Which gut health tests are worth it? Microbiome, stool and SIBO breath tests compared

What is the gut microbiome, and what does it do?

Your gut microbiome includes 30 to 40 trillion bacteria living in your intestine. This is slightly more than the number of cells you have in your entire human body.¹ This microbiome is shaped by food you eat, the medication you take, where you live, your age, stress levels, smoking and alcohol and how long it takes food to move through your bowels.^{2, 3} And two people who feel completely healthy can have very different microbiomes.⁴ Furthermore, over recent generations, our gut microbiome has had a significant reduction in its diversity, linked to a food supply that’s less diverse and more processed, industrialisation, advances in medical practice and sanitisation.^5–7 All of this complicates how to define what a healthy microbiome is.⁸

And whilst a lot of people associate your gut microbiome with bacteria, it also includes viruses, fungi, protozoa and archaea.⁹ And this association has crept into the definition of dysbiosis, where the population of “bacteria” gets out of balance.¹⁰ But balance is what is key here. Even a healthy gut contains bacteria some may label as bad. E. coli, for example, is the classic “bad bacteria”, but some strains produce vitamin K.^{11, 12} This is why I think labelling bacteria as “good” and “bad” is too simplistic, and the same may be true of some parasites.^{13, 14} Nevertheless, a gut microbiome that is out of balance has been associated with a number of problems:

Obesity: In obese mice, and possibly individuals, there may be more bacteria that are more efficient at breaking down carbohydrates and releasing more energy to be stored as fat, which may worsen insulin resistance, making it harder to regulate blood sugar.^{15, 16}

Diabetes: Your gut bacteria’s enzymes and metabolic pathways can influence how effectively you can handle the carbohydrates you eat.¹⁷ Their by-products can help your gut release GLP-1, the hormone that Ozempic and other GLP-1 medications mimic to signal to your pancreas to release insulin.¹⁸ And a deficiency of butyrate producers is linked to diabetes.^19–21

Mental health: Around 90% of your body’s serotonin is made in your gut, and it circulates through the whole body, though it does not enter the brain.²² Some gut bacteria can produce GABA, the calming neurotransmitter,²³ and in animal studies both signal to the brain via the vagus nerve.^{24, 25} And an imbalanced population may contribute to a heightened cortisol response.^{26, 27} This constant communication between the gut and the brain is what we call the gut-brain axis.²⁷ Your gut bacteria can also produce and stimulate hormones like dopamine, which may impact your mood, your stress levels and your quality of sleep.^{28, 29}

Systemic inflammation: Your gut bacteria help control your immune system and inflammation, at a local and a systemic level, and help you obtain energy and vitamins from food.^{30, 31} Short-chain fatty acids made by your gut bacteria, like butyrate, acetate and propionate, reduce inflammation and maintain the integrity of the gut barrier.³² It makes sense that research keeps linking the gut microbiome to a number of additional medical conditions such as inflammatory bowel disease, metabolic disease, cardiovascular disease, colorectal cancer, ADHD and eczema.^33–38

As the public becomes more aware of information such as this and seeks answers to their health issues, there will be more demand for ways to test this, resulting in more research being pushed in this area which companies can monetise. The main question therefore has to be: how useful are these tests?

Conventional stool tests

If you went down the conventional pathway, certain symptoms such as anaemia, loss of weight, loss of appetite, recent or worsening symptoms, black stools or vomiting blood, difficulty swallowing, bleeding from the back passage, waking at night with diarrhoea, a family history of bowel cancer or IBD, or new symptoms over 50 would typically be investigated by the relevant pathways promptly.³⁹ And say you mentioned to a gastroenterologist that you have issues related to your gut, such as bloating, constipation, stomach pain and so on. Some of the specific tests they may order to help determine the next stage of treatment would be:

• Faecal calprotectin: to differentiate between inflammation in your gut, indicative of something like inflammatory bowel disease, or IBS.⁴⁰

• Faecal immunochemical test (FIT): to check if there’s blood in your stools, and assess your risk for colon cancer to decide whether you need a colonoscopy.⁴¹

• Faecal elastase: to see if your pancreas is releasing enough enzymes to help digest fats and protein.⁴²

• H. pylori testing: if upper gut pain or burning to decide whether you need antibiotics and proton pump inhibitors to eradicate this bacterium.^{43, 44}

• Stool microscopy and culture: culture to look for bacteria, and microscopy for parasites, to see which treatment can target it.⁴⁵

• A breath test: to assess for the likelihood of excessive bacterial growth in your small intestine, to see which antibiotics may most likely help.^{46, 47}

• Anti-tTG antibodies and total IgA: if a doctor suspects coeliac disease.^{48, 49}

Commercial testing, however, now claims to take this testing significantly further. But are these tests worth it?

How do gut microbiome tests work?

Commercial microbiome tests typically claim to map the organisms living in your gut, assess the balance between them, measure markers of digestion, immune activity and inflammation at the gut level, and then provide a personalised plan to optimise all of it.

With all of these companies, you order a kit, collect a stool sample at home, and post it to a lab. And you will then often receive a score, an assessment of your gut diversity, and suggested ways of improving it with diet or probiotic recommendations, usually using population-level data and AI algorithms.⁵⁰

The key to whether this could be of use is to first understand these methods. There are six main ways these tests work, and each tells you something different:

16S rRNA sequencing: reads a single gene shared by all bacteria to identify them, but mostly only down to the genus level. It’s like reading only surnames. You learn which families of bacteria live in your gut, usually without their first names (the exact species), and it misses fungi, viruses and parasites. Companies such as Biomesight in the UK use this method to give you a broad bacterial profile of your gut.⁵¹

Shotgun metagenomics: reads a sample of all the DNA of all the bacteria, fungi, viruses and parasites in the sample and pieces them back together. It identifies most microbes down to species and sometimes strain level, and reveals what the microbes are capable of doing. It’s like reading the full census: first names and surnames, plus every resident’s CV, meaning what they’re capable of doing. Zoe in the UK uses this method to identify your “good” and “bad” bacteria and get a broad species-level bacterial map.⁵²

PCR: searches for, detects and amplifies the DNA of a fixed list of named specific, pre-selected organisms and measures how much of each one’s DNA is there. It’s like checking a guest list. So it’s highly sensitive for those targets but blind to everything else in the sample. Tests such as the GI-MAP use PCR to detect microbial DNA, and they claim greater sensitivity in doing so.⁴⁵

PCR plus culture: adds the older method of growing bacteria from the sample in a lab dish. Culture shows which bacteria are alive and lets the lab test which agents kill them. Tests such as Doctor’s Data GI360 and Genova GI Effects combine the benefits of PCR with culture.

Metatranscriptomics and metabolomics: Metatranscriptomics measures the microbes’ RNA (instead of the DNA), which is the short-lived message a microbe makes when it switches a gene on, showing which microbial genes are actively switched on and working in your gut at that moment. Metabolomics measures the chemicals in your stool, many made by microbes, such as short-chain fatty acids or vitamins. It’s like listening in on the town’s phone calls: it shows which jobs are under way today and also checking what the town has produced by the end of the day respectively. Companies such as Viome use metatranscriptomics to measure what your microbes are actively doing.^{53, 54}

In addition to the organisms themselves, some of these panels may also measure additional markers, such as zonulin, secretory IgA, beta-glucuronidase and blood metabolites to provide claimed markers for intestinal permeability, immune activity, hormone and toxin recycling and nutrient conversion respectively.^55–58

The case against most gut microbiome tests

Stool only shows what leaves your gut

I’ll start with the most obvious concern I have with gut microbiome tests: they measure the microorganisms through the stool, which leaves your large intestine. What about the microorganisms further up, in your small intestine, for example? How is this an accurate measure of that, and therefore how can it be an accurate measure of the cause of problems in your gut, which includes your full intestine, not just what leaves at the end of it?^{59, 60}

Same sample, different answers

Even if this were resolved, when standardised human stool material was sent to seven consumer microbiome tests, different providers gave different answers on the same sample.⁶¹ So the validity of the results of these tests comes into question.⁶²

Who sets the reference ranges?

Let’s say a stool sample was able to give a good understanding of what’s happening in your entire digestive system, and the results were standardised. Then who creates the reference ranges?^{63, 64} If you are a company, you could set cut-offs that favour the products you sell, because we don’t even know with confidence, from the most current scientific literature, what is normal in the microbiome.^{8, 50, 65} So how do these companies know? And are they transparent about how they create the reference ranges? Companies do seem to be starting to describe how they determine good and bad bacteria, how they define good and not optimal scores, and how they develop their ranges, which is a step in the positive direction.^66–68

Studies funded by competitors

Between companies, what obscures things even further is that they can fund studies to compete with each other. One example: a study funded by Doctor’s Data, a GI-MAP competitor, whose employee co-wrote it, reported a high number of false positives, with 4 of 7 clean control samples coming back reporting a pathogen at high levels, although disputed.^{69, 70}

Selling the solution

Unfortunately, when patients are vulnerable, they want a solution. With gut health being high on the wellness agenda, and with many patients trying almost anything, companies can use strong marketing tactics to avoid many of these arguments and sell them the solution.⁶² That can lead to unnecessary restrictive diets, antibiotics, long courses of antifungals or supplements, and anxiety from scores.⁵⁰

Why the big trials may never happen

However, there’s a caveat I’d add to all of this. To satisfy the scientists’ criteria for the gut microbiome, you’d have to spend millions on randomised controlled trials. These would have to prove, by keeping most measures the same, that certain medications or supplements, used in a personalised way, can improve patient outcomes. Some personalised trials have been done,^{71, 72} but they are small next to the multi-phase trials needed to change clinical guidelines. The honest truth is, this is hard to do at the scale needed, especially when companies keep their algorithms and data private.^{50, 62} And this method of investigation is very unlikely to work well to account for the personalisation required for individuals, and this is actually one of the problems with our current scientific method.

It’s why, no matter how much gut microbiome research we do, it’s going to be hard to definitively prove what matters in the end: whether patients get better with certain protocols, proven well enough that no specialist can argue with it.

That’s the hardest thing.

The case for gut microbiome tests

Even so, there are some good reasons to consider these tests.

PCR finds what culture misses

Firstly, validated PCR panels are more sensitive than culture for named pathogens and are recognised in hospital laboratories worldwide to guide diagnostics.^{45, 73} And whilst metabolomics and metatranscriptomics may be the frontier, there’s simply not enough good-quality data to base treatment on this. One problem with culture-based testing is that it favours oxygen-loving bacteria, because these grow in a lab dish more easily. In some cases, the bacteria that grow without oxygen are not just more abundant but may be more important clinically to explain the symptoms going on. DNA methods can pick that up.⁷⁴

Choosing antibiotics for H. pylori

Secondly, Helicobacter pylori is often treated with two or more antibiotics and a proton pump inhibitor.^{43, 44} However, stool PCR tests claim to check which antibiotics will work for bacteria such as Helicobacter pylori. If they are as reliable as they claim to be, that could provide real value from a conventional perspective: to rid the body of a bacterium that can contribute to significant long-term health conditions.^{43, 75}

Parasites and fungi

Thirdly, the gut microbiome extends far beyond bacteria, it includes parasites and fungi. Whilst we can check for parasites in the stool through clinical testing, a lot of patients do come back negative with the current methods.^{73, 76} Therefore, if a test such as PCR, which is more sensitive for parasites and fungi, exists, it could fill a real gap in conventional medicine, where a positive result reflects disease and not harmless carriage.^{77, 78} And if this testing became more established, I do believe it could change a lot of current clinical guidelines, especially if what becomes apparent is that more gastrointestinal issues have been contributed by fungi and parasites than we have acknowledged.

This is especially important when you consider that, when infection or overgrowth is suspected, the conventional treatment tends to be antibiotics, which target bacteria. If fungi or parasites are contributing more to a person’s current issues, the remaining question is: could we be making patients worse, encouraging, for example, fungi-associated disease to flourish in such a gut environment?^{79, 80}

Faecal transplants

And finally, even though microbiome sequencing research is roughly 20 years old, in one of the most severe bacterial infections, recurrent C. difficile infection, an endorsed treatment is to replace the intestinal microbiome by transplanting faecal microbiota, first described in China around 1,700 years ago.^81–84 There does seem to be potential growing value in understanding the microbiome.⁸⁵ And the consensus recommendation is that a doctor or clinician should order and interpret any test, and that evidence of clinical value is still scarce.⁵⁰

How is SIBO tested, and how accurate are breath tests?

The biggest problem with stool tests is that they’re measuring the stool that comes out of your large intestine. What about people who have issues with their small intestine? This is where the breath test potentially has some value to add to the diagnosis of SIBO: small intestinal bacterial overgrowth, though breath testing in IBS is contested by specialists.^{86, 87}

How a breath test works

You drink a solution containing either glucose or lactulose, and over the next 2 to 3 hours, you breathe into a bag every 15 to 20 minutes.⁴⁷ The rationale is that if bacteria have overgrown in your small intestine, they will ferment the carbohydrate early and produce hydrogen, whereas archaea would produce methane. The gas travels in your bloodstream, and you breathe it out through your lungs. An early rise in hydrogen, within 90 minutes, is considered a positive glucose or lactulose breath test for SIBO. This has the potential to differentiate between an overgrowth of archaea, something called IMO (intestinal methanogen overgrowth), and small intestinal bacterial overgrowth, which can determine the antibiotic regimen you can be prescribed.^{46, 88}

The only other way is to put an endoscope through your mouth, which already creates a risk of contamination from the bacteria in your mouth, go directly into your small intestine, aspirate the fluid there, culture it, and measure what’s growing. Obviously, because it’s invasive and costly, this is rarely done, which is why the breath test is far more accessible and available.^{46, 88}

False positives and false negatives

The big problem is how long it takes for the glucose or lactulose to go from your mouth to your colon. If it goes very fast, fermentation could be happening in your colon and not your small intestine, which could give you a diagnosis of small intestinal bacterial overgrowth when the fermentation is actually happening further down. A false positive.^{89, 90}

And the opposite: what happens if the glucose or lactulose doesn’t reach the small bowel in time, because of delayed emptying or glucose being absorbed before it reaches the bacteria? You could technically have SIBO, get a negative result, and be given false reassurance.^{47, 88} Nevertheless, taking into account that some people barely produce hydrogen at all, this also provides false reassurance.⁸⁸ And the same issue applies as mentioned above: what happens if it’s not bacteria or archaea in the small intestine at all, but fungi, for example? This test won’t measure that.⁹¹

Do you need the test?

Whilst it’s understandable why a lot of people are referred for and take this test, it really comes down to how you want to be treated in the end. If you get diagnosed with SIBO or IMO, the end solution is typically antibiotics.^{46, 92} Often, at least for the patients I see, the last thing they want is to be treated with antibiotics due to their effect on the gut microbiome, though rifaximin’s lasting effect appears limited.⁹³ So really think it through: if you wouldn’t take the treatment, what does the diagnosis do for you, unless it prompts a search for a further cause, such as slow movement of the gut, low stomach acid, medication or a narrowing after surgery?^{46, 88}

How I assess gut health

There may be ongoing debate between conventional doctors, functional and integrative medicine doctors, natural healthcare practitioners, and scientists for many years to come regarding the usefulness of these tests. But the only thing that matters in the end is: what is the best long-term solution to improve the health of your gut, ideally with as few side effects as possible?

To come to the solution to all of this, I do believe it would be important for modern science, modern medicine, and functional medicine to look at ancient healing traditions such as Ayurveda and Chinese medicine. Their diagnostic and treatment principles for healing the gut go back thousands of years. And I suspect that if and when there is a genuine merging of modern scientific principles with ancient healing philosophy, medicine will return to what it was always meant to be: a healing profession.

Admitting my own bias, considering the way I practise, I do believe the ancient pulse diagnosis, used for centuries in Ayurveda and for thousands of years in Chinese medicine, should be explored in more depth. Having studied and trained in both, I’ve seen how two independent systems, when understood, seem to point to similar ways of understanding what is happening in the entire body through the pulse.^94–97 The same can be said of the tongue. These are typically done as standard during consultations in Ayurveda and Chinese medicine. With both Ayurvedic and Chinese medicine practitioners, the more experienced they are, the more accurate I think they can be. I’d advise anyone with an open mind and curiosity to look more into this.

Furthermore, to resolve gut issues, the philosophy of treatment in the modern West will have to shift to how we’ve been doing it for thousands of years. Why? Because I believe it’s a genuine solution.

Germ theory and the terrain

The best example I can give is a frog that develops gut symptoms whilst it is in dirty water. The current Western testing methodology could be viewed as: let's test the frog's stool. Let's test the frog's breath. Let's test the frog's blood. Let's figure out what bad bacteria, fungi or other microorganisms are causing these gut symptoms. Once we find them, let's kill those bacteria, fungi or parasites.

As you can see, a lot of this article has been based on this modern way of thinking so far, which comes from germ theory.⁹⁸ Ayurveda and Chinese medicine tend to first focus on the terrain: the state of the body the microbes live in.⁹⁹

But when you look at how we’ve been treating human beings for thousands of years, what we actually do is simply figure out how to take the frog out of the dirty water first. If you don’t take the frog out of the dirty water, the same fungi, bacteria, and parasites will reinfect the frog. And in clean water, the frog’s own body grows stronger and better able to fight them off.¹⁰⁰ What I am saying may be controversial now, but I suspect that in the information age, as more and more people become aware, it will be accepted. It’s logical, intuitive, and makes sense.

How I treat gut health

The unfortunate reality is this way of thinking is not as scalable, patentable and profitable as endless testing, medication, supplements and protocols, unlike the simpler solutions ancient healing traditions such as Ayurveda and TCM may provide once the pattern is understood and treated competently.¹⁰¹ You can’t patent ginger, a pulse reading or an acupuncture point. For example:

• If a person has excess heat, simple ingredients like aloe vera may be used.¹⁰²
• If the issue is stemming from the mind, we target the mind, both consciously and subconsciously,^103–106 and through the subtle effects of food and herbs.¹⁰⁷
• If the cause is the environment, the first step may be to leave the environment if practical.
• If there’s a problem with flow in the gut or elsewhere in the body, considering the entire body is interconnected, we can use techniques such as acupuncture, cupping, and massage, which may help release this stagnation.^108–111

At the end of the day, what we’re really trying to do is create balance in the mind, body, spirit, and energy.

And at the forefront of microbiome research, the only solutions experts seem to agree on are that you should have a diverse group of microbes and species, supported by eating a diverse range of plants, probiotic and fermented foods, and keeping active.^112–114

So my question to you is: what will a gut microbiome test, or any of these tests, do for you, and how can they genuinely help your treatment? Could the personalised solution be to keep up to date with the gut microbiome in the scientific literature as much as possible? Could it be to take an interest in more ancient forms of healing? Could it be to combine all of this?

Regardless of my view or yours, the true solution going forward is for patients to become more empowered, to take charge of their health, and therefore their quality of life. As that happens, maybe medicine can return to a more healing profession, maybe the health of the population can change, maybe the health of our society can take a turn for the better. Who would benefit most from this?

I wish you all the best.

Which gut health tests are worth it?