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Microbiome Testing for Gut Health

1 year ago

We’ve all heard of the term 'gut feeling', but have you ever thought about what it is that your gut is trying to tell you?  With the help of microbiome testing, now you can find out.  The microbiome is now being linked to many areas of health, and testing can shed some light on ongoing symptoms and diseases. For example, many people commonly suffer with digestive issues, such as bloating, Irritable Bowel Syndrome (IBS), food intolerances, and discomfort after eating. By understanding how the gut works and by testing its efficiency we can address any imbalances within the ecosystem of the gut and support overall health and vitality. 

The gut revolution is well underway and digestive health will continue to be a significant trend in 2019. Want to know what’s going on inside your gut? Want to boost immunity? Increase energy? Read on to learn about the explosion in microbiome testing and what these tests can tell you about your gut. I will also talk about some simple DIY gut tests that you can do at home, to get you started on your road to better gut health. 


Our health starts in the gut!

Recent science behind functional gut testing

The human gut is home to many different strains and species of microorganisms, which are collectively known as the microbiome.  We now know that these microbial allies are the foundation of health and wellness, and that we need to tend to our gut gardens with a greater awareness of the impact of our diet and lifestyle habits.

Research into gut health has mushroomed as we enter the post-biotic era with a focus on reseeding the gut microbiome as opposed to killing off the bad bugs. Diagnosis of gut conditions has come a long way since the humble food sensitivity test and subsequent elimination diets, and we understand far more now beyond just a standard diagnosis of IBS. As the world of gut testing opens up to us, we can really start to get to know our microbiomes. Our adult bodies harbour ten times more microbial than human cells, and our intestines contain the highest-density bacterial ecosystems, which leaves huge scope for the area of microbial testing.  As medicine moves more towards disease prevention, I believe gut testing, personalised diets and probiotics are set to play a huge part in this. 

We now know that our gut bacteria do more than just digest our food and supply us with energy and nutrients; they affect our whole physiology and susceptibility to diseases, ranging from type 2 diabetes1 to obesity2, to mood disorders. Our intestinal bacteria even contain their own DNA, and our microbiome genomes are a reflection of our state of wellbeing. It is now possible to do testing on the genetics of your microbiome and look for biomarkers in your stool to identify what is happening in your body. The Human Genome Project, completed in 2003, and the Human Gut Microbiome Initiative (HGMI), are both an extension of this and promise to further our understanding of the foundations of human health, delivering genome sequences for hundreds of species and thousands of strains of bacteria. This research will potentially provide insight in to some common diseases and provide treatment modalities.


 What's inside my gut?

What can microbiome testing tell me about my gut?

Our gut microbiome is unique to us, in much the same way as a DNA fingerprint is. These bacteria become a signature of our health and dietary status.  Every time we put something into our mouths, whether that be a healthy, colourful, plant based salad, rich in plant fibre and antioxidants, or a sugary, fried cronut, we are influencing the balance of our gut bacteria for better or worse. It's time for us to make friends with our gut bacteria again!  The 4,000 species of bacteria found in our stool tell us more about the human body than all the other sites put together.3  Testing the diversity and efficiency of your gut will provide valuable insights into our unique microbiomes, and the best ways to support our microbial allies.

diet and bacteria

The science into analysing the microbes in our guts is expanding each year, and testing has become more affordable as research continues into mapping the bacteria of our microbiome. Much of our health and wellbeing relies upon the ability of the gut to digest what we eat and absorb all of the necessary nutrients. Our bodies require a constant supply of nutrients in the form of proteins, fats, carbohydrates, vitamins, and minerals to function at their best, and this is why addressing gut health is always a starting point in my clinical practice. I find labs that show what's happening in the gut to be very useful for helping people understand exactly what is contributing to their symptoms. 

Microbiome tests can tell us about a myriad of things, including:

Gut diversity

Testing can inform you of your levels of beneficial bacteria compared to pathogens (bad microorganisms). It is important to maintain a good diversity of bacteria for optimum health, and knowing which strains you are lacking in can help to inform your dietary choices. To increase your friendly bacteria levels, you may even wish to consider taking a probiotic supplement to support levels of beneficial strains. 

good bacteria


A stool test can confirm whether you have an overgrowth of parasties, yeast, and worms in your body. Diversity scores are useful because the presence of specific pathogenic microorganisms in your microbiome can be associated with certain illnesses. Certain labs use DNA analysis as well as digestive and immune markers to assess gut function.

Gut conditions

Gut testing can provide insight in to the relationship between your gut conditions and your microbiome. Your microbiome might include microorganisms associated with conditions such a IBS, bloating, or other gut-related issues. 

Metabolic disorders

The composition of our gut bacteria is now being linked with certain metabolic disorders, including diabetes, obesity, and non-alcoholic fatty liver disease. The next step in medicine is looking towards protection from diseases conferred by our gut bacteria.

Synthesis of vitamins and nutrients

You can use tests to find out how your body digests certain foods and receive personalised food recommendations based on your results. We can also learn how diet affects gut bacteria. This can be useful as it can tell us how much fibre we need to be healthy.

Leaky gut

Leaky gut, also referred to as intestinal permeability, is a condition in which bacteria and toxins can leak through the gut lining and into the blood stream, causing gastrointestinal imbalances and a range of symptoms in the body. Testing for leaky gut can enable you to assess the correct absorption of nutrients and healthy intestinal barrier function. Multiple food intolerances can be a good indicator that you may have a leaky gut, or there are laboratory tests that are able to detect leaky gut by measuring the ability of sugar solutions to pass through the small intestine. Levels of the sugars are measured in the urine and can give you a clear picture of the permeability of the gut.

leaky gut


Small Intestinal Bacterial Overgrowth is a condition that occurs when the bacteria in your small intestine become out of balance. This can lead to pain, diarrhoea, malabsorption, and other symptoms related to IBS. A breath test is used for diagnosing S.I.B.O; gut bacteria excrete high levels of hydrogen and methane, which are exhaled by your lungs and can therefore be measured.

Food sensitivities (IgG)

Many of us with IBS symptoms have a lot of food triggers and sensitivities. A food symptom diary is often useful for identifying triggers, but tests can help you clarify foods that you may need to avoid for a period of time while you heal your gut.

Another test I like to use in my practice is the Organic Acids test, which looks at the metabolic by-products of bacteria and yeasts as well as other health markers, providing information about your digestive function and overall health. 

DIY digestive home tests

Candida test

Candida is a pathogenic yeast that, in excess, can cause infections. We naturally harbour Candida in our guts, but our natural levels can become unbalanced, and this is when it becomes a problem. This test is a simple and effective way to test for possible Candida overgrowth. 

Put out a fresh glass of water before bed.

  1. First thing in the morning briefly rinse your mouth, swallow, gather some saliva and then spit in to the glass.
  2. Keep an eye on the water for 30 mins, paying particular attention in the first few minutes.
  3. If you have candida overgrowth you may notice:

> strings (legs) hanging down from the saliva

> cloudy specks suspended in the water

> heavy looking saliva at the bottom of the glass.

If you suspect that you may have a Candida overgrowth, I would advise workingwith a practitioner who specialises in gut health, and consider taking a probiotic supplement to restore levels of friendly bacteria.

The stomach acid burp test

Acid reflux and heartburn are often a result of too little stomach acid, which can affect how well you digest your food. Your stomach secretes hydrochloric acid (HCl) and peptic enzymes to digest your food and kill off bugs and parasites before delivering the food to the intestines, and your saliva also contains enzymes to help begin the digestion process. It is important to remember to chew thoroughly and not eat too quickly, or on the run, as this can be one cause of acid reflux or heartburn. If you are suffering from indigestion and have already tried a more mindful approach to eating, it may be due to low levels of stomach acid and so you may wish to try this simple test. 

  1. Mix 1/4 teaspoon of baking soda in 4-6 ounces of cold water first thing in the morning before eating or drinking anything.
  2. Drink the baking soda solution.
  3. Time how long it takes you to belch. Time up to five minutes.

If you have not burped within five minutes, stop timing.


Low stomach acid no burping

Sufficient stomach acid burping

In theory, if your stomach is producing adequate amounts of stomach acid you’ll likely burp within two to three minutes. Any burping after 3 minutes indicates a low acid level. 

If you suspect low stomach acid try diluting a tablespoon of apple cider vinegar in water and drink it 5 minutes before meals, as this may help reflux symptoms in some people. If your indigestion gets worse then stop and consult a doctor to investigate further causes.


apple cider vinegar


How do I know where to start? 

Should I consider gut testing? (signs and symptoms to look out for)

Fixing gut problems primarily involves addressing dietary changes to avoid triggers, but the root cause of IBS symptoms and food sensitivities is often gut infections with parasites, bacteria, and yeast overgrowth. Gut testing can help you understand exactly what you are dealing with so that you can create the appropriate strategy for healing. But you're probably thinking: 'so, how do I know if my microbiome is out of balance?' Well, there are certain signs and symptoms to look out for which could indicate that your good gut bugs may be waging war down below. If you suffer from IBS, food intolerances, weight gain, low energy, low mood, or autoimmunity, you could well benefit from doing some further investigations. On top of this, if you have a history of antibiotic use; a poor diet lacking in diversity, colour, and fibre; if you drink chlorinated tap water; suffer from recurrent colds and infections; or were not breast fed as a baby, then your microbiome may be compromised. 

How does diet affect gut bacteria?

One way we can positively influence our gut bacteria and keep it thriving is through the foods we choose to eat. Finding out about how our diet is affecting our gut bacteria means that we can personalise food recommendations even further.

By eating a greater variety of plant-based foods, we can maintain a good diversity of healthy species, as the fibre found in these foods is digested by these bacteria and supports the growth of these beneficial microbes. Microbes convert polyphenols (substances found in fruits and vegetables) into molecules that are beneficial to our gut and immune system. This is why it is important for us to eat a rainbow of foods, as different coloured foods contain different antioxidants which are beneficial for creating an optimal environment for our microbes.


Our bodies exist as an ecosystem, and our modern lifestyles have reduced the diversity of our microbiomes. It has been found that indigenous communities across the world possess double the amount of microorganism species compared to western cultures, and this is believed to be because they eat a greater variety of foods according to the changing seasons and what is naturally available. In the west, we have a year-round supply of the same convenient foods, shipped in from all over the world to satisfy our food preferences. As a result of this, it can be very easy to get lost knowing what is in season, as the supermarkets provide much of the same produce all year round. Could Brexit potentially save our endangered gut species, with importing food becoming that much more difficult? What this means is that people end up buying and eating the same foods, and as a consequence are reducing the diversity of their microbiomes. Eating a variety of foods provides a greater range of antioxidants and beneficial compounds for our microbes and for us. Eat the Seasons has an excellent comprehensive guide to what foods are currently in season, and Farmdrop is a great supplier of seasonal food boxes without all of the unnecessary plastic packaging. Growing your own veg is also a great way of topping up on your friendly bacteria, as microbe-rich soil may promote the development of a healthy gut.  

Fewer species is not a good thing when it comes to maintaining health, because it increases the risk for opportunistic bacteria and yeasts to take hold in our guts, which in turn weakens our immune defences and increases inflammation in the body. In a recent study4 looking at the effect of the US diet on immigrants, they found a loss of gut microbiome diversity and an increase in obesity. The average number of different kinds of foods consumed by a person used to average at around 100 per year, and now that figure is just 20. There is officially no universal healthy diet because everyone has a unique microbiome that requires different foods to boost certain species of bacteria, so by testing the diversity in your microbiome you can tailor your diet to suit your microbiome with personalised food recommendations.  

Is the future of gut health a personalised diet perfectly matched to your microbiome blueprint?

As microbiome testing companies proliferate, they are now offering individualised ways to improve your health, and I believe this is a valuable tool for addressing long-term gastrointestinal problems. Over the next few years we will find out as research continues, but in the meantime I advise all of my clients to eat a plant-based seasonal diet which supports optimal microbial diversity and a strong immune system.


For more information on the topics discussed please read:

Benefits of Probiotics and Prebiotics

Do I have Irritable Bowel Syndrome?



1. Upadhyaya, S and Banerjee, G (2015). Type 2 diabetes and gut microbiome: at the intersection of known and unknown. Gut Microbes; 6(2): 85-92

2. de la Cuesta-Zuluaga, J, et al. (2018). Gut microbiota is associated with obesity and cardiometabolic disease in a population in the midst of Westernization. Nature, Scientific Reports 8

3 COLLEN, A 10% Human-How your body's microbes hold the key to health and happiness.  William Collins (2015)

4. Vangay, P, et al. (2018) US Immigration westernizes the human gut microbiome. Cell [online] Vol 28:(5) pp. 675-677 Available at https://www.sciencedirect.com/science/article/pii/S0092867418313825 [Accessed 6/2/2019]

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