is indirect, mediated by HRT's influence on metabolism, inflammation, and gut motility.
A smaller 2023 study by Santos-Marcos et al. in Gut Microbes found similar results, with HRT users showing higher Bifidobacterium and Akkermansia levels compared to non-users. Animal studies have shown that estrogen administration to ovariectomized mice partially restores premenopausal microbiome patterns (Org et al., 2016), providing mechanistic support for a direct hormonal effect. But until randomized controlled trials specifically examine HRT's effects on the gut microbiome, the relationship remains associational.
What helps: supporting gut health through the menopausal transition
The evidence base for specific gut-targeted interventions during menopause is still developing, but several strategies are supported by both menopause and microbiome research.
- Increase dietary fiber gradually. Fiber is the primary fuel source for SCFA-producing bacteria, which appear to decline during menopause. A 2020 study in Gut found that a Mediterranean diet rich in fiber increased SCFA producers and reduced inflammatory markers in elderly adults (Ghosh et al., 2020). Aim for 25 to 30 grams per day from varied sources.
- Include fermented foods regularly. A 2021 Stanford study by Wastyk et al. found that a high-fermented-food diet increased microbiome diversity more effectively than a high-fiber diet alone over a 10-week period. Fermented foods include yogurt, kefir, sauerkraut, kimchi, and miso.
- Pay attention to phytoestrogens. Soy isoflavones, flaxseed lignans, and other phytoestrogens interact with estrogen receptors and are metabolized by gut bacteria. Their effects are modest but may be relevant for women experiencing estrogen-related symptoms. A 2021 meta-analysis found that soy isoflavones reduced hot flash frequency by about 20% compared to placebo (Taku et al., 2012, updated by Chen et al., 2021).
- Track your symptoms. GI changes during perimenopause can be confusing because they wax and wane with hormonal fluctuations. GLP1Gut can help you log food, symptoms, and cycle patterns to identify whether specific foods or timing patterns correlate with your worst days.
- Discuss GI symptoms with your healthcare provider. Many women do not mention gut changes during menopause consultations, and many providers do not ask. Bringing it up can lead to appropriate evaluation and management.
The bigger picture: menopause as a gut health turning point
The ZOE data and related research suggest that menopause represents a significant inflection point for gut health. The microbiome changes that occur during this transition are not trivial. Reduced SCFA production, increased pro-inflammatory species, and disrupted estrogen metabolism may collectively contribute to the increased risk of metabolic syndrome, cardiovascular disease, and osteoporosis that women face after menopause. Whether supporting the gut microbiome during this window can meaningfully modify those risks is one of the most important open questions in women's health research.
What is clear is that gut health deserves a place in the menopause conversation, both in clinical settings and in how women approach their own health during this transition. The gut is not separate from hormonal health. It is deeply embedded in it, and the evidence for that connection is now substantial enough that ignoring it does women a disservice.
**Disclaimer:** This article is for informational purposes only and does not constitute medical advice. Always consult with a qualified healthcare provider about your specific health concerns, including decisions about hormone replacement therapy.
Does menopause change your gut bacteria?
Yes. The 2025 ZOE study of over 70,000 women found that menopause is independently associated with changes in gut microbiome composition, including reduced diversity and shifts in species involved in SCFA production and estrogen metabolism. These changes go beyond what would be expected from aging alone.
What is the estrobolome?
The estrobolome is the collection of gut bacteria that produce beta-glucuronidase, an enzyme that influences how estrogen is metabolized and recirculated in the body. It acts as a secondary regulator of circulating estrogen levels, and its disruption during menopause may compound the effects of declining ovarian estrogen production.
Does HRT help your gut microbiome?
Observational data from the ZOE study and smaller studies suggest that HRT users have gut microbiome profiles more similar to premenopausal women. However, this is not proof of causation, and HRT decisions should be based on a full risk-benefit assessment with your healthcare provider, not on microbiome effects alone.
Why do I have more bloating during perimenopause?
Bloating during perimenopause likely results from a combination of factors: fluctuating estrogen and progesterone affecting gut motility, changes in gut microbiome composition, altered visceral sensitivity, and shifts in gut barrier function. These are real physiological changes, not imagined symptoms.