SIBO Testing Explained: What Breath Tests and Stool Tests Actually Tell You

A test result isn't a verdict. It's one piece of information in a conversation, and understanding what each test is actually designed to look for changes how you read your own results.

Breath testing: the first port of call

If SIBO is suspected, a breath test is usually where things start. You drink a sugar solution, either lactulose or glucose, and breathe into a device at intervals to measure hydrogen and methane (and, on some devices, hydrogen sulphide too).

The sugar you're given matters. Lactulose isn't absorbed by the body, so it travels the full length of the small intestine, which means it can pick up overgrowth further along. Glucose, on the other hand, is absorbed early, so it's more accurate for overgrowth near the top of the small intestine but can miss anything further down. Neither one is simply "better," they're looking in different places.

Preparation matters more than people expect. A low-fermentable diet for 24 hours beforehand, an overnight fast, and avoiding smoking or exercise right before the test all affect the result. Methane in particular is slow to appear, sometimes taking up to three hours, so if it shows up at any point during the test, that's meaningful on its own, you don't need to see it rise further.

One detail worth knowing if you've ever been told your test was "normal": a flat, low hydrogen reading in someone who still has real symptoms isn't automatically a clean result. It can point towards hydrogen sulphide SIBO instead, which standard two-gas tests aren't built to catch. If that's your situation, a four-gas test that specifically measures hydrogen sulphide is worth asking about.

Stool testing: a different job entirely

This is where a lot of confusion creeps in. Stool testing isn't actually validated as a way to diagnose SIBO itself, it's not designed to tell you whether bacteria have overgrown in your small intestine. What it's genuinely useful for is building a picture of your wider gut terrain, the underlying factors that may have allowed the overgrowth to happen or that are keeping it going.

There are two quite different technologies behind most stool tests, and knowing the difference helps make sense of results that seem to disagree with each other. One type of test (qPCR, such as GI-MAP) is highly targeted. It looks for a specific, pre-selected list of organisms and gives you an absolute count of how much of each one is present. It's very sensitive for things like H. pylori, Blastocystis, antibiotic resistance markers and dysbiotic overgrowths, but it can only ever report on what it was built to look for.

The other type (shotgun metagenomics, such as Microba's Microbiome Explorer) sequences all the DNA in the sample and reports back proportions, what percentage of the total microbial community each organism makes up. Because it isn't limited to a preset list, it can also report on functional capacity that a targeted test simply can't see: whether you have enough butyrate-producing or GABA-producing microbes, or whether histamine-producing microbes are elevated. Neither test is complete on its own. They're genuinely complementary rather than competing.

This is also why two stool tests done a few months apart can come back looking different, and why that isn't automatically a problem. If real dietary or supplement changes happened between the two tests, the picture is genuinely allowed to have shifted. A single elevated marker, especially something like zonulin (a common leaky gut marker), is worth treating as a prompt for more investigation rather than an instant diagnosis, particularly if a second test doesn't confirm it.

Putting it together

A sensible approach usually looks like this: start with breath testing for classic bloating and altered bowels. If methane and constipation seem to be the picture, lean into methane-specific testing. If sulphur sensitivity is suspected, ask about a four-gas test. If symptoms started after a stomach bug, IBS-Smart alongside breath testing can confirm the post-infectious mechanism. And if you've already had a "clear" breath test but you're still not right, a comprehensive stool test can pick up the terrain issues a breath test was never designed to find.

None of this needs to be worked out alone. If you want a testing plan built around your specific symptoms rather than a generic panel, book a consultation and we'll map it out together.