The Seminal Microbiome: How Bacteria Affect Fertility

By (embryologist).
Last Update: 24/03/2026

The study of male infertility has advanced significantly by analyzing not only the sperm, but also the environment in which they are found. New evidence supports that the male reproductive microbiome influences as a potentially critical component in reproductive health.

This research work has been carried out by the authors Sohei Kuribayashi, Noopur Naik, Aaron W. Miller, and Scott D. Lundy, belonging to the Department of Urology, Glickman Urological & Kidney Institute (Cleveland Clinic); the Cleveland Clinic Lerner College of Medicine of Case Western Reserve University School of Medicine; and the Department of Cardiovascular and Metabolic Sciences of the Cleveland Clinic in the United States.

The different sections of this article have been assembled into the following table of contents.

What is the seminal microbiome?

Due to the ease of obtaining it, semen has been used as a sample to characterize the male reproductive microbiome, in addition to the direct relevance it may have on reproductive outcomes.

Modern sequencing studies suggest that changes in these seminal microorganisms can contribute to inflammation, oxidative stress, and the alteration of spermatogenesis.

Overall, the male reproductive tract is thought to have low-abundance microbial communities, but which are biologically very active. Understanding their composition is essential to more fully evaluate male fertility and improve diagnostic approaches in fertility clinics.

Effect of bacteria on semen

The presence of certain bacteria in the male reproductive tract can be beneficial or detrimental to achieving a pregnancy. Analyzes of seminal samples reveal the following:

These discoveries open new doors in reproductive medicine, indicating that the bacterial environment is one of the many key factors for the sperm to successfully fertilize the egg.

Microbiome in assisted reproduction

The microbiome is not exclusive to a single member of the couple. There is evidence at the couple level showing a rapid and robust exchange of the microbiome, which can modify semen in short periods. This is of great importance in assisted reproduction treatments:

Taking comprehensive care of the bacterial health of both partners could increase success rates in achieving pregnancy.

Treatments to improve semen

Currently, clinical options are being investigated to modulate these bacteria of the male reproductive microbiome and favor fertility. Although larger trials are still needed, current results show some avenues for intervention:

Science continues to advance at a good pace to be able to integrate routine seminal microbiome analysis into fertility consultations in the future and make more precise therapeutic decisions.

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References

Kuribayashi S, Naik N, Miller AW, Lundy SD. Micromanagement: how the male reproductive microbiome shapes male fertility. Fertil Steril. 2026 Jan 27:S0015-0282(26)00048-8. doi: 10.1016/j.fertnstert.2026.01.019. Epub ahead of print. PMID: 41611115. (View)

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