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

What current science says about the microbiome’s role in fertility for those with endometriosis or adenomyosis—plus realistic, patient‑centered steps you can take now.

By Dr Steven Vasilev
A woman in a sunlit kitchen holds a jar of yogurt beside fermented foods while prenatal vitamins and an ovulation test rest on the counter, linked by a faint trail of stylized microbes.

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.


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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.

References

  1. Munyoki SK, Vukmer N, Rios JM, Kallen A, Jašarević E. From gut to gamete: how the microbiome influences fertility and preconception health. Microbiome. 2025. (Review/Commentary). DOI: 10.1186/s40168-025-02230-7

Quick Answers

Is an “endometriosis diet” evidence-based?

Yes and no. The evidence does support the idea that nutrition can influence pathways that matter in endometriosis—like inflammation, oxidative stress, hormone metabolism, and the microbiome—so diet can be a meaningful part of symptom support. What the research does not support (at least not yet) is a single, universally proven “endometriosis diet” that reliably treats the disease or works the same way for everyone.


Most of the strongest signals come from observational research, where higher overall diet quality and Mediterranean-style, anti-inflammatory patterns are associated with better reproductive health and lower likelihood of having endometriosis. That’s encouraging, but it isn’t the same as proof that changing your diet will prevent endometriosis, shrink lesions, or predictably improve pain or fertility for an individual. In our experience, nutrition tends to be most helpful when it’s tailored to your symptom pattern—especially if you have significant bloating, bowel symptoms, or IBS overlap.


If you’re trying to decide what’s worth your time, we recommend focusing on evidence-aligned, sustainable changes rather than long “forbidden food” lists or internet protocols that promise a cure. Our team integrates nutrition and lifestyle strategies into an overall endometriosis plan—so you’re not left experimenting endlessly, and you can evaluate what’s actually helping you.

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Why do endometriosis doctors focus so much on fertility?

Many clinicians focus on fertility because endometriosis can affect it through several pathways—not just “blocked tubes.” Disease can distort pelvic anatomy with adhesions, create an inflammatory environment that interferes with fertilization and implantation, and sometimes impact ovarian reserve (especially when endometriomas are involved). Fertility is also time-sensitive, so teams often raise it early to avoid surprises and to help patients make decisions that still keep future options open.


That said, fertility should never be the only lens. Endometriosis is a whole-body, quality-of-life disease—pain, bowel and bladder symptoms, fatigue, painful sex, and missed work or school are valid reasons to pursue evaluation and treatment whether or not pregnancy is a goal. In our practice, we center the plan on what matters to you—symptom relief, long-term function, and, if relevant, a thoughtful fertility strategy that fits your timeline. If you’re feeling dismissed or “reduced to your uterus,” reach out to schedule a consultation so we can map out an individualized plan that treats you as a whole person.

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Is endometriosis surgery only for fertility?

No—endometriosis surgery is not only for fertility. Excision surgery is often performed primarily to relieve pain and other symptoms, to restore normal anatomy when disease has scarred or “frozen” the pelvis, and to address endometriosis affecting organs like the bowel, bladder, ureters, or diaphragm. Surgery can also be the most definitive way to confirm the diagnosis, because endometriosis isn’t always visible on imaging.


Fertility can be an important goal, but it’s just one possible indication—and it’s not always the reason to operate. For example, removing an ovarian endometrioma before IVF is no longer considered “routine” unless there’s a clear reason such as severe pain, concerning imaging features, or a practical barrier to safe egg retrieval. In our practice, we focus on tailoring excision to what problem we’re trying to solve in your body—symptom relief, organ safety/function, diagnosis, fertility goals, or a combination—so you can make a decision that fits your timeline and priorities. If you’re unsure whether surgery makes sense in your situation, you can reach out to schedule a consultation with our team to review your symptoms, imaging, and goals and map out an individualized plan.

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Can foods worsen endometriosis symptoms?

Yes—certain foods can make endometriosis symptoms feel worse for some people, even though there isn’t one universal “endometriosis diet.” Endometriosis is a chronic inflammatory condition, and eating patterns that push inflammation higher (or trigger gut symptoms) can amplify pain, bloating, and fatigue. We also see that food sensitivities and GI overlap (like IBS-type symptoms) can make endometriosis flares feel more intense, even if the underlying lesions are unchanged.


Rather than assuming you need to cut out a long list of foods, we usually recommend looking for your patterns. Keeping a simple symptom-and-food log for a few weeks can help identify whether certain meals correlate with pelvic pain, bowel symptoms, or a flare around your cycle. Many patients do best focusing on overall diet quality—think anti-inflammatory, Mediterranean-style eating—while avoiding extremes and internet “forbidden foods” lists. If you’d like a structured, evidence-informed approach, our team can help you integrate nutrition and lifestyle strategies into a plan that also addresses the disease itself, not just symptom management.

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Can endometriosis cause inflammation-related weight gain?

Yes—there can be a connection, but it’s usually not as simple as “inflammation makes you gain fat.” Endometriosis is an inflammatory condition, and that inflammation can drive fluid shifts, pelvic and abdominal swelling, bowel slowing/constipation, and the classic waxing-and-waning “endo belly,” all of which can look and feel like weight gain even when body fat hasn’t changed. Pain, fatigue, and stress can also reduce activity or change appetite patterns, which can indirectly affect body composition over time.


What’s also emerging in research is a possible link between endometriosis and certain metabolic risk patterns in some people (like central waist changes and lipid markers). That doesn’t prove endometriosis directly causes metabolic changes—or that metabolic changes cause endometriosis—but it does support why some patients feel their body is harder to “regulate” while the disease is active. If weight changes, bloating, or a new shift in your waistline is part of your story, our team can help you sort out what’s most likely inflammation and GI distension versus longer-term metabolic or hormonal contributors, and build a plan that aligns with your symptoms and goals. If you’d like, you can reach out to schedule a consultation so we can evaluate the full picture and discuss treatment options, including excision and coordinated whole-person care.

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Have a question?

Dr. Steven Vasilev delivers best-in-class endometriosis guidance and a personalized treatment plan—built on evidence and your unique biology.


Led by Steven Vasilev, MD—an internationally recognized endometriosis specialist & MIGS surgeon—Lotus Endometriosis Institute is virtual-forward, with many patients traveling nationally for care. Clinical evaluation and surgical treatment are provided in California.

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