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Enter the Vaginome: Meet the Microbes that Live in Our Vaginas

We've gone way beyond Lactobacillus.
March 3, 2015, 3:00pm
Image: ​Lia Kantrowitz

"Are you here alone?"

It doesn't matter what kind of bar it is, or whether or not you feel inconvenienced by the intrusion; the answer is always the same: "No."

The asinine inspirational posters were right: you're not alone—nobody is. In fact, you are a vast, ecological habitat teeming with trillions of tiny organisms.

Microbes reside in virtually every human bodily system, a mix of about 10,000 different species of bacteria, fungi, and archaea depending on the conditions of the specific body part. This may sound gross and intrusive, but most of the microbes are just hanging out, doing their thing discretely so we don't even notice they're there. While some can wreak havoc, a lot of these tiny organisms actually help us, performing important tasks for their human hosts like defending against infection and helping to digest food. In fact, microbes are so important to human health that we're seeing great results from transplanting healthy poop into the colons of people who suffer from serious gastrointestinal problems.


Now, scientists are exploring the health effects of engineering a different human ecosystem: the vagina. Anyone who has ever referred to the vagina as a garden can pat themselves on the back for their visionary insight.

"It's not a tomato garden," says Jonathan Eisen, who researches microbes at the University of California Davis. "There are things you can do, but it's not like a planter in your backyard with one organism growing in it." Rather, Eisen says a more apt comparison is the Alaskan tundra, which harbors a seasonal battle between icy mosses and lichen and summer marsh vegetation that draws large land mammals. "What we're trying to figure out is: what are the regular patterns?"

The creatures in our "vaginome"—that is, the collection of microbes that live and die in our vaginas—fluctuate too, and have been implicated in a whole host of health outcomes, good and bad, from bacterial vaginosis and chronic urinary tract infections to bolstering women's immune response and reducing the likelihood of transmission of HIV.

By and large, the ecosystem is complex and its residents are turning out to be more difficult to categorize than researchers initially imagined.

"Think of your organisms as very tightly knit."

"Think of your organisms as very tightly knit," says Jacques Ravel, a microbial genomics scientist at the Institute for Genome Science. "They depend on each other. They're like a little community, like a city. You have the police, the fire department—they are all needed for everybody to live safe and well." Ravel explains that if some tragedy were to affect only one role in the community (for example, perhaps the entire fire department gets wiped out in a blast), then there would be no one to extinguish fires. "That affects the community, which makes things start to fall apart."

Western medicine has spent centuries pushing a narrative of health that has more in common with simplified Hollywood plots of heroes versus villains than it does with reality. Up until very recently, health meant eradicating the villains so the heroes could flourish. But what we're learning from modern examinations of our microbes—especially the ones in the vagina—is that health comes from striking and preserving a personalized balance.


In the 19th century, a German gynecologist by the name of Albert Döderlein first identified a bacterial group in vaginal secretions that we soon determined to be the heroes. We now call this group Lactobacillus and right up until about a decade ago, it was the undisputed hallmark of a healthy vagina. Lactobacilli produce lactic acid, which slightly increases the acidity of the vagina, making it less hospitable to invasion. The lactic acid itself may play a role in preventing invasive microbes from getting a foothold.

But as the science advanced, this theory was revealed to be increasingly incomplete. First, we discovered that vaginal infections weren't always caused by some villainous microbes that had managed to sneak in. In fact, a number of so-called villains normally inhabit the vagina, usually without issue.

And then came the whopper: eight years ago, we realized that ethnicity plays a role in the microbial composition of the vagina. In a 2011 study of 394 women, only 59.6 percent of Hispanic women and 61.9 percent of black women had vaginomes dominated by Lactobacillus, compared to 80.2 percent of Asian women and 89.7 percent of white women.

"If accepted at face value, this common wisdom suggests that although most Asian and white women are 'healthy,' a significant proportion of asymptomatic Hispanic and black women are 'unhealthy'—a notion that seems implausible," wrote Ravel and colleagues. "From these data we conclude that vaginal bacterial communities not dominated by species of Lactobacillus are common and appear normal in black and Hispanic women."


When it comes to lactic acid production, Lactobacillus is not the only option. The study discovered that in women lacking Lactobacillus, other lactic acid-producing microbes were found, including Atopobium, a microbe usually regarded as villainous.

Ravel believes that understanding how some women's vaginas can maintain a healthy balance with microbes known generally as "bad actors" will require us to look more closely at these organisms to understand how variations in their genes create strains that affect us differently.

Understanding that difference will make vaginal probiotics a real possibility. This was the stated purpose of a company called SweetPeach, which was thrust out of stealth mode and into a furor last November after an investor completely mischaracterized it as a product to alter the smell of the vagina.

Probiotics, microorganisms consumed to promote a "good" microorganism balance in the body, are nothing new. They already exist as part of the wider dietary supplement industry—which at $32 billion in 2013, dwarfed even porn revenues. But the probiotics industry has been driven more so by rigorous enthusiasm than vigorous science, sometimes with disastrous consequences.

As researchers play catch-up, they've uncovered some intriguing findings. In 2011, a study of 100 women prone to urinary tract infections showed promising response to probiotic vaginal suppositories with Lactobacillus. Of the 50 women who received the treatment, only 15 percent showed a recurrence of infection, whereas among the 50 women who received a placebo, recurrence was seen in 27 percent.


A 2012 study using oral probiotic pills did not show nearly as much promise, but it neglected the younger demographic, focusing mainly on postmenopausal women and using a bacteria that depends on higher estrogen-levels to thrive.

So far, the vast majority of efforts have tried the ham-fisted approach of throwing at the vagina what we believe to be the heroes. The future is likely to be significantly more personalized. This, ultimately, is what makes SweetPeach so promising—the emphasis on characterizing the vagina and providing bespoke probiotics.

We're currently looking at the possibility of vaginal microbe transplants

"Until the integration of health and this big data approach in science, I think we didn't have the information to know how varied 'healthy' really is," says Jessica Richman, founder of uBiome, a company that enables consumers to discover their "microbiome," all the microbes that make up their body. "I think this is a lot more a gateway to personalized medicine than it is to having the one healthy microbiome we're all trying to get to. It's 'where were you when you were healthy?' rather than 'who should you be like?'"

And just as fecal transplants are radically improving the lives of people whose gastrointestinal tracts had been overrun by a single type of bacteria, we're currently looking at the possibility of vaginal microbe transplants to restore the vaginal ecosystem of women with recurrent vaginal infections.


"I don't think there is a universal vaginal secretion you can give to everybody like we see with fecal transplants," said Ravel, emphasizing the need for personalization.

"The area of clinical microbiome transfer is relatively nascent, and a roadmap for testing and implementation has yet to be defined," points out Laura Ensign, who's working to develop vaginome transplants at Johns Hopkins.

Ensign stresses the importance of lobbying for the exploration of vaginal microbial transfer in a clinical setting. The gut has received a lot of attention, mostly because the infections that require a fecal transplant can be fatal. But the vagina is important too—not only for the health of a woman, but for the next generation of humanity.

The vaginal canal is the original site of microbial colonization for babies born vaginally. C-section babies, we have discovered, have much less diverse microbial communities, which have been correlated with an increased risk for obesity, asthma, celiac disease, and diabetes. In light of this relatively new revelation, research is being done to determine how effective it would be to "baptize" C-section babies with vaginal microbes.

Though good researchers are generally cautious about making projections, there is a general undercurrent of excitement among them in the field of microbiomics, especially with regard to recent in-depth longitudinal studies and citizen science.

"We're moving into a world where you actually study yourself and you base treatment options not on the 100 people that were in the clinical trial to test a drug, but on you," says Eisen.

This article is part of Bodies of the Future, a collaboration between Motherboard and LadyBits. Follow LadyBits on Twitter and Facebook.

​Image: Lia Kantrowitz