The Gut and Vaginal Microbiome in Endometriosis sufferers.

By Jessica  Childs

Intimate Health Specialist at Pelvic Relief

The microbiome

The female body is home to trillions of microorganisms, bacteria, yeasts, and viruses that live in the gut, mouth, skin, vagina, cervix, and even the womb lining. These communities actively regulate your immune system, your inflammation levels, and the overall health and function of the local organs. They are absolutely critical for our functioning and support us in health, but can be problematic in cases of imbalance.

Dysbiosis/imbalance of the microbiome.

When the balance of these microbes is disrupted, something commonly referred to as dysbiosis, it can trigger a cascade of inflammatory processes, in many cases resulting in unwanted symptoms such as pain and discomfort, and other wider implications such as poorer food absorption in the gut, and poorer pregnancy outcomes in the reproductive tract as two examples. There are many others!

Unfortunately, women with endometriosis are significantly more likely to have dysbiosis of both the gut and vaginal microbiome than those without the condition.

The relationship is bidirectional. Endometriosis creates a pro-inflammatory environment that disrupts microbial balance. And a disrupted microbiome, in turn, amplifies inflammation, dysregulates oestrogen, and creates conditions that allow endometriosis to thrive. It is a cycle, and one that is attracting research (although more needed) to understand how to break this cycle.

As you know, getting on top of inflammation and improving your diet can be one step to helping with symptom management.

Why does dysbiosis occur in women with endometriosis?

Endometriosis is fundamentally an inflammatory, immune-driven condition. Imbalances in gut and reproductive tract microbiota disrupt normal immune function, leading to the elevation of pro-inflammatory cytokines and altered immune cell profiles, all of which may contribute to the pathogenesis of endometriosis. Over time, this immune dysregulation can progress into a chronic state of inflammation, creating an environment conducive to increased adhesion and tissue growth, which may drive the vicious cycle of endometriosis onset and progression. nih

In short, the chronic inflammatory state of endometriosis actively disturbs the microbial communities in your gut and vagina. And once those communities are disrupted, they start feeding the fire right back.

THE GUT MICROBIOME AND ENDO LINK

What is happening in the gut, and why does it matter?

Research suggests that gut microbiota play a crucial role in the pathogenesis and progression of endometriosis by modulating immune responses and oestrogen metabolism. Studies in women with endometriosis consistently find measurable

differences in gut microbiome composition compared to healthy controls, including an altered bacterial balance and elevated inflammatory markers. MDPI

Here is what that disruption actually does:

1. It produces LPS (lipo-polysaccharides) a powerful inflammatory trigger

When the gut microbiome is imbalanced, harmful gram-negative bacteria proliferate. These bacteria produce a toxic compound called lipopolysaccharide, or LPS. Pathogenic bacteria such as Escherichia coli and Streptococcus can degrade the tight junction proteins that hold the gut wall together, increasing intestinal permeability a condition known as leaky gut. This barrier breakdown allows LPS and other microbial components to translocate from the intestinal lumen into the systemic circulation. Frontiers

Once in the bloodstream, the consequences are significant. This leads to a significant increase in LPS levels in the peritoneal fluid of endometriosis patients, inducing the production of inflammatory factors and angiogenesis factors in the abdominal cavity — enabling the implanted growth of retrograded endometrial fragments to form ectopic lesions. Frontiers

Critically, research has found that LPS concentrations in the menstrual fluid of patients with endometriosis were four to six times higher than in controls, a striking finding that directly links gut dysbiosis to the pelvic inflammatory environment at the heart of this disease. Frontiers

2. It disrupts oestrogen metabolism: the oestrobolome

This is where the gut microbiome has a uniquely powerful role in endometriosis, specifically because endo is an oestrogen-driven disease.

The oestrobolome is a collection of microbial genes involved in the metabolism of oestrogen. The enzyme β-glucuronidase, produced by certain gut bacteria, deconjugates oestrogens in the gut, allowing them to be reabsorbed into the bloodstream. PubMed Central

In a healthy gut, oestrogen is processed and eliminated efficiently. But when dysbiosis is present and β-glucuronidase activity is elevated, processed oestrogen gets reactivated and recirculated, driving oestrogen levels higher. Gut microbiota dysbiosis and alterations in the oestrobolome may play a direct role in the pathogenesis of endometriosis and associated infertility, because excess circulating oestrogen is precisely the hormonal environment in which endometriosis develops and spreads. Springer

3. It drives systemic and pelvic inflammation

When intestinal microbiota is disturbed, β-glucuronidase and β-glucosidase secreted by gut bacteria degrade bound oestrogen, resulting in excessive free oestrogen. The imbalance of intestinal microbiota also leads to an increase in pro-inflammatory cytokines including TGF-β1, IL-8, IL-6, TNF-α, and IL-1β. This local surge of cytokines further promotes the recruitment of immune cells, stimulates the production of VEGF, and drives the growth and survival of ectopic endometrial tissue. Frontiers

In other words, a dysbiotic gut is not just a digestive problem. It is pumping inflammatory signals and excess oestrogen into a body that is already struggling with both.

THE VAGINAL MICROBIOME AND ENDO LINK

We already know that endometriosis is, at its core, an inflammatory condition. So if you also have an inflammatory, dysbiotic vaginal microbiome, you may be adding fuel to a fire that is already burning. That does not cause endometriosis, but it may well be making your symptoms harder to bear and your disease environment harder to control.

What the research actually shows

This field is still early but there is certainly some indication that those suffering with endo are more likely to have less good bacteria, and more opportunistic bacteria and yeasts (resulting in a higher incidence of BV, vaginal yeast infections, and possibly UTIs, as a result of translocation of this opportunistic bacteria from the vagina and gut to the urethra and bladder).

Studies are finding that women with endometriosis have a measurably different vaginal and reproductive tract microbiome compared to those without the condition. Specifically, endometriotic microbiotas have been consistently associated with diminished Lactobacillus, the protective bacteria that form the backbone of a healthy vaginal environment and help keep inflammation in check. MDPI

A 2024 study published in Scientific Reports revealed an endometriosis-specific vaginal microbiota in patients that was entirely distinct from that in a control group, and found complex links between the vaginal microbiome, the body's immune markers, and systemic signs of disease. Nature

The Endobiota Study, comparing vaginal, cervical, and gut microbiota in women with stage 3/4 endometriosis against healthy controls, found that potentially pathogenic species including Gardnerella, Streptococcus, Escherichia, Shigella, and Ureaplasma were significantly elevated in the cervical microbiota of those with endometriosis. Nature

A large systematic review and meta-analysis drawing on multiple major databases confirmed the association between vaginal microbiome dysbiosis and endometriosis — strengthening the case that this is a meaningful biological relationship. nih

We are not yet at the point where we can say that fixing your microbiome will fix your endometriosis. That would be an overstatement entirely. Butwe can say that an inflamed, dysbiotic microbiome is unlikely to be helping, and that is reason enough to pay attention to it.

Endometriosis, the vaginal microbiome, and fertility: why outcomes can be poorer

For women with endometriosis who are trying to conceive, the challenges go far beyond the structural and hormonal effects of the disease itself. The microbiome adds another significant layer.

The incidence of infertility in patients with endometriosis is significantly higher than in the general population, and the reasons involve a variety of factors including abnormal immune function, inflammatory response, hormone imbalance, and impaired endometrial receptivity. Despite advances in assisted reproductive technology, implantation failure remains a major obstacle in endometriosis-associated infertility, suggesting that factors

beyond embryo quality, particularly the uterine microenvironment, are critical determinants of success. Frontiers

Evidence shows that the dominance of Lactobacillus in the female reproductive tract is generally associated with improved chances of successful implantation and an ongoing pregnancy. Conversely, vaginal and endometrial dysbiosis can cause local inflammation and an increase in pro-inflammatory cytokines, compromising the integrity and receptivity of the endometrial lining and potentially hindering successful embryonic implantation. PubMed Central

Women with endometriosis already have depleted Lactobacillus and elevated inflammatory microbes in their vaginal environment. That dysbiosis does not stay contained to the vagina, bacteria and microbial signals can ascend through the cervix into the uterus, directly affecting the endometrial environment where implantation needs to occur. Dysbiosis characterised by enrichment of anaerobic species such as Gardnerella, Prevotella, and Streptococcus is linked to chronic endometritis, implantation failure, and adverse IVF outcomes. nih

A meta-analysis confirmed that Lactobacillus dominance in the vaginal or endometrial microbiota is strongly associated with higher clinical pregnancy rates, with a pooled odds ratio of 9.88, meaning women with a Lactobacillus-dominant microbiome were nearly ten times more likely to achieve a clinical pregnancy. And in women undergoing IVF, a strong positive correlation between Lactobacillus abundance and embryo implantation success has been demonstrated, with lower Lactobacillus consistently linked to implantation failure. BiomedresSpringer

For women with endometriosis, this creates a compounding picture. The disease itself drives inflammation and disrupts the microbiome. That disrupted microbiome then creates a hostile environment for implantation, inflamed, less protective, and less receptive to an embryo. I

For women with endometriosis navigating fertility challenges, understanding the state of their vaginal microbiome is a meaningful piece of the puzzle. Knowing whether dysbiosis is present, and being able to address it, may be one way to support the broader environment in which conception needs to happen.

Testing the vaginal microbiome

What we can confidently say at the moment is that a vaginal microbiome dominated by opportunistic, inflammatory microbes rather than protective Lactobacillus can add to the inflammatory load of one’s endometriosis symptoms.

In those with BV, UTIs, and generalised, recurrent vaginal and vulval symptoms (itching, burning, discomfort, painful sex, unusual discharge, unusual odour etc) its an area to certain consider optimising, because these symptoms indicate an imbalance.

In those with no direct vaginal symptoms, but awful endo symptoms, especially in the uterus, cervix, bladder and bowel, microbiome support is also very relevant.

Vaginal microbiome testing can tell you exactly what is present in your vaginal environment and in what amounts. It will not diagnose or treat your endometriosis, and it is not a replacement for medical care. But it can give you a clearer picture of whether your

microbiome is working with your body or against it, and that is genuinely useful information to have.

The good news.

These microbiome environments are to a good extent, malleable. We can influence them for the better or worse, via diet, lifestyle, supplements etc. So knowing what you can do is also very important.

Based on peer-reviewed research including Jiang et al. (2021), the Endobiota Study (2019), Da Silva et al. (2025), and a 2024 systematic review and meta-analysis on vaginal microecology and endometriosis.