Talking about poo is not something many people are comfortable with. It’s thought to be taboo and uncouth, and even in clinical settings - patients often struggle to describe and articulate the fine details of their bowel movements and habits. Stool samples proposed a nifty way around this - promising an insight into one’s gut health without the awkwardness of verbalising what goes on in the toilet. It’s commercially available, and as interest in gut health continues to rise, clinicians are increasingly being asked by curious and health-conscious patients whether they should get their microbiome tested.

So if a patient presented their microbiome report to you, would you feel comfortable interpreting it and translating that into anything robust and meaningful? It’s tricky.

Without a doubt, there is more value in poo than as a vessel for waste removal. But while the science behind the gut microbiome is fascinating and evolving rapidly, the clinical application of these tests is still catching up. So how do we navigate a conversation around microbiome testing with patients? What can they tell us? How do we interpret reports? Are they clinically useful? And if not (or not yet), should we recommend them?

What does a Stool Sample Report look like?

There is a difference between the stool samples done in clinical settings, and those available commercially. Both, clinical or commercial, can offer a variety of insights depending on what is being measured.

1. Traditional stool tests:

These are used to detect infections (e.g. Salmonella, Giardia), inflammation (e.g. faecal calprotectin), occult blood, pancreatic insufficiency (e.g. faecal elastase), and malabsorption. [1]

For patients presenting with symptoms, these tests can identify severe disturbance to the balance of microbiota due to small intestinal bacterial overgrowth (SIBO), inflammatory bowel disease (IBD), or lifelong antibiotics treatment.  Testing pre and post-dietary intervention to establish the effectiveness of treatment.

2. Commercial microbiome tests:

These tests analyse the diversity and abundance of gut microbes via 16S rRNA sequencing or metagenomics, sometimes offering:
- Bacterial composition.
- Alpha diversity scores (a proxy for microbial richness).
- “Dysbiosis” or balance scores.
- Personalised diet or probiotic recommendations based on proprietary algorithms. [2][3]

How Do We Interpret the Report?

A report comes in the post or via an app, documenting the species of bacteria, fungi and even viruses living in ones stool, with a ‘gut score’ on how healthy the stool is, alongside a list of recommendations on how to improve this. How did it derive those suggestions, and how does knowing the percentage of each species of bacteria at one time point really impact someone’s care? These are some things we need to take into account:

What do they tell us?

‍Commercial gut microbiome tests can tell us the names of microbes present, such as Bifidobacterium, Lactobacillus, Streptococcus and Enterococcus, but depending on what analytical technique, can’t always explain their functionality - which is more important than only knowledge of the compositional data. 16S rRNA sequencing analysis can essentially tell us who is there, but not what they do. Deep shotgun sequencing is more advanced, but interpretation of these results is still a challenge.

There is no defined “healthy/normal” microbiome profile

Unlike how we have reference ranges for blood tests, this doesn’t exist for stool. Microbiome composition varies significantly across age, geography, diet, and lifestyle, and interpreting deviations from a "reference" microbiome may not be meaningful. [4] Even the Human Microbiome Project which started in 2007 has yet to define a “healthy core microbiome”. [5]

Gut Microbiome profiles change all the time
‍
The gut microbiome is in constant flux. It is influenced by diet, exercise, stress, and disease, and can show changes within months or even days. [6] Gut microbiome tests are generally a single measure at a single time point. Depending on when you take a test, it may or may not show any significant findings.

Gut microbiomes are affected by numerous things

Sex, age and BMI have the biggest impact on the gut microbiome .[7]  Stress is another critical factor that can contribute towards “dysbiosis” and disease states such as IBS and IBD. [8] Other factors include sleep, physical exercise, mental health, genetics and diet. [9] Conducting a holistic assessment that takes all these factors into account takes time, but would provide a far better understanding of their gut microbiome profile, and overall health.

Stool is more than just species

While microbiome testing offers a snapshot of gut bacteria, stool consistency and appearance give real-time, actionable clues about gut function. The Bristol Stool Chart (I was from Bristol and am very proud of this!) is a validated tool that helps identify issues like constipation, diarrhoea, or malabsorption based on stool form. There is an established “healthy” type and consistency - Types 3–4 [10]. Unlike microbiome data, stool patterns are easy to observe, track, and respond to, making them just as important in assessing gut health. [11-12]

Commercial tests are not clinical tests

While there is a lot of useful information we can gather from someones stool sample, interpreting these with the lack of symptoms is not diagnostic. Many companies provide risk scores and dietary advice, but few have undergone rigorous scientific validation or peer review. There is evidence that some diseases may have signature profiles -  for example, associations between gut microbial composition and conditions such as colon cancer, depression and obesity (amongst many others) have been observed. [13-15], but it’s currently too premature to be clinically validated.

How it can be helpful

Knowing ones gut composition can offer value for some individuals - particularly those who are very engaged in their health and motivated to make positive lifestyle changes. For these patients, receiving a personalised microbiome report can act as a behavioural nudge, encouraging better dietary habits, such as increased fibre intake, or reduced ultra-processed food consumption. We know that an individual’s diet is a “key determinant” in their microbiome, which, in turn, impacts on how they respond to the food they eat. [16]

It can also help validate symptoms they are experiencing, and may prompt earlier conversations with clinicians. In the context of patient empowerment and encouraging a patient to have a stake in their own health, microbiome testing can lead to a better awareness of their gut-brain and gut-immune connections. The bottom line is that it just needs to be framed appropriately:  not as a diagnostic tool, but as an informative and educational one.

Tips for Clinical Practice:

- Setting realistic expectations - Inform patients about what information these tests can provide. At present, microbiome tests are primarily research tools. They are not yet validated for routine clinical decision-making, and can’t identify or diagnose conditions.
- Focus on established diagnostic tests - Encourage the use of validated stool tests, such as faecal immuno-chemical tests (FIT) for colorectal cancer screening, which have demonstrated clinical utility.
- Personalising care - A personalised approach to health and nutrition is the goal, as every individual we treat is unique. Having information about not only a persons gut microbiome, but their nutrition, sleep, mental health and fitness is useful, and arguably more effective than a generic approach. [17] But at present, further research is needed on how we analyse and interpret these results before personalisation can really be used effectively.
- Stay informed - The field is rapidly growing and evolving, and it is possible that in the not so distant future, there may be clinical applications of microbiome analysis, such as personalised medicine approaches. Patients can be just as well-read (at times, even more so!) as clinicians, so listen up.

Key Takeaways:

1. Stool sampling should be symptom-driven, not curiosity-driven: Stool sampling can give interesting information, but at this point, that information is hard to interpret meaningfully due to inter-individual variation. We also do not yet know what a “healthy” microbiome profile looks like.

2. Holistic care: Gut health is affected by a host of factors, including sleep, hydration, nutrition, physical activity, stress and mental health. [18-22] These are the real game changers with strong evidence backing. Establishing how a patient is doing on these fronts enriches our understanding of their gut microbiome, but also allows us to tailor their care.

3. Tracking changes over time: Using means of assessing changes in someones stool habits - timing, frequency, consistency and appearance (e.g through the use of the Bristol Stool Chart) is important, and may be more beneficial than a one-off test.

How can you track and assess your patient’s stool through the SANNO platform?

To make the most of microbiome testing insights in clinical practice, SANNO offers a powerful clinician portal and patient app that seamlessly support follow-up and monitoring.

Clinicians can invite patients to track their symptoms and stool patterns using the Bristol Stool Chart directly within the SANNO app, with real-time visibility in their clinician dashboard.

In addition to stool tracking, SANNO enables the collection of nutrition, hydration, bloating, urgency, and other key endpoints tied to microbiome health, all within a holistic 360º view that includes sleep, stress, and activity.

For clinicians already using or considering microbiome testing, SANNO offers an integrated and personalised way to follow up with patients and also support lab integrations on request.

Try SANNO here and bring a whole-person approach to your patient care.

Written by Dr. Julia Craggs, May 2025.

References:
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