Search IconSearch
November 5, 2020/Genomic Medicine

Microbiome Reveals Clues to Idiopathic Male Infertility

Bacteria in gut and semen are different in fertile men


At this year’s American Society for Reproductive Medicine’s Virtual Congress, Cleveland Clinic researchers presented their groundbreaking findings about a new aspect of male infertility. They expressed hope that these findings will provide future treatment options for couples struggling with infertility.


Cleveland Clinic is a non-profit academic medical center. Advertising on our site helps support our mission. We do not endorse non-Cleveland Clinic products or services. Policy

“Male infertility causes an incredible amount of stress and anxiety for men,” says lead researcher Scott Lundy, MD, PhD, a urology resident at Cleveland Clinic’s Glickman Urological & Kidney Institute. “We need to remember that when couples are suffering from infertility, nearly half of the time they’re having trouble conceiving due to male factors. And for many of these men, we cannot even give them a reason as to why they’re infertile.”

A growing problem

Recent studies suggest that this problem may be growing. Despite extensive testing, more than half of all men who undergo traditional workups will have no identifiable cause for their infertility.

Despite increased interest in the human microbiome — the genetic material of all the microbes that live on and inside the human body — information on the microbiome in male infertility is lacking. Motivated by this gap in knowledge, Dr. Lundy and a team of researchers at Cleveland Clinic dug deeper.

“We decided to study whether the human genitourinary and gastrointestinal microbiomes are linked with male infertility,” says Sarah Vij, MD, Director of the Center for Male Fertility at Cleveland Clinic. “No other studies to date have looked into the role of the human gut in male reproductive health or explored potential pathways using metagenomics.”

Partnering with microbiome experts

Dr. Lundy approached Charis Eng, MD, PhD, Chair and Inaugural Director of the Genomic Medicine Institute at Cleveland Clinic, about working with her and the microbiome team in her lab. Dr. Eng’s team uses multidisciplinary approaches — genomic modifiers and the human microbiome — to identify therapy and prevention.

“With the help and mentorship of Dr. Eng, we were able to partner with experts who already understood how to analyze the human microbiome,” Dr. Lundy says.

Researching and analyzing bacterial diversity

The team enrolled 25 males with primary idiopathic infertility and compared them with 12 paternity-proven fertile males. Dr. Lundy and his colleagues gathered urine samples, rectal swabs and semen samples. Data and analysis were then sequenced using two approaches: 16S ribosomal RNA, which provides valuable bacterial species (taxonomic) information; and shotgun metagenomics, which allows researchers to evaluate bacterial functional capabilities more comprehensively. Startup company VastBiome assisted researchers with this approach.

“When we investigated the differences in the microbiome between fertile and infertile men, we learned the gut of infertile men included decreased amounts of the bacteria Anaerococcus and increased amounts of Collinsella,” Dr. Lundy explains. “However semen samples of infertile men contained decreased Collinsella and increased Aerococcus.”


To understand the effects of the taxonomic differences, researchers analyzed the metagenomics data and identified seven differentially expressed pathways.

SAM: a differentially expressed pathway

“The most differentially expressed pathway between fertile and infertile males was the S-adenosyl-L-methionine cycle, or SAM cycle, a finding which was confirmed in subanalysis of semen and urine samples independently,” says Dr. Lundy.

SAM is a common metabolite with established roles in methylation, oxidative stress and aminopropylation. It’s the main cellular methyl donor and is critical for the maintenance of the unique methylation patterns seen in spermatozoa. Irregularities in sperm DNA methylation are strongly associated with male infertility. SAM is also a regulator of oxidative stress via conversion to the antioxidant glutathione, which improves sperm motility in infertile men. Furthermore, SAM regulates synthesis of polyamines such as spermidine via the aminopropylation pathway, which plays a key role in spermatogenesis.

Dr. Lundy notes, “It’s not clear whether one or all of these mechanisms play a role in microbiome-mediated male infertility, but this data is nevertheless important and further studies are planned.”

Varicocele linked to differences in seminal microbiome

Researchers also tested the hypothesis that a clinical varicocele, a dilation of the testicular veins associated with infertility, is also associated with differences in the seminal microbiome. They compared semen samples of infertile men with or without a clinical varicocele and identified significant differences in pathway expression.

“Our hope moving forward is that this study forms the foundation for future studies of male infertility and men’s health,” says Dr. Lundy. “We hope this research gives a voice to men and couples dealing with infertility and delivers hope that a resolution is possible.”


Related Articles

Is the MTHFR Gene Mutation Associated With Thrombosis?

The relationship between MTHFR variants and thrombosis risk is a complex issue, but current evidence points to no association between the most common variants and an elevated risk

HVI_Kelley_4277155_Patient Procedure Shoot- First in Human Trial
October 27, 2023/Genomic Medicine
Cleveland Clinic Treats First Patient With Investigational Gene Therapy for Hypertrophic Cardiomyopathy

One-time infusion of adenovirus-based therapy is designed to restore heart muscle function

August 17, 2023/Genomic Medicine
Parkinson’s Disease Research in Women (Podcast)

Studying gender-specific health factors promises new insight into diagnosis, prognosis, treatment

23-NEU-3989309-CQD-Hero-Podcast-650×450 (1)
July 3, 2023/Genomic Medicine
Genetics of Parkinson’s Disease in Latino Populations (Podcast)

Consortium is uncovering risk factors that spur disease development in an understudied group

February 22, 2023/Genomic Medicine/Research
Determining Autism, Cancer Risk in Patients with PTEN Hamartoma Tumor Syndrome

Cleveland Clinic researchers receive $2 million grant from the National Institutes of Health

22-NEU-2638258 genetics_650x450
August 8, 2022/Genomic Medicine
The Case for a Precision Medicine Approach to Training Epilepsy Clinicians

New Cleveland Clinic fellowship fosters expertise in the genetics of epilepsy

21-URL-2361635 CQD 650×450
June 23, 2022/Genomic Medicine
Managing Refractory Hypocalcemia in an Asymptomatic Patient During Pregnancy

Renal genetic testing confirms diagnosis, guides management

April 6, 2022/Genomic Medicine
Prediction Model Aids in the Early Diagnosis of Dravet Syndrome

Integrates genetic and clinical data to distinguish from GEFS+ and milder epilepsies