Menopause and the Microbiome: A Nutritional Therapist’s Perspective on Gut Changes, Stool Testing and Food-First Support
“The Kitchen is your lab and food is your best medicine!”
~ Dr Nina
Perimenopause and menopause are usually talked about in terms of hot flushes, sleep changes, mood changes and weight gain. But one area that deserves much more attention is the gut microbiome. If you have noticed more bloating, constipation, reflux, IBS-type symptoms, or a general sense that your digestion has changed as your hormones have changed, you are not imagining it. Recent literature supports the idea that menopause can alter gut motility and gut microbial composition in ways that affect whole-body health.
Oestradiol and progesterone are not just reproductive hormones. Their receptors are expressed throughout the body, including the gut. As these hormones fluctuate in perimenopause and decline further in menopause, they can affect gut structure, gut barrier function, motility and microbial balance. This matters because the gut is closely linked to immune, metabolic and neuroendocrine systems, so changes here can ripple out into inflammation, energy, weight, cardiometabolic health, mood and even bone health.
What changes in the microbiome during perimenopause and menopause?
One important point is that these changes may begin before periods have fully stopped. In other words, the microbiome story can start in perimenopause, not only after menopause is established. A 2024 study looking at gut microbiota and faecal metabolites in women with menopausal symptoms reported microbial and metabolic differences linked with hormonal change, with microbial diversity beginning to plateau and key shifts starting to appear, including lower Bifidobacterium levels and fewer short-chain fatty acid-producing microbes.
By menopause, the overall pattern is one of lower microbial richness, lower resilience, reduced estrobolome potential, and a shift towards a more pro-inflammatory profile, including lower levels of Lactobacillus, Bifidobacterium, Akkermansia and Faecalibacterium in some studies. At the same time, it is important not to oversimplify this. A large 2024 cohort study found that menopausal differences in the gut microbiome were only modest after adjustment for age, diet and cardiovascular risk factors, and a 2025 study in postmenopausal women suggested that the microbiome may remain relatively resilient in some women. So the fairest conclusion is that menopause can influence the microbiome, but age, diet, body composition, metabolic health and lifestyle still matter enormously.
Why does this matter?
This matters because the microbiome is not just about digestion. Reduced short-chain fatty acid production, poorer barrier integrity and greater endotoxin exposure may all feed into the low-grade inflammation and insulin resistance that so many women notice around menopause. Dysbiosis can increase intestinal permeability and allow lipopolysaccharide (LPS) to enter the circulation, contributing to visceral fat gain, insulin resistance and wider metabolic dysfunction. A study in postmenopausal women with obesity also found that stool microbiota, faecal short-chain fatty acids and calprotectin were associated with cardiometabolic risk factors.
There is also the estrobolome to consider. This is the part of the gut microbiome involved in oestrogen metabolism. Some gut microbes produce enzymes such as beta-glucuronidase and arylsulfatase, which help deconjugate oestrogens in the gut and may influence how much is reabsorbed and recirculated. In a study of healthy postmenopausal women, greater faecal microbial diversity was associated with a higher urinary ratio of hydroxylated oestrogen metabolites to parent oestrogens. Reduced estrobolome activity and gut barrier dysfunction may also affect the gut-vaginal axis, which may help explain why some women notice changes not only in digestion but also in vaginal health and susceptibility to dysbiosis as oestrogen declines.
Can a stool test help?
I do think a stool test can be effective here, but only in the right context. It will not diagnose menopause, and it will not replace a good clinical history. What it can do is help us see patterns that symptoms alone cannot: microbial imbalance, altered fermentation, changes in faecal short-chain fatty acids, inflammatory signals such as calprotectin, and sometimes a gut picture that fits with the bloating, constipation or metabolic changes a woman is experiencing. Research in women with menopausal symptoms has used stool sequencing to identify microbial differences associated with oestradiol, FSH and LH, while work focused on perimenopause has shown faecal metabolite changes alongside hormonal shifts.
The caveat is very important. An international consensus statement published in 2024 concluded that evidence supporting routine microbiome testing in clinical practice is still limited, and that many direct-to-consumer microbiome tests have no proven value. So, for me, stool testing is most useful when there is a clear clinical question to answer and when the results are interpreted alongside symptoms, diet, hormone stage and medical history. Used that way, it can be a helpful tool for personalising food and lifestyle work rather than guessing.
Food-first ways to support the menopausal microbiome
The first dietary shift I would think about is not perfection, but diversity: a Mediterranean-style, plant-rich pattern with more vegetables, fruit, beans, lentils, nuts, seeds and wholegrains. That makes sense to me, because fibre does much more than “keep you regular”. It feeds beneficial microbes, supports short-chain fatty acid production, helps bowel transit and gives the estrobolome the raw material it needs.
I would also pay attention to specific food groups that nourish the microbiome. Soluble fibre from oats, beans and legumes can support transit and metabolic health. Resistant starch from cooked and cooled potatoes or rice, and from green bananas, may help feed bacteria associated with short-chain fatty acid production. Inulin-rich foods such as onions, garlic, asparagus and artichokes can be very useful too, if tolerated. And if constipation has become part of the menopause picture, simple food-based supports such as kiwi fruit, prunes and ground flaxseed can be very helpful.
Polyphenol-rich foods matter as well. Foods such as berries, pomegranate, herbs, spices, cocoa and extra-virgin olive oil provide compounds that interact with gut microbes and may help support microbial diversity and barrier function. Fermented foods are another food-based way to support microbial balance. This is one of the reasons I encourage women not to think only in terms of calories at menopause, but in terms of what their gut bacteria are actually being fed.
Another interesting food angle is phytoestrogen-rich foods, but from whole foods rather than supplements. The benefits of soy foods, flax, sesame, pomegranate and walnuts are partly microbiome dependent. Some women have gut microbes that convert soy isoflavones into equol more efficiently than others, and that may influence how much benefit they notice. One dietary trial found that a low-fat plant-based diet with daily cooked soybeans substantially reduced moderate-to-severe hot flushes over 12 weeks, and an exploratory microbiome analysis suggested the gut may be part of that response. That does not mean every woman needs the same diet, but it does remind us that the microbiome can shape how foods “land” in the body.
Final thoughts
Menopause is not just a hormone story. It is also a gut story, an inflammation story, a metabolic story and, for many women, a bowel habit story too. Looking into the microbiome can be genuinely helpful, especially when symptoms are persistent or the picture feels unclear, but the aim is not to chase a perfect stool test. The aim is to use symptoms, history and, where appropriate, stool testing to guide gentle, achievable food and lifestyle changes that help the body adapt more smoothly to this phase of life. One size rarely fits all here.
If you are navigating perimenopause or menopause and feel that gut symptoms may be part of the picture, I offer one-to-one consultations to help decide whether stool testing would be useful and how to use the results to guide practical food and lifestyle changes.
References
IHCAN Summit. Menopause and the Microbiome: Clinical Strategies for Restoring Digestive and Metabolic Health webinar page.
Bailey C. Menopause and the Microbiome: Clinical Strategies for Restoring Digestive and Metabolic Health slide deck.
Ley D, Saha S. Menopause and gastrointestinal health and disease. Nature Reviews Gastroenterology & Hepatology (2025). (Nature)
Xie X, Song J, Wu Y, et al. Study on gut microbiota and metabolomics in postmenopausal women. BMC Women’s Health (2024). (Springer Nature Link)
Liu Y, Zhou Y, Mao T, et al. The relationship between menopausal syndrome and gut microbes. BMC Women’s Health (2022). (Springer Nature Link)
Łoniewski I, Szulińska M, Kaczmarczyk M, et al. Analysis of correlations between gut microbiota, stool short-chain fatty acids, calprotectin and cardiometabolic risk factors in postmenopausal women with obesity. Journal of Translational Medicine (2022). (Springer Nature Link)
Porcari S, Mullish BH, Asnicar F, et al. International consensus statement on microbiome testing in clinical practice. The Lancet Gastroenterology & Hepatology (2025). (ScienceDirect)
Li VW, Dong TS, Funes D, et al. Mass spectrometric profiling of primary estrogens and estrogen metabolites in human stool and plasma partially elucidates the role of the gut microbiome in estrogen recycling. Molecular and Cellular Endocrinology (2025). (ScienceDirect)
Fuhrman BJ, Feigelson HS, Flores R, et al. Associations of the fecal microbiome with urinary estrogens and estrogen metabolites in postmenopausal women.The Journal of Clinical Endocrinology & Metabolism (2014). (Associations of the Fecal Microbiome With Urinary Estrogens and Estrogen Metabolites in Postmenopausal Women - PMC)
Kahleova H, Holtz DN, Strom N, et al. A dietary intervention for postmenopausal hot flashes: A potential role of gut microbiome. An exploratory analysis. Complementary Therapies in Medicine (2023). (ScienceDirect)
