Wellbeing Blog · Menopause
By Helen James · Nutritional Therapy & Women’s Health
Read time 7 mins
We all know about the gut microbiome — but did you know we also need to be thinking about the other microbiomes that become disrupted by the hormone changes in peri and post menopause?
Our skin, bladder, and vagina all harbour their own ecosystems of bacteria, and declining oestrogen affects every single one of them. The result? A cluster of symptoms that so many women experience but rarely connect to a common cause: skin that breaks out like a teenager’s, recurrent bouts of cystitis or UTIs, and vaginal discomfort that affects daily life and intimacy.
So many of my clients, friends, and colleagues have symptoms related to these specific microbiomes. I’ve been doing further study on these topics and wanted to share what I’ve found. HRT may help to a degree — but I think if we understand what is happening to the bacteria, we can consider other options too.
The Vaginal Microbiome
Of all the microbiome changes that accompany the menopause transition, the vaginal microbiome is perhaps the most well-studied — and the most dramatically affected. In reproductive years, a healthy vaginal microbiome is typically dominated by Lactobacillus species, which keep the environment acidic and inhospitable to harmful pathogens.
As oestrogen declines during perimenopause, the vaginal epithelium undergoes atrophy and loses glycogen content — the food source Lactobacillus relies on — leading to its depletion. This raises vaginal pH, shifting the microbial community towards a more diverse but less protective mix of bacteria. This is known as dysbiosis.
This hallmark shift is directly linked to Genitourinary Syndrome of Menopause (GSM) — a cluster of symptoms including:
- Vaginal dryness and discomfort
- Pain during sex (dyspareunia)
- Increased susceptibility to bacterial vaginosis and infections
- Urinary urgency and recurrent UTIs
“By post menopause, nearly 50% of women show low-Lactobacillus vaginal communities — compared to around 21% before menopause.”
HRT is known to at least partially restore the health of the genitourinary microbiome — but it’s not the only option, and further down I’ll share what else can help.
The Urinary Microbiome
Here’s something that might surprise you — the bladder is no longer considered sterile. We now know it has its own microbiome, and this is an emerging and really important area of research for menopausal women.
Menopause increases the diversity of the urinary microbiome and lowers the proportion of Lactobacillus in urine — and these changes have been shown to precede recurrent urinary tract infections. This matters enormously for so many women who find themselves suddenly plagued by repeated UTIs after years without them.
Dysbiosis of the urinary microbiome is also associated with:
- Urinary urgency and incontinence
- Recurrent UTIs and cystitis
- Interstitial cystitis and bladder pain syndrome
The urinary and vaginal microbiomes are closely interconnected, sharing common bacterial strains — so when vaginal dysbiosis is triggered by falling oestrogen, there is very likely a knock-on effect in the bladder too. This is an area where research is still catching up with lived experience, and I want my clients to know that their bladder symptoms may have a microbial root.
The Skin Microbiome & Menopausal Acne
One of the more surprising — and distressing — experiences for many women in perimenopause is the return of acne after years of clear skin. So let’s break down why this happens, because it’s not random and it’s not just about getting older.
The skin hosts its own complex microbial ecosystem, and it is sensitive to the hormonal shifts of menopause. After menopause, sebaceous gland activity gradually declines, reducing sebum production and limiting the food available for skin-resident microorganisms. The beneficial bacteria that thrive on sebum decrease, while overall bacterial diversity increases — mirroring the pattern we see in the vaginal and urinary microbiomes.
Why does acne come back in perimenopause? The root cause is what is known as “relative androgen dominance.” As oestrogen and progesterone fall sharply, testosterone declines too — but more slowly — and is no longer kept in check by oestrogen’s moderating influence.
Testosterone then:
- Enlarges the sebaceous glands, prompting more sebum production
- Simultaneously makes pores smaller — creating the ideal environment for blockages and trapped bacteria
- Acts alongside falling SHBG (sex hormone-binding globulin), which normally keeps androgens inactive — its decline means more free testosterone is available to act on the skin
The key bacterial player is Cutibacterium acnes — a naturally occurring skin resident. It’s not simply an overgrowth that causes the problem, but a loss of balance between different strains, with a more virulent type becoming dominant and triggering the immune system, leading to inflammation. Stress worsens this further — stress hormones trigger the conversion of DHEA to testosterone — and insulin resistance, which becomes more common in midlife, also promotes sebum production and intensifies breakouts.
Menopausal acne looks different from teenage acne: deep, cystic nodules along the jawline and cheekbones, painful and slow to resolve. And importantly — menopausal skin is simultaneously oily in the pores and dry at the surface, which means harsh drying acne treatments aimed at teenagers are counterproductive. This needs a much more nuanced approach.
Managing GSM Without — or Alongside — HRT
HRT, and particularly localised vaginal oestrogen, remains the most evidence-backed treatment for GSM. But it isn’t the right choice for every woman — and understanding the bacterial picture gives us a much wider toolkit to work with. Here’s what the evidence supports:
pH-balanced vaginal moisturisers & lubricants
Use regularly — not just in response to symptoms. Look for fragrance-free products formulated specifically for vaginal use with a pH of 3.8–4.5. Your pharmacist can point you towards suitable options.
Hyaluronic acid vaginal pessaries or gels
Their strong water-binding properties help maintain hydration and elasticity of vaginal and urethral tissues — well-supported by research and particularly useful for women who cannot use hormones.
Lactic acid pessaries
These directly address the pH problem at the heart of menopausal vaginal dysbiosis. Products combining lactic acid and glycogen work in two ways — lowering vaginal pH to discourage harmful bacteria, while providing Lactobacillus with the glycogen it needs to thrive. Think of it as preparing the soil before planting. They are hormone-free, available over the counter, and worth using regularly rather than just when symptoms flare.
Probiotic pessaries
These introduce live Lactobacillus bacteria directly into the vaginal environment — bypassing the gut entirely.
Research shows that vaginal probiotic pessaries can increase Lactobacillus abundance, decrease undesirable anaerobic bacteria, and have an immune-modulatory benefit to the vaginal epithelial barrier. L. crispatus is considered the most protective strain — supporting the vaginal immune barrier without causing inflammation and producing antimicrobial compounds that inhibit pathogens.
Strain specificity matters. Not all probiotic products are equal. Look for products listing specific, named, clinically-studied strains — not generic “Lactobacillus blend” formulations. For vaginal health, the best-evidenced strains are L. crispatus, L. rhamnosus GR-1, and L. reuteri RC-14.
Oral probiotics
Specific strains including L. reuteri RC-14 and L. rhamnosus GR-1, taken orally, have shown benefits for vaginal and urinary microbiome health. Combine with fermented foods to support overall microbial diversity: kefir, kimchi, natural yoghurt, sauerkraut, kombucha.
Phytoestrogen-rich foods
Soy, red clover, legumes, and linseeds contain plant compounds that mimic oestrogen in the body and can help moderate symptoms including vaginal dryness. They also act as prebiotics — feeding beneficial bacteria throughout the gut and beyond.
Pelvic floor physiotherapy
Underused and highly effective. A women’s health physiotherapist can significantly improve blood flow and tissue health in the genitourinary area — reducing both discomfort and urinary symptoms. Well worth asking for a referral.
CO₂ laser therapy
An emerging clinical option showing meaningful improvement in GSM symptoms, particularly for women who cannot use hormones. Requires referral to a specialist — more large-scale trials are ongoing, but results so far are promising.
⚠ A note on coconut oil
Many women turn to coconut oil as a natural lubricant — it sounds like a gentle, natural option. But it is best avoided. Its antimicrobial properties are indiscriminate, meaning it can suppress the very Lactobacillus bacteria you need to protect vaginal health, while its alkaline pH further disrupts an already fragile acid balance. It also degrades latex condoms. Opt instead for a fragrance-free, pH-balanced lubricant or vaginal moisturiser specifically formulated for vaginal use.
The key takeaway? There is a genuine menu of options available, and a layered approach — combining microbiome support, targeted moisturisation, dietary changes, and where appropriate professional therapies — can make a meaningful difference. You don’t have to simply manage symptoms in the dark. Understanding what is happening to your bacteria means you can make informed, targeted choices. We can now also test these microbiomes in more detailed tests, using PCR and NGS (more accurate than just culture) showing us more specifically which bacteria are causing issues. Armed with this information, you can get more targeted interventions.
If you’d like support working through what’s right for you personally, I’d love to help. Find out more about working with me here.
This blog is for educational purposes and does not constitute medical advice. Always consult a qualified healthcare professional before starting new supplements or treatments, particularly if you have a history of hormone-sensitive conditions.
© Find Your Healthy · Helen James · Nutrition Therapy & Women’s Health