The microbiome no one talks about: UTIs, BV and the menopause transition

We talk a lot about the gut microbiome now. We talk far less about the genitourinary microbiome — the bacterial community of the vagina and urinary tract — even though it shapes some of the most common, frustrating and rarely-discussed issues women face. So, let's talk about it.

A quick, honest note first: infections often need proper medical diagnosis and, medical treatment. However, a holistic genitourinary practitioner is a supportive player here — helping create the conditions for balance.

What “healthy” looks like down there

In most women of reproductive age, a healthy vaginal microbiome is dominated by Lactobacillus species. These beneficial bacteria produce lactic acid, helping to maintain a mildly acidic environment (ideally a pH. between (3.8-4.5), that naturally discourages the growth of potentially harmful microbes.

When Lactobacillus levels decline — a state known as vaginal dysbiosis — the vaginal environment becomes less resilient. This shift can increase the risk of bacterial vaginosis (BV), aerobic vaginitis (AV), vulvovaginal candidiasis (VVC) or recurrent urinary tract infections (UTIs), along with increased susceptibility to certain sexually transmitted infections. Many persistent vaginal and urinary conditions have far more complex drivers than a single infection, which is why it's so important to identify what's contributing to the imbalance.

It's important to remember that there is no single “perfect” vaginal microbiome. What's considered healthy varies between women and their community sub-type. Hormonal fluctuations during the menstrual cycle, pregnancy, sexual intercourse, the postpartum period and menopause all influence the microbial community, with oestrogen playing a major role in supporting Lactobacillus dominance.

I often suggest an advanced vaginal microbiome test to uncover valuable insights for treatment. Unfortunately, the traditional standard cultures and microscopy through your GP are outdated, they miss microbes and fail to detect biofilm communities. Advanced next generation sequencing (NGS) is available which can test over 10,000 species, also advanced polymerase chain reaction (PCR) tests through Nutri-path here in Australia are the tests I rely on, that reveal the pesky pathogenic microbes at play.

The role of antibiotics and microbiome balance

Antibiotics remain an important and often necessary treatment for acute bacterial infections and can be lifesaving when appropriately prescribed. However, antibiotic resistance has become a growing global health concern, and repeated antibiotic exposure can also have unintended effects on the body's microbial ecosystems.

The “antibiotic rollercoaster” — cycles of treatment followed by recurring symptoms — can disrupt the beneficial bacteria that help maintain balance. This loss of microbial diversity can create an environment where opportunistic organisms are more likely to thrive, potentially contributing to ongoing dysbiosis and recurrent infections.

For this reason, addressing the underlying factors that contribute to imbalance — including hormonal changes, immune function, gut health, lifestyle factors and vaginal microbiome resilience — is often a more effective long-term approach than relying on repeated courses of antibiotics alone.

Recurrent UTIs: what the evidence actually says

UTIs are extraordinarily common — more than half of women will have at least one, and a sizeable proportion go on to recurrent episodes (generally defined as three or more in a year, or two in six months). When something is this common, the internet fills with confident claims. The real evidence is more measured, and I think you deserve the honest version:

Whilst uncomplicated UTI’s can often be easily treated, chronic, relapsing and intracellular embedded UTI’s present with more complex clinical features. Uro-pathogens like E.coli can form sticky biofilms contributing to antibiotic resistance, most recurrent UTI’s are caused by the same strain.

It is also important to consider the vagina as a potential reservoir for pathogenic microbes, so I will often suggest a vaginal microbiome test.

• Hydration helps. A good-quality trial found that simply drinking more water each day reduced recurrent UTIs in women prone to them. Unglamorous, free, and worth doing.
• Cranberry (specifically its proanthocyanidins) is widely used and may offer some benefit for women with recurrent UTIs, but the overall evidence is mixed and often low quality. It's reasonable to try; it's not a guarantee.
• D-mannose has been shown to provide systemic relief and can help prevent bacterial adhesion.
• Prebiotics & Probiotics (lactobacillus) female patient’s experiencing UTI’s have a bladder population of markedly reduced lactobacilli. Prebiotics and L. Crisptus probiotic strain in vitro has plausible rationale, for reducing intracellular E.coli load.

Note; Please seek medical advice if you develop blood in urine, fevers, flank pain or back pain. Untreated UTI’s can travel up to the kidneys.

BV and the balance of the vaginal microbiome

Bacterial vaginosis reflects a shift away from that protective a Lactobacillus-dominant state with a change in bacterial species. Symptoms will depend on what type of bacteria present, however the most common symptoms are; unusual greyish discharge, fishy odour, and a pH above 4.5.

Standard medical treatments for BV are usually (metronidazole or clindamycin) however reoccurrence is extremely high, so we need to find out why it keeps coming back.

Recurrent BV is influenced by hormonal changes and the menstrual cycle, stress, lifestyle and sexual interaction. Finally, the new research attributes re-infection to untreated male partners, suggesting that BV has a sexually transmitted component, therefore treating both partners could be crucial in breaking the cycle of reinfection.

Menopause changes the landscape

Here's something many women aren't told: as oestrogen falls through perimenopause and menopause, the genitourinary tissues change. The lining thins, glycogen (which feeds those helpful lactobacilli) declines, and Lactobacillus levels tend to drop. This is part of what's now called genitourinary syndrome of menopause (GSM) — and it helps explain why recurrent UTIs and vaginal discomfort become more common in this stage of life.

This is also where conventional medicine has a genuinely effective tool: vaginal oestrogen, which research shows can reduce recurrent UTIs in postmenopausal women. If this is your situation, it's well worth a conversation with your GP — and nutrition can sit comfortably alongside it.

This is an area I have specific training in, and it's one women are so often left to navigate alone. If it's something you're dealing with, you don't have to. Book a consult.