The Vaginal Microbiome: Its Role in Conception and Fertility

Version For Professionals

The vaginal microbiome, a complex community of microorganisms, plays a critical role in reproductive health, particularly in the context of conception. Its composition and balance significantly influence the vaginal environment, which in turn affects sperm motility and viability. A healthy vaginal microbiome dominated by Lactobacillus species creates an optimal environment for sperm, facilitating successful fertilization. Conversely, dysbiosis, characterized by an overgrowth of pathogenic bacteria such as Gardnerella vaginalis, disrupts this delicate balance, potentially impeding conception.

Composition and Function of the Vaginal Microbiome

  1. Composition

The vaginal microbiome is predominantly composed of Lactobacillus species, particularly Lactobacillus crispatus, Lactobacillus jensenii, Lactobacillus gasseri, and Lactobacillus iners. These bacteria play a crucial role in maintaining an acidic vaginal environment (pH 3.5-4.5) through the production of lactic acid, which inhibits the growth of pathogenic microorganisms. In addition to lactobacilli, the vaginal microbiome includes anaerobic bacteria such as Gardnerella vaginalis, Atopobium vaginae, and various Bifidobacterium species, as well as fungi like Candida species and viruses.

  1. Function

The primary functions of the vaginal microbiome include:

Protection against Pathogens: Lactobacillus Species and Vaginal pH

Lactobacillus species are predominant in a healthy vaginal microbiome and are crucial for maintaining an acidic vaginal pH (approximately 3.5-4.5). They achieve this through several mechanisms:

  • Lactic Acid Production: Lactobacilli ferment glycogen, a polysaccharide stored in the vaginal epithelial cells, to produce lactic acid. This acidification is essential for creating a hostile environment for pathogenic microorganisms.
  • Hydrogen Peroxide Production: Certain Lactobacillus species, such as L. crispatus and L. jensenii, produce hydrogen peroxide, which further inhibits the growth of anaerobic bacteria and pathogens.
  • Bacteriocin Production: Lactobacilli secrete bacteriocins, which are antimicrobial peptides that target and inhibit the growth of competing bacterial species

Immune Modulation: The microbiome interacts with the host’s immune system, modulating inflammatory responses and maintaining mucosal immunity.

Reproductive Health: The microbiome influences vaginal health, affecting lubrication, pH balance, and the integrity of the vaginal epithelium, which are critical for fertility and healthy pregnancy outcomes. 

The Dynamics of the Vaginal Microbiome During the Menstrual Cycle

The vaginal microbiome is a dynamic ecosystem that undergoes significant changes throughout the menstrual cycle. These fluctuations are influenced by hormonal variations, particularly oestrogen and progesterone levels, which can alter the vaginal environment and, consequently, the composition and function of the microbiome. 

Each phase is characterized by distinct hormonal profiles that influence the vaginal microbiome in specific ways.

  1. Menstrual Phase
  • Hormonal Changes

During the menstrual phase, levels of oestrogen and progesterone are low as the endometrial lining sheds. This decrease in hormones creates a unique environment within the vagina.

  • Microbiome Dynamics

Lactobacillus Reduction: There is often a temporary decrease in Lactobacillus species due to the influx of menstrual blood, which raises vaginal ph. Lactobacilli thrive in an acidic environment, so a higher pH can reduce their abundance.

Increased Diversity: The reduction in Lactobacillus dominance can lead to a temporary increase in microbial diversity, including anaerobic bacteria such as Gardnerella vaginalis and Atopobium vaginae.

  • Infection Susceptibility: The menstrual phase may increase susceptibility to infections as the protective acidic environment is temporarily altered.
  1. Follicular Phase
  • Hormonal Changes

Oestrogen levels begin to rise during the follicular phase, preparing the body for ovulation and the potential for fertilization.

  • Microbiome Dynamics

Lactobacillus Recovery: As oestrogen levels increase, so does the production of glycogen in vaginal epithelial cells. Lactobacilli ferment glycogen to produce lactic acid, restoring the acidic pH and promoting Lactobacillus dominance. 

Stabilization: The vaginal microbiome stabilizes with Lactobacillus species regaining dominance, which helps maintain a protective environment against pathogens.

  1. Ovulatory Phase
  • Hormonal Changes

The ovulatory phase is marked by a peak in oestrogen and a surge in luteinizing hormone (LH), triggering ovulation.

  • Microbiome Dynamics

Enhanced Lactobacillus Activity: The high oestrogen levels further support Lactobacillus proliferation, ensuring an acidic environment conducive to sperm survival and motility.

Optimal Conditions for Conception: The vaginal microbiome is typically at its most stable and Lactobacillus-dominant state during ovulation, providing optimal conditions for fertilization.

  1. Luteal Phase
  • Hormonal Changes

After ovulation, progesterone levels rise while oestrogen levels decline, preparing the endometrium for potential implantation of a fertilized egg.

  • Microbiome Dynamics

Potential Dysbiosis: The rise in progesterone can alter vaginal secretions and pH, potentially leading to a slight dysbiosis or increase in microbial diversity.

Immune Modulation: Progesterone has immunomodulatory effects that can influence the microbiome by reducing local immune responses, which might allow for transient increases in non-Lactobacillus species.

Stabilization Toward Cycle End: As the luteal phase progresses and progesterone levels peak, the microbiome may stabilize again, although this can vary among individuals.

Effects of the Vaginal Microbiome on Fertility

The vaginal microbiome plays a pivotal role in conception by influencing the vaginal environment, which can affect sperm motility and viability. An optimal balance of Lactobacillus species maintains a low pH, which is conducive to sperm survival and motility. 

Importance for Sperm Survival and Motility

A low vaginal pH maintained by Lactobacillus species is conducive to sperm survival and motility for several reasons:

  • Protection Against Pathogens: The acidic environment inhibits the growth of pathogenic bacteria and fungi, reducing the risk of infections that could harm sperm or interfere with their motility.
  • Enhanced Sperm Motility: An optimal pH supports sperm motility, allowing sperm to navigate through the cervical mucus and reach the egg for fertilization.
  • Preservation of Sperm Viability: The acidic environment helps maintain the integrity of sperm membranes, protecting them from damage and enhancing their viability during their journey through the female reproductive tract.

Dysbiosis and Its Impact on Conception

Conversely, dysbiosis, characterized by an overgrowth of pathogenic bacteria such as Gardnerella vaginalis, can lead to an elevated vaginal pH, creating a hostile environment for sperm. 

Causes of Dysbiosis

Dysbiosis refers to an imbalance in the vaginal microbiome, where there is a decrease in beneficial Lactobacillus species and an overgrowth of pathogenic microorganisms. Several factors can contribute to dysbiosis:

  • Antibiotic Use: Antibiotics can indiscriminately kill both beneficial and harmful bacteria, leading to a reduction in Lactobacillus populations and an increase in pathogenic bacteria.
  • Hormonal Changes: Fluctuations in oestrogen and progesterone levels during the menstrual cycle, pregnancy, and menopause can affect glycogen availability and pH, impacting the microbial balance.
  • Lifestyle Factors: Poor diet, stress, smoking, and douching can disrupt the vaginal microbiome, leading to dysbiosis.
  • Sexual Activity: Unprotected sex and multiple sexual partners can introduce new bacteria, potentially disrupting the existing microbial balance.

Consequences of Dysbiosis on Vaginal Environment

Dysbiosis can significantly alter the vaginal environment, making it less favourable for sperm:

  • Elevated Vaginal pH: An overgrowth of pathogenic bacteria such as Gardnerella vaginalis can raise the vaginal ph. These bacteria produce enzymes that degrade protective mucus and proteins, leading to a less acidic environment.
  • Pathogen Overgrowth: An increase in pathogens like Gardnerella vaginalis, Atopobium vaginae, and other anaerobic bacteria can result in infections such as bacterial vaginosis (BV). These conditions create an inflammatory environment, producing substances like proteolytic enzymes and sialidases that degrade cervical mucus and disrupt sperm function.
  • Increased Inflammation: Dysbiosis can trigger an inflammatory response, leading to the production of cytokines and other inflammatory mediators. This inflammation can damage the vaginal and cervical tissues, creating a hostile environment for sperm.
  • Biofilm Formation: Pathogenic bacteria can form biofilms, which are protective matrices that harbour bacteria and make them more resistant to treatment. Biofilms can further disrupt the vaginal environment and hinder sperm motility and survival.

Implications for Fertility

Reduced Sperm Motility

The elevated pH and presence of pathogens associated with dysbiosis can reduce sperm motility. Sperm require an optimal pH to maintain their motility and the acidic environment maintained by Lactobacillus species supports this. Dysbiosis disrupts this balance, making it more difficult for sperm to move efficiently towards the egg.

Decreased Sperm Viability

Dysbiosis can lead to conditions that are detrimental to sperm viability. The presence of pathogens and the resulting inflammation can damage sperm membranes, reducing their lifespan and ability to fertilize the egg. The degradation of cervical mucus by enzymes produced by pathogenic bacteria further hampers sperm survival.

Increased Risk of Infections

Dysbiosis increases the risk of vaginal infections, such as bacterial vaginosis, which can have a direct negative impact on fertility. Infections can cause inflammation and damage to the reproductive tract, making it more difficult for sperm to reach and fertilize the egg. Moreover, certain infections can ascend to the upper reproductive tract, leading to conditions like pelvic inflammatory disease (PID), which can cause scarring and blockages in the fallopian tubes.

Implications for Assisted Reproductive Technologies (ART)

For couples undergoing assisted reproductive technologies (ART) such as in vitro fertilization (IVF), the state of the vaginal microbiome can also influence outcomes. Dysbiosis may reduce the success rates of ART by creating an unfavourable environment for embryo implantation. Addressing microbiome imbalances before ART procedures can potentially improve outcomes.

Diagnostic Testing for Vaginal Microbiome Imbalances

Standard Methods

  1. Microscopy: Microscopic examination of vaginal discharge can reveal the presence of clue cells (indicative of BV) and assess the overall composition of the microbiome.
  2. Culture Techniques: Traditional culture methods can identify and quantify specific bacteria and fungi present in the vaginal microbiome.

Advanced Methods

  1. PCR (Polymerase Chain Reaction): PCR-based methods can detect and quantify specific bacterial species, providing detailed insights into the microbiome composition.
  2. Next-Generation Sequencing (NGS): NGS allows for comprehensive profiling of the vaginal microbiome, identifying both known and novel microorganisms with high accuracy.
  3. 16S rRNA Gene Sequencing: This method targets the 16S ribosomal RNA gene, providing detailed taxonomic information on bacterial communities within the vaginal microbiome.

Treatment Approaches


Probiotics, particularly those containing Lactobacillus strains, have been shown to restore and maintain a healthy vaginal microbiome. Probiotic supplements can be administered orally or vaginally, promoting the growth of beneficial bacteria and reducing the prevalence of pathogenic species. Clinical studies have demonstrated the effectiveness of probiotics in preventing and treating BV, yeast infections, and improving overall vaginal health.

Antibiotics and Antifungals

In cases of severe dysbiosis or infections, antibiotics and antifungals are commonly prescribed. Metronidazole and clindamycin are frequently used to treat BV, while antifungal agents like fluconazole are used for Candida infections. However, these treatments can disrupt the natural balance of the microbiome, necessitating the use of probiotics to restore microbial equilibrium post-treatment.


Prebiotics are non-digestible carbohydrates that promote the growth of beneficial bacteria in the vaginal microbiome. They can be used in conjunction with probiotics to enhance their efficacy. Prebiotics like fructooligosaccharides and galactooligosaccharides support the growth of Lactobacillus species, helping to maintain a healthy vaginal environment.

Lifestyle and Dietary Modifications

Diet and lifestyle factors can significantly impact the vaginal microbiome. A balanced diet rich in fibre, fruits, and vegetables supports overall microbial health. Avoiding excessive use of antibiotics, practicing good hygiene, and reducing stress levels can also help maintain a healthy vaginal microbiome.