Our microbiome stool test review is back!

In 2020 we did this review, where we sent a fecal sample from the same person on the same day to various fecal microbiome analysis companies. One major take-away from the review was the in part large discrepancy in the results between the companies, even though the stool sample was taken from the same specimen at the same time.

This time around we build somewhat on the 2020 test review, but the angle and methodology are different in several aspects. In the current review, no split fecal samples were sent to the different companies for analysis, and we have not included aspects such as ease of sampling and shipping the test to the companies, and time until results are sent back. Rather, we have looked at the science behind the different types of analyses that the companies use, how the results are interpreted and how the results are put into a wider context (such as the diet-microbiome-health interactions) in the test report.

We chose companies and tests that were included in our previous review, and new ones that are among the most popular or have features that we find interesting.

The evaluation is done based on our understanding of the field and does not constitute a highly systematic approach.

What kinds of tests are currently available?

Tests fall into two major categories: Those that include an analysis of the fecal/stool microbiome only, and those that include clinical markers or other non-microbiome analyses, in addition to the analysis of the fecal microbiome. Such markers are for instance blood in feces, immune system markers, food remnants, microbial fermentation products and digestive enzymes. Given the significant limitations (see below the individual test evaluations for more on this) in what a fecal microbiome composition can tell about health and disease, and what actions to take based on it, the addition of other markers is at this point in time almost a requisite if one is using the test as a guide to do changes in diet or other lifestyle factors.

The tests in the current review differ widely in what information you will get about the composition and function of your microbiome. Some tests go into much more depth than others (There is a big difference between so-called targeted PCR and meta-genomics methods for instance). Despite these differences, it is not clear that more depth equals better guidance for the consumer, simply because the knowledge isn’t ripe, for the most part, for use in such a detailed manner.

How did we do the test?

No formal grading of the different aspects of the test was made. The test is just as much meant to give an overview of the available tests on the market and what they offer, as a giving a verdict on which tests are the best ones. Furthermore, tests differ in their aims – some tests have deliberately excluded some types of analysis because they do not fall within the purpose of the test. We have not “disqualified” tests for having a narrow scope. In other words, it is up to the user to discern which test is comprehensive enough for the purpose the user has for taking the test.

For more on the science behind fecal/stool microbiome tests and the limitations and caveats to using these tests, see the comments below the evaluation of the individual companies. It is highly recommended that you read this, because the limitations and caveats are far from small in some respects.

Caveats and other comments on commercial stool microbiome testing

Without a doubt, these are early days in the field of microbiome testing. Thus, interpretation of the results must be done with caution and seen within the bigger picture of the patient’s health and lifestyle. Microbiome testing can as of today not by far be used as a stand-alone tool to guide medical decisions, and these tests should only be used under the guidance of a physician or somebody else with clinical experience and education. We do not find fecal microbiome testing useless, but below are some important limitations and aspects to consider when ordering a fecal microbiome test.

One major question, which we at MyMicrobiome seldom find is emphasized enough, is what fecal microbes can tell about how the microbes in the different parts of our gastrointestinal tract affect our health. Sure enough, fecal samples will provide some kind of footprint of the microbes throughout the gastrointestinal tract, but is it so coarse that it is not really useful? Is the footprint even so coarse that a fecal sample tells no more about the upper parts of the intestine or the mucosal microbiome, than the content of the sorted organic waste bin from a household tells about the diet of the ones living in the house? After all, the mucosal and the small intestinal microbiome may also be of large interest when doing these analyses.

Without going too much into detail on this issue, it is worth mentioning that the microbiome in the small intestine close to the mucosa is vastly different from the luminal microbiome in the colon for instance (https://pubmed.ncbi.nlm.nih.gov/33772148/). Also, most of the immune system in the gastrointestinal tract sits closest to the small intestine, not the colon, which speaks to the different local and systemic immune effects microbes can have in the small intestine versus the colon.

One could thus take the approach that there is just too much uncertainty to the microbiome tests that one should just shy away from them (https://www.gutmicrobiotaforhealth.com/why-microbiome-tests-are-currently-of-limited-value-for-your-clinical-practice/). That would be the easy way to go for someone who is not in dire need of help with regard to their health issues, for instance. For others, on the other hand, it may not matter much that a few hundred euros is spent on a test in the hope that some kind of insight will be gained.

No matter how pressing it is for someone to find solutions to their health issues, are there any clear examples at all that a commercial microbiome-focused fecal sample can give more insight than what a standard fecal sample that you take at your GP’s office can give? It is evident that fecal samples that are taken to guide microbiome related conditions that pertain to the colon can have some merit. Therefore, a fecal sample can give some indications as to what is wrong in the colon.

But the major reason for most people to do such a test is because they have issues that are just as likely to have the small intestine or stomach as the hotspot for them not feeling well. Or that they have few gut related symptoms, but wonder whether their gut microbes could be influencing for instance their skin condition or their depression.

While several connections between microbes and extracolonic disease have been found in individual studies, the overall picture across different populations and studies is more muddled. Researcher and microbiome expert Colin Hill speaks to this at gutmicrobiotaforhealth.com where he says that “the gut microbiome is unique to each person and is relatively stable and resilient, so it is difficult to predict if someone would benefit from a specific gut microbiome composition or from changing their current gut microbiome to a new composition.” (https://www.gutmicrobiotaforhealth.com/why-microbiome-tests-are-currently-of-limited-value-for-your-clinical-practice). Even the much lauded indicators richness and diversity of the microbiome is not the straight forward indicator of a healthy microbiome that is claimed in some of the tests included in our review, since these measures far from always are correlated with good health.

In spite of the limitations that Colin Hill and others speak to, we find that there are some parts missing in the argumentation for why one should or should not do a fecal microbiome test at this point in time. What is missing can be illustrated by the following example: Let’s say that a health practitioner does a microbiome test on a patient, and then the test comes back and “everything” is off the charts, or, on the other hand: nothing is abnormal. In the first instance the practitioner would be comfortable targeting the treatment at the microbiome, and in the second case one would to a larger degree look in other places. It does not have to matter all that much then, exactly what is off the charts – which a scientific study tends to have as a soul focus – because the info can be seen in the light of the overall, unique picture of the patient, and other knowledge that the practitioner has, and use all of this in a plan for the patient that can be adjusted based on the response to treatment.

In conclusion, several of the available fecal microbiome tests have intriguing features that can be of general interest to those that are curious about what is in their feces and serve as an entry point to learn more about the fascinating world of the microbes. The limitations and caveats with these tests are so big however, that one should be very careful in doing lifestyle changes or make medical decisions based on these tests. While, in general, the advice given are not in conflict with other standard advice that is given elsewhere, some of the advice is restrictive and can lead to a more complicated diet than necessary.

Overview Test Kits with and without clinical markers - Just click on the respective company to get to the test result.
With clinical markers With clinical markers
TOP choice: GI MAP - Diagnostic Solutions TOP choice: Digital Gut - Unseen Bio
TOP choice: GI 360 - Doctor’s Data GA-map Dysbiosis Test Lx - Genetic Analysis
TOP choice: GI Effects Comprehensive Profile - Genova Diagnostics myBioma - Biome Diagnostics
CSAPx2 - Doctor’s data Viome - Viome Life Sciences
  Biomes - Biomes NGS
  Elsavie - Elsavie ÖU
  Atlas Biomed - Atlas Biomed Group
  ZOE - ZOE Limited

TOP choice among tests that include clinical markers, in this review:

GI MAP - Diagnostic Solutions

Methodology: quantitative PCR (only specific predetermined microbes are searched for with this method)

Clinical markers and other additional analyses: yes

Scope of microbes searched for: bacteria, yeasts, viruses, parasites (protozoa and worms)

Option to get a consultation with dietitian or other health professionals with the test: no

Other comments: One of the newest tests on the market. This test includes markers that few other fecal tests do, such as zonulin, different bacterial toxins, beta glucoronidase and a broad range of H pylori virulence factors.

Verdict: This test is a top choice for individuals with gut issues where pathogens are suspected to be the cause.

TOP choice among tests that include clinical markers, in this review:

GI 360 - Doctor's Data

Methodology: PCR (only specific predetermined microbes are searched for with this method), microscopy and culture

Clinical markers and other additional analyses: yes

Scope of microbes searched for: Bacteria, viruses, yeast, parasites

Option to get a consultation with dietitian or other health professionals with the test: no

General comments: This test is most useful for those who have moderate to strong symptoms from the gut, since the scope of the microbes searched for are geared towards microbes that are known to be causing disease in the gastrointestinal tract. While other microbes are also included in the test, metagenomics is not carried out, meaning that a large number of microbes will not be detected with this test. Clinical markers that are included in this test that seldom are found in other tests are: stool mucus, Charcot-Leyden crystals, carbohydrate digestion/absorption, lactoferrin, and lysozyme.

Verdict: A very comprehensive review of gut related health, with a broad range of clinical markers.

TOP choice among tests that include clinical markers, in this review:

GI Effects Comprehensive Profile - Genova Diagnostics

Methodology: PCR (only specific predetermined microbes are searched for with this method), microscopy and culture

Clinical markers and other additional analyses: yes

Scope of microbes searched for: Bacteria, viruses, yeast, parasites

Option to get a consultation with dietitian or other health professionals with the test: no

General comment: The inclusion of the bacteria Methanobrevibacter (the dominant methanogen in the human gut) and Desulfovibrio (one of the most common hydrogen sulfide producers) is unique to this test. Methane producing microbes are linked to constipation, and hydrogen sulfide producers are linked to diarrhea. The test also includes a wide range of other markers. The test report neatly presents the main conclusions of what needs to be done based on the results, in five categories: Need for digestive support, inflammation modulation, microbiome support, prebiotic support and need for antimicrobial support.

Verdict: A very comprehensive review of gut related health, with a broad range of clinical markers. The inclusion of methanogens and hydrogen sulfide producers makes this a slightly better choice than GI 360, which is quite similar to this test in other respects.

TOP choice among tests that do not include clinical markers, in this review:

Digital Gut - Unseen Bio

Methodology: Metagenomics (Shallow Shotgun Metagenome Sequencing) (In plain language: all bacteria, archea (a type of “bacteria”), viruses and parasites can potentially be found with this method)

Clinical markers and other additional analyses: No

Scope of microbes searched for: Bacteria, archea, yeast and parasites

Option to get a consultation with dietitian or other health professionals with the test: Yes

General comment: An intriguing feature of the Unseen Bio test is how the results are presented. In their test report you can see how your microbiome compares to those who have a non-industrial lifestyle, the healthy Danish population and other populations, whatever is your most relevant comparison. You also get an overview of which commercial probiotics that contain the species that are in low abundance in your feces sample.

It should however be noted that while the personal microbiome-probiotics overview is potentially very interesting, the usefulness in terms of what actions that can be made based on this probiotics list is a non-substantiated concept at the moment. It is not necessarily so that a probiotic will find its place in your ecosystem of microbes and stay there, nor that you don’t already have microbes that have a different name but fulfill the same functions in your gut, or that you in fact need the “missing” microbes at all. 

The lifestyle recommendations they provide are generally sound, and take into account some of the latest findings when it comes to how lifestyle interacts with the microbiome. The diet advice is in part based on the diet registration that is a part of the test, but the microbiome results have no influence on the dietary advice given, which is not necessarily a bad thing, given the state of the art: The knowledge simply isn’t there yet when it comes to tailoring the diet based on fecal microbial species analyses only, apart from perhaps a few factors. Still, the diet registration is lacking questions on meal frequency and timing, and level of processing, which arguably is just as important as the actual food items eaten. 

Verdict: The test is a very good value for money option for those who are just curious to see what microbes reside in them and don’t have gut complaints, for whom a test that includes other markers would be advisable.

CSAPx2 - Doctor's data

Methodology: PCR (only specific predetermined microbes are searched for with this method)/microscopy/culture

Clinical markers and other additional analyses: Yes

Scope of microbes searched for: Bacteria, viruses, yeast and parasites

Option to get a consultation with dietitian or other health professionals with the test: No

General comment: This test is most useful for those who have moderate to strong symptoms from the gut, since the scope of the microbes searched for are geared towards microbes that are known to be causing disease in the gastrointestinal tract. While other microbes are also included in the test, metagenomics is not carried out, meaning that a large number of microbes will not be detected with this test.

Verdict: A good test for clinical markers, parasite screening and detection of known pathogenic bacteria. Limited information on the totality of the bacterial composition, and, the culture based part of the analysis is too uncertain to pay much attention too, except for finding out if certain bacteria are present at all.

GA-map Dysbiosis Test Lx - Genetic Analysis

Methodology: PCR (only specific predetermined microbes are searched for with this method)

Clinical markers and other additional analyses: No

Scope of microbes searched for: Bacteria

Option to get a consultation with dietitian or other health professionals with the test: No

General comment: The test has been described and tested clinically and published in several peer review papers, something which is quite unique to this test. The claim is that it can be a useful tool with regard to diseases such as IBS (irritable bowel syndrome) and IBD (inflammatory bowel syndrome), but a recent study questions this. In that study this test was not able to distinguish between neither different types of IBD, nor healthy individuals from IBD patients. This study was carried out in children however, which could indicate that this test is not suitable for children, while still being useful for adults. More research is needed to clarify reasons for discrepancies between studies in this regard.

The test results are presented in an easy to understand manner in one main domain – their own Dysbiosis Index, and five subcategories in terms of “Functional Imbalance”.

Verdict: This is one of the most researched tests on the market, and provides an indication as to what degree dysbiosis of the fecal microbiome is present.

ia, viruses, yeast and parasites

Option to get a consultation with dietitian or other health professionals with the test: No

General comment: This test is most useful for those who have moderate to strong symptoms from the gut, since the scope of the microbes searched for are geared towards microbes that are known to be causing disease in the gastrointestinal tract. While other microbes are also included in the test, metagenomics is not carried out, meaning that a large number of microbes will not be detected with this test.

Verdict: A good test for clinical markers, parasite screening and detection of known pathogenic bacteria. Limited information on the totality of the bacterial composition, and, the culture based part of the analysis is too uncertain to pay much attention too, except for finding out if certain bacteria are present at all.

MyBioma - Biome Diagnostics

Methodology: PCR (only specific predetermined microbes are searched for with this method)

Clinical markers and other additional analyses: No

Scope of microbes searched for: Bacteria

Option to get a consultation with dietitian or other health professionals with the test: No

General comment: The test report is mainly concerned with dietary advice, based on the microbiome findings in the sample. The dietary advice is in some respects outdated. For instance, a low-fat diet and a low cholesterol diet is recommended for prevention of heart disease and obesity. A high cholesterol intake is something that has been thoroughly refuted as a cause of these diseases, and the evidence for a high fat diet doing the same is weak. Also “complex sugars” used in the report is a term that has little relevance for how a healthy diet should be composed. The test also mentions trimethylamine N-oxides (TMAO) as a contributor to heart disease. But this is most certainly not a causative factor in heart disease (https://pubmed.ncbi.nlm.nih.gov/35606406/) and the claim by MyBioma that TMAO enhances absorption of cholesterol appears unfounded. In fact, the opposite has been found (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6543245/).

Verdict: While the test report is more detailed in terms of interpretation of the results than many other tests, the relevance of the interpretation is for a large part ahead of the science or has been shown to be wrong. It is unclear if this test will hamper health more than improving it, compared to general dietary advice. We do not recommend this test.

Viome - Viome Life Sciences

Methodology: Meta-transcriptomics

Clinical markers and other additional analyses: No

Scope of microbes searched for: Mostly bacteria show up on the test report, but the test can also detect viruses, archea, fungi and parasites.

Option to get a consultation with dietitian or other health professionals with the test: No

General comment: This test is marketed as a test that primarily is a guide to how you should eat to get or maintain a healthy microbiome.

The use of the method meta-transcriptomics makes this test stands out among other commercial tests. Viome’s methodology has not been made public to any large degree however, and no clinical trials have been carried out based on their methods. In other words, it is not possible to properly assess what effects people who take this test will have when they follow their recommendations.

Several of the interactions between the body, diet and the microbiome that Viome addresses are based on the latest science, and has potential in assessing how a person’s microbiome and gene expression (meta-transcriptomics, which measure which genes are at work at a given point in time) affect health. But, there is quite a lot of uncertainty both regarding what actual impact the findings in this test will have for the individual, and most importantly: What can be done to fix the specific aberrations in the gut microbiome.

The specific mentions of different foods that are supposed to be good for the person having done the test is based on vague reasoning and is oversold. For instance, in one test report that MyMicrobiome received from Viome, bone both is recommended, mostly due to the content of amino acids. This hints at a very limited understanding of nutrition, and is confusing in terms of how a person getting this advice should go about the practicalities of this recommendation, given that many other foods are far better sources of amino acids/protein. There is also no mention of how the processing of foods affects the quality of the foods, and in turn the microbiome. Any microbiome test that claims to be a guide to what foods and meal patterns to have that excludes this part is not reassuring as to the science and thinking behind the test.

Verdict: This test is ahead of the science, and the dietary recommendations appear, in part, to be both arbitrary and narrow, and have not been validated in clinical trials. It is highly questionable that it is recommended that certain foods, that are in other respects considered healthy, are avoided based on this test. We do not currently recommend this test, but hope that their methodology will have more data behind it in the future.

Biomes - Biomes NGS

Methodology: Not stated on the website. Probably PCR.

Clinical markers and other additional analyses: No

Scope of microbes searched for: Bacteria

Option to get a consultation with dietitian or other health professionals with the test: No

General comment: The test report provides a good overview of what the fecal microbiome findings can tell about the state of some aspects of your gut and overall health, given the limitations of all fecal microbiome composition tests in this regard. However, although the complete recommendations are not available on the website, the dietary advice is not in line with the science on some central topics, such as advising against red meat based on the levels of TMAO that some microbes produce. As mentioned in the MyBioma evaluation TMAO has no clear role in causing disease. Furthermore, advising against a high caloric intake is a rather vague concept and a high caloric intake is not a cause of obesity per se.

Verdict: The dietary recommendations part that is based on the specific microbes found in a sample are not as far ahead of the science as Viome’s or MyBioma’s, but the overall quality of the diet recommendations is too poor to recommend this test.

Elsavie - Elsavie ÖU

Methodology: PCR (only specific predetermined microbes are searched for with this method)

Clinical markers and other additional analyses: No

Scope of microbes searched for: Bacteria and archae

Option to get a consultation with dietitian or other health professionals with the test: No

General comment: This test is primarily concerned with how the composition of the fecal microbes can guide what you eat.

The dietary recommendations in this test are probably more to the detriment of getting better health than the opposite, in addition to the fact that there still is so little that can be stated in general about how the diet should be changed based upon a microbiome test. Some of the questionable and, in part, wrong advice that is given is: warning against a high fat intake, to eat many meals per day and to reduce the amount of cholesterol in the diet. There is also no mention of how food processing affects the quality of foods, and in turn the microbiome. Any microbiome test that claims to be a guide to what foods and meal patterns to have that excludes this part is not reassuring as to the science and thinking behind the test.

Verdict: The dietary recommendations part that is based on the specific microbes found in a sample are not as far ahead of the science as Viome’s or MyBioma’s, but the overall quality of the diet recommendations is too poor to recommend this test.

Atlas Biomed - Atlas Biomed Group

Methodology: PCR (only specific predetermined microbes are searched for with this method)

Clinical markers and other additional analyses: No

Scope of microbes searched for: Bacteria

Option to get a consultation with dietitian or other health professionals with the test: Yes

General comment: The test report includes many different features and are presented in an easy-to-understand manner. You can even find out which country’s average diet your diet resembles the most. A more confusing aspect is the presentation of the amount of vitamins that are to be found in your feces. The significance of knowing something about this is not clear.

A central feature of the test are the diet recommendations, that are based on your fecal microbiome results. Since no peer reviewed paper has shown that a microbiome guided single food-based recommendation will improve health over recommendations to follow a general healthy diet, Atlas Biomed would have needed to present in detail just how they can give advice that will improve the microbiome composition and health. The test includes a free consultation with a nutritionist however, which could safeguard against too strict an implementation of the advice for the customer.

Verdict: The test holds some interesting features in their way of presenting the results, but just like other tests that give food advice based on the microbiome composition the usefulness is limited at this point in time. The manner in which the advice is given is however not as far ahead of the science as is the case with other tests in this review.

ZOE - ZOE Limited

Methodology: Shotgun metagenomics

Clinical markers and other additional analyses: No

Scope of microbes searched for: Bacteria, viruses, yeast, parasites

Option to get a consultation with dietitian or other health professionals with the test: No

General comment:

ZOE has a strong science base in terms of how their methodology was and still is developing. Researchers involved in ZOE are also some of the ones that have carried out the clinical studies that the test ZOE provides is based upon.

Just like Viome this test is primarily focused on how your diet interacts with your microbiome. A basic tenet for the test is that how different foods affect you acutely and uniquely, especially with regard to blood sugar and blood fat, can impact both short- and long-term health. ZOE claims that the larger the blood sugar spikes after meals the greater is the potential for adverse health effects. While more or less constant blood sugar elevations such as seen in diabetes can have deleterious effects, the hypothesis that blood sugar spikes in healthy or even prediabetic people can lead to a deterioration of health is not substantiated by concrete findings. This makes what stands to be gained by swapping an apple with a banana for instance, based on your personal microbiome and blood sugar results, an even bigger leap of faith. Only future studies can indicate with more certainty if their approach will actually lead to better health outcomes.

The test does not only take blood sugar and blood fat into account. You will also get a balance chart of ZOEs researched and selected 15 “bad” and 15 “good” bacteria, and how to make the right species thrive, by selecting the right foods. Again, the efficacy of changing your diet in a specific manner based on these results remains to be tested in clinical trials. One major question is if the results found in the studies that they have done to date is applicable to mixed meals, and not just single foods.

ZOE is not available in all countries at the moment, but will expand in the future.

Verdict: The amount of research and effort that go into this test is huge. The test is however not ready for prime time in terms of knowing with sufficient certainty that dietary changes based upon this test will lead to better health outcomes than other more standard dietary advice.

Certification consultant for probiotics
Inge Lindseth
registered dietitian

Inge Lindseth is a registered dietitian from the University of Oslo with over 20 years experience in nutrition. His special areas are diabetes, obesity, ME and those who want to get more out of exercise and perform the maximum in sports.

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