The human body is home to trillions of microorganisms that coexist with us in a delicate balance. Among these, the vaginal microbiome plays a crucial role in maintaining a woman’s reproductive and overall health. 

The vaginal microbiota is a complex ecosystem primarily composed of Lactobacillus species, which help regulate pH, prevent infections, and support fertility. However, various factors—such as hormonal changes, lifestyle, and external influences—can alter this balance, leading to conditions like bacterial vaginosis, recurrent infections, and even implications for fertility and pregnancy outcomes.

Understanding the vaginal microbiome is essential not only for treating gynecological conditions but also for preventing them and promoting overall well-being.

Composition of the vaginal microbiome

In healthy women, the vaginal microbiome is primarily dominated by Lactobacillus species. These beneficial bacteria play a protective role by producing lactic acid, which maintains an acidic vaginal pH (between 3.8 and 4.5). This acidity creates an environment that inhibits the growth of pathogenic bacteria and fungi.

The five vaginal Community State Types (CST)

Scientific studies have classified the vaginal microbiota into five distinct community types, known as Community State Types (CSTs):

  • CST I – Dominated by Lactobacillus crispatus (associated with strong protection and stability)
  • CST II – Dominated by Lactobacillus gasseri
  • CST III – Dominated by Lactobacillus iners (less stable, can shift toward dysbiosis)
  • CST IV – Low levels of lactobacilli, high presence of Gardnerella vaginalis and anaerobic bacteria (linked to bacterial vaginosis)
  • CST V – Dominated by Lactobacillus jensenii

The presence or absence of lactobacilli significantly influences vaginal health. CST I and III are considered the most protective, while CST IV is associated with an increased risk of infections and gynecological disorders​.

Functions of Lactobacilli in the vaginal microbiome

Lactobacilli serve as the first line of defense against vaginal infections and play several critical roles:

  • pH Regulation: By producing lactic acid, they maintain an acidic vaginal environment, which prevents the overgrowth of harmful bacteria.
  • Production of Hydrogen Peroxide (H₂O₂): Some lactobacilli, such as Lactobacillus crispatus, synthesize H₂O₂, which has antimicrobial properties against pathogens like Gardnerella vaginalis and Escherichia coli.
  • Production of Bacteriocins: These are proteins with antibacterial activity that help control the growth of harmful microorganisms.
  • Biofilm Formation: Lactobacilli can form protective biofilms on vaginal epithelial cells, preventing the adhesion of pathogenic bacteria​.

The vaginal microbiome across life stages

The vaginal microbiome is not static; it evolves throughout a woman’s life in response to hormonal changes.

Childhood and adolescence

At birth, the vaginal microbiota is diverse and lacks dominant lactobacilli. However, with the onset of puberty and increased estrogen production, glycogen accumulates in vaginal epithelial cells, providing a substrate for lactobacilli to thrive.

Reproductive years

During the fertile years, the microbiome stabilizes, with Lactobacillus crispatus and Lactobacillus iners being the most common species. This stability is essential for:

  • Preventing bacterial and yeast infections
  • Supporting fertility and embryo implantation
  • Reducing the risk of sexually transmitted infections (STIs)​

Pregnancy

Pregnancy triggers hormonal and immune changes that increase the dominance of lactobacilli. This stabilization serves to protect against preterm birth and infections that could harm the fetus​.

Menopause

After menopause, the decline in estrogen reduces vaginal glycogen levels, leading to a decrease in lactobacilli and an increase in anaerobic bacteria such as Gardnerella vaginalis and Mobiluncus spp.. This change can cause symptoms like vaginal dryness, infections, and increased risk of bacterial vaginosis​.

Dysbiosis: when the balance is lost

Dysbiosis refers to an imbalance in the vaginal microbiome, where harmful bacteria outnumber beneficial lactobacilli. This condition is linked to:

  • Bacterial Vaginosis (BV): characterized by an overgrowth of anaerobic bacteria such as Gardnerella vaginalis, Atopobium vaginae, and Prevotella spp. Symptoms include unusual discharge, a fishy odor, and increased susceptibility to infections.
  • Yeast infections (Candidiasis): overgrowth of Candida albicans, often due to antibiotic use, stress, or hormonal fluctuations.
  • Urinary Tract Infections (UTIs): the vaginal and urinary microbiomes are closely linked, and dysbiosis can increase UTI risk​.

The Intestinal-Vaginal axis

The intestinal-vaginal axis refers to the intricate relationship between the gut and vaginal microbiomes. While these microbial ecosystems are distinct, they are closely connected through immune signaling, microbial translocation, and metabolic interactions. Increasing evidence suggests that gut health directly influences vaginal health, affecting susceptibility to infections, inflammation, and even reproductive outcomes.

Microbial migration: the gut as a reservoir for vaginal bacteria

One of the most significant links between the gut and vagina is the transfer of bacteria from the gastrointestinal (GI) tract to the vaginal and urinary tracts. This occurs primarily through:

  • Fecal-Perineal-vaginal transmission: the proximity of the anus to the vaginal opening allows for the migration of gut bacteria to the vaginal area. While this process helps maintain a natural reservoir of beneficial lactobacilli, it also increases the risk of pathogenic bacteria like Escherichia coli, Enterococcus spp., and Clostridium spp. colonizing the vagina and urinary tract, potentially leading to infections such as bacterial vaginosis (BV), urinary tract infections (UTIs), and yeast infections.
  • Oral probiotic influence: studies have shown that orally consumed probiotic strains, such as Lactobacillus rhamnosus and Lactobacillus reuteri, can colonize the gut and later migrate to the vagina, contributing to microbial balance​.

Gut dysbiosis and vaginal infections

When the gut microbiome is imbalanced (a state known as gut dysbiosis), it can negatively affect vaginal health. Several mechanisms explain this connection:

  • Inflammation and immune crosstalk: a disrupted gut microbiome can lead to chronic low-grade inflammation, which affects the immune defenses of the vaginal mucosa. This can make the vaginal environment more susceptible to infections, particularly bacterial vaginosis, yeast infections, and sexually transmitted infections (STIs).
  • Endotoxemia and vaginal health: dysbiosis in the gut can cause an increase in lipopolysaccharides (LPS), bacterial endotoxins that enter the bloodstream due to increased intestinal permeability (“leaky gut”). LPS-induced inflammation can alter vaginal immunity, reducing the protective effects of lactobacilli and making the vaginal microbiome more susceptible to pathogenic overgrowth.
  • Estrobolome regulation: the estrobolome, a subset of gut bacteria responsible for metabolizing estrogens, plays a significant role in regulating estrogen levels. Since estrogen directly affects vaginal health by promoting glycogen production (the main energy source for lactobacilli), a disrupted gut microbiome may lead to reduced estrogen metabolism, causing vaginal dryness, increased vaginal pH, and a higher risk of infections​.

Diet, the gut microbiome, and vaginal health

What we eat has a profound impact on both gut and vaginal health. A diet rich in processed foods, sugars, and unhealthy fats can promote inflammatory gut bacteria, whereas a fiber-rich, plant-based diet supports beneficial microbes that indirectly benefit the vaginal microbiome. Some dietary influences include:

  • Prebiotic-rich foods (fiber, polyphenols): support the growth of beneficial gut and vaginal lactobacilli.
  • Fermented foods (Yogurt, Kefir, Kimchi, Sauerkraut): provide probiotic strains that can migrate from the gut to the vagina.
  • High-Sugar diets: promote Candida overgrowth, increasing the risk of recurrent yeast infections.
  • Omega-3 fatty acids: help reduce inflammation and maintain mucosal immunity, benefiting both the gut and vaginal microbiome​.

The role of probiotics and the intestinal-vaginal axis

Since the gut serves as a primary reservoir for Lactobacillus species, maintaining a healthy gut microbiome through probiotics and prebiotics can have a direct positive impact on vaginal health. Clinical studies suggest that probiotics:

  • Restore vaginal lactobacilli levels: orally administered L. rhamnosus and L. reuteri can colonize the vagina and reduce the recurrence of BV and UTIs.
  • Modulate inflammation: probiotics help reduce systemic inflammation, which can otherwise weaken vaginal defenses.
  • Improve hormonal balance: by regulating estrogen metabolism via the estrobolome, probiotics can support vaginal health during menopause and pregnancy​.

Clinical implications: the gut as a therapeutic target for vaginal disorders

Given the strong connection between gut and vaginal health, treating gut dysbiosis could be a novel approach to managing recurrent vaginal infections. Some promising strategies include:

  • Probiotic and prebiotic therapy: supporting both gut and vaginal microbiomes.
  • Dietary interventions: reducing inflammatory foods and increasing gut-friendly nutrients.
  • Fecal microbiota transplant (FMT): some studies are exploring whether FMT could restore balance in cases of severe gut dysbiosis and vaginal disorders​

Given the importance of lactobacilli in vaginal health, probiotics (live beneficial bacteria) have gained attention as a strategy to restore balance. 

For example, probiotic species such as L. rhamnosus and L. reuteri have been shown to help restore a healthy vaginal microbiota. Clinical studies suggest that oral and vaginal specific probiotics strains may reduce  the recurrence of BV and UTIs.

A balanced microbiome is also crucial for successful embryo implantation and pregnancy​.

Challenges and future research

Although probiotics hold promise, research is ongoing to determine:

  • The most effective strains for specific conditions
  • The ideal dosage and delivery method (oral vs. vaginal)
  • The long-term impact on women’s health​

Conclusion

The vaginal microbiome is a dynamic and essential component of female health. It interacts with hormonal changes, immune function, and even gut bacteria. While the dominance of lactobacilli is a key factor in maintaining vaginal health, disruptions can lead to various infections and reproductive challenges. 

By understanding the complex interactions within this microbial ecosystem, we can develop better strategies—including probiotics, diet, and lifestyle interventions—to support women’s health across different life stages.