Gut Microbiome Testing: Everything You Need to Know

There is no doubt that the human microbiome plays a pivotal role in health and disease. Countless research studies have been published on the intricate relationship between the microbial communities residing within and on our bodies and a myriad of health conditions. Among the diverse human microbiome communities, the gut microbiome takes center stage, with extensive studies affirming its undeniable role in shaping our well-being. It is estimated that up to 90% of diseases are correlated with the health of our gut and the microorganisms that live there.

Unfortunately, our microbiome is constantly at the receiving end of various assaults. Suboptimal diet and lifestyle practices, urban living, medication, smoking, alcohol, stress, antibiotics, extreme hygiene practices, a lack of exposure to healthy soil and nature, air pollution, and other environmental toxins collectively contribute to unfavorable shifts in the composition of our intestinal microbial ecosystem. These changes can, in turn, negatively impact immune system function, digestion, heart health, nutrient status, brain function, detoxification, metabolism, hormonal balance and more.

This realization continues to drive both scientific research and commercial endeavors. In recent years, there has been an exponential surge in companies offering microbiome health solutions. A vast and growing number of microbiome-targeted products including fermented foods, probiotics, prebiotics, postbiotics, as well as services like direct-to-consumer gut microbiome testing, are now readily available. Ordering a test kit online, collecting a stool sample in the comfort of your home, shipping it back to the lab, and receiving a comprehensive analysis of your gut microbiota, accompanied by detailed diet and supplement recommendations, has become an accessible option for those looking to nurture their inner ecosystem back to health.

The allure of peering into the intricate world of our intestinal microbiota is undeniable. From a health practitioner perspective, gut & microbiome testing can be highly beneficial as a part of a personalized health optimization approach. As a functional nutrition & lifestyle consultant, I have been using practitioner level gut microbiome tests with clients for many years. These tests, when used at the right time, under the right circumstances, and in conjunction with a thorough health assessment, history, and symptom review, can help uncover underlying gut and microbiome imbalances driving various symptoms. This, in turn, facilitates a more targeted and personalized approach to building overall health.

It is important to note that practitioner-grade gut & microbiome tests differ from direct-to-consumer options. Practitioner level GI tests include host GI markers that reflect gastrointestinal imbalances as well as an analysis of certain micro-organisms that are well understood and researched in terms of their impact on digestive health and health in general.  Commercial gut microbiome tests on the other hand analyse the entire collection of microbes found in your stool sample.

In this article, I aim to explore the latter, given the growing array of testing options and the need for a clearer understanding of their uses and benefits. I will delve into what commercial gut microbiome tests are, what to expect when purchasing a test, and the strengths and limitations associated with them. Drawing from research and personal experience, I will also provide insights and tips on selecting the right test, should you decide to embark on an exploration of your mysterious inner microbial world.

What is gut microbiome testing?

A gut microbiome test analyses your stool sample to assess the different kinds and amounts of micro-organisms inhabiting your gut. With over 10,000 microbial species identified residing within and on the human body, this comprehensive analysis sheds light on your unique microbial composition. Commercial gut microbiome tests use DNA (or sometimes RNA) analysis techniques to pinpoint and quantify the various microbes inhabiting your gut. Different labs use different genomic sequencing methods, each with its unique advantages and drawbacks (see the overview at the end).

Companies providing direct-to-consumer gut microbiome testing typically have one (or both) of the following primary motivations:

1. For laboratories, a key driver could be research. In scientific research, the more samples you have, the more accurate and valuable the information drawn from these samples is going to be. A lab may aim to expand its reference database, leveraging the findings for academic research projects or selling data to product and pharmaceutical companies. By offering testing to companies and the general population, the lab is building a sizable dataset.
2. The main driver for most companies offering gut microbiome testing is a commercial goal. While revenue from the tests is one aspect, another objective often is to capture the buyer and use the test as a steppingstone to something else – be it a service such as a gut health consultation package or a product, like supplements designed to support gut health.

What can you expect when you order a gut microbiome test?

Upon purchasing a microbiome test online, a test kit will be shipped to your home. This kit contains stool sample collection instructions, collection tools such as gloves, disposable collection paper and a sample storage container with a preservative. Typically, the kit features a scannable code for easy registration, usually via an app. As part of the intake process, a brief health questionnaire is to be completed. Once you have collected your stool sample you can inform the lab or use the return shipping label to send the test kit back to the lab via post or arrange a courier pick-up.

Upon receipt, the lab processes the sample to identify the microbes. Following the identification of the microbes through genomic sequencing, the lab uses a large database of information from research studies, its proprietary dataset, and computational tools to generate a comprehensive report. This report typically includes the following:

1. The overall health of your gut microbiome based on the types of micro-organisms that are present and their relative abundance levels in comparison with a reference dataset of other samples.
2. A diversity score.
3. An overview of the most abundant bacteria: beneficial species, pathogenic species, opportunistic species.
4. An overview of other micro-organisms such as viruses, fungi, archaea, and prokaryotes (this depends on the lab and the genomic sequencing method used).
5. An analysis of the microbiome’s functionality: this is assessed based on the gut microbiota composition and looks at its potential for producing metabolites such as short chain fatty acids, vitamins, neurotransmitters, toxins, nutrients and its potential impact on detoxification, inflammation, gut permeability, food intolerances, and longevity.
6. Diet recommendations.
7. Supplement recommendations.

Some microbiome testing companies or labs offer an additional free consultation with an in-house microbiome consultant to explain the report. Other companies have a database of consultants that you can hire should you feel the need for further support.

Why do a gut microbiome test?

People who opt for a gut microbiome test often struggle with chronic digestive issues, like gas, bloating, GERD, abdominal pain, IBS, or constipation. Often these gut issues linger on a subclinical level prompting people to seek answers independently. A quick search on Google underscores the crucial role of gut bacteria in addressing many of these digestive concerns, making testing seem like an intuitive next step. Another subset of people turns to gut microbiome testing not due to specific digestive complaints but with broader health improvement objectives or concerns related to conditions like autoimmunity, metabolic issues, skin problems or cognitive function. When reading or researching about these health conditions or health in general, the role of the gut microbiome as a key player fuels the desire to learn more.

While there are some useful insights to be gleaned from commercial gut microbiome tests, there are several limitations that I want to cover first:

Limitations of commercial gut microbiome testing

1. Microbiome science is incomplete.

While we recognize the pivotal role of the gut microbiome in both health and disease, our scientific understanding remains incomplete. We simply do not yet have a full and complete understanding of all the types of microbes that exist, their functionality, inter-microbial interactions, and host-microbiome interactions. Although numerous studies establish correlations between microbiome composition and various diseases, there is not yet enough insight into causation and the intricate mechanisms by which microorganisms influence our biology. Given the rapid evolution of scientific knowledge in this area, it is crucial to approach gut microbiome test results with caution, recognizing that what holds true today may undergo revision in the future.

A great example of this is H Pylori. This bacterium can cause damage to the gastric mucosa, ulcers, GERD, and other GI symptoms and was thought for a long time to be a pathogenic microorganism that needed to be eradicated. More recent research has shown that around 70% of people with H Pylori in their gut are healthy and have no symptoms. Some studies have found certain protective effects of this bacteria on the body (1).

Given the evolving science and the dynamic interplay between the gut microbiome and the host, it is important to interpret a microbiome report in conjunction with your overall health status, prevailing symptoms, health history, and various environmental factors. A good direct-to-consumer microbiome testing company goes beyond mere data collection, striving to incorporate as much personalized information as possible into their analysis. Additionally, they may provide the option of a consultation with a qualified practitioner well-versed in the nuances, strengths, and limitations of these tests. Importantly, such practitioners take the time to familiarize themselves with your unique situation while helping you to interpret the results.

2. The microbiome is personal.

Each of us carries few hundreds of species out of which 30-40 make up the bulk of the microbial population. Between individuals there is a certain degree of similarity on the level of phyla (which are the main groupings of bacteria), less on a genus level and much less on a species and strains level. In other words: your microbiome is unique. It is as unique as your fingerprint. And the way this unique microbiome “performs” depends on other personal factors, such as your unique genetic make-up. Simply put there is no perfect gut microbiome, and you can’t “ace” a gut microbiome test. There are, however, patterns that help to identify potential problem areas and scope for improvement (as detailed below).

3. The microbiota composition does not necessarily reflect its function in the body.

Studies have shown that there is about 43% similarity in the composition of gut microbiota between two different people. However, the metabolites that are produced by these different microbiomes is on average 82% similar (2). Metabolites are the compounds through which microorganisms impact their host: they act as signaling molecules in the body and influence metabolic pathways. In one study there were about 6 times more associations found between host metabolic pathways and fecal metabolites as compared to species (2). What this means is that the actual function of the microbiome as measured through metabolites is potentially more important than the microbiome structure or which micro-organisms are in the gut microbiome.

Most gut microbiome tests take an inventory of the microorganisms found in a stool sample and use computational tools to predict their function in the gut based on what we know about microbial metabolites. Not only are metabolites a growing area of research, using algorithms to assess functionality may not be fully accurate as microbial genes may or not be expressed. It is important to realize that our understanding of gut microbiome structure and functionality is incomplete and that test results need to be interpreted accordingly. There are microbiome testing companies that use RNA analysis or metatranscriptomics (like Viome) to determine the active microbes and the microbiome’s functional profile but as of now there are certain other potential drawbacks associated with this methodology (see review at the end).

4. Lack of standardized testing guidelines.

Between different labs gut microbiome testing results can be very different. This is because of the use of different technologies, microbiome profiling methods, references databases, computational tools, and other processes (3). There are several anecdotal reports of practitioners who have sent in portions of the same stool sample to different labs and received back widely differing and sometimes contradictory results. A 2023 study published in Nature Journal highlighted significant differences in bacterial diversity and composition results between 6 labs that received the same DNA sample (3). This lack of consistency has prompted a need for uniform reporting standards such as STORMS (Strengthening The Organization and Reporting of Microbiome Studies) (4). Sample collection and preparation processes, quality control, validation steps, and careful interpretation of results are critical. Selecting a reputable microbiome testing company that follows good testing guidelines is therefore important.

5. The microbes in a stool sample do not represent your entire gut microbiome.

The adult GI tract is about 9 meters long and different areas in the digestive tract house different local microbial communities. A stool sample captures only a portion of the microbiota from within the colon. It may miss microbes that are present in other areas in the colon, as well as microbes that reside in the small intestinal tract or those that adhere to the gastrointestinal mucosal lining and are not shedded in stool (5). In a study done with healthy individuals stool microbiome results were found to be a poor indicator of the actual microbiome composition and its function in the gut (6, 7).

6. The microbiome composition is dynamic.

The microbiome composition can go through rapid shifts, depending on diet and lifestyle factors and even diurnal patterns. Everyone has a core microbiome structure, but the overall microbiome ecology is dynamic. Which means that the results of today’s sample may be quite different from last week or next week depending on what is going on with your diet and lifestyle (5).

The benefits of commercial gut microbiome testing

Despite the above-mentioned limitations, there are benefits to gut microbiome testing. Here are some reasons to do a test:

1. Increase understanding of your gut microbiome’s role in health or disease.

The gut microbiome is intimately connected to our state of health and disease. Your gut microbiome test results can reveal certain trends that correlate with symptoms and your diet and lifestyle choices. This could be the presence or overgrowth of potentially harmful species, the lack of beneficial ones, or the inflammatory profile and the impact of your microbiome’s functionality on your metabolism, aging, brain function, or health in general. Understanding how your inner ecosystem relates to how you feel can be an eye-opener and give you the motivation to take your microbiome seriously and take steps to restore it to a healthy state. 

2. Assess microbiome diversity.

It is well established that microbial diversity as measured in stool samples is an important indicator of gut microbiome health (8). In general, a more diverse range of micro-organisms means a healthier ecosystem. A lack of diversity is associated with increased risk of allergies and asthma in children, obesity, insulin resistance, dyslipidemia, and inflammation (9, 10, 11). All of us have been exposed to factors that reduce gut microbial diversity: like medications, antibiotics, monotonous diets, stress, pollution and more. All gut microbiome tests report a diversity score, based on the number of species found and their abundance levels. If your diversity score is low, you can take steps to help build a more robust microbial ecosystem.

3. Assess the impact of dietary and supplement interventions.

You can use a series of gut microbiome tests to track the impact of diet and lifestyle interventions. Tracking is a powerful biohacking tool for supporting a personalized health optimization approach. Wearable devices such as the Fitbit, Apple Watch, Oura ring, Whoop band and Continuous Glucose Monitors have gained popularity for that same reason. Some of the benefits reported by users of health tracking devices include increased motivation to engage in healthy behaviors, improved health literacy, and positive behavior change. Through access to real live data such as HRV balance, heart rate, activity levels, sleep quality, blood sugar levels and, in this case, gut microbiome composition and functionality, you can connect aspects of your health to diet & lifestyle habits and learn what works for you (or not).

4. Contribute to science.

Granted, it may not be your main reason to engage in testing, but the knowledge that you are contributing to science by submitting your stool sample is a nice added benefit. Microbiome science is an active and important area of research that helps us to connect the gut microbiome to diet, predict the development of disease, identify targeted therapeutics such as precision probiotics and microbiome precision medicine.

How to choose a gut microbiome test

Once you have decided to learn more about your gut microbiome and how it relates to your health, you are going to have to choose a microbiome testing company. As outlined earlier, it makes sense to do some due diligence before ordering your test kit. There are new microbiome testing companies appearing constantly and your experience is going to be impacted by factors such as business model, processes, and testing standards. Here are some points to consider:

• Is the company in it for the testing, or is their main objective to sell you their products or other services?
• What is the company’s reputation?
• What do customer reviews look like?
• Does the company / laboratory readily share information about sequencing methods and primers used, as well as bioinformatics tools and databases for interpreting results?
• Does the sample collection tube contain stabilisers?
• Does the laboratory perform regular quality control testing?
• Can you get access to a sample report? Are the results easy to read, actionable, are meaningful next steps being communicated?
• Does the company try to correlate the results to your unique situation? For example, by capturing your unique data or food habits or through a personal consult?
• What kind of support is being offered after the testing is done and who provides this support: what is their experience, background in microbiome research and functional healthcare?
• What are the privacy and security measures in place for handling personal health data? Is there a privacy policy?
• What is the size and nature of the dataset that is used to compare your sample with? I learned the importance of this when I sent my Northern European microbiome sample to a lab in India that uses a reference dataset comprised solely of Indian samples.
• Watch out for over-promises. If a microbiome testing company claims that their test is the answer to all your issues, I would consider that a red flag, for all the reasons I have mentioned above.

Microbiome Test Reports – Diet Recommendations

I do want to spend a moment to discuss the diet recommendations that these gut microbiome tests reports provide. Most of the reports I have seen provide a staged diet plan that begins with the elimination or reduction of inflammatory foods like sugar, refined carbs, refined vegetable seed oils, and an increase in the intake of vegetables, fruits, and fiber-rich plant foods in your diet. If you are eating an inflammatory diet that is low in plant foods, making such diet changes is going to positively impact your gut microbiome and your health. These broad diet recommendations are found in every commercial gut microbiome test report and, if adhered to, will ensure positive microbiome – and health changes.

Then there are the more nuanced diet recommendations, such as the elimination of certain otherwise healthy wholesome foods that can feed the overgrowth of a particular pathobiont, or the inclusion of foods that have been shown to support the growth of keystone bacteria. If you are already eating a healthy, wholesome, plant-powered diet you can certainly experiment with these nuanced diet recommendations that the microbiome tests offer. I am, however, skeptical of treating gut microbiome test diet recommendations like gospel for several reasons, most of which have been outlined above. Microbiome science, like nutrition science, is hugely complex, still evolving and only a part of the entire health and wellness puzzle. Much of it may be true but partial. To get as close as possible to crafting a truly ideal and personalized nutrition and lifestyle strategy you need to look at the gut microbiome in conjunction with your health history, life history, current health status, genetics, the environment you live in, and your lifestyle habits. It is for those reasons that I advocate working with a functional/integrative health practitioner who is trained in incorporating gut microbiome data and all these other aspects and who uses standard lab tests, as well as advanced functional and genetic testing to inform personal nutrition and lifestyle recommendations. They should have the ability to gauge which patterns in your stool test are clinically relevant to you and help you navigate that complexity in a personalized manner.

Summary

First things first: if you are dealing with worrisome chronic symptoms, digestive or otherwise, a direct-to-consumer gut microbiome test should not be your first step. In this case, you want to engage with a qualified, functional healthcare practitioner who can guide you appropriately. They may recommend (as I often do) to run a GI test and/or a complete gut microbiome analysis as part of the investigative process and to determine the best personalized approach.

If, despite seeking medical help, you reach a dead end and you continue to deal with sub-clinical nagging symptoms, or you are just curious about your gut microbiome and you want to understand how to look after it better, do your research first and pick a reputable testing company, while keeping in mind the points listed above. I am of the opinion that gut microbiome testing is best done as part of a comprehensive health building approach under the guidance of a qualified practitioner who understands the clinical relevance of your test results and is able to integrate test data in your carefully curated, personalized health strategy.

Finally, even if there are limitations to gut microbiome testing currently, I am hugely optimistic and excited about the rapid advances in the microbiome research field and its application in personalized healthcare. Carefully selected practitioner- and commercial gut microbiome tests do and will continue to play a key role in my practice and my ability to gain deeper and fuller insights into my clients’ microbiome and its impact on their health and wellbeing.

Be Well.

 

_______

A quick overview of Genomic sequencing methods:

There are different sequencing methods that can be used by labs. All of them have their own unique advantages and disadvantages.

16s rRNA Sequencing

Most microbiome testing companies today use 16s sequencing. The 16s rRNA gene is a gene that is present in all bacteria and archaea. This sequencing method was used by the National Institute of Health’s Human Microbiome Project and thousands of laboratories worldwide. Hundreds of scientific studies based on the 16s gene are published every year. This has resulted in a sequence database unmatched in size compared to other sequencing methods: more than 3 million 16s gene sequences. A downside of this method is that it can detect at the phylum and genus level and sometimes species. Eukaryotes, which include fungi and parasites can be detected by the 18s rRNA gene and some labs combine 16s and 18s in their sequencing to report these different species. It is the most cost-effective sequencing technique.

Shotgun metagenomic sequencing

In shotgun metagenomic sequencing all the DNA in a sample is analyzed and this allows for sequencing of different microbial organisms, including bacteria, parasites, fungi, viruses, etc. down to the species and even strain level. Besides providing information on the taxonomic diversity it provides insight into the functional potential through the presence of genes and pathways and the use of computational tools. It cannot, however, distinguish between active and non-active microorganisms. It is comparatively more expensive and computationally intensive as compared to 16s sequencing. Furthermore, the reference database is comparatively smaller with over 100,000 genomes.

Metatranscriptomics (RNA)

Metatranscriptomics focuses on analysing the RNA in a sample. RNA transcripts reveal which genes are expressed and what are the metabolic activities and functional processes in the microbial community. In other words, it reports on the actual function of the microbiome. It is comparatively a newer technique and therefore there it has less supporting research literature. Additionally, there are certain other technical challenges associated with this technique. It is computationally demanding and therefore costly, microbial species that are present in low abundance can be challenging to detect and RNA is generally less stable than DNA and therefore prone to degradation. Furthermore, it can be challenging to distinguish microbial RNA from host RNA, potentially resulting in host RNA contamination (12).

_______

References:

1. Reshetnyak VI, Burmistrov AI, Maev IV. Helicobacter pylori: Commensal, symbiont or pathogen? World J Gastroenterol. 2021 Feb 21;27(7):545-560. doi: 10.3748/wjg.v27.i7.545
2. Visconti, A., Le Roy, C.I., Rosa, F. et al.Interplay between the human gut microbiome and host metabolism. Nat Commun 10, 4505 (2019). https://doi.org/10.1038/s41467-019-12476-z
3. Roume, H., Mondot, S., Saliou, A. et al.Multicenter evaluation of gut microbiome profiling by next-generation sequencing reveals major biases in partial-length metabarcoding approach. Sci Rep 13, 22593 (2023). https://doi.org/10.1038/s41598-023-46062-7
4. Mirzayi, C., Renson, A., Genomic Standards Consortium. et al.Reporting guidelines for human microbiome research: the STORMS checklist. Nat Med 27, 1885–1892 (2021). https://doi.org/10.1038/s41591-021-01552-x
5. Allaband C, McDonald D, Vázquez-Baeza Y, Minich JJ et al. Microbiome 101: Studying, Analyzing, and Interpreting Gut Microbiome Data for Clinicians. Clin Gastroenterol Hepatol. 2019 Jan;17(2):218-230. doi: 10.1016/j.cgh.2018.09.017. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6391518/
6. Michael Blaut, Thomas Clavel, Metabolic Diversity of the Intestinal Microbiota: Implications for Health and Disease1,2, The Journal of Nutrition, Volume 137, Issue 3, 2007, Pages 751S-755S, ISSN 0022-3166, https://doi.org/10.1093/jn/137.3.751S.
7. Jensen BAH, Heyndrickx M, Jonkers D et al. Small intestine vs. colon ecology and physiology: Why it matters in probiotic administration. Cell Rep Med. 2023 Sep 19;4(9):101190. doi: 10.1016/j.xcrm.2023.101190.
8. Lozupone CA, Stombaugh JI, Gordon JI et al. Diversity, stability and resilience of the human gut microbiota. Nature. 2012 Sep 13;489(7415):220-30. doi: 10.1038/nature11550.
9. Le Chatelier, E., Nielsen, T., Qin, J. et al.Richness of human gut microbiome correlates with metabolic markers. Nature 500, 541–546 (2013). https://doi.org/10.1038/nature12506
10. Abrahamsson TR, Jakobsson HE, Andersson AF et al. Low gut microbiota diversity in early infancy precedes asthma at school age. Clin Exp Allergy. 2014 Jun;44(6):842-50. doi: 10.1111/cea.12253.
11. Abrahamsson TR, Jakobsson HE, Andersson AF, Björkstén B, Engstrand L, Jenmalm MC. Low diversity of the gut microbiota in infants with atopic eczema. J Allergy Clin Immunol. 2012 Feb;129(2):434-40, 440.e1-2. doi: 10.1016/j.jaci.2011.10.025.
12. Shakya M, Lo CC, Chain PSG. Advances and Challenges in Metatranscriptomic Analysis. Front Genet. 2019 Sep 25;10:904. doi: 10.3389/fgene.2019.00904.