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The seminal microbiome in health and disease


Owing to the fact that there are more microbial than human cells in our body and that humans contain more microbial than human genes, the microbiome has huge potential to influence human physiology, both in health and in disease. The use of next-generation sequencing technologies has helped to elucidate functional, quantitative and mechanistic aspects of the complex microorganism–host interactions that underlie human physiology and pathophysiology. The microbiome of semen is a field of increasing scientific interest, although this microbial niche is currently understudied compared with other areas of microbiome research. However, emerging evidence is beginning to indicate that the seminal microbiome has important implications for the reproductive health of men, the health of the couple and even the health of offspring, owing to transfer of microorganisms to the partner and offspring. As this field expands, further carefully designed and well-powered studies are required to unravel the true nature and role of the seminal microbiome.

Key points

  • Semen has a unique microbiome; however, its origin and function need to be further investigated in order to understand its role in health and disease.

  • Alterations in the bacterial composition of semen have been linked to a variety of disorders, including subinfertility and poor semen quality, prostatitis and HIV infection.

  • The seminal microbiome might influence a couple’s health and even that of their offspring, as well as affecting pregnancy outcomes.

  • When studying the male seminal microbiome, the partner’s reproductive tract microbiome and the sexual behaviours of both partners should also be considered.

  • Study of the seminal microbiome is still in its infancy, and further well-designed, large-cohort, functional studies are required.

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Fig. 1: Effects of the seminal microbiome on the male, the couple and their offspring.
Fig. 2: Population and lifestyle factors affecting the seminal microbiome.
Fig. 3: Bacterial communities found in the urogenital tract in males.


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S.A. is funded by the Spanish Ministry of Economy, Industry and Competitiveness (MINECO) and the European Regional Development Fund (FEDER): grants RYC-2016-21199 and ENDORE SAF2017-87526; Programa Operativo FEDER Andalucía (B-CTS-500-UGR18) and by the University of Granada Plan Propio de Investigación 2016 —Excellence actions: Unit of Excellence on Exercise and Health (UCEES) — and Plan Propio de Investigación 2018 — Programa Contratos-Puente, and the Junta de Andalucía, Consejería de Conocimiento, Investigación y Universidades, European Regional Development Funds (ref. SOMM17/6107/UGR). R.M. is funded by the Estonian Research Council (grant No. IUT34-19), the Estonian Ministry of Education and Research (grant No. KOGU-HUMB) and Enterprise Estonia (grant No. EU48695).

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A community of microorganisms present in a defined environment.

Next-generation sequencing

(NGS). Technique to detect microbial communities.


Transient microbial population that is readily eliminated.


Microorganisms that are present in particular diseased states, a transient population that contribute to disease.


‘Healthy’ bacterial residents that maintain homeostasis, a stable population.


The entire habitat that includes the microorganisms (bacteria, viruses, archaea, and lower and higher eukaryotes), their genomes and the surrounding environmental conditions, including the products of the microbiota and the host environment.

Seminal microbiome

The microbiome of the male ejaculate and reproductive tract.


Metabolic by-products of live (probiotic) bacteria.


Quantitative polymerase chain reaction (to detect specific microorganisms).

Decomplementary activity

Microbial inhibitor of complement.


The collection of microorganisms capable of metabolizing oestrogens.

Shannon Index

A measure of the richness and evenness in a given sample.


Whole set of nucleic acid methylation modifications in genome.


Whole set of messenger RNA molecules expressed from the genome.


Compounds in food that induce growth or activity of beneficial microorganisms.


Live bacteria and yeasts promoted as having various health benefits.


Food ingredients or dietary supplements combining probiotics and prebiotics in a form of synergism.

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Altmäe, S., Franasiak, J.M. & Mändar, R. The seminal microbiome in health and disease. Nat Rev Urol 16, 703–721 (2019).

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