Perimenopause, Menopause & Your Gut: When Hormones, Microbes, and Identity All Shift at Once

15 Sept

"I don’t know who I’m becoming… but I know I need to take care of her."

If you’re in perimenopause or menopause and feel like your body has changed the rules without warning - gut flares, food reactions, skin outbreaks, fatigue that doesn’t lift - you’re not imagining it.

For many women, this transition can feel like a perfect storm: hot flushes, night sweats, brain fog, mood swings… and digestive chaos - IBS flare-ups, SIBO relapses, histamine intolerance, MCAS reactions, or IBD flares. It’s distressing, exhausting, relentless, and it can leave you wondering, “Will I ever feel like myself again?”

The truth is, there are clear, physiological reasons for this - and your gut microbiome is right at the centre of the story.

Why Hormone Changes Can Hit the Gut So Hard

Perimenopause and menopause aren’t just about periods stopping. The drop in oestrogen and progesterone reverberates through every system - nervous, immune, metabolic, and digestive.

Research shows that menopause is linked to reduced gut microbiome diversity, shifts toward a more inflammatory composition, and changes in how gut bacteria help process hormones. This recent review notes:

“Declining oestrogen which occurs during menopause appears to influence the microbiota, which may in turn contribute to menopause-related conditions such as weight gain, bone health, cancer risk and cognitive health. The modulation of estrogen through the gut's 'estrobolome', a collection of bacterial genes involved in estrogen metabolism, may offer explanation for some of the interindividual differences observed during menopause (e.g. length, symptoms and disease risk)”. (Liaquat & Minihane, 2025).

This means that your gut isn’t just a bystander in menopause - it’s an active participant in how your symptoms show up, how long they last, and how intense they feel.

Research has also shown that menopause is linked to:

Reduced gut microbiome diversity and shifts toward a more inflammatory composition. Loss of Lactobacillus and rise in pathogens like Enterobacteriaceae are seen in menopause-related dysbiosis, with links to cardiovascular and metabolic diseases (Peters et al., 2022) (Liu & Zhou, 2022)
Changes in beta-glucuronidase activity - an enzyme produced by gut microbes that can recycle estrogens in the body. Menopause was associated with lower microbiome diversity and a shift toward a male-like profile. Depletion of beneficial taxa like Akkermansia muciniphila and reduction in β-glucuronidase activity were observed, possibly impairing estrogen recycling. When this process is disrupted, estrogen metabolism and hormone balance can shift further, sometimes aggravating symptoms. (Peters et al., 2022)
Weakened gut barrier function (“leaky gut”), allowing bacterial components like lipopolysaccharide (LPS) into the bloodstream. LPS can trigger inflammation throughout the body, contributing to fatigue, joint pain, and worsening gut sensitivity (Shieh et al., 2019).
Altered production of short-chain fatty acids (SCFAs) like butyrate, which are vital for nourishing the gut lining, regulating inflammation, and supporting nervous system health. Some studies suggest that menopause-related microbiome shifts may reduce butyrate-producing bacteria, making the gut lining more vulnerable (Liaquat & Minihane, 2025).
Reduction in Bifidobacteria in postmenopausal women: A study in Brazil found that Bifidobacterium levels were significantly correlated with hormonal and metabolic parameters during menopause. Specifically, postmenopausal women had altered correlations between Bifidobacterium and alkaline phosphatase levels, indicating changes in abundance and function during menopause (Silva Gonçalves et al., 2022)

If you’ve felt like your gut has gone from “sometimes sensitive” to “hyper-reactive to everything,” the science says you’re not overreacting, your body’s signalling systems are genuinely changing.

On the bright side:

A 2025 RCT showed that this traditional food reduced menopausal symptoms and improved gut microbial profiles, particularly increasing beneficial bacteria in postmenopausal women (Han et al., 2025)
The gut microbiota in menopause - therapeutic potential of pre/probiotics. Reviews evidence that menopause-induced estrogen decline impacts microbiota, increasing disease risk. Suggests targeting the gut microbiome (e.g. estrobolome) using prebiotics and probiotics as a novel, personalised, and potentially effective treatment strategy for managing menopause-related symptoms and disease risks. (Liaquat & Minihane, 2025)

When Gut Symptoms Collide with Hormone Symptoms

In clinical practice, I often see women in midlife whose existing gut conditions (IBS, SIBO, histamine intolerance, MCAS, IBD etc) flare dramatically during perimenopause or menopause.

Why? Because these shifts in microbiome diversity, gut barrier integrity, and microbial metabolism don’t happen in isolation. They collide with:

Nervous system changes - hormonal fluctuations can amplify stress sensitivity, and the gut–brain axis means stress can directly alter motility and gut sensation (Nachtigall & Nachtigall, 2019).
Immune reactivity - increased gut permeability allows more LPS into circulation, priming the immune system and worsening inflammatory and/or allergic-type responses.
Histamine load - reduced microbial breakdown of histamine plus hormonal changes can tip sensitive individuals into a constant “high histamine” state.

It’s not “just stress.” It’s not “just getting older.” This is a physiological cascade, and understanding it can be the first step in reclaiming your health.

Supporting the Microbiome in Midlife

While we can’t stop the hormonal changes, we can work with your microbiome to reduce symptom intensity and rebuild resilience. Evidence-based strategies include:

Rebuilding diversity - A fibre-rich, plant-varied diet (when tolerated) supports a broader microbial community, including butyrate producers that calm inflammation.
Targeting SCFA production - Certain prebiotic fibres and polyphenols can boost butyrate-producing species and reduce inflammation.
Reducing LPS burden - Supporting gut barrier health with nutrients (like glutamine), stress modulation, and anti-inflammatory foods can reduce the leakage of inflammatory compounds.
Balancing beta-glucuronidase activity - Supporting healthy microbial metabolism with dietary variety and, where needed, targeted probiotics may help regulate oestrogen recirculation.
Gentle nervous system regulation - Trauma-aware, slow-paced care reduces gut flares linked to stress signalling.

This Transition Is About More Than Symptoms

For many, perimenopause and menopause trigger a deep identity shift. Gut flares and hormone swings are part of it, but so is the quiet, unsettling question: “Who am I becoming?”

In my work, I see this stage as both a becoming and a reclaiming, a time when something new is emerging, even as you gather back the parts of yourself you may have set aside along the way. Supporting your microbiome isn’t just about reducing bloating or histamine reactions. It’s about restoring trust in your body, clearing the noise so you can hear yourself again, and walking into the next chapter with grounded, unwavering energy.

If you’re ready for care that sees the whole picture - gut, hormones, and the person you’re becoming - book a Discovery Call and let’s create a plan that works with your body’s pace, not against it.

Or join me for my Microbiome Retreat this October - there are still a couple of spaces available. If you’re ready to slow right down (even stop for a while), rest deeply, and be nourished inside and out, this is your space. If reading this sparks that quiet, glimmering yes in you - reach out, and let’s make it happen.