The Gut-Endo Connection: When IBS Is Actually Endometriosis

I spent three years being told I had IBS. Three years of elimination diets, FODMAP protocols, and a GI specialist who was genuinely kind but fundamentally looking at the wrong patient. The bloating, the urgency, the unpredictable cramping — it was all endometriosis. My gut wasn't broken. My gut was being tortured by lesions in my peritoneum.

This is so common I almost don't know where to start. If I had to guess, I'd say 60–70% of the endo patients I've worked with spent years being diagnosed with IBS before someone asked the right question. Not because gastroenterologists are incompetent — they're not — but because endometriosis masquerades as a digestive disease. And the mechanisms are so clever, so interconnected, that you can't actually understand your gut symptoms without understanding your endometriosis.

The Estrobolome: Estrogen's Recycling Program

Let me introduce you to your estrobolome. That's your gut bacteria, specifically ones that produce an enzyme called beta-glucuronidase. This enzyme's job is deconjugated estrogen — meaning it breaks down estrogen that your liver already tried to clear out of your body. Your liver packages estrogen up, sends it to the gut, and hopes you'll poop it out. But if you have too many beta-glucuronidase-producing bacteria, those bacteria say, "Nope," and recycle that estrogen straight back into your bloodstream.

This is called the estrobolome, and in one study, it was significantly altered in people with endometriosis.

Think of it like a landfill where someone keeps rescuing the garbage and putting it back on the truck. Your body is trying to get rid of used estrogen. Your gut bacteria are bringing it back. And that recycled estrogen fuels endometriosis growth. This is why endo patients often don't feel better with hormonal suppression alone — the disease is feeding itself through its own biological pathways.

SIBO and the Intestinal Permeability Problem

Here's what keeps me up at night: in one study, 91.9% of endometriosis patients tested positive for SIBO (small intestinal bacterial overgrowth). SIBO isn't "just" an endo symptom — it's a mechanism that makes endo worse.

SIBO creates inflammation in your small intestine. That inflammation damages the intestinal barrier. A damaged barrier means molecules that shouldn't cross into your bloodstream start crossing anyway — bacterial lipopolysaccharides, partially digested proteins, antigens. This is called "leaky gut," and it's not pseudoscience. It's a measurable physiological state.

Now your immune system is in constant alert mode. There are invaders. The alarms go off. Cytokines flood your system. And that systemic inflammation? That's the environment where endometriosis thrives.

So the cascade looks like this: dysbiosis → SIBO → leaky gut → systemic inflammation → endo progression. It's not linear. It's a loop. And conventional IBS treatment — even good IBS treatment — doesn't interrupt this loop if endo is the root cause.

The Gut-Immune Axis: Your Defense System Under Siege

Your gut does something most people don't realize: it's your largest immune organ. About 70% of your immune system lives in your gut-associated lymphoid tissue (GALT). This is where your body learns what's dangerous and what's safe.

When you have endo, that boundary between the "safe" and the "dangerous" gets blurry. Endometrial tissue where it shouldn't be is triggering your immune system. That triggers inflammation. That changes which bacteria can thrive in your gut. Those bacteria further alter your gut lining and immune tolerance. It's a bidirectional conversation, and both sides are sending panic signals.

One study found that people with endometriosis have altered immune profiles that persist in the gut microbiome. This isn't about rebalancing bacteria with the right probiotic. This is about addressing the inflammatory environment that's selecting for dysbiotic bacteria in the first place.

Why Your IBS Diagnosis Masked Your Endo

The reason this matters clinically is this: if your provider is only treating the gut symptoms, you're treating the downstream consequence, not the upstream cause. You can follow a pristine FODMAP diet and still have endo. You can take rifaxomicin for SIBO and feel better for three months, then relapse, because the estrogen-driven inflammation that created the dysbiosis is still there.

I'm not saying dietary modifications are useless. I'm saying they're incomplete. It's like trying to bail water out of a boat while someone's still poking holes in the hull.

And — this is important — some of your gut symptoms might actually be from endo directly. Lesions on your sigmoid colon, your rectum, your small bowel. Those cause urgency, cramping, pain with bowel movements. That's not IBS. That's endometriosis of the gut. Your gastroenterologist's colonoscopy might not even visualize it if it's in the submucosa.

What to Ask Your Provider

If you have IBS symptoms and haven't been evaluated for endometriosis: Ask your gynecologist or primary care provider specifically about endo. Ask if your bowel symptoms cycle with your menstrual cycle. Ask if they're worse during your period or in certain phases of your cycle.

If you have a confirmed endo diagnosis and are being treated for IBS: Ask your GI provider whether they've coordinated with your gynecologist about your endo location. Ask if your gut symptoms are cyclical. If they are, that's a clue that hormones and endo are involved.

Before you try another elimination diet: Ask for a baseline: inflammatory markers (CRP, ESR), a fecal calprotectin if IBS-D is suspected, and be honest about symptom timing. You might not have IBS. You might have endo affecting your gut.

The work of addressing the gut-endo connection requires coordination. Your gynecologist, your gastroenterologist, and you all need to be looking at the same patient — not the same symptoms in isolation. That's rare, I know. But it's the only way to actually interrupt the cycle.

Heather Yoshimura, MSN, AGNP-BC

UCSF-trained nurse practitioner specializing in endometriosis. Founder of Luteal Health. Author of The Endo Dilemma.