Our Journey to Developing VS-01™: The First-of-Its-Kind Vaginal Probiotic

From her Baltimore apartment in the privacy of the early morning hours, a woman sits on the toilet. She picks up a long cotton swab, still in its sterile paper packaging, and peels the pouch open gingerly. Then, she spreads her legs, hunches forward, and, using the fingers of her free hand to clear the way, swabs her vaginal tract in a few deft motions. It’s been eight weeks—she’s practically a professional at this point.

An hour later, she drops off a tube with the morning’s swab, along with six others, identical but for their labels, at the University of Maryland’s medical school. Her work for the week is done—but the tubes she passed off are just beginning their journey.

Next, they will be frozen at a temperature of -80°C, plunging their bacteria into a state of suspended animation: cryostasis, like the kind entered by science-fiction astronauts. And just like sci-fi space voyagers, the organisms frozen inside these tubes will eventually go on to expand our understanding of the world.

They’ll join thousands of others—each indexed and neatly nestled in boxes in a laboratory freezer—to have their data analyzed by metagenomic sequencing. The results of this sequencing will then help bring stability and order to ecosystems that have gone awry. It’s all made possible largely by the work of one enterprising scientist named Jacques Ravel, Ph.D. 

This is the story of how we partnered with Dr. Ravel to bring microbial science out of the lab and into the real world with a first-of-its-kind innovation for restoring and repopulating the vaginal microbiome.

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The Beautiful Simplicity of the Vaginal Microbiome 

To appreciate Dr. Ravel’s feat, you’ll first need to understand how microbiomes work, and what makes the vaginal microbiome (VMB) so extraordinary.

Every part of the human body, from your gut to your skin, to the hair follicles of your armpit, is home to an ecosystem of bacteria: a unique microbiome adapted to its ecological niche. Of these, the gut is the most complex. It’s like a rainforest—chaotically rich, thick with life of every kind, bound in dizzyingly complex webs of interaction. At the other end of the spectrum, there’s the vaginal microbiome, which is less like a jungle and more like a row of pines.

In the claustrophobic density of a rainforest, plants grow on top of other plants. But walk through a pine forest, and you’ll notice a conspicuous, almost eerie absence of other kinds of trees. 

These forests owe their peculiar uniformity to their trees’ ability to produce chemical compounds that are toxic to most other plants. A steady-state vaginal microbiome works much the same way. It’s dominated by certain species of Lactobacillus that outcompete competitors using lactic acid, which helps keep the environment’s pH too low for most other microbes.¹ 

Researchers first learned of the existence of lactobacilli in the vaginal microbiome back in 1892, thanks to the work of a German gynecologist named Albert Döderlein.² Much more recently, we learned that specific Lactobacillus strains in the vaginal tract, such as Lactobacillus crispatus, also carry an arsenal of sophisticated defenses against specific foes.³

Without this microbial legion, VMBs are vulnerable to imbalances and unwanted issues. Nine out of 10 women now have an unstable vaginal microbiome due to everyday agitators such as certain prescriptions, “feminine washes,” lubricants, contraception, and sex (just to name a few vaginal microbiome disruptors—the list goes on).⁴ As a result, millions suffer from discomforts and have to choose between short-term solutions—which can wipe out protective bacteria and leave the vagina more susceptible to future pH imbalances—or remedies of dubious efficacy, like drinking cranberry juice or soaking tampons in yogurt.^5,6

Dr. Ravel knew that repopulating vaginal ecosystems that had fallen prey to invaders would require zooming out and examining the structure of the vaginal microbiome as a whole.

Towards a More Nuanced Understanding of the VMB

Dr. Ravel didn’t set out to become one of the world’s foremost experts on vaginal ecology; he spent his early career tracing the source of the bacteria used in the 2001 anthrax terrorism plot and inventing computational tools to “mine” bacterial genomes for new medicines. He was also working at the Institute for Genome Research when they sequenced the first gut metagenome. It was, in effect, a million-dollar project to understand a single piece of poop. 

“We didn’t get much insight from that,” Dr. Ravel says. “There was all this data, all these genes that nobody had ever seen before, and no annotation.”

Annotation, in the context of genomics, refers to the collective knowledge of what a gene does—what kind of protein or enzyme a given string of nucleotides will create when transcribed by a cell. In some senses, the diversity of the gut microbiome was an immense discovery—a library-at-Alexandria’s worth of information, but written in an alien language that could only be translated through painstaking experimental work, one word at a time. It would be years or even decades, Dr. Ravel realized, before the mess of data could be decoded and applied for good. The question became: How could he leverage his microbial knowledge to improve people’s lives today? 

Dr. Ravel found his answer when he met another scientist, Larry Forney, PhD, who had been applying the burgeoning science of genomics to understand the differences among the various lactobacilli that dominate the vaginal ecosystem.

Seen through a microscope, the Lactobacillus species found in a vagina might look no different from one that helps turn milk into yogurt, and even the complex chemical tests that microbiologists have long used to define bacterial species can rarely tell the difference.⁷ Until the early 2000s, with the advent of cheap gene-sequencing methods, there was no way to know what we know now: that Lactobacillus is a genus as diverse as the genus Canis, which includes not only every breed of dog, but also wolves, dingoes, and coyotes. 

It is composed of hundreds of sub-species and strains, each playing a unique role in vaginal health and dysbiosis.⁸ To understand just how different certain strains within the same microbial family can be, consider Escherichia coli: a species with hundreds of strains, many of which live in our intestines and are considered healthy—but at least 200 of which are pathogenic, causing foodborne illness and diarrhea.

Using then-newfangled gene-sequencing methods, Dr. Ravel and Dr. Forney endeavored to map the microbial forest of the vagina, so to speak, and gain new insights into vaginal health in the process. In 2006, they received the first-ever NIH grant dedicated to the study of the vaginal microbiome. In the decades that followed, they became familiar with billions of microorganisms that call the vagina home—thanks to the help of hundreds of women who volunteered to self-sample in the name of scientific discovery.

Identifying the 5 Types of Vaginal Microbiomes 

Through a massive feat of science at scale, Dr. Ravel and his team created a detailed map of the vaginal microbiome using samples from 396 reproductive-age women, like the Baltimore resident we met earlier.⁹ 

The team asked participants to swab their vaginas at home and store those swabs in their freezers until they could be dropped off at the lab. It might seem like an obvious move, but the same protocol once cost Dr. Ravel a research grant. “We once had a proposal to the Human Microbiome Project turned down because there was a reviewer—a clinician—who believed that women couldn’t sample themselves, even though there was already published literature at the time showing that physician-collected samples are equivalent to donor-collected ones,” he shares. It’s a demonstrative anecdote: a reminder of how subtle internalized biases—masquerading as technical or procedural concerns—have stalled progress in the women’s health space for decades.

After analyzing thousands of samples from diligent citizen scientists, Dr. Ravel was able to identify five subgroups, or “community state types” (CSTs), of the vaginal microbiome:

• CST I: Lactobacillus crispatus dominant
• CST II: Lactobacillus gasseri dominant
• CST V: Lactobacillus jensenii dominant
• CST III: Lactobacillus iners dominant
• CST IV: Non Lactobacillus dominated 

Four of these CSTs are dominated by a single Lactobacillus species (CST I, II, III, and V), while the fifth (referred to, somewhat confusingly, as CST IV) is a catchall category for any microbiome where the less friendly denizens of the vagina—which typically play only a marginal role—have supplanted the usual predominant Lactobacillus species. When that happens, the lactobacilli can no longer exert their protective effect, putting their host at risk of vaginal microbiome imbalance.¹⁰

One of Dr. Ravel’s foundational discoveries was that some CSTs appear to be more stable than others. For example, about 20-40% of vaginal microbiome samples fall into the category CST III, which is characterized by a bacterium called Lactobacillus (L.) iners.¹¹ CST III is considered healthy, but it’s significantly more prone to disruption than most of the other types, and can more readily transition to CST IV under the influence of things like sex, hormonal fluctuations, or certain prescriptions.¹² 

In CST I, on the other hand, the dominant bacterial species is L. crispatus, which appears to confer the most resilience against disruptions out of any of the four common species.¹⁰ 

Hormone levels seem to fluctuate throughout the menstrual cycle, impacting the secretions of the cells that line the vagina—and influencing the community’s architecture in turn.¹³ At menstruation, the ecosystem is inundated with blood and sloughed uterine lining, which can provide nutrients that can feed unwanted bacteria. As a result, a vagina that is Lactobacillus-dominated in one part of the cycle may transition to CST IV in the weeks during and after a person’s period, gradually reverting as the cycle progresses.¹⁴ Lifestyle factors also impact the vaginal microbiome: Take up smoking, for example, and you’re multiple times more likely to find yourself in the upwards of ~37-42% of women categorized as CST IV.^15-17

Translating Vaginal Microbiome Science Into a First-Of-Its-Kind Probiotic

Dr. Ravel’s work helped demonstrate that the vagina is a dynamic environment, and CSTs are far from a fixed feature. This foundational insight meant that it would be possible to restore L. crispatus dominance in vaginal microbiomes that had been ambushed by unwanted bacteria and fungi.

Doing so, however, would require isolating the exact strains of L. crispatus that had the most protective influence—a feat of strain-level science that was unprecedented in the probiotic industry. 

To bring back the dog analogy, two strains of L. crispatus can be as biologically distinct as a greyhound and a dachshund—both part of the species Canis familiaris. And up until this point, very few “vaginal health”-branded probiotics contained strains that had actually been tested and proven on the vaginal microbiome. 

“People have tried putting multiple different species of Lactobacillus in a single product, even though that doesn’t represent what happens in vivo (in the human body). People have tried different species that aren’t even human vaginal species,” Dr. Ravel says. The majority of these probiotics were also administered by mouth, despite the lack of any plausible mechanism for them to reach the vaginal tract. 

In 2016, we partnered with Dr. Ravel to found LUCA, a metagenomics platform and gene catalog that would leverage Seed’s end-to-end product platform to fully realize the potential of his research. The first innovation: a clinically validated probiotic that would restore an optimal vaginal microbiome.

In order to find the ideal strains of  L. crispatus, our team—helmed by Dirk Gevers, Ph.D., Seed’s Chief Scientific Officer—analyzed more than 10,000 samples, including daily vaginal swabs from hundreds of women over a period of 10 weeks. 

Once a consortium of L. crispatus strains was identified, it was time for months of preclinical validation that culminated in a double-blind, randomized, placebo-controlled clinical trial that pitted a handful of possible designs against one another and included one of the leading vaginal health probiotics currently on the market as a benchmark.

The clear winner: a pressed tablet, designed to be inserted directly into the vagina, containing LUCA’s three strains of L. crispatus along with a proprietary Lactobacillus-specific nutrient complex. It was 10 times more effective at increasing the abundance of beneficial bacteria than the leading oral probiotic for vaginal health, resulting in an optimal vaginal microbiome in 90% of participants who started with a low baseline of L. crispatus.

Introducing VS-01™: a vaginal synbiotic rooted in enterprising science and supported by clinical trials involving hundreds of citizen scientists. We’ve used 15+ years of metagenomic research and cutting-edge microbiome technology to unlock the exponential impact that is possible when science is inclusive of a woman’s point of view—and we’re just getting started. VS-01™ is just the beginning of a vaginal health movement—one that will take us from harsh, reactive treatments towards proactive, sustainable care.