From Gut to Gamete: What the Microbiome May Mean for Fertility in Endometriosis and Adenomyosis

For people living with endometriosis or adenomyosis, fertility concerns often feel layered and complex. Hormones, inflammation, pain, prior surgeries, medications, and immune dysfunction can all intersect—sometimes in ways that are difficult to fully explain. A growing area of research suggests that another system may also be part of this picture: the microbiome, the community of microbes living in and on the body.

A 2025 review published in Microbiome explores how microbial communities—particularly in the gut and reproductive tract—may influence fertility and preconception health. Importantly, the authors emphasize caution: much of the evidence is still early, and while associations are compelling, cause‑and‑effect relationships in humans have not yet been proven. For patients with endometriosis or adenomyosis, this research offers context rather than promises—but it may help explain why whole‑body approaches to care matter.

What is the microbiome—and why might it matter in endometriosis and adenomyosis?

The microbiome refers to trillions of bacteria, viruses, and fungi that live primarily in the gut, but also in the reproductive tract, skin, and other tissues. These microbes are not passive passengers. They actively produce metabolites and signaling molecules that influence:

• Immune regulation and inflammation
• Estrogen metabolism and hormonal balance
• Energy use and metabolic health

For patients with endometriosis or adenomyosis—conditions strongly linked to chronic inflammation, immune dysregulation, and estrogen‑dependent pathways—these microbiome‑mediated processes are particularly relevant. The review suggests that microbial signals may influence reproductive tissues during the preconception period, potentially affecting ovulation, implantation, and early pregnancy physiology.

That said, the authors stress that researchers do not yet have a complete mechanistic map showing exactly how microbial signals travel from the gut to the ovaries, uterus, or endometriotic lesions in humans. This remains an active area of investigation.

Distinct microbiome patterns have been observed in endometriosis

The review summarizes evidence that people with certain reproductive conditions may have distinct microbiome “signatures,” including those with:

• Endometriosis
• Polycystic ovary syndrome (PCOS)
• Primary ovarian insufficiency
• Recurrent pregnancy loss

For endometriosis patients, this aligns with earlier research suggesting alterations in both gut and reproductive‑tract microbiota. However, it is critical to interpret this carefully. A different microbiome does not mean the microbiome caused endometriosis or adenomyosis. Instead, it suggests that these conditions may be associated with systemic changes—including immune and inflammatory shifts—that also affect microbial ecosystems.

In other words, the microbiome may be part of the broader biological environment in which endometriosis exists, rather than a single root cause.

What animal studies suggest—and why human relevance is still uncertain

Much of the mechanistic insight in this field comes from animal models. The review highlights studies showing that disrupting the gut microbiome in animals can accelerate ovarian aging and impair reproductive function.

These findings are biologically intriguing, especially for patients concerned about diminished ovarian reserve or early fertility decline. However, the authors repeatedly caution against over‑extrapolating these results. Key limitations include:

• Animal reproductive physiology differs from humans
• Microbiome manipulations in animals are often extreme and artificial
• Fecal microbiota transplantation (FMT) studies in mice do not prove human causality

For patients, this means that while headlines about “fixing fertility by fixing the gut” may sound appealing, they often oversimplify what the science actually shows.

Diet: a practical lever that may matter more than supplements

One of the most relevant takeaways for patients with endometriosis or adenomyosis is the role of diet. According to the review, diet is the most direct and modifiable factor shaping microbiome composition and function.

Key points include:

• Dietary patterns can shift the microbiome within days
• High‑fiber diets support production of beneficial metabolites such as short‑chain fatty acids (SCFAs)
• Western‑style diets (high in ultra‑processed foods and saturated fats, low in fiber) are associated with microbiome disruption and reduced beneficial metabolites

Because inflammation plays a central role in endometriosis, these dietary effects may be particularly relevant—even though direct fertility benefits have not yet been proven in clinical trials.

Patient‑centered takeaway

Rather than focusing on calories or restrictive rules, the review supports emphasizing diet quality, especially in the months leading up to conception. For many patients, this may overlap with dietary strategies already used to help manage endometriosis‑related inflammation and gastrointestinal symptoms.

Antibiotics and preconception planning: why history matters

The review also discusses how broad‑spectrum antibiotics can significantly disrupt the gut microbiome and reduce microbial diversity. Some human studies have linked preconception antibiotic exposure with outcomes such as:

• Interactions with hormonal contraceptives
• Increased risk of infertility
• Miscarriage
• Certain congenital anomalies

The authors do not recommend avoiding antibiotics when medically necessary. Instead, they emphasize thoughtful use and awareness—especially for patients who have required repeated antibiotic courses, which is not uncommon in people with chronic pelvic pain or recurrent infections.

Patient‑centered takeaway

If you have endometriosis or adenomyosis and are considering pregnancy:

• Share your recent antibiotic history with your clinician
• Let your care team know if you are trying to conceive or plan to soon
• Ask whether timing or antibiotic choice matters in your specific situation

Do probiotics or microbiome treatments improve fertility in endometriosis?

At present, there is no strong evidence that probiotics or microbiome‑targeted treatments improve fertility outcomes, including IVF success. The review notes that in studied examples, microbiome interventions did not outperform placebo in reproductive endpoints.

This is especially important for endometriosis patients, who are often targeted by supplements and programs promising to “heal the gut to restore fertility.” While the biology is intriguing, the clinical data are not yet there.

Patient‑centered takeaway

If you are considering probiotics or microbiome‑focused fertility products:

• Be cautious of strong marketing claims
• Review ingredients with your clinician
• Prioritize interventions with clearer evidence while research continues

What you can reasonably do now—without overpromising

Based on this review, these steps are considered low‑risk and reasonable to discuss with your care team:

• Begin preconception planning early, including medication and nutrition review
• Emphasize fiber‑rich, minimally processed foods to support a healthier microbiome profile
• Limit ultra‑processed dietary patterns associated with microbiome disruption
• Review antibiotic history as part of fertility planning
• Approach microbiome “fixes” with healthy skepticism

These steps align with broader principles of endometriosis‑informed care, even as fertility‑specific microbiome research continues to evolve.

The bottom line for endometriosis and adenomyosis patients

The microbiome may represent one of the missing links connecting diet, immune balance, hormones, inflammation, and reproductive health—all areas deeply relevant to endometriosis and adenomyosis. The 2025 Microbiome review presents a thoughtful, measured message:

• Associations and animal data are compelling
• Human causality and effective treatments are not yet established
• Practical focus should remain on evidence‑based care, diet quality, and informed medication use

For patients, this research does not offer a quick fix—but it reinforces the importance of whole‑body, personalized approaches to fertility and reproductive health.