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Role of Vaginal Microbiome and Fertility

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Introduction

Our human body is covered with billions of micro-organisms. From the skin, nose, mouth, intestine, to the genital areas, we are covered with bacteria colonies which play pivotal impact on our overall health. It is increasingly known that a healthy microbiome over our genital region protects one against various infectious diseases including STDs.

In this article, we want to explore further the relationship of genital microbiome and fertility, potential long term effect of genital microbiome in conception- both naturally and in assisted reproductive treatments.

Healthy Vaginal Microbiome

A healthy vagina is predominantly covered with Lactobacilli spp bacteria. Lactobacilli spp produces lactic acid in the vaginal canal, keeping the pH in an acidic level, preventing bad bacteria, fungus or even viruses from thriving.

The healthy Lactobacilli spp vaginal flora serve functions as:

  • Protecting against bad micro-organisms
  • Maintain and control inflammation and immune response of the vagina tract
  • Facilitates reproductive process such as improve motility of the sperm, increase survival of the sperm, helps fertilization and implantation of embryos

Abnormal Vaginal Microbiome

The vaginal ecosystem can turn into a hostile environment with depletion of healthy Lactobacilli spp, making the pH of the vaginal canal higher and conducive for pathogens to grow. In an abnormal vaginal canal, the bacteria colonies are more diversified with the presence of bacterial-vaginosis-related bacteria (Gardnerella vaginalis), and fungus (Candida spp).

The alteration of the vaginal flora also leads to the loss of innate vaginal mucosal barrier, resulting in an unstable vagina susceptible to external insults such as infection and inflammation.

A diversified vaginal bacteria flora also predisposes one to form biofilm- which is a layer of diversified micro-organism colony that is resistant towards treatment and difficult to eradicate them.

What are the factors that can affect the vagina microbiome?

Vaginal microbiome can change due to

1. Hormonal fluctuation/ menstrual cycle

Changes of estrogen and progesterone levels can be associated with changes in the vaginal microbiome.

Hormonal Phase Vagina flora Health Impact
Follicular phase Lactobacillus levels getting more

Overall flora getting stable

Generally feeling well, minimal vaginal discharge
Ovulation phase Lactobacillus levels high

Stable flora

Reproductive environment is suitable for fertilization, ideal for sperm movement and survival
Luteal Phase Lactobacillus starts to deplete

Flora becomes more diversified

Noticeable heavier vaginal discharge, Susceptible to infection and inflammation
Menstruation Lactobacillus depletedMore alkaline pH

Flora diversified

Susceptible to infection and inflammation

2. External lifestyle factors

Unhealthy lifestyle such as chronic stress, smoking, poor dietary intake, certain intense exercises such as biking/ cycling, tight clothing can result in vaginal microbiome disruption. Also, medications such as antibiotics can also inadvertently disrupt the healthy vaginal flora by stripping off the good lactobacillus bacteria as well.

3. Infections/ STDs

Untreated STDs are known to cause persistent inflammation in the lower genital tract, resulting in disruption and displacement of the normal healthy vaginal flora. Overtime, one can develop permanent scarring of the reproductive organs.

4. Sexual intercourse 

Frequent unprotected intercourse, different and multiple sexual partner(s) tend to diversify the vaginal microbiome. This is due to changes of the microbiome pH, leading to depletion of healthy lactobacillus and increase the overgrowth of bad bacteria. Without the innate vaginal mucosal barrier protection, one is also susceptible to various STDs.

Healthy Uterus (Endometrium) Microbiome

The uterus is long believed to be a sterile, internal part of the human body. Increasing evidence has shown that the uterus has its own micro-ecosystem, and this is not a carry-over ecosystem from the vaginal microbiome.

Similar to vagina microenvironment, lactobacilli spp can be found in abundance in the uterus healthy lining. Contrary to vagina flora, the uterus normal flora also consists of non-lactobacilli bacteria such as bacteroides spppseudomonas sppacinetobacter spp and etc.

The uterus microbiome is now proven to play a vital role in the outcome of fertility. When there is a dysregulation of the ecosystem, the uterus has a significant reduction in number of lactobacilli spp and increase growth of bacterial-vaginosis-related bacteria. Overtime, the uterus mucosal lining that serves as a protective barrier can be impaired with increased risk of inflammation and infection.

A uterus with predominant lactobacilli spp has a higher success chance in natural conception and assisted reproductive treatments. Those with unhealthy uterus microbiome is associated with poorer reproductive outcome, higher risk of infertility, embryo implantation failure, miscarriages and other obstetric complications.

Impact of Abnormal Vaginal Microbiome on Fertility

Vaginal flora disruption is associated with poorer reproductive outcome.

In early part of fertilization or conception, the vaginal microbiome plays a vital role in sustaining the sperm and facilitating the sperm to reach the egg. In a less conducive vaginal microbiome, the sperm is unable to move and swim in the vaginal tract and it may also unable to survive long enough in the woman's genital tract due to an abnormal vaginal environment that is hostile, inflammatory and present of pathogens.

To further insult to the reproductive process, due to susceptibility and increase risk of infection in an abnormal vaginal microbiome, one can have irreversible genital tract/ tube scarring and damage, leading to difficult fertilization of the sperm and egg.

Surfacing medical evidence shows that the imbalance of vaginal flora is associated with pregnancy complications such as recurring miscarriages, failure of implantation, pre-termed labor, low birth rate and etc. In those seeking assisted reproductive treatments/ IVF, an abnormal vaginal micro-environment has lower success rate, with more risk of failure in embryo transfer and implantation.

How can we improve our vaginal microbiome?

Lifestyle

  • As the genital microbiome is a self-sustaining, self-cleaning organ, avoid douching or chemical washing of the vaginal canal.
  • Minimizing sexual partner(s) is imperative to avoid cross-contamination of male and female genital microbiome, or even contracting STDs.
  • Consider condom during intercourse as barrier contraception can reduce the risk of vaginal flora disruption.
  • Avoid physical activities, tight clothing that can disrupt the genital flora.

Medical Health

  • Long term vaginal and genital probiotics can be beneficial in maintaining a high level of lactobacilli spp in the genital tract, reducing risk of external factors that may disrupt the microbiome constituents.
  • Regular vaginal health testing is useful in detecting any abnormal flora, thereafter allowing the appropriate treatment to be delivered.
  • Regular STD testing is useful to pick up any concurrent infection(s) from partners that potentially can affect the normal vaginal flora.
  • Any underlying medical conditions such as hormonal imbalance or chronic conditions (diabetes) should be addressed in order to improve overall vaginal health.

Common Concern for Vaginal Checkup

One may be hesitant to see or discuss such concerns with your healthcare providers. The medical checkup is usually less apprehensive than we thought. Vaginal checkup with vaginal tests and STD tests can be performed at clinic settings. A sterile speculum device is carefully inserted into the vagina to open up the vagina canal. This is followed by a gentle swab test over the vaginal and cervical walls.

Over the years, reliable vaginal smear tests, cultures and PCR tests allow patients and health care physicians to determine accurately any underlying vaginal pathogens. Do consider exploring your vaginal health with your healthcare providers.

What have I learnt today?

  • The vagina and the uterus have innate microenvironment.
  • Genital microbiome can be tampered by various factors including hormone levels, stress, medication, STD infections and lifestyle reasons.
  • Understanding of our vaginal microbiome with vaginal swab screening can be useful in detecting any pathogens in the vagina and allow targeted individual antimicrobial therapy to be given to eradicate the pathogens.
  • Supplementary probiotics are encouraged to restore and maintain healthy vaginal-uterus microbiome, reduce risk of dysbiosis of the microsystem of the vagina.
  • Healthy genital microbiome promises long term benefit in fertility- both natural and assisted conception.

Contact DB Clinic

The vaginal microbiome plays an important role in fertility and overall reproductive health. If you would like to discuss this further, consultations are available at DB Clinic to help you discuss your concerns and possible care options.

References:

  1. Chen X, Sui Y, Gu J, Wang L, Sun N. The Implication of The Vaginal Microbiome in Female Infertility and Assisted Conception Outcomes. Genomics Proteomics Bioinformatics. 2025 May 5:qzaf042. doi: 10.1093/gpbjnl/qzaf042. Epub ahead of print. PMID: 40323322.
  2. Gullo G, Satullo M, Billone V, De Paola L, Petousis S, Kotlik Y, Margioula-Siarkou C, Perino A, Cucinella G. The Role of the Genital Tract Microbiome in Human Fertility: A Literature Review. J Clin Med. 2025 Apr 24;14(9):2923.
  3. Zhao H, Wang C, Narsing Rao MP, Rafiq M, Luo G, Li S, Kang Y. 2025. Effects of vaginal microbiota on in vitro fertilization outcomes in women with different infertility causes. Microbiol Spectr. Jan 2025;13:e01255-24.
  4. Günther V, Allahqoli L, Watrowski R, Maass N, Ackermann J, von Otte S, Alkatout I. Vaginal Microbiome in Reproductive Medicine. Diagnostics (Basel). 2022 Aug 12;12(8):1948.
  5. Venneri MA, Franceschini E, Sciarra F, Rosato E, D'Ettorre G, Lenzi A. Human genital tracts microbiota: dysbiosis crucial for infertility. J Endocrinol Invest. 2022 Jun;45(6):1151-1160.
  6. Vitale SG, Ferrari F, Ciebiera M, Zgliczyńska M, Rapisarda AMC, Vecchio GM, Pino A, Angelico G, Knafel A, Riemma G, De Franciscis P, Cianci S. The Role of Genital Tract Microbiome in Fertility: A Systematic Review. Int J Mol Sci. 2021 Dec 24;23(1):180.

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