Sperm microbiome revealed with RNA sequencing

A new study reports the first-ever detailed description of the human sperm microbiome, using newer RNA sequencing techniques that are capable of discriminating between sperm RNA and that of bacterial contamination or colonization.

The study, published in the Journal of Assisted Reproduction and Genetics in January 2020, shows that non-targeted RNA sequencing has the potential to identify the presence of infection, as well as to detect the presence of sperm. This could thus offer opportunities for better and more personalized care, during a routine evaluation of infertile people.

3D illustration of sperm. Rost9 / Shutterstock
3D illustration of sperm. Rost9 / Shutterstock

What is RNA sequencing?

RNA sequencing is a genetic technique in which the amount of RNA and the sequences are found using next-generation sequencing (NGS) techniques. It is basically an exploration of the transcriptome, the sum of all the RNA transcribed from the DNA, including mRNA, tRNA and rRNA. This helps to link the DNA information, or gene expression, with the actual proteins synthesized, that determine actual cell function. It shows the level of gene activity in the sample being analyzed – which genes are actually being transcribed, at what level, and at what period of the cell’s activity. This is of great help in finding out how the cell functions, what proteins become active at different stages and for different purposes, and some of the changes that accompany or precede disease conditions. There are a number of techniques based on RNA sequencing, including transcriptional profiling, SNP identification, RNA editing and differential analysis of gene expression.

RNA sequencing is superior to DNA sequencing in that it captures more closely the actual manner of expression of the genetic data. For instance, it could help understand what an unknown gene does by showing in which tissues it is active. It shows how a single gene can give rise to two or more different RNA sequences by means of mechanisms like alternative splicing, a discovery that is impossible with DNA sequencing. It can also show how RNA is processed to produce molecules with different functions, such as the addition of a polyadenyl chain or a 5’cap.

Originally based on Sanger sequencing, RNA sequencing was slow, costly and unreliable – though the Sanger method was an incredible innovation for its time. It is only with the development of newer technologies like NGS that RNA sequencing has become practically viable and extremely useful.

NGS is an umbrella term for multiple high-throughput sequencing technologies that can sequence DNA and RNA easily, accurately and inexpensively.

The study

The study was carried out in collaboration between the Wayne State University School of Medicine, the CReATe Fertility Centre and the University of Massachusetts Amherst.

The purpose of the study was to find out if non-targeted RNA sequencing was sensitive and specific enough to detect the presence of microbes, a task which current techniques that use targeted culturing are incapable of doing. The researchers took 85 samples of semen and extracted the RNA of the sperm. This was then sequenced using their enhanced technology. The RNA sequences that were not part of the human genome were matched to microbial genes. These reads were used to create a picture of the microbes found in each semen sample.

The findings

They found that all the samples showed similar levels of bacteria normally found in the male reproductive tract. These come from 11 genera, forming part of 4 phyla. Only one exception was found, which was quite different from all the other microbial reads.

Specifically, this specimen harbored a large number of bacteria of the species Streptococcus agalactiae and S. dysgalactiae. S. agalactiae is a bacterial species that is linked to many newborn infections, as well as infections occurring in pregnancy and after delivery. It is also the cause of many deaths among babies born prematurely. Moreover, it also causes serious infection in elderly adult patients. The presence of this bacteria in sperm is therefore of considerable concern.


At present, the presence of microbes in the male reproductive organs is diagnosed by culture techniques. However, most of the microbes typically found to infect this tract are fastidious in their culture requirements, meaning that they cannot be cultured under the usual laboratory conditions.

On the other hand, RNA sequencing is a much more reliable and now more widely available technique, which is also becoming more affordable by the day. The use of this technology is likely to provide a better idea of the bacteria and other microbes inhabiting the human body. The researchers say, “We show that non-targeted sequencing of human sperm RNA has the potential to provide a profile of micro-organisms (bacteria, viruses, archaea). This information was recovered from the data typically cast aside as part of routine nucleic acid sequencing.”

The clinical picture shows that infections with S. agalactiae are on the rise and are becoming more severe than before. Other microbes are also causing more frequent infections in newborns and adults. In this situation, says researcher Stephen Krawetz, “Non-targeted human sperm RNA sequencing data may, in addition to providing fertility status, prove useful as a diagnostic for microbial status."

Journal reference:

wanson, G.M., Moskovtsev, S., Librach, C. et al. What human sperm RNA-Seq tells us about the microbiome. Journal of Assisted Reproduction and Genetics, January 2020. https://doi.org/10.1007/s10815-019-01672-x. https://link.springer.com/article/10.1007%2Fs10815-019-01672-x

Dr. Liji Thomas

Written by

Dr. Liji Thomas

Dr. Liji Thomas is an OB-GYN, who graduated from the Government Medical College, University of Calicut, Kerala, in 2001. Liji practiced as a full-time consultant in obstetrics/gynecology in a private hospital for a few years following her graduation. She has counseled hundreds of patients facing issues from pregnancy-related problems and infertility, and has been in charge of over 2,000 deliveries, striving always to achieve a normal delivery rather than operative.


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