Vaginal Microbiome Sequencing
- emilyharari
- Sep 16
- 7 min read
"23andMe for your cooch" 🫢 An explanation of the vaginal microbiome and how to interpret test results
In 2019, I was both working on and participating in a research study by Juno Bio, a biotech company sequencing the vaginal microbiome.
The vaginal microbiome is uncharted territory. It’s a community of microbes living in your body. It’s another exciting frontier of science to better understand the female body. For a high level explanation of the study, watch my video. To acquire all the knowledge you need to really prove you're a feminist in cocktail chitchat, keep reading!
Why is the vaginal microbiome important? According to this review, the state of the vaginal microbiome has been linked to preterm birth (PTB), miscarriages, recurrent urinary tract infections (UTIs), sexually transmitted infections (STIs), endometriosis, polycystic ovary syndrome (PCOS), infertility, and gynecological cancers. To understand this microbiome could mean the ability to better treat or even prevent these problems.
The Science
But what makes this microbiome different from all other microbiomes? If you're reading this blog, you've obviously heard about the gut microbiome. You've probably heard the common advice to maximize microbial diversity in your gut by eating a variety of colorful fruits and vegetables. What's interesting about the vaginal microbiome is that this advice is flipped. According to this meta-analysis, more microbial diversity in the vagina actually meant greater risk of contracting STDs. Why is microbial diversity positively correlated with good health in the gut microbiome and negatively correlated with good health in the vaginal microbiome?
If we think about a microbiome as an ecosystem of microbes, then we can start to appreciate each one's unique features. For example, the ecology of a rain forest is different from that of a desert. The healthy gut microbiome is like a rain forest, flourishing with up to 400 different bacterial species. Meanwhile, the healthy vaginal microbiome is like a desert, characterized by just a handful of different species. You'll see what those species are in my Juno Bio Report, but I haven't yet finished singing my praises of the vaginal microbiome.
How did we end up with a rainforest for a gut and a desert for a vagina? How did these distinct ecosystems emerge? A big clue is pH.
A quick explainer on pH:
What is pH, if not another buzzword to market overpriced bottled water? It's a way to talk about acidity.
Think of pH as an acidity score. (It’s actually the concentration of hydrogen molecules. Acids give away hydrogens like free candy. The more acidic a solution, the more hydrogens there are floating around the environment.) Vinegar, for example, is super acidic, loaded with hydrogens. Just to make things extra confusing, the pH "score" is calculated by dividing by the concentration of hydrogens.
A low pH of 1 is super acidic. A high pH of 14 is not acidic; it's super basic. And 7 is smack in the middle-- neutral. Acidic things are sour, like lemon juice. Basic things are slippery & bitter, like soap. And water is neutral.
When we talk about the gut microbiome, we're usually focusing on the colon in the large intestine. The hard work of extracting nutrients in the small intestine is done and your microbes can feast on the fibrous leftovers. You poop out some microbes, but those bacterial colonies hang around. Pooping doesn't clear the rainforest, but it does get us a biological sample-- an idea of what the ecosystem looks like.
So let's characterize that ecosystem. What's the pH of the colon? It's 5.5-7. That's pretty close to neutral, like sparkling or still water. What's the pH of a healthy vaginal microbiome? It's 3.5-4.5. That's like apple juice (more acidic). Not exactly apples to apples, comparing the gut to the vaginal microbiome!
I know apple juice doesn't sound hard core (pun intended), but everything is relative. Look across the entire body and you'll find that the vagina is the second-most acidic microbiome in the human body. First it's the upper GI/stomach (obvious to anyone who's experienced the wrath of a fiery heartburn). Then it's the vagina. Then the skin, the mouth. The gut microbiome star, the colon. And finally the small intestine.
No wonder just a handful of different species live in the vaginal microbiome. You'd have to be specifically adapted to survive that environment, which is why I compare it to the desert ecosystem. You've got plenty of organisms surviving the desert, maybe some vultures and lizards, but not as much variety as the rainforest, with its toucans and parrots and iguanas and... you get the point. (Just for comprehensiveness, the upper GI/stomach would be like Mars or like the bottom of the ocean. There actually are some microbes, but it's limited.)
We know a lot about the vaginal microbiome, but I say it's uncharted territory because there are still a lot of pieces we haven't connected to women's health. Luckily, progress is underway.
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Applications in Women's Health (including my test results!)
What happens when the ecosystem is disrupted? In the vagina that's called vaginal dysbiosis. What’s the harm in a bit of dysbiosis? Even if you don’t experience symptoms, a state of dysbiosis means your defenses are down: Your immune system is unable to fend off viruses, keep in check the nefarious microbes already residing in your microbiome, or catch sneaky cancer cells that may emerge from all this inflammation. Often, however, you do encounter symptoms. For example, BV and STIs.
Disease deep dive! In case you haven't already experienced a WebMD doom scroll while waiting for your test results from the clinic... Bacterial Vaginosis (BV), a bacterial infection:
One in three women of reproductive age will have bacterial vaginosis, an infection caused by an overgrowth of certain harmful bacteria in the microbiome. When I helped recruit for the Juno Bio study, I joined various BV Facebook groups to understand what women were going through. The symptoms can be awful: odor, discharge, burning. A lot of women are embarrassed about their BV. What’s worse, BV can be persistent. Even after antibiotics, it can come back with a vengeance.
STIs:
Having BV has been associated with higher risk of both getting and transmitting certain viral infections like HPV and HIV, as well. What if we lived in a world with at home test kits that didn’t just tell you once it was too late that you did or didn’t have an STD? What if we had tests that would give us early warnings about our vulnerability to contract them in the first place? Once we shift to these preventative models, we’ll wonder why we ever settled for less.
The Juno Bio report presented my individual results but then contextualized it relative to the other study participants in their database. They observed 4 buckets of common vaginal microbiome profiles, what are called “community state types” (CST). I fell into the majority: CST 1, L. crispatus dominant. It’s considered the most stable microbiome. In fact, L. crispatus is what one researcher calls the “‘golden child’” of all the microbes. So, yeah, I'm kind of the microbiome "golden child." Is that not the nerdiest humble brag?
I'm happy with those results now, having researched for this article and knowing what I know about microbial diversity in the vaginal microbiome. But, to be honest, when I first got my results, it was pretty anticlimactic. The first thing I saw was 98.11% Lactobacillus crispatus. I just thought, "That's it? Like, all that, just for 2 microbes?"
In the other 2% I was humbled to find some L. iners, too. It's fine in small amounts, but if it grows out of control, it can cause BV. This highlights the nuance of microbial analysis. It’s all about relative abundance. The mere presence of a pesky microbe doesn’t warrant sounding the alarms.
My friends joined the study too and we compared our results. That was fun. It kind of reminded me of those Buzzfeed quizzes or personality tests. Or the reports from 23andMe (RIP). I joke in my video that vaginal microbiome sequencing is like "23andMe for your cooch." I don't think we have enough info to make these reports quite as engaging as 23andMe's genetic reports, but I'd love for us to get to that point, because this would be such a fun Galentine's Day party activity lol.
Beyond the fun and silly science parties, this kind of science could help a lot of women, too. So many have been prescribed too many antibiotics and totally messed up their microbiomes. Data like Juno Bio’s can fuel research to develop better treatments for women.
For example, Osel is developing treatments, similar to probiotics, to restore the vaginal microbiome. If you’ve struggled with BV and want some hope, I highly recommend this article spotlighting Dr. Cohen’s work spearheading treatments in this space.
Juno Bio was one of the first kids on the block when it came to mapping the vaginal microbiome. Now, giants like Evvy are blasting the message far and wide: Vaginal healthcare is here. We’re emerging from the dark ages of the “whiff test”! (If you don’t know what the “whiff test” is, watch my video lol).
I’d love to try an Evvy kit. Given what this paper says about copper IUDs’ impacts on the vaginal microbiome, I bet my L. crispatus numbers have gone down. Hint hint, Evvy, if you’re reading this and want to do a follow up experiment to that study, you know how to reach me!
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