Your IBS Diagnosis Might Be Missing the Point: SIBO, Endo, and the Gut-Hormone Axis

You were told you have IBS.

Maybe after a colonoscopy that came back clear. Maybe after months of symptom tracking and a referral to a gastroenterologist. Maybe just at a GP appointment where the investigation had run out of options.

The diagnosis felt like an answer. But over time, it started to feel like a full stop placed somewhere that should have been a comma.

Because the low-FODMAP diet helped for a while. And then it did not. Because the symptoms come back every month, in a pattern you could almost set your calendar to. Because you have a quiet suspicion that there is something else going on, and nobody has looked for it.

That suspicion is worth investigating.

What IBS actually is

IBS, or irritable bowel syndrome, is a functional gut diagnosis. It is defined by a combination of symptoms: abdominal pain, bloating, altered bowel habits (constipation, diarrhoea, or both) persisting for at least three months.

It is also, by definition, a diagnosis of exclusion. It is given when other causes have been ruled out.

The problem is that the list of what gets ruled out varies significantly depending on which practitioner you see and how comprehensive the workup is. Many women are diagnosed with IBS after standard investigations that do not include functional pathology, microbiome testing, SIBO breath testing, or a thorough hormonal assessment.

Which means the IBS diagnosis is sometimes accurate. And sometimes it is given because the right questions have not been asked yet.

The SIBO and endometriosis overlap

SIBO, small intestinal bacterial overgrowth, is a condition in which bacteria that should be present mainly in the large intestine migrate into and proliferate in the small intestine. The result is fermentation of foods in the wrong location, producing gas and leading to bloating, cramping, altered motility, and pain.

SIBO symptoms and IBS symptoms look almost identical. Bloating, distension, gas, unpredictable bowels, abdominal discomfort. This is why SIBO is significantly underdiagnosed in women who have received an IBS label.

Now add endometriosis.

Research has found higher rates of SIBO in women with endometriosis compared to those without. The proposed mechanisms include the inflammatory environment created by endo lesions affecting gut motility and intestinal permeability, immune dysregulation altering the gut microbiome, and adhesions or lesions near the bowel directly affecting function.

Women with endometriosis affecting the bowel, the rectovaginal septum, or the uterosacral ligaments are particularly likely to have significant gut symptoms. These symptoms are often attributed to IBS rather than to the endo itself.

The questions that change the picture

These are the questions I ask when a woman comes to me with an IBS diagnosis:

• Do your symptoms follow a cyclical pattern? Do they worsen before or during your period?

• Do you have pain with bowel movements, particularly during menstruation?

• Have you had a laparoscopy, or has endo been considered?

• Have you been tested for SIBO?

• Does your bloating tend to worsen throughout the day and improve overnight?

• Do you experience significant pain, not just discomfort, with gas or bloating?

Cyclical symptoms are a key differentiator. IBS symptoms can fluctuate, but symptoms that reliably worsen in a hormonal pattern suggest that hormones are a driver, not an incidental feature.

What standard investigation misses

A standard workup for IBS-type symptoms in New Zealand typically includes a colonoscopy or flexible sigmoidoscopy, coeliac serology, and basic blood work. Sometimes a gastric emptying study.

It rarely includes SIBO breath testing. It rarely includes comprehensive stool analysis. It rarely includes a hormonal assessment, a DUTCH test, EndoMAP, or a conversation about whether the pattern is cyclical.

These are not exotic tests. They are clinically relevant investigations that change the treatment approach. In my practice, I use them routinely when the picture suggests that something broader is being missed.

A different starting point

If you have an IBS diagnosis and a gut feeling (literally) that there is more to the story, you are worth investigating further.

That does not mean dismissing the IBS diagnosis. It means asking what is causing it, and whether there are contributing factors that have not been explored.

In some cases, addressing SIBO is the primary step. In others, treating the hormonal picture, particularly oestrogen metabolism and the gut-hormone axis, is what shifts the gut symptoms. In many cases, both need to be addressed, in the right order.

The order matters. Treating gut symptoms without understanding the underlying driver is why so many women cycle through protocols that work briefly and then stop.

Read more about the gut-hormone mechanism here → Why Your Gut Symptoms Follow Your Cycle

If you are ready to look at the full picture, the Endometriosis Clarity Quiz is a useful starting point.

Take the Endometriosis Clarity Quiz →Click here

Or book a Clarity Call to talk through your specific history.

Book a Clarity Call → Click here