The Gut-Vagina Axis: Is There a Relationship Between Your Gut and Your Vaginal Microbiome?

The first “microbiome” you likely ever heard of was that of the gut. And while the gut microbiome owns the spotlight in popular culture and in scientific research, microbial communities actually exist in every area of the human body that’s exposed to the outside world. Your skin, mouth, nose, and eyes all have a microbiome, and, of course, so does your vagina. 

As scientific researchers have learned more about the gut microbiome’s influential relationship with almost every other element in the body (from your hormones to your brain), increasing conversation and curiosity have emerged about the gut’s relationship to its downstairs neighbor: the vaginal microbiome. 

And it’s not just scientists. People with vaginas from around the world have begun to ask their doctors, the internet, and Evvy’s community and experts — is there a relationship between my gut and vaginal microbiome?

Thankfully, we’ve got some answers. Evvy’s Senior Scientist, Krystal Thomas-White, a microbial maven (with a PhD, no less), breaks down existing research on the gut-vagina axis and explains how you can use this information to better understand what’s up down there as it relates to your body. 

What is the gut-vagina axis?

As we learn more and more about the vaginal microbiome, researchers are beginning to understand that a connection exists between the gut microbiota and the vaginal microbiome. 

There are three different ways the gut microbiota can have an impact on your vaginal health: 

• The gut microbiome acts as a reservoir for pathogens that can disrupt your vaginal microbiome. 
• Poor gut health causes systemic inflammation, including in the vagina.  
• Your gut microbiome can change the levels of hormones, like estrogen which can affect the vaginal microbiome. 

Pathogens from your gut can travel into your vaginal microbiome 

Many of the pathogens we worry about disrupting the balance of your vaginal microbiota (i.e., Candida albicans, E. coli, Prevotella) get into the vagina by way of the gut. This is known as a reservoir — a place where a stable community of potentially harmful bacteria hangs out. Periodically those harmful microbes will colonize the vaginal microbiome (and then maybe even the bladder) and cause symptoms. 

We also know that lactobacilli levels in the gut correlated with levels of vaginal lactobacilli. So to put it simply, a healthy gut microbiota means your vagina will likely be in a protective state as well. This is the current hypothesis as to how taking an oral probiotic might help improve your vaginal symptoms. 

Oral probiotics are showing real promise when it comes to supporting vaginal health, especially when they include strains that are naturally found in the vaginal microbiome, like certain species of Lactobacillus. While it might seem unlikely that something you swallow could affect your vaginal environment, the body’s microbiomes are more connected than they appear.

Think of it this way: while the gut may seem like a long and winding road away from the vagina, the gut, vaginal, and urinary microbiomes are actually in constant conversation. So, when you improve the balance of bacteria in your gut, you may be indirectly influencing what happens elsewhere, too.

One of the current theories in microbiome science is that by nurturing the gut, you reduce the likelihood of “bad actors” like E. coli or Candida growing out of control. Since these microbes can migrate from the gut to other areas (like the vagina or bladder), keeping them in check upstream can help protect those downstream ecosystems. 

Emerging research even shows that oral probiotics containing vaginal-native strains may directly influence the vaginal microbiome. With consistent use, some clinical studies suggest these strains can help maintain a healthy vaginal environment from the inside out. While more research is still needed to fully understand the mechanics, the evidence so far is encouraging and points to a future where whole-body microbiome care is the new normal.

Oral antibiotics, gut health, and inflammation

The gut microbiome is in charge of training your immune system. A healthy gut = a healthy immune system. Therefore, inflammation around the gut microbiome could cause a change in inflammation throughout your whole body. Unfortunately, there isn’t much research into how this gut-microbiome-training of the immune system directly affects vaginal symptoms.  

We do know that taking oral antibiotics for urogenital infections (like bacterial vaginosis or urinary tract infections) will deplete bacteria in your gut as well as your vagina. And the loss of intestinal bacteria can affect your immune system. 

This is why it’s important to help recolonize your gut with good bacteria after taking antibiotics — you can do this by taking an oral probiotic. A probiotic can not only help with symptoms of nausea and gastrointestinal distress, but it will also help get your immune system back to a health-balanced state (known as homeostasis). 

Gut microbiome and hormone levels

Researchers are beginning to understand that the gut microbiome can influence the levels of estrogen circulating in your bloodstream. Why does this matter for vaginal health?

Estrogen is an essential hormone for many reasons, but it’s particularly important for vaginal health because it helps your body provide a food source for protective bacteria called Lactobacilli. 

Lactobacilli act as the local heroes of the vaginal microbiome, helping to keep your vaginal pH acidic. 

When estrogen levels go up (like in pregnancy), levels of Lactobacilli go up because there is an increase in their food source (called glycogen) in the vagina. When estrogen levels decrease (like with menopause), the food source decreases, and so too do levels of Lactobacillus. Side note — it’s thought that this is why some people have cyclical symptoms because Lactobacilli levels change as your hormones change throughout the menstrual cycle. 

When estrogen is low, and therefore Lactobacilli are low, this creates a more optimal environment for pathogens to colonize because the vaginal microbiome is less protective. 

Circling back to the gut-vagina axis, a healthy and diverse gut microbiome can help keep estrogen levels higher because it can keep estrogen (otherwise marked for removal by the liver) in your system. This increases overall levels of circulating estrogen in the body, which works to provide a food source for the Lactobacilli in your vaginal microbiome. 

Wait, my gut microbiome can change my hormones? Yep, this is a really new discovery, and we are only starting to understand it. But here are the basics:

Normally, hormones exit your body when you pee. This helps your body maintain healthy levels of hormones in the bloodstream. The way your body does this is by adding a flag or marker to the estrogen molecule that tags it for waste disposal. This tagging process naturally occurs in the liver. You can think of the liver as the bouncer at a club making sure that only people with the correct wristband/stamp get in. This marker “or wristband” is called glucuronic acid. Estrogen molecules with glucuronic acid exit the body and ones without will be kept around. 

Certain bacteria in the gut microbiome can add or remove these tags on estrogen molecules. Your gut microbiome is the friends helping sneak people into the club by sharing wristbands. It has been shown that the presence of these molecules (called either β-glucuronidases or β-glucuronides) is directly related to the levels of circulating estrogen. 

That is how the gut microbiome can change the levels of circulating hormones. And an increase in estrogen in your system can improve your vaginal microbiome. 

Is my gut contributing to my vaginal symptoms? 

While there is sadly no two-in-one, gut-vagina axis microbiome test, there are a few things you can do to take care of your gut and vaginal microbiomes. 

First up, do a loving assessment of your diet. There’s no need to shame yourself or swear off your favorite comfort foods, but it’s worth taking a moment to notice what you’re eating day to day. Are you getting enough vegetables (especially leafy greens)? A balanced, fiber-rich diet supports your gut microbiome, which can in turn influence your vaginal and urinary health. Even if everything feels fine down there, good nutrition is foundational for whole-body wellbeing.

If you’re dealing with recurrent vaginal symptoms, though, it might be time to go deeper. A vaginal microbiome test like Evvy’s Vaginal Health Test can give you a full picture of what’s really going on. Unlike traditional tests that just flag the presence of a few bacteria or yeast, Evvy uses metagenomic sequencing to identify all bacteria and fungi in your vaginal microbiome, and shows you their relative abundance. That matters because symptoms can arise from imbalances, not just infections.

For example, high levels of Lactobacillus are often seen as a good thing, but too much of a good thing can cause irritation, too. Understanding your unique microbiome can help you make more informed choices, including what type of probiotic (if any) is right for you.

And if you’re also noticing gut symptoms (like bloating, constipation, or indigestion) it could be a sign that your gut microbiome is off balance, too. A healthcare provider can help you get to the bottom of what’s going on and guide you toward testing options or treatment strategies that address both the gut and vaginal ecosystems.

To support both, Evvy created the Women’s Complete Probiotic, a daily supplement formulated with the gut, vaginal, and urinary microbiomes in mind. Whether you’re addressing an imbalance or simply staying proactive, this multi-strain formula is designed for anyone with a vagina, at any life stage.

Even if you’re generally healthy, factors like stress, your menstrual cycle, sex, or antibiotics can disrupt your microbiome. The Women’s Complete Probiotic helps support resilience and balance across systems, with strains like LA-5® and UALp-05 for digestion, and vaginal-native strains for targeted support.

With consistent daily use, many people notice improvements in digestion, like reduced bloating and more regular bowel movements, within the first month. Over time, users often report better vaginal comfort, fewer or urinary symptoms, and a greater sense of balance across their gut, vaginal, and urinary health, especially around common disruptors like periods, sex, or antibiotics.

Can I test my gut microbiome at home?

Outside of testing you can get through your provider, companies like Viome provide comprehensive gut microbiome tests. 

Specifically, Viome’s Gut Intelligence Test uses RNA sequencing to assess if you're having trouble breaking down certain foods, if opportunistic microbes are causing problems, if your microbes are impacting your blood sugar response, and much more. 

With your Viome results, you’ll receive 20+ gut health scores along with personal recommendations that target the areas of your gut health that need specific nutrients to support and that may be the root cause of symptoms such as GI issues, occasional gas and bloating, irregular bowel movements, skin irritation, hormone imbalances, trouble sleeping, trouble losing weight, and other symptoms associated with poor gut health. 

(Since posting this article, we heard from many of our community that you’re interested in testing your gut microbiome, so we’ve recently partnered with Viome to offer you $100 off their Gut Intelligence Test — just use EVVY100 on Viome.com!)