• The gut microbiome has a surprisingly strong impact on fertility in both women and men.
• For women, miscarriages and implantation failure can be linked to the microbiome.
• Conditions such as PMOS (formerly PCOS), endometriosis, and adenomyosis are also influenced by the microbiome.
• In men, reduced testosterone levels and poor sperm quality are frequently the consequence of a disrupted microbiome.
• Probiotics can be a sensible therapy in certain cases, but improvement can also be achieved through other measures.

The gut microbiome has increasingly been viewed as a cause—or at least a culprit—behind many different complaints for some time now. More and more often, the gut microbiome is also blamed for reduced fertility. But can bacteria in the gut really have an influence on your family planning journey?

What Throws the Microbiome Off Balance?

The gut microbiome can be influenced by a wide variety of causes. Poor diet, overuse of antibiotics, or obesity can particularly affect the microbiome (Barnea, E. R., et al., 2026). Regarding diet, attention should be paid to a high intake of dietary fiber, among other things. These are found in whole grain products, legumes, fruits, and vegetables. Naturally, the microbiome can also be affected by other factors such as illnesses.

Effects of the Microbiome on Female Fertility

The effects of the microbiome on female fertility are almost always underestimated. Contrary to what many expect, these bacteria are extremely important and affect the entire body—and thus also the reproductive system. The gut flora and reproductive system can influence each other and exist in constant interaction (Tahtouh Zaatar, M., et al., 2026).

When the microbiome is out of balance, ovulation dysfunction can occur. Furthermore, through various hormonal and metabolic mechanisms (mechanisms related to metabolism), egg quality can be reduced (Balagoni, S., et al., 2026).

The success rates of artificial insemination are also determined by the microbiome. If the microbiome causes problems, artificial insemination is also less likely to be successful (Tahtouh Zaatar, M., et al., 2026).

Chronic inflammation of the uterine lining—known as chronic endometritis—can also be promoted by a disrupted microbiome. A lack of Lactobacillus is particularly responsible for this (Hiratsuka, D., et al., 2026).

PMOS

Patients suffering from PMOS (formerly PCOS) particularly often show a disrupted microbiome that negatively affects fertility (Hiratsuka, D., et al., 2026). However, a disrupted microbiome also has a negative impact on PMOS itself. This makes it especially important for women with PMOS to focus on improving their microbiome. In addition to probiotics, dietary fiber and metformin are likely to be particularly beneficial for PMOS patients (Tahtouh Zaatar, M., et al., 2026).

As part of a study with patients preparing for insemination, experts were able to demonstrate that probiotic intake can positively influence the thickness of the endometrium. This may potentially facilitate implantation. The probiotics were taken over a period of 8 weeks (Behroozilak, T., et al., 2026).

Endometriosis and Adenomyosis

Both endometriosis and adenomyosis can be promoted by an imbalance in the microbiome (Balagoni, S., et al., 2026; Hiratsuka, D., et al., 2026). For these patients, scientists particularly recommend therapy with vaginal antibiotics or vaginal probiotics. Whether antibiotics or probiotics are the more suitable therapy should be decided individually in consultation with a doctor (Hiratsuka, D., et al., 2026).

Recurrent Implantation Failure (RIF), Recurrent Miscarriages (RPL), and the Microbiome

Unfortunately, an imbalanced gut flora can also have dramatic consequences regarding implantation and maintaining a pregnancy. A lack of Lactobacillus (sometimes called lactobacilli)—a specific genus of bacteria—appears to promote recurrent implantation failure (RIF). This deficiency is particularly serious when it can be detected not only in the gut microbiome but also in the vaginal microbiome (Hiratsuka, D., et al., 2026)

(Recurrent) miscarriages can also be caused by an imbalanced microbiome. Recurrent miscarriages or habitual abortions are defined as two or more miscarriages occurring before the 20th week. Worldwide, approximately 1–5% of couples are affected by recurrent miscarriages (RPL). Particularly, a lack of Lactobacillus and reduced diversity of the microbiome can be the cause of pregnancy loss. The background may involve increased inflammation or an imbalance in the immune system triggered by the disruption of the microbiome. The maternal-fetal immune tolerance can also be influenced by the disrupted microbiome. As a result, it is possible for the mother's body to reject the unborn child. Regarding recurrent miscarriages, however, not only the gut microbiome but also the vaginal and oral microbiome appear to play a decisive role (Bahia, W., et al., 2026).

Antibiotics and Female Fertility

Antibiotics are intended to kill bacteria that cause certain illnesses. Unfortunately, antibiotics also always kill health-promoting bacteria. This harm is accepted because the benefit of killing the harmful bacteria—in cases where antibiotics are prescribed—is considered greater than the reduction of beneficial bacteria. Despite the justification of this approach, the effects of antibiotic use on your fertility can unfortunately be serious: due to changes in the microbiome, there is a higher probability of infertility, miscarriages, and abnormalities in child development. Fortunately, your microbiome can (and should) be rebuilt and improved after a course of antibiotics. You therefore do not need to fear long-term damage. If you are still concerned, seek medical advice and question whether alternative treatment options exist (Alemu, B. K., et al., 2024).

Probiotics as a Miracle Cure?

Probiotics are increasingly touted as a miracle cure for improved fertility. However, in which cases the intake of probiotics is actually sensible has not yet been sufficiently researched (Tahtouh Zaatar, M., et al., 2026).

In some cases, however, scientists are increasingly convinced of the positive effects of taking probiotics. The benefits that probiotic intake can have for PMOS patients or women with endometriosis or adenomyosis are already described above.

There is consensus among experts that vaginal application of probiotics can be more effective for fertility patients than oral application (i.e., classically in the form of a tablet that is swallowed). This allows the probiotic to exert its effect directly where it is most needed (Tahtouh Zaatar, M., et al., 2026).

Particularly, the intake of Lactobacillus crispatus appears to positively influence fertility in many ways (Li, L., et al., 2026). Especially noteworthy is the positive effect on miscarriage rates (Barnea, E. R., et al., 2026). However, the study authors also point out that probiotics must meet certain requirements in order to positively influence fertility, and these criteria are often not (sufficiently) met (Li, L., et al., 2026).

Depending on the microbiome disruption, a combination of antibiotics and prebiotics may be necessary, for example in cases of recurrent implantation failure (Hiratsuka, D., et al., 2026).

Effects of the Microbiome on Male Fertility

Male fertility is also not unaffected by the microbiome. Increasingly, supposedly idiopathic infertility (i.e., unexplained infertility) can be explained by a disruption of the microbiome (Luo, C., et al., 2026). Through various changes in microbial metabolites, a disrupted microbiome can negatively affect your fertility. In addition, for example, the energy metabolism of the testes or the blood-testis barrier can be impaired by the microbiome (Pan, M., & O'Flaherty, C., 2026).

Oxidative stress also increases due to an altered microbiome, as does DNA fragmentation. DNA fragmentation refers to one or more breaks in the strands of genetic material in sperm (Kuribayashi, S., et al., 2026).

Sperm Quality

Particularly sperm quality, which is ultimately decisive for successful fertilization, is influenced by the state of the microbiome. For example, the concentration, motility (movement of sperm), and morphology (sperm shape) of sperm decrease due to a microbial disruption (Pan, M., & O'Flaherty, C., 2026). The number of sperm that are mobile at all is also reduced in men with a disrupted microbiome (Kuribayashi, S., et al., 2026).

Disruption of Testosterone Metabolism

Testosterone metabolism is responsible for the amount of available testosterone, which—like sperm quality—affects fertility. Through a disruption of the gut flora, endocrine functions are also influenced, resulting in less testosterone than usual being produced (Pan, M., & O'Flaherty, C., 2026). The Leydig cells, which play an important role in testosterone production, are also influenced by the microbiome (Shim, Y. H., et al., 2025).

Probiotics as Therapy

As part of an innovative study, it was found that additional probiotic intake improved testosterone synthesis (i.e., production) and the mitochondria of Leydig cells also functioned better. Mitochondria are often described as the powerhouses of cells (Shim, Y. H., et al., 2025).

Regarding the improvement of sperm quality, a change in diet is primarily described as a successful therapy (Pan, M., & O'Flaherty, C., 2026).

Ultimately, therefore, it should be decided individually whether and to what extent the intake of probiotics is sensible. However, a change in diet is clearly recommended.

Frequently Asked Questions on the Topic

What does the gut have to do with fertility?

The gut microbiome influences the entire body—including the reproductive system. The gut flora and reproductive organs exist in constant interaction. In women, a disrupted microbiome can impair ovulation, egg quality, and implantation. In men, sperm quality and testosterone levels are affected.

What causes the microbiome to become imbalanced?

Common causes include a low-fiber diet, excessive use of antibiotics, and obesity. Illnesses can also alter the gut flora. An increased intake of dietary fiber through whole grain products, legumes, fruits, and vegetables is a central lever.

Can a disrupted microbiome cause miscarriages?

Yes, a lack of Lactobacillus bacteria as well as reduced diversity of the microbiome can promote recurrent miscarriages (RPL). The underlying causes are often inflammation and a disrupted maternal-fetal immune tolerance, in which the maternal body can reject the embryo. Both the gut and the vaginal and oral microbiome are affected.

How does the microbiome affect sperm quality?

In men with a disrupted microbiome, the concentration, motility (movement), and form (morphology) of sperm decrease. Oxidative stress and DNA fragmentation—i.e., breaks in the genetic material of sperm—also increase. Infertility previously classified as "idiopathic" can often be explained by a microbial disruption.

Can the microbiome lower testosterone levels?

Yes, through the influence on endocrine functions and the Leydig cells, which are significantly involved in testosterone production, a disrupted microbiome can lead to reduced testosterone levels.

References

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