Gut Health Testing – All Your Questions Answered (2024)

You know gut health is important—but you’ve been wondering if a gut health test is right for you.

We get it. You’d like to have a better idea of what’s going on in your gut, but you also want to make sure a gut health test is worth your time and money. Is it easy? Is it evidence-based? Is it even useful?

This is a huge and fascinating topic—and this article is designed to give you an introduction.

Here we’ll discuss the importance of gut flora, the science behind testing (including its limitations), how to test your gut health, how to interpret the results and what to do afterwards.

If you’ve already had a gut health test in the UK, you’re a health practitioner or you want more than an introduction, check out ‘Microbiome Test UK – In-Depth and Advanced Testing‘.


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How do you know if your gut is healthy?

Why test for gut bacteria?

Can you get your gut bacteria tested?

What does a DNA gut health test do?

How do doctors test gut health?

How to test your gut health online or at home?

How to interpret a gut health test?

How long does it take to receive the results of a gut health test?

What happens after a gut health test?

How to test gut health of a baby or child?

Which is the best gut health test?

How do you know if your gut is healthy?

A key belief in Functional Medicine is that the gut is the seat of your health. If something is ‘off’ in your gut, it can lead to problems with your digestion, such as:

  •      Bloating
  •      Flatulence
  •      Constipation
  •      Diarrhoea
  •      Abdominal cramps
  •      Nausea

This is an obvious connection. If you experience any sort of digestive symptom, it’s logical to wonder if your gut is working properly. After all, we’ve all eaten something dodgy and not felt great.

But—here’s the interesting part—more and more research is showing that gut health can influence symptoms outside the digestive system too. Our digestive capacity and our gut bacteria have been associated with a range of conditions1. Examples include:

  •      Obesity
  •      Diabetes
  •      Eczema
  •      Psoriatic arthritis
  •      Breast cancer
  •      Autism
  •      Arterial stiffness

Let’s be clear: we’re not saying that poor gut health causes these conditions. Researchers have found that there’s a correlation between impaired gut health (specifically impaired gut bacteria) and these conditions. Whether gut bacteria are influencing these conditions or it’s the other way around, we don’t yet know—but we do know there’s a link.

What this means is that you can’t assume your gut is healthy just because your digestion seems fine. Your gut bacteria have a much broader impact on your health.

The only way to be sure your gut is healthy is to test it.

Why test for gut bacteria?

Testing gut bacteria can be interesting for anyone—but it’s particularly helpful if you suffer from digestive issues or any of the other conditions listed above.

You have 100 trillion bacteria, yeasts, archaea and other microbes living in your gut. Together they weigh 2kg, which is roughly the same as your brain2.

These microbes and their genetic material are known as the ‘gut microbiome’. Funnily enough, they’ve also been dubbed ‘the second brain’—simply because they play a role in so many bodily functions3. These include:

  •      Digesting your food
  •      Modulating your immune system
  •      Producing neurotransmitters
  •      Synthesising vitamins

This is what we know so far. The gut microbiome is a new area of research and it’s developing all the time. Although we don’t yet have all the answers, we do know that healthier people tend to have richer and more diverse gut microbiomes4.

An easy way to understand this is to picture your gut microbiome as a meadow. The best meadows don’t just have one type of living thing—they have trees, grass, flowers, bees, butterflies and animals. Your inner meadow is the same. For a strong ecosystem, it needs not only high numbers of individual microbes but also lots of different types. They work together and help to keep each other in balance.

Taking a gut test is like taking a photograph of a meadow. You get a snapshot of what’s there, and you get to see how plentiful individual species are and whether they seem to be in balance. But knowing which microbes you’re harbouring is only one part of it. You then need personalised advice on how to tweak your diet and lifestyle to make your microbiome as rich and diverse as possible.

Find the root cause of your symptoms.

View our gut health tests

This is where the value of gut health testing lies. Through assessing your bacteria taking action, you can have a positive knock-on effect on your health as a whole.

Can you get your gut bacteria tested?

It’s now simple to get your gut tested, as advanced methods have made it easier, faster and less expensive to examine bacteria and other microbes.

All types of gut tests involve sending off a sample of your stool (poo). This is analysed in a lab to find out which bacteria and other microbes are present.

Let’s look at two commonly used methods and their advantages/disadvantages:


This is where a bit of the stool is put in a petri dish to see what grows.

Advantages: it’s widely available and inexpensive.

Disadvantages: it’s slow, and not all bacteria survive and grow in oxygen—leading to skewed results.


This is where a special ‘probe’ is used to look for a specific bacterium. This is the main method used by the NHS.

Advantages: it’s quick and precise, and the bacteria don’t have to be alive to be detected.

Disadvantages: you have to know what you’re looking for, so it can’t give an overview of all bacteria.

You can also take a breath test for gut health, but this is more relevant if you suspect you have SIBO. We’ve written a comprehensive guide to SIBO testing.

As you can see, culturing and qPCR both have values and limitations. But there’s a third method, called 16s rRNA sequencing, which is even more comprehensive. This is because it identifies bacteria by looking at their DNA.

What does a DNA gut health test do?

A DNA gut health test allows you to see both the types and number of all the bacteria in a stool sample.

All bacteria (and archaea) have the 16s rRNA gene, and the gene remains detectable whether the bacteria are dead or alive5. By using 16s rRNA sequencing, you can see which species and strains of bacteria you’re carrying, and in what ratios.

This method is quicker than culturing, and it gives a broader overview than qPCR—which means it’s currently the best method available for looking at all bacteria in a stool sample.

But a stool carries more than bacteria. It may also have yeasts, digestive residues and perhaps even parasites. That’s why a Healthpath Gut Health Test uses a combination of 16s rRNA sequencing and qPCR to identify all types of microbes in your gut. We also use immunochemical assays and near-infrared spectroscopy to assess how well your digestion is working.


How do doctors test gut health?

Analysing your gut microbiome isn’t yet common practice in the NHS.

Most doctors will arrange a test if they think something is wrong and they want to investigate it. They can ask you to provide a stool sample so they can look for something specific, such as:

  •      Blood
  •      Parasites
  •      Parasite eggs

You can also have other procedures—such as a colonoscopy, a sigmoidoscopy or an ultrasound—to investigate polyps, cancer and other forms of bowel disease.

But none of these tests is required to investigate IBS according to NICE guidelines. What this means is that you can receive a diagnosis of IBS without having any sort of gut test.

This may well change. More and more studies are showing the microbiome disruption or dysbiosis is a driving factor of IBS6.

How to test your gut health online or at home?

You can order a gut health test from several online providers.

Do your research. You want to make sure that your gut health test kit provider a) looks at bacteria, yeasts, parasites and digestive markers, and b) will help you understand what they mean for your health. If you don’t have those two elements, you’ll be left with set of data that’s both incomplete and baffling.

Here’s how the process works at Healthpath:

  1.     Order your gut health test kit online, which will arrive at your home within three days.
  2.     On the day of your test, attach a special stool collector to your toilet. Pass stools (poo) as normal. Using the spoon and test tubes provided, take a sample from a few areas of your stool.
  3.     Pop the lid on the test tubes and place them in the returns envelope provided. Post them back to the lab within 12 hours of collection.

You’ll also fill in a detailed symptom survey on your Healthpath account. We encourage this because you’re more than just data—how you feel is an important part of your health picture.

After that, the lab will analyse your sample, and you’ll receive a report detailing which microbes have been found. In your Healthpath report, a practitioner will consider both your results and your symptoms to give you personalised, practical advice.

To make results as accurate as possible, it’s also important to prepare for the test properly. You should:

  •      Eat your normal diet for at least a week before the test. This will enable you to get an accurate picture of your ‘baseline’ microbiome.
  •      Stop taking any probiotics three days before the test.
  •      Make sure you take the test on a day you can get to the Post Office (and check it will be open!).

At-home microbiome testing is popular in the UK because it’s easy, convenient and non-invasive. It also gives you a level of detail not yet offered by standard NHS tests.

How to interpret a gut health test?

A good gut health test will not only tell you which microbes you house, but it will also explain the research behind those microbes. That second part is essential—otherwise you’re just left with a huge list of funny bacterial names.

Broadly speaking, you want to look at:

1)    Your overall diversity. That means how many different types of bacteria you have. Healthpath makes this easy by providing a diversity score.

2)    Whether you have dysbiosis. This means an imbalance in bacteria. Again, Healthpath provides a dysbiosis scale so you can tell at a glance.

3)    The bacterial phyla. These are six large categories of bacteria. A good gut health test will let you know if these are in the expected ranges. An out-of-range bacterial phylum, such as high Proteobacteria, can contribute to symptoms—even if everything else on the test is normal.

4)    Individual species and strains of bacteria. The balance of bacteria is important, but some individual strains and species are especially useful. Appropriate levels of the species Akkermansia muciniphila, for example, can be regarded as a general marker of intestinal health7. But too much of another species, Clostridium difficile, is known to contribute to diarrhoea8. Your report should give you evidence-based details about each bacterium.

5)    Other microbes and markers. These include yeasts, parasites and digestive biomarkers. These create a comprehensive view of your gut function.

The most important part of interpreting a test is making it actionable. Again taking Akkermansia muciniphila as an example: if you know you have low levels of this species, you also need to know what to do to increase it.

A Healthpath gut health test report shows you when you have out-of-range bacteria (or other markers), explains what the research says they could mean, and gives you personalised advice on how to get them back in the optimum range.

How long does it take to receive the results of a gut health test?

UK providers of gut health tests vary in their turnaround times. It usually takes about four weeks to get your results, but some can take up to eight weeks. This may be because the provider is relying on slower methods such as culturing, or because they have to ship the sample to a lab in the US.

Here at Healthpath, we’ve partnered with a German lab who use speedy and reliable 16s rRNA sequencing and qPCR technology. This means that Healthpath customers usually receive their gut health test results within two weeks.

What happens after a gut health test?

After you’ve sent off your sample, you should receive your test report within a few weeks (depending on the provider). Your test should show you which microbes you have and explain the current research findings on each. It should also tell you how to optimise the richness and diversity of your microbiome.

The specifics of this guidance will vary according to what’s found in your sample. Here at Healthpath, we give personalised recommendations for:

Diet You may be eating too much of a food type that encourages dysbiosis, or you might not be eating enough of a food type that encourages the growth of healthy bacteria. A good test report should tell you which foods will benefit your microbiome.

Lifestyle Although your dietary habits shape your microbiome, other habits have an impact too. These include your sleep, stress and level of activity. A Healthpath gut health report gives you extra resources to help you improve all three.

Supplements You should always optimise your diet and lifestyle first, but supplements can be a helpful tool to support your gut health. Typical recommendations include probiotics, prebiotics and antimicrobials—but this will vary depending on your specific results.

You should expect to follow these recommendations closely for eight to 12 weeks. After that, the goal is to make your diet as relaxed and as inclusive as possible, all while continuing to support a healthy microbiome.

Some characteristics of your microbiome are fixed. But, according to current scientific knowledge, you can change yours for the better by making long-term adjustments to your diet and lifestyle9. A good gut health test report should show you how to do this.

How to test gut health of a baby or child?

Technically, you can perform a gut health test a person of any age. You could perform a gut health test on a baby who’s currently breastfed or formula-fed—but it would be worth re-testing down the line, as their microbiome will shift when solid foods are introduced.

The testing process is the same, except the parents would have to make sure their baby or child is properly prepared for the test. The parents would also have to collect the stool samples and send them off to the lab as directed.

Microbial populations change naturally during early childhood—but by the time a child reaches age 3, their microbiome more or less resembles that of an adult10.

But it’s important to realise that not all advice for influencing the microbiome is suitable for children. Eliminating or reducing certain foods isn’t appropriate when a person is growing, and supplement dosages need to be adjusted depending on a child’s age.

For that reason, it’s best to test a baby or child’s gut health while working in conjunction with a Nutritional Therapist or Functional Medicine Practitioner. They will be able to further tailor the advice to the child.

Which is the best gut health test?

There is a lot to consider when choosing a gut health test provider: what methods they use, which microbes they look at, and how they explain the findings to you.

Here at Healthpath, we strive to offer the best gut health test on the UK market. But whichever provider you use, you should ask three questions:

1)    Do they provide meaningful results?

Some gut health tests on the market include certain bacteria just because they can. They don’t necessarily explain what they mean or how they might be contributing to your symptoms. They also give percentage values for each bacterium, which are meaningless unless you know how many bacteria you have in total.

The best gut health test reports give evidence-based explanations for each out-of-range bacterium. Here at Healthpath, we also turn percentage values into colony forming units (or CFUs, the typical measurement for bacteria), so you have a clearer idea of the richness and distribution of your bacteria.

Most crucially of all, we also give you personalised advice to change your microbiome for the better.

2)    Do they look at more than just bacteria?

The gut microbiome is important, but it’s just one part of the picture. You also need to know how your digestion is functioning.

Many gut tests look at just bacteria, yeasts and parasites. Here at Healthpath, we look at those—but we also look at markers for digestive enzymes, inflammation and immune responses. These provide a more useful overview of your gut health as a whole.

3)    Are they upfront about the limitations?

At the present time of writing (December 2019) the gut microbiome is a new area of research. We haven’t yet identified all types of microbes that live in our guts. Of those we have identified, we can’t definitively say how they influence our health.

A good provider should never suggest that a gut health test is a ‘diagnosis’. But they should show they’re committed to keeping on top of research related to gut health—because there’s still so much more to learn.

Find the root cause of your symptoms.

View our gut health tests


Testing your gut health can be valuable whether you’re experiencing digestive problems or not. This is because research shows that our gut health has a knock-on effect on our health as a whole.

At-home gut testing is an easy, convenient option, and it gives you a depth of insight into your gut health that’s not available via normal NHS tests.

But a gut health test is only valuable if you know what to do with the results. The best test reports explain the research behind each bacterium or marker, and show you what to do to get them back in the optimum range.

Here at Healthpath, we strive to bring true meaning to your results. We provide comprehensive reports, and you have the option to speak to one of our in-house practitioners for further support. If you’re unsure about whether a gut health test is right for you can even get started with our  15-Minute Consultation.



Fiona Lawson BA (Hons) DipCNM mBANT is a Registered Nutritional Therapist and health writer. She is a member of the Complementary and Natural Healthcare Council (CNHC) and the Institute for Functional Medicine (IFM). As Content Director of Healthpath, Fiona is on a mission to help people take charge of their own health. Read more about Fiona on her practitioner page.













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