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Gut microbiome testing
A gut microbiome test reads the DNA of the bacteria in a stool sample to show which kinds are present and how varied they are. It can add useful detail to the care of selected people with long-standing gut symptoms. It cannot diagnose a disease, and there is no single normal result. In my practice it is ordered after a consultation and standard tests, when the result is likely to change the plan.
At a glance
What it shows
Which bacteria are present in a stool sample, in what proportions, and how varied the community is.
Sample
A small stool sample, collected with a kit and written instructions.
Preparation
Your usual diet. Ideally no antibiotics in the four to six weeks before.
Results
A few weeks. Explained in a consultation, together with your symptoms and standard tests.
What is a gut microbiome test?
A gut microbiome test is a laboratory analysis of the genetic material of the microbes in a stool sample. Most gut bacteria cannot be grown in a routine culture, so the laboratory reads their DNA to identify them.
Three methods are in use:
- 16S sequencing reads one marker gene that all bacteria carry. It identifies groups of bacteria, usually to the level of the genus.
- Shotgun sequencing reads all the DNA in the sample. It identifies individual species and the genes they carry, and it also detects fungi and viruses.
- Targeted quantitative PCR does not survey the whole community. It measures the amount of DNA from a fixed list of bacteria, parasites and yeasts, and is usually reported with stool markers of digestion and inflammation.
The method is chosen for the question. A broad picture of the community calls for sequencing. A search for particular organisms calls for a targeted panel.
It is different from the standard stool tests, which answer other questions:
| Test | The question it answers |
|---|---|
| Stool routine and culture | Is there an infection or a parasite? |
| Stool calprotectin | Is the bowel inflamed? |
| Stool occult blood | Is there hidden bleeding? |
| Hydrogen breath test | Are bacteria overgrowing in the small intestine? |
| Microbiome test | Which bacteria live in the colon, and how varied are they? |
When do I advise a microbiome test?
An international expert panel has reported that evidence for the usefulness of microbiome tests in everyday care is still scarce, and has set out standards for how they should be ordered and reported. I therefore use the test selectively.
Long-standing symptoms with normal standard tests
Bloating, irregular bowels or food reactions that continue after infection, inflammation and overgrowth have been looked for.
After repeated antibiotics
The result shows how varied the community is, which helps to set priorities for food.
Symptoms or overgrowth that keep returning
Alongside a breath test, to look for a pattern that would change the plan.
To make a food plan more specific
For example, how much fibre to begin with and which fermented foods to add first.
When I do not advise it
- As a first test for new symptoms
- As a health check in a person without symptoms
- To diagnose IBS, colitis, coeliac disease or cancer
- In place of a colonoscopy when there is bleeding, weight loss or anaemia
How do I prepare?
Keep to your usual diet
Eat as you normally do in the week before, so that the result reflects your usual state. Gut bacteria shift within days of a change in diet.
Antibiotics
Ideally, wait four to six weeks after a course of antibiotics. Tell me about any course in the last six months.
Probiotics and medicines
Do not stop a prescribed medicine. Tell me what you take, including probiotics, acid-blockers, laxatives and diabetes medicines, because each can change the result.
Timing
Avoid collecting the sample during a bout of acute diarrhoea, unless that is the reason for the test.
How is the sample collected?
You are given a collection kit with written instructions. A small amount of stool is placed in a tube that contains a preserving liquid, and the tube is sealed, labelled and returned as instructed. There is no fasting and no bowel preparation.
Depending on the test, the sample is analysed by a laboratory in India or sent to a laboratory abroad. Reports take a few weeks, and longer when the sample travels abroad. You will be told which laboratory is used, and why, before you decide.
What does the report show?
Diversity
How many different kinds of bacteria are present, and how evenly they are spread. Higher diversity is generally linked with better health, but a number on its own is not a diagnosis.
The main groups
Which groups of bacteria dominate. In Indian studies, people on largely plant-based diets carried more Prevotella, and people on mixed diets carried more Bacteroides. Neither pattern is a disease.
Specific organisms
Bacteria flagged as high or low against the laboratory’s reference group. These are associations, and a reference group drawn from another population may not fit an Indian patient.
What the bacteria can do
Some reports estimate functions, such as the capacity to make butyrate from fibre.
This is how I read a report:
- As one sample on one day. The stool community changes with recent meals and from day to day.
- Against your own history, not against a perfect score. Summary scores such as a “dysbiosis index” have no agreed standard.
- Together with everything else: your symptoms, examination, food and standard tests.
- Without comparing laboratories. Methods differ, so two reports from two laboratories cannot be compared directly.
What happens after the result?
The result is explained in a consultation. It may change the order of the food plan, support a decision to test for overgrowth, or show that no change is needed. It is never a reason on its own to start antibiotics, antifungal medicines or a long list of supplements.
What are the limits and risks?
The test carries no physical risk. Its limits matter more:
- It cannot diagnose a disease.
- It describes the bacteria in stool, which reflects the colon. It does not show what is happening in the small intestine.
- It shows associations. It cannot tell whether a pattern is the cause of your symptoms or the result of them.
- A report full of red and green flags can cause worry that is out of proportion to what the result means.
Questions patients ask me about microbiome testing
Is a gut microbiome test worth doing?
For most people with new gut symptoms, standard tests answer the important questions first. A microbiome test can add useful detail in selected people with long-standing symptoms, when it is read by a doctor who knows the rest of your history.
Can I order a gut microbiome test kit online and read it myself?
You can, but I advise against acting on a report alone. Reports list associations, and it is easy to restrict foods or take supplements that you do not need. Bring the report to a consultation.
Does a microbiome test diagnose SIBO, leaky gut or candida?
No. SIBO is diagnosed with a breath test. There is no validated routine test for “leaky gut”. Candida lives in the gut of many healthy people, so finding it in stool does not show that it is causing symptoms.
What does a gut microbiome test cost in India?
The cost depends on the method and the laboratory. Shotgun sequencing costs more than 16S sequencing, and a test sent to a laboratory abroad costs more than one done in India. Please ask the clinic for current details. I advise the test only when it is likely to change your plan.
Which type of microbiome test do I need: 16S, shotgun or PCR?
It depends on the question. Sequencing gives a broad picture of the whole community. A targeted PCR panel looks for a fixed list of organisms and adds stool markers. I choose the method after the consultation, and many people need none of them.
Is my sample tested in India?
Some tests are done by a laboratory in India and some samples are sent abroad. You will be told which before the test is ordered.
Should I repeat the test after treatment?
Rarely. We judge progress by symptoms. A repeat is considered only when the answer would change what we do next.
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.
- International consensus statement on microbiome testing in clinical practice. Porcari S et al. Lancet Gastroenterol Hepatol. 2025. PubMed 39647502
- Multi-omics study of the Indian gut microbiome. Dhakan DB et al. Gigascience. 2019. PubMed 30698687
- Pan-India profile of the human gut microbiome. Dubey AK et al. Sci Data. 2018. PubMed 30375992
- Study of how quickly diet changes the gut microbiome. David LA et al. Nature. 2014. PubMed 24336217
- Study of gut bacteria recovery in healthy adults after antibiotics. Palleja A et al. Nat Microbiol. 2018. PubMed 30349083
- North American consensus on hydrogen and methane breath testing. Rezaie A et al. Am J Gastroenterol. 2017. PubMed 28323273
- Review of Candida albicans as a normal resident and occasional pathogen of the gut. Kumamoto CA et al. Curr Opin Microbiol. 2020. PubMed 32604030