Bloating, diarrhoea, constipation, and abdominal discomfort can all have very different causes. Unfortunately, there isn’t a single test you can take to identify the underlying cause.

Most tests for gut health look for specific markers to understand what’s going wrong. They’re trying to answer one of four questions:

• Who is living in the gut?

• Where and how is fermentation occurring?

• Is the gut barrier functioning normally?

• Is inflammation present?

No single test answers all four questions. Depending on your symptoms, either a single test or a combination of tests is needed to make a diagnosis. But what’s the best gut health test? How does a gut microbiome test compare to other tests? And when is each test recommended? Find out below.

A Stool Test Is Not One Specific Test

The term “stool test” is often used as a catch-all for several different tests. It refers to what’s being collected, not what is being measured.

For example, both microbiome sequencing and faecal calprotectin use stool samples but answer completely different questions. Other stool tests may investigate infection, digestive function, or blood.

Because of this difference, it’s important to understand why your doctor is recommending a specific test, not just what they’re asking you to provide.

Gut Health Tests Compared

What Does a Gut Microbiome Test Show?

A gut microbiome test sequences microbial genetic material found in the stool. It can identify the types and relative abundance of microorganisms present.

That’s important because low diversity or the overgrowth of a particular species can cause symptoms like bloating, diarrhoea, or flatulence. However, it cannot independently diagnose SIBO (small intestine bacterial overgrowth) or prove that symptoms are caused by a particular species.

What Does a Breath Test Show?

Certain microbes produce hydrogen, methane, and or hydrogen sulphide when they ferment carbohydrates. These gases enter the bloodstream and are eventually exhaled.

That means they can be measured in your breath.

Glucose or lactulose breath testing is used specifically when SIBO is suspected. Other substrates can investigate lactose or fructose malabsorption. However, without a gut microbiome test, it’s impossible to know the specific gut microbes behind the overgrowth.

What Does a Gut Permeability Test Show?

The gut lining prevents the harmful microbes and molecules in the gut from entering the bloodstream. It works as a selective barrier that absorbs nutrients while limiting the passage of unwanted materials.

Permeability tests assess how readily specific probe substances or markers cross the barrier. If the barrier is too “leaky,” it could explain bloating, inflammation, and other symptoms. An abnormal result does not explain all symptoms, however.

What Does a Faecal Calprotectin Test Show?

Calprotectin is released by inflammatory cells and can be measured in the stool. It’s primarily a test to confirm gut inflammation and can help diagnose conditions like inflammatory bowel disease.

Unfortunately, the test is not diagnostic and only helps point doctors in the right direction.

Which Is the Best Gut Health Test?

There is no single best gut health test. The right choice depends on what you are trying to discover.

A gut microbiome test shows which microorganisms are present and their relative abundance. Breath testing investigates fermentation and may help identify SIBO or carbohydrate malabsorption.

A permeability test examines how well the gut barrier is formed, while faecal calprotectin checks for intestinal inflammation.

Because these tests answer different questions, the most comprehensive option is not automatically the most useful. Your symptoms, medical history, and suspected condition should guide the decision, ideally with advice from a clinician experienced in digestive testing services.

Book a Gut Health Check in the UK

If you’re struggling with symptoms like bloating, diarrhoea, constipation, or abdominal discomfort, getting your gut tested is the best first step. Our team can help advise you on the best gut health test based on your symptoms and medical history.

The Functional Gut Clinic offers a full range of gut health tests. We’re the UK’s first fully integrated full-spectrum microbiome clinic. Learn more about our testing options and take control of your health.

Check out the next article: Gut Health for Athletes and Regular Exercisers