The Gut Microbiome and Menopause: What’s Happening Inside, and How to Support Your Health
Did you know that women spend, on average, one-third of their lives in menopause? It’s a natural and inevitable transition - but that doesn’t mean it’s without challenges. While hot flushes, sleep disruption, and mood changes tend to steal the spotlight, fewer women are aware of what’s happening deeper within: significant shifts in the gut microbiome.
The gut microbiome - a diverse community of bacteria, fungi, and other microorganisms that live in your digestive tract - plays a vital role in everything from digestion and immunity to metabolism and even mental wellbeing. And during menopause, when hormone levels, particularly oestrogen, fluctuate dramatically, this internal ecosystem can also undergo meaningful changes.
Understanding these shifts is key to protecting your gut health, and by extension, your overall wellbeing during this phase of life.
1. Declining Oestrogen Alters Gut Microbiota Composition
As oestrogen levels fall during menopause, they don’t just affect hormones—they impact your gut too. Oestrogen plays a key role in supporting a healthy, diverse microbiome.
Studies show that lower oestrogen is linked to gut dysbiosis—an imbalance in bacteria that can lead to bloating, digestive issues, inflammation, and weight gain (Baker et al., 2017; Lindheim et al., 2021).
In short: when your hormones shift, your gut does too—and looking after your microbiome can help ease the ride.
2. Menopause May Contribute to "Leaky Gut" and Inflammation
Another downstream effect of lower oestrogen is increased gut permeability - commonly referred to as leaky gut. In this state, the tight junctions lining your intestinal wall become compromised, allowing toxins and bacteria to “leak” into the bloodstream, triggering inflammation.
According to a 2019 study in Frontiers in Endocrinology, oestrogen has protective effects on the intestinal barrier, and its decline during menopause may exacerbate inflammation and compromise gut integrity Sharma et al., 2019. Chronic inflammation, in turn, is linked to many menopause-related symptoms, including joint pain, fatigue, and mood changes.
3. Changes in Gut Motility Can Lead to Digestive Discomfort
Gut motility—the coordinated muscle contractions that move food through the digestive tract—often slows down during menopause. This may be due to hormonal shifts that affect the enteric nervous system and the gut-brain axis.
A study by Sanna et al. (2018) in Nature explored how changes in hormonal signalling during menopause could impact microbial function and digestive transit, leading to common complaints such as constipation and bloating Sanna et al., 2018.
When gut transit slows, fermentation of undigested food increases, potentially contributing to gas, bloating, and further disruption of the microbiome.
4. The Gut-Brain Axis and Mental Health During Menopause
The gut-brain axis—the bidirectional communication network between the central nervous system and the gastrointestinal tract—plays a crucial role in mental wellbeing. It’s why your gut is sometimes referred to as your “second brain.”
Hormonal fluctuations during menopause can alter this gut-brain dynamic. Lower oestrogen levels are associated with an increased risk of anxiety and depression, and research suggests that dysbiosis of the gut microbiome may be a contributing factor. A 2015 study published in Brain, Behavior, and Immunity found that individuals with depressive symptoms had significantly different gut microbiota compared to those without, suggesting a possible microbial link to mood disorders Jiang et al., 2015.
Supporting gut health may therefore help buffer against emotional lows during this time of transition.
How to Support Gut Health During Menopause
Thankfully, there are practical and natural ways to care for your gut microbiome as you navigate menopause:
✅ Prioritise a Fibre-Rich Diet
Fibre feeds your good gut bacteria. Aim for a variety of colourful fruits, vegetables, legumes, and whole grains. These prebiotic foods nourish the microbiota and promote regular digestion, helping to maintain a diverse and resilient gut environment.
✅ Incorporate Probiotic-Rich Foods
Fermented foods such as yoghurt, kefir, sauerkraut, kimchi, and miso are excellent sources of probiotics—live bacteria that can help restore balance in the gut.
🔗 NHS overview of probiotics and fermented foods
✅ Manage Stress to Protect the Gut-Brain Axis
Chronic stress has a direct impact on gut health. It can alter microbial balance and increase gut permeability. Stress-reduction techniques such as mindfulness meditation, yoga, walking in nature, and deep-breathing exercises can help re-regulate the gut-brain axis and support emotional equilibrium.
🔗 Mental Health Foundation: Managing Stress
✅ Consider Supplements for Additional Support
In some cases, supplements can help bridge nutritional gaps or offer targeted support. These may include:
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Probiotic and prebiotic blends to improve microbial diversity
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Omega-3 fatty acids to reduce inflammation
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Adaptogens and mushroom-based supplements like itmushbegood’s ‘pause’, designed to balance the nervous system and digestive health during menopause
(As always, consult a healthcare provider before starting a new supplement routine.)
Final Thoughts
Menopause is more than a hormonal event - it’s a full-body shift that includes complex interactions between your endocrine system, gut, brain, and immune response. The changes in your gut microbiome during this time can affect everything from your digestion and immunity to your mood and energy levels.
But you’re not powerless. By understanding what’s happening within your body and making simple, consistent changes to your diet, lifestyle, and self-care habits, you can support your gut health - and feel more grounded, resilient, and well throughout the menopause transition.
Your microbiome is talking. During menopause, it’s more important than ever to listen.
