The Three Faces of SIBO: Why Hydrogen, Methane and Sulphide SIBO Need Completely Different Treatment

One of the most common reasons SIBO treatment doesn't work isn't that the person didn't try hard enough. It's that nobody worked out which type of SIBO they actually had.

SIBO isn't one condition wearing different masks. It's three genuinely different presentations, produced by different microbes, needing different diets, different antimicrobials and different timelines. Get the type wrong and you can do everything "right" and still not shift.

Hydrogen-dominant SIBO

This is the classic version, and usually the easiest to work with. It tends to show up as loose stools, diarrhoea and urgency, often several times a day, along with pronounced bloating. It's frequently post-infectious, tracing back to a bout of gastroenteritis, and it's the most straightforward type to track on testing, with hydrogen rising more than 20 parts per million above baseline within 90 minutes of a breath test.

The encouraging news is that hydrogen-dominant SIBO tends to respond well to a low FODMAP or SIBO biphasic diet. Left unaddressed, though, it can progress into methane-dominant SIBO over time, so it's worth taking seriously even when it feels manageable.

IMO, methane-dominant SIBO

Methane isn't actually made by bacteria at all. It's produced by a completely different type of organism called Archaea, which feed on the hydrogen that bacteria produce when they ferment carbohydrates. This is why it's now more accurately called IMO, intestinal methanogen overgrowth, rather than SIBO.

Methane slows the gut down. That means constipation, bloating and slow transit, sometimes with faecal impaction present even in people who go to the toilet "regularly." Here's the twist that catches people out: methane also creates conditions that favour histamine production, and histamine has the opposite effect, speeding transit up. So someone can have both processes cancelling each other out, look like they have completely normal bowel movements, and still be significantly constipated underneath. Most people with this pattern underestimate how backed up they really are.

Before reaching for antimicrobials with this type, it's worth actually confirming transit time, either with a charcoal capsule test or the classic sweetcorn test. A healthy transit time sits somewhere between 12 and 24 hours. Faster than that suggests malabsorption, slower suggests constipation, and either way, that number changes the treatment plan.

ISO, hydrogen sulphide SIBO

This is the type most likely to be missed, because standard breath tests don't measure it directly. It tends to show up as variable bowels, fatigue, brain fog and dizziness (hydrogen sulphide is a vasodilator, which is part of why it makes people feel so foggy and lightheaded), joint pain, skin redness, bad breath, gum issues, real trouble with alcohol, and a noticeable reaction to high-sulphur foods like eggs and broccoli. Rotten-egg smelling gas is a classic clue, though it isn't always present.

It tends to build up in people eating a lot of animal fat and protein, those with a genetic predisposition around how their body handles sulphur, and, somewhat counterintuitively, in people on very restrictive low-carb or ketogenic diets for a long stretch of time. The body actually needs some carbohydrate, and going without any for too long can itself tip someone into this pattern. On a standard test, this type often shows up as a flat, unremarkable hydrogen line, which is exactly why it gets waved through as "normal" when the symptoms say otherwise. A flat hydrogen reading with ongoing symptoms deserves a second look, not a clean bill of health.

Why this matters for your treatment

Each type needs a different combination of antimicrobials, a different diet emphasis, and a genuinely different timeline. Someone with hydrogen-dominant SIBO might see real change within a few weeks. Someone with methane-dominant SIBO is working against biofilm-forming organisms that are naturally more stubborn, and needs a plan that also addresses motility and stool movement, not antimicrobials alone. Treating all three the same way is one of the quickest routes to a frustrating, expensive round of supplements that doesn't move the needle.

If you recognise a pattern here but you've never actually had it confirmed which type you're dealing with, that's the missing piece. Testing is what turns a guess into a plan, and that's what I'll cover next.

If you'd rather skip the guesswork altogether, book a consultation and we'll work out exactly which pattern fits you.