How does the Microbiome Impact Fertility?

How does the Microbiome Impact Fertility?

The human body is a complex ecosystem, home to trillions of microorganisms collectively known as the microbiome. These microscopic inhabitants, including bacteria, viruses, fungi, and other microbes, play a crucial role in maintaining our health. Recent research has highlighted the significant impact of the microbiome on various aspects of human physiology, including fertility. 1

Understanding the Microbiome

The microbiome is a diverse community of microorganisms residing in specific sites of the body, each with unique characteristics and functions. Key microbiomes include:

  • Gut Microbiome: Located in the digestive tract, it aids in digestion, immune function, and the production of essential vitamins.
  • Oral Microbiome: Found in the mouth, it helps in digestion and protects against harmful pathogens.
  • Skin Microbiome: Located on the skin surface, it acts as a barrier against pathogens and helps in wound healing.
  • Breast Microbiome: Located in the breast tissue and ducts, it contributes to maintenance of healthy breast tissue by stimulating resident immune cells.  
  • Vaginal Microbiome: Found in the female reproductive tract, it plays a crucial role in protecting against infections and maintaining reproductive health.
  • Semen Microbiome: Present in male reproductive fluids, it influences sperm quality and fertility.


The Vaginal Microbiome and Fertility

The vaginal microbiome is a dynamic community predominantly composed of Lactobacillus species. These bacteria produce lactic acid, maintaining an acidic environment (pH 3.5-4.5) that protects against infections. The balance of this microbiome is crucial for reproductive health and fertility.2

Impact on Fertility

1. Protection Against Infections:
A healthy vaginal microbiome prevents the overgrowth of pathogenic bacteria and viruses, reducing the risk of infections such as bacterial vaginosis (BV) and sexually transmitted infections (STIs), both of which can negatively impact fertility.

2. Cervical Mucus Quality:
Lactobacilli influence the production and consistency of cervical mucus, which is essential for sperm survival and transport. Optimal mucus quality facilitates sperm motility and enhances the chances of successful fertilisation.

3. Embryo Implantation:
A balanced vaginal microbiome supports a healthy endometrial environment, crucial for embryo implantation. Disruptions in this microbiome can lead to conditions such as endometriosis and pelvic inflammatory disease (PID), adversely affecting fertility.

Research Insights

Studies have shown that women with a high abundance of Lactobacillus in their vaginal microbiome have better fertility outcomes compared to those with dysbiosis, an imbalance in the microbial community. Further, studies have shown that the vaginal microbiota can influence vulnerability to sexually transmitted infections, 4 and that it may play a role in outcomes of assisted reproductive technology (ART).5 The vaginal microbiota has also been reported to have a different composition in pregnant women who deliver preterm compared with those who do not.6

The Semen Microbiome and Fertility

The semen microbiome is less well-known but equally important. It comprises a variety of bacteria, with the dominant genera being Lactobacillus, Pseudomonas, and Prevotella. The composition of this microbiome can significantly affect sperm quality and male fertility.


Impact on Fertility

1. Sperm Quality:
The presence of beneficial bacteria such as Lactobacillus is associated with better sperm motility, morphology, and concentration. Conversely, pathogenic bacteria like Escherichia coli can cause sperm agglutination, reducing motility and fertilisation capability.

2. Inflammation and Immune Response:
An imbalanced semen microbiome can trigger inflammation and an adverse immune response, leading to conditions such as prostatitis, which can impair sperm function and decrease fertility.

3. Transmission to Partner:
The semen microbiome can influence the vaginal microbiome through sexual intercourse. A healthy semen microbiome helps maintain the partner's vaginal microbiome balance, promoting overall reproductive health.

Research Insights

Research published highlights that men with fertility issues often exhibit significant differences in their semen microbiome compared to fertile men. Advances in our understanding of the semen microbiome may contribute to potentially new therapeutic avenues for correcting impairments in sperm parameters and improving male fertility.3

The microbiome's impact on fertility is an emerging field of research, revealing that these tiny organisms play a vital role in reproductive health. A balanced vaginal and semen microbiome supports fertility by protecting against infections, ensuring optimal sperm function, and maintaining a conducive environment for conception and pregnancy. As research progresses, understanding and manipulating these microbiomes could offer new avenues for treating infertility and enhancing reproductive outcomes.



1. Dekaboruah, E., Suryavanshi, M., Chettri, D. et al. Human microbiome: an academic update on human body site specific surveillance and its possible role. Arch Microbiol 202, 2147–2167 (2020).

2. Krog, M. C., Madsen, M. E., Bliddal, S., Bashir, Z., Vexø, L. E., Hartwell, D., Hugerth, L. W., Fransson, E., Hamsten, M., Boulund, F., Wannerberger, K., Engstrand, L., Schuppe-Koistinen, I., & Nielsen, H. S. (2022). The microbiome in reproductive health: protocol for a systems biology approach using a prospective, observational study design. Human reproduction open, 2022(2), hoac015.

3. Osadchiy, V., Belarmino, A., Kianian, R. et al. Semen microbiota are dramatically altered in men with abnormal sperm parameters. Sci Rep 14, 1068 (2024).

4. van Houdt, R., Ma, B., Bruisten, S. M., Speksnijder, A. G. C. L., Ravel, J., & de Vries, H. J. C. (2018). Lactobacillus iners-dominated vaginal microbiota is associated with increased susceptibility to Chlamydia trachomatis infection in Dutch women: a case-control study. Sexually transmitted infections94(2), 117–123.

5. Koedooder, R., Singer, M., Schoenmakers, S., Savelkoul, P. H. M., Morré, S. A., de Jonge, J. D., Poort, L., Cuypers, W. J. S. S., Beckers, N. G. M., Broekmans, F. J. M., Cohlen, B. J., den Hartog, J. E., Fleischer, K., Lambalk, C. B., Smeenk, J. M. J. S., Budding, A. E., & Laven, J. S. E. (2019). The vaginal microbiome as a predictor for outcome of in vitro fertilization with or without intracytoplasmic sperm injection: a prospective study. Human reproduction (Oxford, England)34(6), 1042–1054.

6. Kindinger, L. M., Bennett, P. R., Lee, Y. S., Marchesi, J. R., Smith, A., Cacciatore, S., Holmes, E., Nicholson, J. K., Teoh, T. G., & MacIntyre, D. A. (2017). The interaction between vaginal microbiota, cervical length, and vaginal progesterone treatment for preterm birth risk. Microbiome5(1), 6.