Menopause and Your Microbiome: How Gut Health Shapes Weight, Mood, and Hormones

While the changes we experience around menopause and its many symptoms are primarily related to shifting hormone levels, your body also goes through other important changes that can affect your health, physical function, and sense of well-being.

One of the most important – and often overlooked – changes occurs in your gut. See how changes in your gut microbiome during perimenopause and menopause can affect your weight, mood, digestion and hormone profile.

Basic Takeaways

• Perimenopause and menopause can reduce gut microbial diversity, which can affect digestion, inflammation, mood and metabolism.
• Estrobol—the group of gut bacteria involved in estrogen metabolism—plays a role in how estrogen is recycled in the body.
• Changes in the gut may explain why many women notice changes in waist circumference, energy, constipation, sleep and emotional resilience during midlife.
• Diet, exercise, fiber, fermented foods and targeted supplements can help support a more resilient microbiome.

Why the gut microbiome matters in menopause

We know that our microbiome—the trillions of bacteria that live in our gut—does more than just help digest food and absorb nutrients.

These beneficial bacteria influence metabolism, mood, immune and brain function, inflammation, body composition and bone density. In women, gut bacteria also help recycle estrogen during our reproductive years.

As such, the microbiome is deeply connected to our overall health, important bodily functions, performance and recovery.

READ MORE | Take creatine during menopause to improve your quality of life

What happens to the microbiome during perimenopause?

During perimenopause, the transitional, often symptom-heavy phase leading up to menopause, your microbiome changes in ways that can affect your entire body.

Usually starting in your 40s or 50s, fluctuating estrogen and progesterone levels cause irregular periods, hot flashes and emotional swings.

However, these hormones don’t just regulate your reproductive cycle. They also have receptors all over your body, including the lining of your gut.

One of the most overlooked consequences of perimenopause is the decline in gut microbial diversitywhich often starts years before your last period.

Research¹ suggests that falling levels of sex hormones—particularly estrogen and progesterone—are associated with reduced gut microbiome diversity and changes in the estrobulus, the collection of bacteria involved in estrogen metabolism.

Additionally, a decrease in estradiol (the most potent and abundant form of estrogen) and progesterone can lead to gut permeability, which allows gut bacteria to escape the digestive system and enter the body, leading to problems like leaky gut syndrome.

Progesterone can also slow down bowel motility, potentially contributing to constipation, which is common during menopause.

READ MORE | Hormones, menopause and cancer: An invitation to consider breast cancer risk

How gut changes can affect weight, mood and digestion

Studies² link these menopause-related microbiome changes to higher waist circumference, blood pressure, and markers of cardiometabolic risk.

An unbalanced microbiome also affects the gut-brain axis – a two-way communication pathway between your gut and brain. This disorder has been linked to anxiety, depression and cognitive changes, which may be more prevalent during menopause.

This is a major reason many women notice changes in weight, energy, digestion and mood during the menopause transition.

READ MORE | Don’t let perimenopause stop your life: thrive through change

How to support gut health during menopause

The good news is that you can actively support and nurture your microbiome during perimenopause and menopause through diet and lifestyle choices.

The best thing women can do at this stage of their lives is to eat foods and make lifestyle changes that promote a diverse gut microbiome and help maintain the integrity of their gut barrier.

A comprehensive approach should incorporate these four powerful interventions:

1. Eat more plants

Eat a wide variety of plants each week, including vegetables, fruits, herbs, legumes, nuts, seeds and whole grains, as foods provide the compounds that gut bacteria thrive on.

Plants contain different forms of fiber, which are the preferred food sources for beneficial gut bacteria. Aim for at least 25-30 grams of fiber per day from a variety of sources.

Eating a wide variety of brightly colored fruits and vegetables also provides polyphenols – natural compounds that act as antioxidants.

2. Include fermented foods

Fermented foods contain live probiotics, which can help replenish and maintain a healthy gut microbiome. Consider incorporating:

• Yogurt (make sure it contains live cultures)
• Kefir
• Sauerkraut
• Kimchi
• Tempeh
• Hate

3. Move with intention and intensity

Movement doesn’t just support muscle and bone health. it also stimulates the microbiome.

Exercise, especially high-intensity training and strength training, has been proven³ to improve microbial diversity and metabolic signaling.

4. Complete your approach

A fiber supplement can help rebuild your gut microbiomeespecially if you find it difficult to eat a variety of natural plant foods or have suffered from a recent illness that required antibiotics.

Look for a supplement that includes different sources of fiber, providing both soluble and insoluble fiber and resistant starch.

When it comes to supporting your gut lining, do your research⁴ shows that Glutamine supplements may improve gut health supporting the microbiome and gut wall integrity by reducing inflammation.

Probiotics are another supplement that can help support and promote gut diversity through this transitional stage of life.

These products contain live microorganisms that can provide health benefits when consumed in sufficient amounts. Look for products that list the specific strains and have a colony forming unit (CFU) count.

Before starting any new supplement, including probiotics, talk to your doctor or a registered dietitian. They can help you determine if probiotics are right for you and recommend specific strains based on your individual needs.

Frequently Asked Questions

1. Can Menopause Affect Gut Health?

Yes. Changing estrogen and progesterone levels during perimenopause and menopause can affect gut microbial diversity, gut motility, inflammation, and the gut-brain axis.

2. What is a strobe?

The estrabolome is the group of gut bacteria involved in estrogen metabolism and recycling. When this microbial community changes, it can affect the amount of estrogen circulating in the body.

3. What foods support the gut microbiome during menopause?

A wide variety of plant foods, fiber-rich whole grains, legumes, nuts, seeds, colorful fruits and vegetables, and fermented foods such as yogurt, kefir, sauerkraut, kimchi, tempeh, and miso can all help support microbial diversity.

4. Should you take probiotics during menopause?

Probiotics may help support gut diversity for some women, but the right product depends on your symptoms, health history, and needs. Talk to your doctor or a registered dietitian before starting any new supplement.

References:

1. Peters BA, Santoro N, Kaplan RC, Qi Q. Spotlight on the Gut Microbiome in Menopause: Current Insights. Int J Womens Health. 2022 Aug 10, 14:1059-1072. doi: 10.2147/IJWH.S340491. PMID: 35983178; PMCID: PMC9379122.
2. Gumpeny N, Gumpeny L, Gumpeny SR. Metabolic syndrome in menopause. Explore Endocr Metab Dis. 2025? 2: 101440.
3. B. Charlesson, J. Jones, C. Abbiss, P. Peeling, S. Watts, CT Christophersen. Training load affects the gut microbiome of highly trained rowers. Journal of the International Society of Sports Nutrition2025? 22 (1) DOI: 10.1080/15502783.2025.2507952
4. Zhou Q, Verne ML, Fields JZ, Lefante JJ, Basra S, Salameh H, Verne GN. Randomized placebo-controlled trial of dietary glutamine supplementation for postinfectious irritable bowel syndrome. Intestine. 2019 Jun;68(6):996-1002. doi: 10.1136/gutjnl-2017-315136. Epub 2018 Aug 14. PMID: 30108163; PMCID: PMC9549483.