Menopause and your gut microbiome

What researchers have found

A 2022 study in mSystems analyzed stool samples from about 2,300 adults in the Hispanic Community Health Study/Study of Latinos. Postmenopausal women had lower gut microbiome diversity than premenopausal women, and their overall microbial makeup was somewhat closer to that of men. The differences were real but modest; sex explained much more variation than menopause did.

Several specific bacteria differed by menopause status. Some that were less common after menopause were linked, among postmenopausal women, with more favorable cardiometabolic measures, such as smaller waist size.

What the estrobolome is

Your liver packages estrogen and other sex hormones for removal, partly by sending them into the gut with bile. Some gut bacteria make enzymes that can unpack these hormones so they are reabsorbed. Researchers call the bacterial genes involved the estrobolome.

In the same study, postmenopausal women had lower levels of one of these bacterial enzyme genes, and some microbes correlated with hormone metabolites in the blood. The authors suggested gut bacteria may help recycle sex hormones after the ovaries slow down, but the study could not show cause and effect.

Important limits of this research

• The main study was cross-sectional, a snapshot rather than following women over time
• Menopause status was self-reported, and perimenopausal women could not be separated out
• Estradiol levels were not measured directly
• The results may not apply to all populations
• No study has shown that changing your microbiome changes your hormone levels or symptoms in a useful way

Digestive changes you might notice

Bloating, constipation, looser stools or new reactions to foods are common complaints in perimenopause and after. Hormonal fluctuations, changes in sleep and stress, medications and shifts in diet and activity can all play a role. It is usually impossible to pin symptoms on the microbiome alone.

New or persistent digestive symptoms, especially with weight loss, bleeding, or bloating with early fullness or pelvic pain, should be evaluated medically before any microbiome testing.

Can a microbiome test help?

A microbiome test can describe the bacteria in your stool and give a diversity score. What it cannot do yet is measure your estrobolome in a clinically meaningful way or tell you whether hormone therapy is right for you. An international consensus statement published in 2025 concluded that microbiome testing still has limited proven clinical value.

If you are curious about your gut and diet patterns, it can be interesting context. Your hormone treatment decisions are still based on your symptoms, history and risks.

Does hormone therapy change the microbiome?

This is an open question. Some small studies have looked at it, but there is no reliable evidence that hormone therapy improves gut health or that gut bacteria should guide hormone dosing. The Menopause Society's guidance on hormone therapy focuses on symptoms such as hot flashes, vaginal changes and bone protection, not the microbiome.

Medications common in midlife that affect the gut

Midlife often brings new prescriptions, and several can affect both bowel habits and gut bacteria. Antibiotics have the clearest effect on microbial diversity. Acid-suppressing drugs, iron supplements, some antidepressants, pain medications and GLP-1 weight medications can change bowel habits. If your digestion changed around the time a medication started, mention it, because adjusting the medication may help more than any dietary change.

Do not stop a prescribed medication on your own; your clinician can help weigh the options.

Supporting gut health in midlife

• Eat a wide variety of plant foods; the American Gut Project linked eating more than 30 plant types a week with greater microbial diversity
• Increase fiber gradually, with enough fluids
• Keep active, which helps bowel regularity
• Protect sleep, which affects appetite and gut comfort
• Limit alcohol
• Keep up with colorectal cancer screening

How HealifyMD approaches it

Your clinician looks at digestive symptoms alongside menopause symptoms, rules out red flags, and explains what a microbiome test can and cannot add. The Gut Biome Analysis is $625 as a one-time test, confirmed after your eligibility review. Labs are priced separately from treatment, and there is no membership fee.