Gut Testing: What’s Worth Doing - and What’s Not

If you’ve been struggling with bloating, irregular bowel habits, IBS-type symptoms or persistent digestive discomfort, it’s natural to start wondering:

Should I get a gut test?

A quick search online brings up everything from microbiome mapping and stool tests to SIBO breath testing, food sensitivity panels and parasite cleanses. It can be hard to know what’s evidence-based, what’s genuinely useful, and what might simply add more confusion (and expense).

In this blog, I’ll walk you through the most common gut tests people ask about, what they can and can’t tell us, and when it’s essential to involve your GP to rule out medical causes.

First: testing should match your symptoms

One of the biggest mistakes I see is people ordering tests before they’ve clarified what they’re trying to understand.

Gut symptoms can be driven by many factors, including:

• low stomach acid or low digestive enzyme output
• gut-brain axis dysregulation and stress physiology
• constipation and slow transit
• dysbiosis (microbial imbalance)
• post-infectious gut changes
• coeliac disease
• inflammatory bowel disease (IBD)
• medication effects (e.g., PPIs, antibiotics)

A sensible testing strategy should always begin with:

• a detailed symptom history
• diet and lifestyle review
• bowel habit assessment
• screening for red flag symptoms (more on this below)

For many people, we can make significant progress without extensive testing. But for others, testing can help us build a much more targeted plan.

Comprehensive stool and microbiome testing 

One of the most commonly used functional tests is comprehensive stool testing, often referred to as microbiome testing.

A test like Genova GI Effects Stool Test or GI Map can provide insight into:

• the balance of key bacterial groups
• markers linked to digestion and absorption
• indicators of inflammation
• microbial metabolites (such as markers linked to short-chain fatty acids)
• potential pathogens or opportunistic overgrowth patterns
• immune activity in the gut (e.g. secretory IgA)

When this type of test may be useful

In practice, comprehensive stool testing may be worth considering if:

• gut symptoms are long-standing or complex
• you’ve tried dietary changes but haven’t improved
• there are signs of dysbiosis or microbial imbalance
• bowel habits remain irregular despite foundational support

What it can’t do

Microbiome tests are not there to:

• diagnose IBS, IBD or coeliac disease
• replace medical investigations
• provide a complete picture of the entire gut microbiome (it’s a snapshot)
• give a guaranteed solution

However, they can be useful when interpreted in context, particularly when results are combined with symptom patterns, diet quality, lifestyle factors and health history.

SIBO breath testing

SIBO (small intestinal bacterial overgrowth) is one of the most talked-about causes of bloating online. SIBO occurs when bacteria that normally live in the large intestine overgrow in the small intestine.

The most common test is a breath test, typically measuring hydrogen and methane (and sometimes hydrogen sulphide depending on the test available).

When SIBO testing might be appropriate

SIBO testing may be worth considering if there is:

• significant bloating soon after meals
• excessive wind
• constipation or diarrhoea that doesn’t respond to standard support
• symptoms that noticeably worsen with fermentable fibres
• history of food poisoning, antibiotics or GI infections
• sluggish gut motility or chronic constipation

A note on limitations

SIBO is complex. Breath testing has limitations and results need careful interpretation. Not all bloating is SIBO, and it’s common for people to go through multiple restrictive protocols unnecessarily when the driver is something else entirely (for example constipation, stress patterns, or weak digestion).

Asking your GP to test for coeliac disease 

This is one of the most important points in the entire gut testing conversation:

If you have ongoing gut symptoms, especially diarrhoea, bloating, persistent fatigue, or nutrient deficiencies, it is sensible to rule out coeliac disease early.  NICE guidelines recommend coeliac disease testing in people with persistent unexplained GI symptoms consistent with IBS, among other presentations.

If you suspect coeliac disease, it’s important that you continue eating gluten before testing. If gluten is removed before the blood test, results may become falsely normal.

This is one reason I don’t recommend removing gluten “just in case” without a clear plan, especially if symptoms are significant.

Your GP can arrange coeliac screening blood tests. If positive (or strongly suspected), further medical follow-up is needed.

FIT testing via your GP (especially if there is blood in stool)

If you notice blood in your stool, it’s important to speak to your GP promptly.

Other red flag symptoms include:

• black/tarry stools
• unexplained weight loss
• persistent diarrhoea
• severe abdominal pain
• night-time bowel movements
• ongoing fatigue with low iron levels

A FIT test (faecal immunochemical test) may be used in primary care to help assess the need for further investigation when symptoms suggest possible bowel disease.

This is not something to self-manage with supplements or elimination diets.

Food sensitivity testing: is it worth it?

Food sensitivity testing is often one of the first things people try when gut symptoms don’t improve. It’s understandable, because it feels like it might give a clear list of foods to avoid.

However, this is an area where it’s easy to spend money and end up more confused (and more restricted) than before.

Why food sensitivity tests often “light up”

With ongoing gut issues, especially if the gut lining is irritated or intestinal permeability is increased (sometimes referred to as “leaky gut”), food sensitivity tests can come back with long lists of positives.

This can happen because the immune system is more reactive when the gut barrier is not functioning optimally. In that situation, results can “light up like a Christmas tree” and leave you feeling like you can’t eat anything at all.

The downside

If we remove lots of foods based on a test result without addressing the underlying gut issue, it can lead to:

• unnecessary restriction (which can impact microbiome diversity)
• increased anxiety around food
• missing the real drivers of symptoms such as constipation, dysbiosis, low digestion, or stress

In clinic, it’s usually better to:

1. support gut function first (digestion, motility, microbiome support, gut lining support)