Hot flashes and sleep problems get the most attention in midlife, but many women also notice changes in their gut. Bloating appears out of nowhere, once-reliable toilet routines go completely off track, and foods that once seemed fine now feel heavy.
Is it just getting older? Or is something else going on? Research shows that hormone shifts during perimenopause and postmenopause can throw the gut out of balance in some women. “The gut microbiome influences many parts of your health, including your immune system, your metabolism and even your brain function,” said Dr. Charis Chambers, board-certified gynecologist and founder of The Period Doctor. “In short, the gut microbiome plays a key role in staying healthy in middle age.”
Learn what changes occur in your gut microbiome in midlife and get simple tips to help you keep it under control.
How perimenopause and menopause can affect the gut microbiome
“Hormonal levels, particularly estrogen levels, decrease and become more variable, and this can change the type of microbes that thrive in your gut,” explained specialist Kate McLean, MD, MPH, FACOG. Some small studies have shown lower diversity and a gut profile more similar to that of men, even when researchers take age and lifestyle into account.
Scientists use the term estrobolome to describe the group of gut bacteria and enzymes that help process and recycle estrogen. Changes in these bacteria could affect how much estrogen is recycled or excreted from the body, Chambers said. “This means less estrogen is absorbed and available to the body, which can further worsen menopause symptoms and increase the risk of osteoporosis, metabolic syndrome and cardiovascular disease.”
In some studies, these changes are also associated with signs of cardiac and metabolic risk. Daily habits, aging, medications, and changes in sleep, stress, activity, and diet can all influence which microbes thrive in the gut, Chambers explained.
How microbiome changes during menopause can affect your everyday life
Reduced microbiome diversity and changes in gut bacterial species during menopause can lead to a range of symptoms. These symptoms can be different for everyone, but there are some that are common. “Women may notice digestive symptoms such as bloating, constipation and diarrhea,” Chambers said.
Because your microbiome plays a large role in regulating neurotransmitters that affect your mood and cognition, symptoms can extend beyond the gut. According to McLean, you may notice brain fog, low energy, trouble sleeping, or mood swings.
Keeping a simple symptom log of your diet, sleep times, exercise, and stress levels in addition to symptoms can make clinic visits more useful and help you determine exactly what impact your symptoms are having.
How to improve your gut microbiome
To improve the diversity of your gut microbiome, start with daily habits that support a healthy mix of gut bacteria. Small steps add up.
- Eat more fiber. Add fruits, vegetables, beans, and whole grains to most meals and try to fill half of the plate with plants. Fiber feeds helpful microbes and supports regularity.
- Choose simple fermented foods that you enjoy. Yogurt, kefir, sauerkraut, kimchi, or tempeh can add helpful microbes to your gut. Choose options that suit your taste and budget. A spoonful or two with meals is enough to start with.
- Exercise most days. Walking, strength training, or aerobic exercise such as cycling, running, and swimming support digestion and overall health, even for short workouts. Moderate, regular exercise supports a healthy gut microbiome. But don’t overdo it—prolonged, high-intensity exercise can actually throw your microbiome out of balance.
- Protect sleep and reduce stress. Try to go to bed and get up at the same time every day. Brief relaxation and simple stress tools like breathing or stretching can help. Both sleep and stress can affect how you feel in your gut.
- Be careful with alcohol. Reducing your alcohol consumption supports (among other things) gut health. That’s because drinking alcohol upsets the balance of bacteria in your gut microbiome. It can also lead to leaky gut because your gut microbiome sometimes starts to eat away at the intestinal lining when it gets out of balance. Your gut microbiome also creates metabolites when it processes alcohol – and some of these metabolites are toxic.
- Consider Probiotics or prebiotics with care. “Food-first fiber” is a good place to start. Some people find supplements helpful, but results vary. If you want to try it, look for human-studied strains, clear CFU quantity, and quality testing. Be sure to consult your doctor if you are immunocompromised or taking certain medications. “[Probiotics and prebiotics] may help some people, but the benefit depends on the product and the person,” McLean said.
- Do you know where hormone therapy makes sense?. Menopausal hormone therapy is used to treat symptoms such as hot flashes and sleep problems, and scientists are still studying how it might affect the gut. “From a gut perspective, restoring estrogen may indirectly affect the microbiome and some symptoms, but hormone therapy is a medical decision based on overall risks and benefits, so discuss it with your doctor,” McLean said.
- A simple step to try this week. “Add an extra serving of high-fiber food every day and drink a little more water,” McLean said. “It’s easy, inexpensive, and instantly supports a healthier gut.”
Menopause care looks different for everyone
Access and cost can impact your options in midlife. Menopausal care and use of hormone therapy differ based on race, ethnicity, income, and insurance. These gaps can increase symptom burden and limit treatment options for many people. Many families also suffer from food insecurity, making it more difficult to regularly purchase fiber-rich foods or fermented foods.
Practical tips for a gut microbiome-friendly diet:
- Choose inexpensive sources of fiber and protein such as beans, lentils, oats, brown rice, frozen vegetables, canned fish – choose store brands and bulk containers when possible.
- Try inexpensive fermented foods like plain yogurt, store-brand kefir, and jarred sauerkraut.
- If supplements aren’t in your budget, focus on whole-food-based fiber first and skip packaged foods with added fiber that promise quick fixes.
- Look for community resources such as WIC and SNAP benefits, food co-ops, community refrigerators, and relay clinics.
- If you don’t have access to a menopause-trained doctor, search directories of major companies and telemedicine providers that accept your insurance.
When to call a healthcare provider
Seek medical help if any of the following symptoms occur or do not improve with simple measures:
- New or heavy vaginal bleeding, new or foul-smelling discharge, or severe pelvic pain.
- Severe abdominal pain, blood in the stool, unexplained weight loss, or persistent vomiting.
- Intestinal symptoms that prevent you from daily activities or that do not improve after a few weeks of fundamental changes.
Talk to your doctor about the full range of treatments for symptom relief, including menopausal hormone therapy if appropriate.
“It’s a myth that menopause automatically ruins your gut and there’s nothing you can do about it,” McLean said. “The gut is adaptable and diet, exercise, sleep and targeted care can significantly improve gut health at any age.”
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