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What can a stool or microbiome test really tell me?
It depends on the test. Standard stool tests reliably detect infection, inflammation, hidden bleeding and poor digestion of fat. Microbiome sequencing shows which bacteria are present in your gut, but it cannot yet diagnose a disease or prescribe a diet by itself. I use both as pieces of a larger picture, alongside your history and examination.
In short
- Stool tests answer specific questions well: is there an infection, inflammation or bleeding?
- A stool inflammation marker helps to tell inflammatory bowel disease from IBS.
- A stool test for hidden blood is a screening test for bowel cancer. A positive result needs a colonoscopy.
- Microbiome reports describe which bacteria are present. There is no agreed “healthy” profile yet, so they are interpreted with care.
- A test is worth doing when its result would change the plan.
Which stool test answers which question?
| Test | The question it answers |
|---|---|
| Microscopy, culture and DNA-based infection panels | Is there an infection or a parasite? |
| Faecal calprotectin | Is the bowel inflamed? A normal result makes inflammatory bowel disease unlikely. |
| Test for hidden blood (FIT) | Is there bleeding too small to see? Used to screen for polyps and bowel cancer. |
| H. pylori stool antigen | Is this stomach infection present, and has treatment cleared it? |
| Faecal elastase | Is the pancreas making enough digestive enzymes? |
| Microbiome sequencing | Which bacteria are present, and in what proportions? |
The first five are well established and are used in gastroenterology clinics everywhere.
What does a microbiome test measure?
The gut holds trillions of bacteria, roughly as many as there are human cells in the body. A microbiome test reads the genetic material in a stool sample and lists the bacteria it finds, usually with a diversity score and a comparison against a reference group.
How should a microbiome report be read?
There is no single healthy pattern
Healthy people differ widely from one another. Diet, region, age and medicines all shape the result.
It is a snapshot
The mix of bacteria shifts from week to week, and after an infection, antibiotics or a change in diet.
Laboratories differ
The same sample can give different results at different laboratories, because their methods and reference groups differ.
Association is not cause
Finding less of a particular bacterium in people with a condition does not show that it caused the condition, or that replacing it will help.
For these reasons a microbiome report does not diagnose disease, and it should not be used alone to choose a probiotic or a diet.
When do I find it useful?
In selected patients with long-standing symptoms, after standard tests are complete. Very low diversity after repeated courses of antibiotics, an overgrowth of particular organisms, or markers of poor digestion can support what the history already suggests and help to set priorities. I read it with the person in front of me, never on its own.
Microbiome testing is available through my clinic. It starts with a consultation, so that the right test is chosen and the report is read alongside your history. See gut microbiome testing.
What should I ask before paying for a test?
- What question will this test answer?
- Would the result change my treatment?
- Is there a simpler, validated test for the same question?
- Who will interpret it, together with my history?
Questions patients ask me
Can a stool test diagnose IBS?
No. IBS is diagnosed from its pattern of symptoms. Stool tests are used to rule out conditions that look like it, such as infection and inflammatory bowel disease.
Should I have a microbiome test to choose a probiotic?
It is not reliable for that purpose at present. Probiotics are chosen by the condition being treated and the evidence for a particular strain.
If my stool looks normal, can there still be bleeding?
Yes. Small amounts of blood are invisible. That is what the test for hidden blood detects, and why it is used for screening.
How is a sample collected?
You are given a clean container and instructions. Avoid mixing the sample with urine or water, and deliver it within the time stated. For some tests, recent antibiotics or bowel-cleansing preparations affect the result, so mention them.
Sources
This page is written for patients and is based on the guidelines and studies below. It is for education and does not replace a consultation.
- American College of Gastroenterology guideline on irritable bowel syndrome. Lacy BE et al. Am J Gastroenterol. 2021. doi:10.14309/ajg.0000000000001036
- American College of Gastroenterology guideline on colorectal cancer screening. Shaukat A et al. Am J Gastroenterol. 2021. PubMed 33657038
- Maastricht VI/Florence consensus on Helicobacter pylori infection. Malfertheiner P et al. Gut. 2022. PubMed 35944925
- Revised estimates of human and bacterial cell numbers in the body. Sender R et al. PLoS Biol. 2016. PubMed 27541692
- North American consensus on hydrogen and methane breath testing. Rezaie A et al. Am J Gastroenterol. 2017. PubMed 28323273