What a gut microbiome test can tell you, and what it can’t
A gut microbiome test, sometimes called a gut flora test, reads the DNA in a small stool sample to show which microbes live in your gut, and in what proportions. It can add context to ongoing gut symptoms. It can’t tell you on its own what is causing them, and there is still no agreed healthy range to compare the results against.
If you have spent months on probiotics and cutting out foods and still feel unsettled, wanting a test that finally shows what is going on makes complete sense. None of that is a lack of effort.
Written and reviewed by Georgina Waugh, Clinical Nutritionist. Updated 11 September 2026.
General information, not medical advice. A microbiome test does not diagnose any condition, and new or worsening gut symptoms belong with your GP first.
The short version
- A gut microbiome test is a home stool test that sequences the DNA in your sample and reports the microbes it finds as percentages of that sample.
- In a 2025 consensus, 69 microbiome experts found there is not yet enough evidence to recommend routine testing, or to set strict healthy ranges for gut species.
- When seven home testing services analysed the same stool material, the number of species their reports identified ran from 20 to 1,701.
- It does not diagnose IBS, SIBO or food intolerance, and it is not bowel cancer screening.
- It earns its place after the ordinary checks, read alongside your symptoms and history, when the answer would change what you do next.
What the test actually measures
You collect a small stool sample at home and send it back to the lab, which reads the microbial DNA in it. There are two accepted ways to do that. One reads a single marker gene that bacteria share, usually called 16S sequencing. The other reads all the DNA in the sample, called whole genome or shotgun metagenomic sequencing.
An international consensus panel accepts both as proper microbiome profiling, and notes that they produce different findings.
The part most people don’t expect is that the results are shares, not amounts. Sequencing works out what fraction of the DNA came from each microbe, so every result is a percentage of your sample. When one group goes up, every other group’s share goes down, even if nothing else changed. The same panel recommends reporting results as percentages for exactly that reason, so nobody mistakes them for counts.
A comprehensive stool test adds two other kinds of result to that profile, and they are worth keeping separate:
| Part of the report | What it can add | What it can’t do |
|---|---|---|
| Microbiome profile | Which bacteria and other microbes were found, in what proportions, how varied the community is, and groups researchers track, such as short-chain fatty acid producers. | Tell you whether that mix is causing your symptoms, or measure you against a settled healthy range. No such range exists yet. |
| Gut environment markers | Markers such as faecal calprotectin, which reflects white blood cells in the stool, and a check for hidden blood. | Tell you what a result means medically. A raised calprotectin or any blood in the sample is a result for your GP, not a nutrition plan. |
| Pathogen screen | A PCR check for a set list of specific bacteria and parasites. | Stand in for the microbiome profile. PCR panels are good at finding named organisms, but they are not microbiome testing. |
The test we use is Microba’s Microbiome Explorer Comprehensive, which puts all three into one at-home sample. The markers it covers and the ways to order it are on our Microbiome Explorer Comprehensive test page.
What the research says about testing
In 2025 an international panel of 69 microbiome experts published a formal consensus on how microbiome testing should be used in medicine. Their conclusion was plain: at present there is insufficient evidence to widely recommend routine microbiome testing in clinical practice.
The same panel found there is not yet enough information to set strict healthy reference ranges for gut species, and not enough evidence to put any dysbiosis index, a single score for how “off” a gut looks, on a report. Keep that in mind if a report colour-codes you against a healthy population.
Australian guidance lands in the same place. A 2026 review of irritable bowel syndrome in Australian Prescriber notes that a less diverse gut microbiome may be present in IBS, but that routine testing is not of clinical value.
Then there is the question of whether two tests would even agree. Researchers from the US National Institute of Standards and Technology and the University of Maryland ordered three kits from each of seven home testing services and gave every kit a portion of the same standardised stool material. The differences between services came out on the same scale as the natural differences between different people.
None of that makes the science worthless. It means a report is one lab’s reading of one sample on one day. If you ever repeat a test, repeat it with the same lab, so you are comparing like with like.
When a microbiome test is the wrong first step
Some symptoms need a doctor before they need a test. Healthdirect’s advice is to see your doctor about stomach pain, nausea or diarrhoea that won’t go away.
See your GP first if any of these apply
- blood in your stools, black stools, or vomiting blood
- weight loss you weren’t trying for
- symptoms that wake you from sleep
- abdominal pain that keeps getting worse
- symptoms that began after the age of 50
- a family history of inflammatory bowel disease, coeliac disease or cancer
- blood results that came back abnormal, such as low iron, raised inflammation markers or a positive coeliac test
These alarm features come from Australian Prescriber. A microbiome test is not bowel cancer screening either. That is the free National Bowel Cancer Screening Program kit, offered every two years to people aged 45 to 74, and Cancer Council’s advice for anyone with symptoms is to speak to their doctor.
A microbiome test also answers a different question from the other gut tests, so it helps to know which question is yours:
| If your main question is | A more useful place to start |
|---|---|
| Is my bloating coming from bacteria in the small intestine? | A breath test, which measures hydrogen and methane. A stool test does not answer that question. Our guide to what SIBO is explains the breath test. |
| Do certain foods seem to set me off hours later? | An IgG food intolerance screen, which is a separate test again and does not test for allergies. Swelling or trouble breathing after food needs urgent medical care. |
| Could this be coeliac disease, low iron or inflammation? | Your GP. These are ordinary blood tests, and faecal calprotectin, the stool test for bowel inflammation, is rebated by Medicare. |
| What does my wider gut community look like, once the basics are covered? | This is where a microbiome test can add context. |
Is a gut microbiome test worth it?
It can be, when three things are true. The ordinary explanations have been looked at with your GP. Your symptoms have been going on long enough that you want a wider picture. And the answer would change what you actually do next, rather than sit in a folder.
How it gets read matters as much as the test. The consensus panel’s position is that any change to someone’s care based on a microbiome result should be made by the health professional who requested it, looking at the whole history rather than a single test. Your bowel habits are part of that history: gut transit time can influence the microbiome, and the panel notes that how often you go and what your stools look like are simple clues to it.
What I look at first. When someone brings me a microbiome report, I don’t start with the species list. I start with the gut environment markers, because a raised calprotectin or any blood in the sample changes the conversation, and that conversation belongs with their GP.
Then I go back to their story. How often their bowels move and what that looks like. What an ordinary day of eating is. Every medicine and supplement. What changed around the time the symptoms started.
The microbiome profile gets read against all of that, never the other way round.
If bloating or unsettled bowels are the main thing you are living with, our page on how we work with bloating and gut symptoms lays out the wider approach.
If you have decided it is the right next step, our gut microbiome test page has the options, including having your report read with a clinical nutritionist.
Not sure a microbiome test is the right next step?
Bring your symptoms, any bloods you already have and whatever you have tried. A short call is usually enough to work out whether a microbiome test, a different test or your GP comes first. No test is booked on that call.
Book a free 15-minute callFifteen minutes on the phone with Georgina, at no cost.
Common questions about gut microbiome testing
Is a gut flora test the same as a gut microbiome test?
In practice, yes. Gut flora is the older name for the microbes living in your gut, and plenty of people still search for it that way. Tests sold today read the DNA of that community from a stool sample, which is what a gut microbiome test does.
Will a microbiome test show whether I have IBS or SIBO?
No. A 2026 Australian Prescriber review of irritable bowel syndrome says routine microbiome testing is not of clinical value, and SIBO, which is about bacteria in the small intestine, is investigated with a breath test rather than a stool test. A microbiome report can add context, but it does not identify either condition.
Can a microbiome test tell me which probiotic to take?
Not on its own. Australian Prescriber lists probiotics among IBS therapies with limited or controversial evidence, and the international consensus panel’s view is that decisions about someone’s care should rest on their whole history rather than a single test. Any supplement suggestion belongs in a conversation with whoever is managing your care.
Why do different microbiome tests give different results?
Because the method changes the answer. Kits collect stool differently, labs read different stretches of DNA, and companies compare you with different reference groups. When researchers sent the same stool material to seven home testing services, the differences between services were on the same scale as the differences between different people. If you retest, use the same lab.
Do I need a GP referral for a gut microbiome test?
No, you do not need a GP referral to order one through Wellbeing George. New, severe, worsening or unexplained gut symptoms should still go to your GP first.
Sources
- Porcari S, Mullish BH, Asnicar F and colleagues. International consensus statement on microbiome testing in clinical practice. Lancet Gastroenterology and Hepatology, 2025;10(2):154-167. A Delphi consensus of 69 experts. Statement 32 on routine use, 28 on healthy reference ranges, 27 on dysbiosis indices, 12 and 13 on sequencing versus PCR and culture, 3 on who changes care, and the reporting of results as percentages.
- Servetas SL, Gierz KS, Hoffmann D and colleagues. Evaluating the analytical performance of direct-to-consumer gut microbiome testing services. Communications Biology, 2026;9:269. Seven services, three kits each, one standardised stool material. Table 1 is the source for the species counts in the chart.
- Morrison S, Talley N. Australian Prescriber, 2026;49:93-8. doi:10.18773/austprescr.2026.018. A 2026 review of irritable bowel syndrome, and the source for routine microbiome testing in IBS, faecal calprotectin and its Medicare rebate, probiotics, and the alarm features.
- Microba. Microbiome Explorer Comprehensive, practitioner product information. The three panels, the gut environment markers and the pathogen markers.
- Healthdirect Australia. Gut microbiome and your health. When to see a doctor about ongoing stomach symptoms.
- Cancer Council Australia. National Bowel Cancer Screening Program: frequently asked questions. Eligible ages, how often, and what to do about symptoms.
Important: This page is general information written by a clinical nutritionist. It is not medical advice and does not replace care from your GP or another qualified health professional. A gut microbiome test does not diagnose, treat, cure or prevent any condition. Read our full disclaimer.
Written and reviewed by Georgina Waugh
Clinical Nutritionist, BHSc Nutritional Medicine
Last updated: 11 September 2026
Sources reviewed: the 2025 international consensus on microbiome testing, Australian Prescriber, Cancer Council Australia, Healthdirect and the published testing literature