Vaginal Microbiome 101

Your vagina is as mysterious and mesmerizing as the ocean. Much like the depths of the sea, we’ve barely scratched the surface of the more than 10,000,000,000 (that’s ten billion) bacteria, fungi, and other microscopic organisms that currently traverse it.^1,2

This enigmatic ecosystem is constantly changing with your hormones, your genetic makeup, and your lifestyle. When ebbing and flowing in synch, its microbiota act as a first line of defense against genital and urinary tract infections, bacterial vaginosis (BV), infertility, pregnancy loss, and even some cancers.^3,4,5,6,7 

Clearly, the vagina is so much more than a reproductive organ—it’s a living shield, a vital health metric, a pleasure and arousal center, and a landscape worthy of increasing study. Let’s submerge into the depths of the vaginal microbiome to explore what it is, how it functions, and how to protect yours.

Our bodies are home to multiple microbiomes, from the gut microbiome to the skin microbiome to the axillary microbiome (within our armpits).⁸ Some organisms can be found in multiple biomes, while others tend to stick to a specific region.⁹ 

The moist, humid conditions of the vaginal canal have attracted unique microscopic residents over the lengthy course of human-microbe coevolution.¹⁰ While this vaginal microbiome (VMB) is a busy bacterial hub, it tends to have less diversity than other biomes of the body like the gut microbiome.^1,11 In a peak state of equilibrium, vaginal microbiotas are dominated by the genus Lactobacillus, which produce lactic acid to maintain a moderately acidic environment (typically at a pH level between 3.8—5.0 during reproductive years).^1,12

You might associate acidity with decay and corrosion, but in the vaginal microbiome’s case, it’s a really good thing. A more acidic microenvironment has a suppressive effect on disruptive bacteria that can lead to issues like BV, urinary tract infections, and yeast infections.¹³ More acidic VMBs also tend to be more resilient against other infections, like STIs. Vaginal discharge—a combination of cervical mucus, bacteria, dead cells from the vaginal epithelium, and vaginal fluid—also creates an environment for beneficial bacteria to thrive.^12,14 (Yep, seeing discharge in your underwear is totally normal and not at all “gross.”)

Acidity-regulating lactobacilli are considered a “keystone species” (a species that other organisms in an ecosystem depend on for life) for the vaginal ecosystem—but there is immense variety within this one bacterial family. Within the larger Lactobacillus genus, there are hundreds of species with characteristics that are distinct from other bacterial groups.¹⁵ (And within those species, there are also subsets of strains that share certain genetic information—see where this gets as mind-boggling as ocean exploration now?). 

Some species, like Lactobacillus crispatus, appear to offer a heightened level of protection thanks to strains that produce molecules to neutralize pathogens, known as bacteriocins.^1,13 Think of bacteriocins as having targeted, naturally occurring antibiotic (killing the bad guys) and probiotic (feeding the good ones) functions that help prevent “dysbiosis” or disorder.¹⁶ Overall, they help defend vaginal walls and cell tissues against disease-carrying microbes, and help Lactobacillus species to establish themselves and survive.¹⁷

Other types of Lactobacillus species, like Lactobacillus iners, don’t offer the same protection and seem to be more vulnerable to disruption.^18,19

Ideally, your vagina is teeming with microbes that keep predators at bay and filter out threats in real time.²⁰ 

Research suggests that most (but not all) vaginal microbiomes are dominated by one Lactobacillus species.¹ This dominance makes us humans markedly different from other mammals.¹ Many bacterial species that are common in the human vaginal microbiome have not been found in the vaginal microbiome of other mammals, including non-human primates.

The uniqueness of the human vaginal microbiome makes it tricky to study. Animal models can’t necessarily stand in for human VMBs, so in order to analyze the microbiomes of real humans, scientists need to collect samples from, well, real humans. Over the last few years, this has given rise to large-scale citizen science projects that ask people from around the world to collect vaginal samples to be processed in a lab. 

This exhaustive sequencing work has shown that no two vaginal microbiomes are the same—though they can be generally categorized into five “groups” that share similar characteristics and themes. 

No vaginal microbiome will fit neatly into a box. However, the Community State Type (CST) grouping system is used as a point of reference. First established by Jacques Ravel, Ph.D., a leading expert in vaginal microbiome science, it catalogs vaginal microbiome compositions into five main types:²¹

CST I — Lactobacillus crispatus dominant

CST I, dominated by Lactobacillus crispatus, produces high levels of lactic acid and appears to be most resistant to BV, STIs, and other vaginal infections, as well as protective against preterm birth.^{22,23,24,25,26,27} You could say it’s the holy grail of VMBs, and it’s found in about 10% of women.²⁸

CST II — Lactobacillus gasseri dominant

Lactobacillus gasseri dominates CST II, which is a relatively rare CST that seems to be less stable and protective than CST I.^1,26

CST V — Lactobacillus jensenii dominant

Lactobacillus jensenii rules in this domain, and it seems to promote a vaginal ecosystem that is acidic with a low chance of dysbiosis.^21,29 Like CST II, CST V is relatively rare and not quite as protective as CST I.²¹

CST III — Lactobacillus iners dominant

Lactobacillus iners takes center stage within CST III, one of the most common VMB states.²¹ This somewhat fickle strain is not solidly categorized as either harmful or beneficial—it can swing either way.³⁰ All in all, CST III seems to offer less protection against dysbiosis and be more prone to disruption than other Lactobacillus types.^18,19

CST IV  — Non Lactobacillus dominated

You can think of this CST as the chaos category. It’s not dominated by a Lactobacillus species. Instead, it’s governed by a more diverse array of bacteria that might include Atopobium, Prevotella, or Gardnerella.⁴ 

While having this type doesn’t necessarily mean you have an active vaginal infection (or even vaginal symptoms), CST IV has been linked to a higher likelihood of several health conditions, including BV, STIs, as well as infertility, and preterm birth.^4,31,32,33 

The latest science shows that CSTs are fluid, rather than static. Your CST might change at certain points of your menstrual cycle, for example, since lactobacilli abundance tends to drop and vaginal pH creeps up slightly during your cycle.^12,34 Your age, pregnancy status, and lifestyle habits (including sexual activity) can influence your VMB makeup, too, potentially shifting it in or out of dysbiosis.³⁵ While some change is to be expected, people who switch between CSTs more rapidly (spending less than 2-3 weeks in one CST) seem to be more prone to dysbiosis, according to some research.³⁶

This means that reductionist terms such as “healthy” and “unhealthy” or “good” and “bad” just aren’t fit to describe the vaginal microbiome. It’s too versatile for that. Instead, healthy or not, balanced or not, will look different from one VMB to the next. Just like its host (you!), the vaginal microbiome is complex and ever-evolving.

Since the vaginal environment is far from fixed, there are plenty of things you can do to shape yours. Taking daily steps to keep beneficial bacteria in and harmful pathogens out—from only using antibiotics as needed to using protection during sex to avoiding douching—will be a great first line of defense.

And for the approximately 5-9% of women who suffer from recurring (at least 3 per year) vaginal infections, “just deal with it” hopefully won’t be the default advice for much longer.³⁷ As vaginal probiotics become more meticulously designed, some are starting to include L. crispatus bacterial strains that have been clinically shown to restore a healthy balance of vaginal microflora. 

In the future, vaginal microbiome transplants (which transfer vaginal fluid from a healthy host to a patient with dysbiosis), could also be a viable option for some.³⁸ A 2023 proof-of-concept case study transplanted vaginal fluid into a woman who suffered from vaginal irritation and a complicated pregnancy history.³⁹ Her VMB went from being 90% dominated by Gardnerella species to being 81.2% L. crispatus and 9% L. jensenii dominated after the procedure. Five months after the transplant, she became pregnant and went on to deliver a healthy baby at term.

Stories like this show that the vaginal microbiome is the next frontier of vaginal healthcare. It’s all within reach: increased prevention, highly personalized care, and more effective treatments for symptoms we used to think just “came with the territory” of having a vagina.

Here’s to entering a new era of exploration—this time, into the depths of the landscapes within.

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