Is Your Microbiome Menopausal?
Exploring how hormonal changes during perimenopause and menopause may influence the gut, vaginal microbiome, digestive health, and wider body systems
The relationship between midlife hormonal transition and the microbiome is becoming one of the most interesting emerging areas of women’s health research. Studies are beginning to show that hormonal shifts during perimenopause and menopause may influence both the gut and vaginal microbiome, with potential implications on varying aspects of health including digestive, metabolic and vulvovaginal health & bone density.
The microbiome appears to interact closely with hormones throughout life and shifts in oestrogen levels during the menopause transition may influence both the gut and vaginal microbiome in complex and interconnected ways.
What Is the Microbiome?
The terms microbiome and microbiota are often used interchangeably, although they have slightly different meanings. Generally speaking, microbiota refers to the microorganisms themselves — including bacteria, fungi, viruses, and other microbes — while microbiome more broadly refers to the microorganisms, their genetic material, and their surrounding environment within the body.
For ease of discussion, the term microbiome will be used more generally throughout this article.
The human body contains multiple microbiome sites, each with distinct microbial communities and functions. In women’s health research, two of the most studied are:
The gut microbiome, found predominantly within the large intestine
The vaginal microbiome, which plays an important role in vulvovaginal and urinary health
These microbial communities influence many aspects of health, including immune function, inflammation, metabolism, nutrient absorption, intestinal barrier integrity, and hormone metabolism.
Importantly, hormones also influence the microbiome in return.
How Hormonal Changes May Influence the Gut Microbiome and Digestive Health
Oestrogen has wide-ranging effects throughout the body, including influence on the gastrointestinal tract and gut microbiome. During perimenopause and menopause, hormonal changes may influence gut motility, intestinal barrier function, immune signalling, visceral sensitivity, and microbial composition.
Several human studies suggest the gut microbiome changes across the menopause transition, including alterations in microbial diversity and short-chain fatty acid-producing bacteria in some women. Emerging research has also linked these changes with aspects of metabolic, inflammatory, skeletal, and gastrointestinal health.
For some women, these physiological and microbial shifts may contribute to digestive symptoms becoming more noticeable during midlife, including:
Bloating
Reflux
Constipation
Altered bowel habits
Abdominal discomfort
Heightened gut sensitivity or visceral hypersensitivity
Stress, sleep disruption, dietary changes, and the close relationship between the gut and nervous system may also contribute. While not every digestive symptom during midlife is directly hormonal, the menopause transition can create a physiological environment where pre-existing gut issues may become more noticeable.
The Vaginal Microbiome and Menopause
The vaginal microbiome is particularly sensitive to hormonal change.
In reproductive years, oestrogen helps maintain healthy vaginal tissue thickness, glycogen production, and an acidic vaginal environment that supports Lactobacillus species — beneficial bacteria associated with vaginal and urinary health.
As oestrogen declines during menopause, changes may include:
Reduced Lactobacillus dominance
Increased vaginal pH
Greater microbial diversity associated with microbial imbalance
Increased susceptibility to irritation, dryness, and infections
Changes in urinary and vulvovaginal health
This shift may contribute to symptoms associated with genitourinary syndrome of menopause (GSM), including:
Vaginal dryness
Burning or irritation
Pain with intercourse
Recurrent UTIs
Urinary urgency or discomfort
Research increasingly suggests that supporting the vaginal environment — alongside addressing hormones where appropriate — may play an important role in symptom management and long-term vulvovaginal and urinary health.
The Gut–Hormone Connection: The “Estrobolome”
Researchers sometimes use the term estrobolome to describe gut bacteria involved in oestrogen metabolism.
Certain gut microbes produce enzymes and metabolites, including beta-glucuronidase, which may influence how oestrogen is metabolised, recycled, and excreted within the body through enterohepatic circulation. This means the gut microbiome may play a role in modifying circulating oestrogen exposure and hormone metabolism — while hormones simultaneously influence the microbiome in return.
This two-way relationship may partly explain why gut health, metabolic health, inflammation, and menopausal symptoms ar
What Might Help to Support the Microbiota During Perimenopause and Menopause?
While research in this area is still evolving, emerging evidence suggests that factors such as diet, sleep, stress, and hormone balance may all play a role in shaping the microbiome during perimenopause and menopause. Starting with simple, sustainable diet and lifestyle changes can is a great start.
What might help:
A high-fibre, plant-diverse dietary pattern (a ‘plant forward’ Mediterranean style diet)
Aiming for at least 30 different plant foods per week (if you’re easily reaching this, you can aim for 40!)
Regular intake of polyphenol-rich foods such as berries, pomegranate, pink dragonfruit, extra virgin olive oil, herbs, spices, cacao, green tea, legumes, colourful vegetables, nuts, and seeds
Adequate intake of whole plant foods including legumes, vegetables, fruit, nuts, seeds, and whole grains
Omega-3-rich foods such as salmon, sardines, trout, walnuts, chia seeds, and ground flaxseeds
Fermented foods where tolerated, such as yoghurt, kefir, kimchi, or sauerkraut
Therapeutic phytoestrogen intake where appropriate, including soy foods and flaxseeds (individual thyroid health and iodine status matters here)
Supporting sleep, nervous system regulation, and stress management
Medically prescribed menopausal hormone therapy (MHT) where appropriate
Vaginal topical oestrogen or estradiol preparations where indicated
Evidence-informed microbiome testing where appropriate
Final Thoughts
Research increasingly suggests that hormonal changes may influence both the gut and vaginal microbiome, with potential downstream effects on digestion, inflammatory balance, skeletal, metabolic & vulvovaginal health.
While this field is still rapidly evolving, supporting the microbiome through dietary diversity, adequate fibre intake, sleep, stress management, and seeking professional support early may help support resilience and overall health during the menopause transition.
If you would like to assess and understand your individual gut or vaginal microbiome, Amy offers evidence-based gut and vaginal microbiome testing as part of a personalised and integrative approach to care.