The importance of the gut microbiome in male fertility

1 Jun

Research is suggesting that there is a growing issue of declining male fertility in the modern era, attributing it partly to factors like poor nutrition and lifestyle. Historically, male infertility was often overlooked, but it is now understood to account for a significant percentage of cases, with many causes remaining unknown. One thing I focus on in depth with my male fertility clients is their gut health - why? Because it really matters!

Recently I reviewed a 2025 paper named ‘Lower Semen Quality Among Men in the Modern Era-Is There a Role for Diet and the Microbiome?’ by Magoutas, K. et al. One of the main summaries from this paper was that male factors account for 40-50% of infertility cases. In half of these cases, the proximal cause for male infertility is unknown. Sperm contributes half of the nuclear DNA to the embryo, and its quality is known to impact fertilisation rates, embryo quality, pregnancy rates, risk of spontaneous miscarriage, de novo autosomal-dominant conditions, psychiatric and neurodevelopment conditions, and childhood diseases.

Recent studies have suggested that both the microenvironment of the testes and diet quality may play an important role in fertility; however, there is limited research on the combination of these factors. This review summarises current known causes of male infertility and then focuses on the potential roles for diet and the seminal microbiome. Future research in this area will inform dietary interventions and health advice for men with poor semen quality, potentially alleviating the need for costly and invasive assisted reproduction treatments and allowing men to take an active role in the fertility conversation which has historically focussed on women individually.

One thing that emerging research is starting to shed more light on is the bi-directional impact of the gut microbiome on the quality of the seminal microbiome. The composition of the seminal microbiome is an emerging area of research with increasing evidence suggesting specific associations with male fertility and semen quality parameters. While the testes were historically considered sterile, newer sequencing techniques have identified microbial DNA in testicular tissue and comprehensive microbial communities in semen. So how does the gut microbiome impact the seminal microbiome and therefore fertility outcomes?

DIET, WEIGHT + THE GUT mICROBIOME

Diet is a key driver in the health of the gut microbiome. High-fat diets have been associated with changes in the gut microbiome. Being overweight or obese, often linked to dietary habits, is strongly associated with impaired semen quality and increased sperm DNA fragmentation. This relationship is thought to be linked to inflammation and metabolic issues, and the gut microbiome is posited as a potential intermediary in this pathway. A poor-quality diet, characterized by high fat and low fiber/antioxidants, is proposed to potentially interact with the gut microbiome, leading to reduced sperm quality.

INFECTIONS

Genital tract infections account for approximately 15–20% of male infertility cases. The most frequent causative agents mentioned are Chlamydia trachomatis, Mycoplasma hominis, Mycoplasma genitalium, and Ureaplasma urealyticum. These infections, which are often asymptomatic and can be sexually transmitted, can directly damage the testes or seminiferous tubules or indirectly cause inflammation leading to tissue damage, scarring, or obstruction, ultimately impacting spermatogenesis. Typically the gut microbiome is the ‘master’ microbiome and can have a positive impact on the policing of these microbes that can negatively impact fertility. Improving your gut microbiome is imperative in reducing the negative impact that infections can have.

HORMONAL REGULATION

Gut bacteria influence testosterone levels. Certain microbes affect the metabolism of sex hormones, particularly testosterone and oestrogen, via the gut-liver axis. A disrupted gut microbiome may alter levels of SHBG, which regulates the availability of testosterone.

OXIDATIVE STRESS + INFLAMMATION

Imbalanced microbiome (dysbiosis) leads to increased gut permeability ("leaky gut"), allowing endotoxins (like LPS) into the bloodstream. This triggers chronic low-grade inflammation and oxidative stress, both of which are known to impair:

Sperm motility
Sperm morphology
DNA integrity

Nutrient absorption

The gut microbiota is essential for synthesizing and absorbing key nutrients for sperm production, such as:

Zinc (critical for sperm quality)
Folate (important for DNA synthesis)
Vitamin B12, selenium, and omega-3 fatty acid

Dysbiosis can lead to suboptimal nutrient absorption, affecting sperm development (spermatogenesis).

IMMUNE SYSTEM MODULATION

The gut influences the hypothalamic-pituitary-gonadal (HPG) axis, which regulates reproductive hormone signalling. Changes in microbial composition can affect neurotransmitters (like serotonin and dopamine), which in turn impact hormone balance and libido.

The gut microbiome trains and regulates the immune system. Gut dysbiosis can lead to an overactive immune system that may attack sperm or impair testicular function. A balanced immune response is necessary for:

Preventing anti-sperm antibodies
Maintaining testicular immune privilege

Gut-Friendly & Fertility-Supportive Foods

So what can you do to positively impact your gut microbiome to be supportive of your fertility? Prebiotic-Rich Foods are really beneficial to feed gut bacteria to improve microbiome diversity and support hormone balance. Prebiotic-rich foods include: jerusalem artichokes, chicory root, leeks, onions, garlic, asparagus, green bananas or slightly underripe plantains, oats, legumes (soaked/sprouted for easier digestion). Prebiotic foods feed Bifidobacteria and Akkermansia, linked to metabolic and hormonal health.

Polyphenol-rich foods are anti-inflammatory, antioxidant compounds that reduce oxidative stress in the gut and reproductive system. Polyphenol-rich foods include berries (especially blueberries, raspberries, blackcurrants), green tea, pomegranate, extra virgin olive oil, dark chocolate (min. 70%), herbs: rosemary, turmeric, oregano. These reduce systemic inflammation and protect sperm DNA.

Omega-3 rich foods are crucial for sperm membrane fluidity and anti-inflammatory action. Omega-3 rich foods include: fatty fish: sardines, salmon, mackerel; chia seeds, flaxseeds (freshly ground), walnuts. These improve sperm motility and morphology.

Fertility boosting nutrients that support spermatogenesis (production of sperm) and DNA integrity include zinc, selenium, vitamin B12 and folate. These nutrients require good gut function to be optimal so it’s important you include gut specific and supportive foods too (listed below). Food sources of these micronutrients include:

Zinc: Pumpkin seeds, oysters, beef, chickpeas
Selenium: Brazil nuts (1–2/day max), eggs
Vitamin B12: Eggs, fish, dairy, liver
Folate: Leafy greens, lentils, avocado

Probiotic rich + fermented foods help to enhance testosterone regulation, lower gut inflammation. They help populate the gut with beneficial bacteria and improve gut-immune function. Probiotic + fermented rich food sources include:

Kefir (goat or coconut milk-based if dairy-sensitive)
Sauerkraut, kimchi
Miso, tempeh
Natural yogurt (unsweetened, with live cultures)

LIFESTYLE TIPS TO MAXIMISE GUT + FERTILITY BENEFITS

We cannot ignore the fact that our lifestyles also positively or negatively impact gut health. Some things to focus on to improve your gut health in order to support your fertility include:

Daily movement: walking supports gut motility and sperm quality.
Prioritise sleep: Gut microbiome diversity is tied to circadian rhythms.
Stress reduction: High cortisol affects both microbiome balance and reproductive hormones.