#TransgenderAwarenessWeek | Trans Folks and the Vaginal Microbiome

While the role of the vaginal microbiome in cisgender women has been (and continues to be) investigated, there is a troubling lack of knowledge and research on the vaginal microbiomes of trans people.

Highlights from this article: 

  • The medical community knows very little about the vaginal microbiome in trans folks.
  • Neovaginas have a microbial community, just like the vaginas of cisgender women.
  • Some research has shown that neovaginal flora in trans women with gender-confirming surgery have higher levels of anaerobic bacteria associated with BV. 
  • One study found that trans men on testosterone have less Lactobacilli in their vaginal microbiomes.
  • The lack of research on transgender vaginal microbiomes is a barrier to trans folks accessing medical care.


Thanks to decades of evidence, we now know that vaginal flora is a major component of long-term health.

The vaginal microbiome plays a role in everything from fertility and pregnancy outcomes to your risk of getting infections to your likelihood of certain cancers progressing. But while the role of the vaginal microbiome in cisgender women has been (and continues to be) investigated, there is a troubling lack of knowledge and research on the vaginal microbiomes of trans people. 

We sat down with Dr. Diana Currie, OB/GYN and pioneering advocate for gender-specific and gender-expansive care (in addition to being an Evvy advisor!), to discuss the latest research on transgender vaginal health.

“Generally, there is a dearth of data on the vaginal microbiome for any group of patients,” noted Dr. Currie, “We are stumbling in the dark for everyone — and with respect to trans people, there are even fewer studies, as is the case on all topics for this group.” 

Trans folks have been historically underrepresented in scientific literature due to stigma and discrimination. Gender confirming surgery — sometimes referred to as sex reassignment surgery or gender reassignment surgery — has been around for over 70 years and is becoming more and more common, but there’s still a lack of evidence into how transfeminine bottom surgery or masculinizing hormone therapy affect the vaginal microbiome of trans folks. 

What does the vaginal microbiome look like in trans folks who have undergone gender confirming surgery? 

Research on the vaginal microbiome of cisgender women has shown that the majority have a vaginal microbiome dominated by Lactobacilli, a type of protective bacteria that plays an important role in regulating vaginal health.

One of the key questions around the vaginal microbiome of trans folks has been if Lactobacilli are present in a similar way, but the existing research has shown conflicting results.

In one study in 2009, a group of researchers enrolled 50 transgender women who had undergone neovaginoplasty, a type of surgery where a neovagina is created through penile inversion and genital skin grafts. 

The study, published in BMC Microbiology, analyzed vaginal swabs from each woman and found that much like the vaginas of cis women, neovaginas also have a microbial community — albeit a different one. There was a high presence of aerobic bacteria usually associated with bacterial vaginosis (BV), while Lactobacilli were found in only one of the study participants.

The researchers concluded that “the environment of this penile skin-lined neovagina, does not support the growth of Lactobacilli,” and added that this might be “due to the absence of glycogen rich epithelial cells.” 

However, a different study published in 2014 in the peer-reviewed journal Scientific Reports, contradicts this theory. Researchers took vaginal samples from 63 trans women and looked at whether Lactobacilli strains could survive in the neovagina, and if so what the most dominant Lactobacilli species were.

Similar to the vaginal microbiomes of cis women, the researchers found Lactobacilli present in 75% of study participants, specifically Lactobacillus gasseri, Lactobacillus crispatus, Lactobacillus johnsonii, and Lactobacillus iners. This was the first study to find Lactobacilli in neovaginal microbiomes, opening up a “new discussion about the origin of Lactobacilli  in the penile skin-lined neovagina.” 

Whether or not Lactobacilli can thrive in the neovaginal microbiome remains a question in the existing research, and answering this question can help us better understand what “healthy” looks like and how we can prevent infections and other negative health outcomes in people with neovaginas.

How does sex affect the neovaginal microbiome? 

The 2009 BMC Microbiology study linked the presence of bacteria in neovaginas with sexual intercourse. The researchers found the presence of Enterococcus faecalis — fecal bacteria that live in the gastrointestinal tract — in the neovaginas of straight trans women. 

E. faecalis was present in 78.6% of trans women who had sex with men, while it was only present in 14.2% of homosexual trans women and in 12.5% of bisexual trans women. According to the authors, “the migration of this uropathogen to the vagina is strongly enhanced by intercourse, an observation that has previously been made for E. coli and Enterococcus species.

Sex is known to affect the vaginal microbiome in cis women, and this link suggests that it can similarly affect the microbiome of trans women too. Better understanding this link can tell us a lot about preventing and treating vaginal infections in trans women!

What treatment options exist for the vaginal infections in the neovagina?

Vaginal infections are super common, and while BV, yeast infections, and UTIs are well understood in cis women, the same can’t be said for trans women. The lack of knowledge on neovaginal microbiomes makes diagnosis and treatment of vaginal infections either challenging or completely impossible.

“The most frustrating knowledge gap for me is whether or not vaginal estrogen helps improve integrity, function, comfort etc. for trans women. Because we use vaginal estrogen for cis women, many providers who are caring for trans women that have vaginal complaints will prescribe vaginal estrogen, myself included,” said Dr. Currie.

“I find myself saying ‘we don't know whether this will help but let's try it anyway.’  This is a most unsatisfying situation. I wish I had good data regarding the benefits (or not) of using vaginal estrogen in trans women with neovaginas.”

One study examined the neovaginal microbiome of five women with a Candida infection. The women in the study presented with symptoms like unusual discharge, vaginal odor, and itching and were successfully treated with miconazole (AKA, ol’ faithful: Monistat). The researchers behind the study stressed that “although neovaginal candidiasis does not seem to be a major health problem in transgender women, it may cause significant discomfort to individual patients, who subsequently seek professional medical care.”

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Where does research stand on the vaginal microbiomes of trans men? 

Unsurprisingly, it’s not just trans women’s microbiomes that have been neglected—trans men have equally been left out of the equation. Only one study to date has looked at the impact of masculinizing hormone therapy on the vaginal microbiome. 

It found that trans men taking testosterone were less likely to have Lactobacilli in their vaginal microbiome, but it’s unclear whether trans men are at higher risk of developing vaginal infections. 

However, the role of estrogen in the vaginal microbiome may shed more light on how changing hormones might affect the vaginal microbiome. More specifically, estrogen promotes stability in the vaginal microbiome because it promotes the production of glycogen, which is a key factor for the growth of beneficial Lactobacilli bacteria. If estrogen levels are altered, the good bacteria’s ability to flourish may be hindered and it may be easier for pathogens to cause trouble.

Considering the importance of Lactobacilli in preventing infection and disease, this is another area that desperately needs more research.  

Dr. Currie explains,“I frequently have trans men who experience vaginal discomfort, we presume due to atrophy of epithelial cells similar to postmenopausal women experiencing estrogen depravation — assuming BV, yeast, and other infections are ruled out.” 

“We have no solid data about the vaginal microbiome in trans men and how changes may contribute to symptoms, and whether the use of vaginal estrogen or Prasterone reverses these changes, etc. It is mostly all guesswork and extrapolation based on studies in postmenopausal women.”

How can people help advocate for more research on the vaginal microbiome for trans folks?

We know the vaginal microbiome is a fundamental component to overall health — it can determine the risk of STI acquisition, fertility & pregnancy complications, and even the progression of certain cancers — so understanding how it affects trans folks’ health is a necessary component of transgender healthcare. 

“We all need to advocate for more research on trans people, both MtF and FtM. We recognize there is a lack of data on women's health (especially vaginas) and trans health — likely related to the social taboos and personal discomfort that mainstream, cis male, heterodominant people feel when these topics come up.” said Dr. Currie. 

“We need to keep talking about vaginas until it is just as acceptable to show Super Bowl commercials for products that treat vaginas as it is to show ads for penis problems such as erectile dysfunction.” 

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