Microbiome stool testing: why you shouldn’t do them if you have IBS

Spending hundreds on a stool test promising 'personalized' answers? Before you click 'buy,' let's talk about what that expensive report actually tells you.

Your gut microbes play a very important role in the health of the whole body and the gut. If you want to be healthy and live long, it is vital that you take good care of your beneficial microbes. Gut dysbiosis, on the other hand, has been linked to most chronic illnesses, including IBS. Your gut microbes deserve to be noticed!

Home poop tests that measure microbial composition promise that by seeing what microbes there are in your poop, it can help you understand your gut better and give you precise and individualized recommendations to improve gut health.

We all want that silver bullet, but unfortunately, the current science behind these home tests simply doesn't support the marketing claims. Read on to find out the critical reasons why testing your gut microbiome today is premature, and possibly even harmful.

1. The tests are not accurate. 

There are multiple different kinds of tests out there, some better than others, but they all have the same issue: they are not accurate. Here are various problems of multiple tests:(a) Some tests only measures bacteria (not fungi/viruses), (b) Functionality is often guessed from diversity, (c) Many microbes go undetected, (d) Contamination with human DNA complicates results.

Also, different tests give different results. Take all the different tests with the same sample and you’ll get different results. This can happen even with testing the same sample with the same test multiple times.

2. Challenges stemming from the microbiota itself

• Your gut microbiome fluctuates even WITHIN A DAY. The relative amounts of different microbes, species and strains are changing constantly. You microbes are different based on the season, your lifestyle, your diet and even the time of day. This means that a test taken in the morning shows a different result than a test taken in the evening. What conclusions can you really draw from this?

• We don’t have a standard with which to compare: science doesn’t know everything about the gut microbiome yet. Including what is ideal, or a healthy gut microbiota. Every person has their own individual microbial fingerprint and we know that diversity is good. But, even IBS doesn’t have an identified microbial signature yet, even though some trends can be detected. If a testing company has a scoring system, it’s not based on sound scientific evidence.

• Correlation does not mean causation: studies can show that in some illnesses, higher numbers of specific bacteria are present. However, this does not prove that those bacteria are what are causing the illness. 

Your gut microbiota is highly complex and the truth is that microbiome test results are very difficult to truly interpret, even if they were accurate. This makes providing science-based recommendations based on test results virtually impossible.

Some companies provide dietary recommendations based on the results, however, but the scientific backing to prove them is thin. I contacted a company once to find out how they came up with their "foods to avoid and to eat" lists for different results and they couldn’t provide any real evidence for this.

And what’s worse, making big diet changes and restricting a lot of foods based on these tests can be harmful. They increase malnutrition risk, they increase stress and they can lead to disordered eating and food fears, all of which are damaging to gut health. 

Ways to support gut microbe health (evidence-based)

1. Lots of diet variety, especially plants
2. Feed your gut microbes with fiber and prebiotics
3. Fermented foods, potentially probiotics
4. Avoid low-quality foods, like certain ultraprocessed foods
5. Proper sleep 
6. Exercise
7. Stress reduction

The gut microbiota is hugely important in IBS and in health in general, but testing your poop to see what bacteria it has is not the answer. Rather focus on the foundational lifestyle and diet habits that we know help your gut. It might not be exciting, but it is powerful.  

If you need help building these solid lifestyle and diet foundations, join my group program in January 2026! Together we will take 15 gut health steps in 15 days that are designed to take only 15 minutes per day to get through. It’s a low threshold program with no fluff and only evidence-based practices to soothe your digestion. Go here to sign up! 

PS. The program has also a version in Finnish, here’s the sign-up page.

References:

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Wensel CR, Pluznick JL, Salzberg SL, Sears CL. Next-generation sequencing: insights to advance clinical investigations of the microbiome. J Clin Invest. 2022 Apr 1;132(7):e154944. doi: 10.1172/JCI154944. PMID: 35362479; PMCID: PMC8970668.

Heiman ML, Greenway FL. A healthy gastrointestinal microbiome is dependent on dietary diversity. Mol Metab. 2016 Mar 5;5(5):317-320. doi: 10.1016/j.molmet.2016.02.005. PMID: 27110483; PMCID: PMC4837298.

So D, Whelan K, Rossi M, Morrison M, Holtmann G, Kelly JT, Shanahan ER, Staudacher HM, Campbell KL. Dietary fiber intervention on gut microbiota composition in healthy adults: a systematic review and meta-analysis. Am J Clin Nutr. 2018 Jun 1;107(6):965-983. doi: 10.1093/ajcn/nqy041. PMID: 29757343.

Leeuwendaal NK, Stanton C, O'Toole PW, Beresford TP. Fermented Foods, Health and the Gut Microbiome. Nutrients. 2022 Apr 6;14(7):1527. doi: 10.3390/nu14071527. PMID: 35406140; PMCID: PMC9003261.

Pérez-Prieto I, Plaza-Florido A, Ubago-Guisado E, Ortega FB, Altmäe S. Physical activity, sedentary behavior and microbiome: A systematic review and meta-analysis. J Sci Med Sport. 2024 Nov;27(11):793-804. doi: 10.1016/j.jsams.2024.07.003. Epub 2024 Jul 9. PMID: 39048485; PMCID: PMC12510671.

Hantsoo L, Zemel BS. Stress gets into the belly: Early life stress and the gut microbiome. Behav Brain Res. 2021 Sep 24;414:113474. doi: 10.1016/j.bbr.2021.113474. Epub 2021 Jul 16. PMID: 34280457; PMCID: PMC8380711.

Morwani-Mangnani J, Giannos P, Belzer C, Beekman M, Eline Slagboom P, Prokopidis K. Gut microbiome changes due to sleep disruption in older and younger individuals: a case for sarcopenia? Sleep. 2022 Dec 12;45(12):zsac239. doi: 10.1093/sleep/zsac239. PMID: 36183306; PMCID: PMC9742900.

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