Commercial gut microbiome testing

09 Nov 2021
by Julie Thompson, Linda Thomas FIFST FRSB

Members of the British Society of Gastroenterology’s Gut Microbiota for Health Expert Panel offer advice on how to support patients using commercial microbiome test kits.

Since the publication of the human gut genome sequencing report in 2012,1 our understanding of the interrelationship of our gut microbiota with health and disease has increased.

At the end of 2019, there were more than 9,500 gut microbiome citations on the Web of Science database, 30 times more than in 2001.2 There has also been rapid development in methods to improve the understanding of the complex interaction between the microbes and the host over the last 20 years.

The general public’s awareness of gut health has also grown, and people are very interested in what lifestyle changes they can make to improve the composition of their gut microbes and, therefore, their overall health. Certain commercial companies are currently offering to test faecal samples and to provide a report of the customer’s gut microbiome and microbial metabolites (such as butyrate levels).

The programme offered also can include tests such as faecal calprotectin, a measure of gut inflammation. The company might then provide suggestions about lifestyle changes, including supplements to improve the gut microbiota profile. Thus, they provide a complete complex testing service and treatment plan, but at a cost. It should be questioned whether current scientific knowledge is at a stage that can support these tests, reports and dietary advice.

This article describes what we know now and suggests what dietitians can advise patients who might attend a clinic with such a report in their hand and an expectation of receiving advice about lifestyle changes that might improve their gut microbiota profile.

“It should be questioned whether current scientific knowledge is at a stage that can support these tests.”

The human large bowel is home to over 100 trillion bacteria, representing over 1,000 different species.3 This number does not account for other types of microbes that may be present, such as viruses, protozoa and fungi. The gut microbiota could be considered a microbial organ of the body2 that, through a complex interaction, regulates physiology at both local and systemic levels.2

Considerable variations 

The Human Microbiome Project was founded in 2009 and was expected to measure the standard human gut microbiome. Even at the early stage of the project, there was an understanding that the researchers would look at what was considered ‘normal’ and not necessarily what was considered ‘healthy’.1 Two-hundred-and-forty-two participants took part. The investigators undertook a 16s RNA gene analysis at various body sites and at two time points during the study in a subgroup to assess variability. The result of this extensive study was the discovery that there was considerable variation in the microbiota of ‘healthy’ individuals, and there was little correlation with biometric measures such as BMI.1

The Human Microbiome Consortium study1 was published in 2012; what do we know now? A body of evidence has been reported,4 for instance, on the interaction of the microbiome in energy homeostasis and development of metabolic syndrome in individuals with obesity-related metabolic disease. However, the gut microbiota is only one environmental factor in what is a complex multifactorial disease, but perhaps a promising one for future investigation.

A link has also been reported between non-alcoholic fatty liver disease and an altered gut microbiome,4 and the scientific literature suggests gut dysbiosis may be a factor for diseases such as inflammatory bowel disease,4 autoimmune liver disease,4 colorectal cancer4 and irritable bowel syndrome.5,6 Although it is still considered early in our understanding of how the gut microbiome might influence its host’s health and disease, this is an exciting prospect for future research.

The Human Microbiome Study1 investigators suggested other factors that needed consideration in future research, including diet, plus other possible confounding variables. Research to date indicates there is no ‘standard’ microbiome composition that can be used as a baseline for health and few instances where there is a definitive association between any gut microbe and disease risk.

This therefore does not support the commercial tests that are currently being offered. Whilst it is hoped that future research can enable treatments to be developed based on beneficial manipulation of the gut microbiota and its host interactions, we are not at that stage yet.4

Case study

Her GP has referred Mrs Jones to you at her request for weight management. During the consultation, she reports that she purchased a gut microbiome test after reading in a magazine that unhealthy gut microbes could cause obesity.

The commercial test has shown that she has low levels of bifidobacteria, and also identified Escherichia coli in her stool, which she thinks is a “nasty bacterium”, and she is very concerned about this.

Her test report suggests that changing lifestyle can help, and advised she see a nutritional therapist, take their proprietary probiotic, then have another test after she has made the changes.

She is aware that the best option is a registered healthcare practitioner, hence her request to her GP. On assessment, her Bristol Stool Chart type is two, and she opens her bowels every other day with no reported symptoms of bloating or abdominal pain. Her diet history suggests that she is managing two portions of fruit and vegetables per day, her diet is high in energy, plus she has one meal containing wholegrain carbohydrates per day. Her fluid intake is currently adequate. What would you advise?

It can be a challenging situation if patients attend the clinic with a report in hand and expect the dietitian to use the results to advise and measure lifestyle change benefits. A way to approach this problem is to say that, whilst the results are interesting, there is currently insufficient research to tell us how any specific changes to lifestyle and/or diet may result in changes to her gut bacteria that would directly affect her health and risk of obesity.

However, we do know that positive changes to diet and activity have worthwhile benefits for overall health. We don’t know what a healthy microbiome is yet, as the microbe populations vary from person to person plus, a one-off sample of faeces will not necessarily give a good picture of an individual’s gut microbes.4

What is generally accepted is that a wide range of bacteria is a good indication for your gut microbiota. The gut microbiota will generally include some types of microbes that, whilst they can cause illness under certain circumstances, can be present without causing any problem. Escherichia coli is a good example of this. These bacteria are commonly found in the gut and most are harmless. In fact, some strains of E. coli help to digest food and can produce vitamin K.

Her interest in dietary and lifestyle changes for the better, however, should be encouraged. Discuss goals she might choose, such as increasing fibre intake and fruit and vegetable portions slowly, plus strategies to reduce her energy intake. If she wishes to try a probiotic, there has been a recent review that suggests some strains might be useful in reducing BMI and weight.7 Choice should include a product delivering a minimum dose of 1 x 109 CFU (colony forming units) of the probiotic strain with quality assurance that the probiotic strains remain viable at this level at the end of shelf life, plus proof from human intervention studies that the probiotic strain(s) reaches the gut alive. Ideally, the probiotic chosen should be supported by evidence such as that reported in Tome-Castro et al (2021).7 Consider goals with outcomes that she can easily measure herself, such as stool type and weight or waist circumference, if appropriate to her circumstances.

In conclusion, commercial gut microbiota testing and lifestyle change programmes based on the test results cannot be advised currently as the science is not at a stage that can support testing and treatments programmes. Any reports of high faecal calprotectin results should be reported to the patient’s GP, although these commercial tests may not reflect similar tests that are used to test for inflammatory bowel disease in clinical practice.

Gut Microbiota for Health Expert Panel

The Gut Microbiota for Health (GMfH) Expert Panel of the British Society of Gastroenterology is a multidisciplinary group of healthcare professionals, including dietitians. The panel aims to promote research and raise awareness of the gut microbiome and its health effects among healthcare professionals and the general public. To this end, they have produced a booklet9 in collaboration with Guts UK Charity that can help to explain in lay terms what we currently know about microbiome testing.

Copies of the booklet can be requested or downloaded free from the Guts UK website. If you are interested in the GMfH group and further reading, then relevant and key papers on a range of topics can be found here. The GMfH panel is very active. For instance, it has been instrumental in helping to establish guidelines for faecal microbiota transplantation (now called intestinal microbiota transplantation) and their review on the influence of the gut microbiota on health and disease4 has been highly cited.


  1. Human Microbiome Project Consortium. Structure, function and diversity of the healthy human microbiome. Nature. 2012 Jun 13;486(7402):207-14. doi: 10.1038/nature11234. PMID: 22699609; PMCID: PMC3564958.
  2. Li et al. (2020) Seven facts and five initiatives for gut microbiome research. Protein & Cell 11: 391-400
  3. Guts UK Charity (2018) All you need to know about gut bacteria in health and disease GUTS_Bacteria_In_Health_And_Disease_A5_V1.92.pdf ( accessed 26.08.21
  4. Marchesi et al. (2016) The gut microbiota and host health: A new clinical frontier. Gut 65(2): 330-339
  5. Ahluwalia, Iribarren , Magnusson, Sundin, Clevers, Savolainen, Ross, Törnblom, Simrén, Öhman A Distinct Faecal Microbiota and Metabolite Profile Linked to Bowel Habits in Patients with Irritable Bowel Syndrome. Cells. 2021 Jun 10;10(6):1459. doi: 10.3390/cells10061459. PMID: 34200772; PMCID: PMC8230381.
  6. Liu, Li, Yang, Zhang, Wang, Jia, Xiang, Wang, Miao, Zhang, Wang, Wang, Song, Sun, Chai and Tian (2021) Leveraging 16S rRNA Microbiome Sequencing Data to Identify Bacterial Signatures for Irritable Bowel Syndrome. Front. Cell. Infect. Microbiol. 11:645951. doi: 10.3389/fcimb.2021.645951
  7. Tomé-Castro XM, Rodriguez- Arrastia M, Cardona D, Rueda-Ruzafa L, Molina-Torres G, Roman P. Probiotics as a therapeutic strategy in obesity and overweight: a systematic review. Benef Microbes. 2021 Feb 24;12(1):5-15. doi: 10.3920/BM2020.0111. Epub 2021 Jan 17.PMID: 33459204.
  8. Hill C, Guarner F, Reid G, Gibson GR, Merenstein DJ, Pot B, Morelli L, Canani RB, Flint HJ, Salminen S, Calder PC, Sanders ME. Expert consensus document. The International Scientific Association for Probiotics and Prebiotics consensus statement on the scope and appropriate use of the term probiotic. Nat Rev Gastroenterol Hepatol. 2014 Aug;11(8):506-14. doi: 10.1038/nrgastro.2014.66. Epub 2014 Jun 10. PMID: 24912386.
  9. Long version of the gut microbiome testing leaflet:

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