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You’ve Heard About the Gut-Brain Axis—But What About the Gut-Vagina Axis?

Inside the superhighway that spans from your vagina to your gut.

7 minutes

19 Citations

Historically, vaginal health was a taboo topic largely avoided by the scientific community.1 Vaginas were usually only a medical concern in two contexts: first, as a baby-maker (during pregnancy and birth) and second, when something was very obviously, and often painfully, wrong. The vagina during steady-state, non-pregnant times is only now starting to get the scientific attention it deserves—and it’s even more fascinatingly complex than you might think.

Meet: Your vaginal microbiome, which is currently teeming with bacterial communities working to protect their host (that’s you!) against disease and infection.2 The importance of this inner ecosystem spreads far beyond the vagina. The vaginal microbiome also communicates with your gastrointestinal tract (GI) via a network called the gut-vagina axis. This means that the health of your vaginal microbiota can impact the health of your gut, and vice versa. 

Here, we explore the microbial landscape of the vagina, how it shifts over time, and how it exerts its influence on the gut via the gut-vagina axis. Let’s dig in. 

What Is the Vaginal Microbiome and How Does It Relate to the Gut? 

Just like the ecosystem of microbes that live in your gut, there is also a community of (hopefully) beneficial microbes currently residing in your vagina.

Compared to the gut microbiome, which is characterized by a sprawling neighborhood of microorganisms, the vaginal microbiome has fewer community members and is ideally dominated by one type of bacteria called Lactobacillus.3 However, it’s not simple by any means. In a sampling of the vaginal microbiome of reproductive-age women, 135 subspecies were identified, each performing its own function and cohabitating with other strains.4 

Meet your vaginal microbiome’s mayor: Lactobacillus

In an optimal vaginal microbiome, various Lactobacillus strains limit any newcomers that shouldn’t be there.3 They also help produce the lactic acid needed to maintain a vaginal pH that is conducive to life and resilient against infection.5 You can think of Lactobacillus as the mayor of your one-of-a-kind vaginal community.


Research shows that microbiomes that are low in lactobacilli are more susceptible to a variety of vaginal health concerns, including preterm birth (PTB), bacterial vaginosis (BV), and increased risk of sexually transmitted infections.6

While the vagina is not a part of the gastrointestinal tract, the proximity of the vaginal opening (vestibule) to the rectum can facilitate some physical cross-contamination of microbes between the gut and urogenital area. The existence of this axis means that issues in the vagina can make their way to the gut, and vice versa. The gut microbiome of babies born vaginally also seems to contain some of the Lactobacillus species from their mother’s vaginal microbiota after a process called seeding (the inspiration for our name, Seed!).7

The Dangers of Dysbiosis, From BV to IBD

Dysbiosis in the vaginal microbiome occurs when the composition of bacteria shifts from a healthy baseline; maybe lactobacilli are in low supply or there is an overgrowth of pathogenic bacteria. 

Vaginal dysbiosis may not lead to pain or other symptoms, and by itself, it does not necessarily need to be treated medically. But, as mentioned earlier, it can lead to other vaginal health issues such as BV and STIs, as well as have downstream impacts on fertility and obstetric outcomes.

Emerging research also shows that thanks to the bidirectional relationship between the vagina and the gut, vaginal dysbiosis might also correlate with GI concerns. For example, species of E. coli that typically reside in the gut sometimes find their way to the urethral opening, causing a urinary tract infection (UTI).8 A recent study also found that pregnant women with IBD are more susceptible to bacterial vaginosis and Candida colonization, which might pose a risk for preterm birth.9 And in an online survey of 1,250 women conducted in 2019, those who had active IBD were more likely to report vaginal discomfort than those who did not.10

We also know that microbes in our gut produce enzymes that help us ferment certain foods into short-chain fatty acids (SCFAs), which have an anti-inflammatory effect.11 This process helps keep the gut wall strong and prevents a “leaky gut” from which microbes can escape. If certain microbes leave the gut and enter the bloodstream, it can set off an inflammatory response that affects the entire body, including the vagina. 

If you experience pain during everyday tasks, while urinating, or during intimacy, your vaginal microbiome could be to blame. Noticing that your vaginal discharge all of a sudden takes on a gray, green, or yellow color or starts to smell foul, fishy, or rotten? This could also signal a vaginal microbiome imbalance.6 

Research suggests that up to 90% of women have unstable vaginal microbial makeups that are susceptible to imbalances and infection.12 So even if you aren’t currently experiencing any pain or funky symptoms, you may still benefit from “feeding” your whole-body microbiome the ingredients it needs to thrive. 

You can foster a healthy gut and vaginal microbiome by eating a plant-rich, high-fiber diet, loading up on fermented foods, being mindful of antibiotic use, and drinking in moderation. Avoid using intimate washes and douches, as they may negatively affect the microbial community in the vagina and cause inflammation.6 

Taking a vaginal probiotic that contains clinically studied Lactobacillus strains can also help colonize the vaginal microbiome with beneficial bacteria. Suppositories that are inserted directly into the vagina are preferable to oral capsules, as they have been more effective in clinical research.13

Where Hormones Come In: The Role of the Gut-Vagina Axis In Regulating Estrogen

Scientists use the term “steady state” to describe a healthy, non-pregnant female reproductive tract—but many people with a vagina will raise an eyebrow at the word “steady.”

On a roughly monthly basis, menstruators may notice changes in mood, energy levels, sleep quality, and other symptoms thanks to shifts in the reproductive hormone estrogen. The gut-vagina axis seems to play a role in regulating this key hormone. That’s because a subset of microbes that reside in your gut are able to chemically modify (add or remove) circulating estrogen in the body.14 

You might be thinking, how do the microbes in my intestine alter estrogen in the blood? Well, as estrogen cycles through the body, it actually passes through the gastrointestinal tract.15 Your liver filters out estrogen in the bloodstream, then chemically modifies it to be discarded and secretes it into the intestines through bile. Without any gut microbiome involvement, all of this discarded estrogen is secreted out of the body in the feces. However, we now know that a network of microbes that can chemically modify estrogen (known as the estrobolome) interrupt this secretion by “undoing” the liver’s chemical modifications, allowing the estrogen to be reabsorbed back into the bloodstream.15

Furthermore, some foods contain estrogen-mimicking compounds, which can be modified by gut microbes as well, allowing for absorption. So, whether or not you have estrogen-modifying microbes present in your gut, which ones, and how active they are, ultimately influences how much estrogen is in your body.  This can have downstream effects on your vaginal microbiome health, as higher estrogen levels correlate to more lactobacilli.16 Your estrogen levels also affect the overall health, thickness, and mucus production of the vaginal lining. 

Estrogen isn’t the only sex hormone implicated in the gut-vagina axis. Researchers are now looking into how others, such as progesterone, are involved.

What Happens During Menopause? 

As we age, our body produces less estrogen. This coincides with the end of menstruation and potentially the beginning of other unpleasant sensations such as hot flashes and vaginal dryness. Yes, we’re talking menopause. Unfortunately (but unsurprisingly), research on the gut microbiome’s influence on post-menopausal vaginal health is scant. But we do know a few things so far. 

First, multiple studies have shown that the composition of the gut microbiome usually shifts during menopause. It becomes higher in some strains and lower in others, but less diverse overall (and actually more similar to the average male gut microbiome). Second, we know that progesterone and estrogen, two sex hormones that are affected by the gut (and decrease during menopause), influence the permeability and strength of the vaginal mucosal barrier.17 A weaker mucosal barrier in the vagina allows more inflammation, so it’s possible that gut microbes influence vaginal inflammation related to menopause. However, scientists are unable, at this point, to disentangle menopause-specific changes in vaginal immunity with overall changes in inflammation associated with aging.

The Gut-Vagina Axis: An Essential Superhighway for Women’s Health  

The vagina doesn’t exist in isolation. Emerging science demonstrates just how closely tied it is to whole-body health—from your gut, all the way up to your mouth. (Yep, dysbiotic conditions in the vagina have even been associated with gum disease.)18 

Researchers are just beginning to scratch the surface of how the bacterial communities in your vagina ebb and flow throughout your life—and what these changes might mean for you in pregnancy, menopause, and beyond. There are also advancements being made in studying how you can cultivate healthier vaginal microbiomes through lifestyle choices, probiotics, and even microbial transplants.19 The gut-vagina axis represents a long-awaited new frontier in vaginal health research that’s just getting started. 


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