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Watercolour drawing of three identical jars holding the same small garden of bacteria. Behind each jar is a sheet of paper with a different, squiggly pattern, as if three readings of the same thing give three different pictures.

Gut flora tests: Same sample, seven different answers

By Published 4 min read

You send a small stool sample by post, and a few weeks later you get a report: which bacteria you have, a score for your gut health and perhaps a suggestion of what you should eat or which supplements to take.

It sounds like precise knowledge about your own body. But how reliable are the answers, and can you use them for anything?

Same sample, different answers

The US standards institute NIST tested this directly. An employee set up a private account with seven companies that sell gut flora tests to consumers, and ordered three tests from each company. The companies did not know they were part of a study. All the samples came from the same, thoroughly mixed stool material [1].

So the answers should have been the same. They were not:

  • The difference between the companies was as large as the difference between different people's gut flora. In other words: which company you choose can matter as much for the answer as which gut the sample comes from [1].
  • One company called the gut flora healthy in two of the samples and unhealthy in the third, even though it was the same material. In the third report, 7 out of 10 measured areas were below average, compared with only one in the other two [1].
  • Three companies reported that the bacterium Clostridioides difficile was present. The other four reported that it was not [1].

The researchers explain the differences by the companies using different methods and not having sufficient quality control. They also note that some companies recommended expensive supplements, such as probiotics, that they sold themselves and for which there is very little evidence [1].

What the experts say

In 2024, an international group of 69 experts from 18 countries, among them researchers from Aarhus University Hospital and the University of Copenhagen, put together joint guidance on gut flora tests [2]. These are expert opinions, not trial results, but the message is clear:

  • There is not enough evidence to recommend gut flora tests routinely in the treatment of patients.
  • You should not order a test on your own initiative without a medical reason.
  • Treatment advice from the test company is strongly discouraged. Interpreting the results belongs with the doctor who ordered the test. The experts note that this kind of advice is common in the tests sold today.
  • There is no direct evidence that the tests improve the treatment of any disease in humans.

Three things in the report you can ignore

The experts also go into detail about what a report should not contain [2]. Three of these often turn up in tests for consumers:

  1. The ratio between Firmicutes and Bacteroidetes. The experts advise against using the ratio between these two large groups of gut bacteria in a report. Such broad groups do not capture the variation in the gut flora and can give misleading results.
  2. A "dysbiosis index" or an overall health score. There is not enough evidence to use any of them.
  3. "Normal ranges" for how much of each bacterium you should have. There is not enough knowledge to set fixed limits for what is healthy.

The experts also write that tests which only culture bacteria, or look for a few selected ones with PCR, cannot be called a gut flora test. They only see a small part of the picture [2].

Why is it so difficult?

Your gut flora is made up of hundreds of species. A test measures how large a proportion each bacterium makes up, not how many there are [2]. If one group rises, the others automatically fall on paper, even if they have not actually changed.

On top of that, according to the experts, there is not enough knowledge to set fixed limits for what is a healthy amount of each bacterium [2]. Even if the measurement were completely accurate, it would often be unclear what the numbers mean for you.

What you can do

  • If you have stomach problems, start with your doctor. Persistent symptoms can have many causes, and some of them need to be investigated with completely different methods. See, for example, the section on warning signs in the article on a bloated stomach.
  • If you have already received a report, take it for what it is: a snapshot measured with one method. Do not make big decisions about diet or medicine based on it alone.
  • Be extra sceptical if the report ends by recommending supplements from the same company, or if it puts weight on a Firmicutes/Bacteroidetes ratio, a dysbiosis index or fixed normal ranges.
  • If you want to do something good for your gut flora, varied food with fibre is a better place to spend your money. Read more about prebiotics and types of fibre.

The bottom line

  • When the same sample was sent to seven companies, the difference between the companies was as large as the difference between different people's gut flora.
  • One company called the same sample both healthy and unhealthy.
  • 69 international experts advise against ordering a gut flora test without a medical reason and strongly advise against treatment advice from the test company.
  • There is still no evidence that the tests improve the treatment of any disease.

Sources

  1. Servetas SL et al. Evaluating the analytical performance of direct-to-consumer gut microbiome testing services. Commun Biol. 2026. PMID 41748906
  2. Porcari S et al. International consensus statement on microbiome testing in clinical practice. Lancet Gastroenterol Hepatol. 2025. PMID 39647502

This article is general information and not medical advice.