Microbiome Testing: What Is It? And How Does It Work?
Your gut is home to trillions of bacteria and other microbes from over 100 different species. Known as the “gut microbiome,” these microorganisms — including bacteria, viruses, archaea, fungi, and more — are specific to you. No one else has the same composition of species.
But they’re not all harmful. In fact, your gut microbiome actively supports your health. The “good” bacteria are associated with positive health indicators. These microbes aid in digestion, release compounds that prevent heart disease, lower the risk of diabetes, and may even protect your brain and lift your mood.
Unfortunately, your microbiome can be disrupted, leading to the “bad” microbes taking over your gut. Gut microbiome testing analyses the species and composition to see if this is the underlying problem behind your symptoms.
Below, we’re explaining microbiome testing, from what it is to how it works.
What Is Microbiome Testing?
Microbiome testing examines a person’s stool sample to determine the species composition within their colon. It uses advanced DNA sequencing techniques to analyse the DNA from these species, identifying all the species present.
There’s a lot of genetic material.
It’s estimated that the trillions of bacteria in your gut contain around 3 million genes collectively. But by comparing these genes to known species, we can track down who’s living in your gut.
Based on this information, we can create an action plan to improve your gut microbiome. We can support certain species while trying to reduce the numbers of others, restoring your microbiome to a state that’s perfect for you.
How Does Microbiome Testing Work?
The most common form of microbiome testing is a stool microbiome analysis.
The patient provides a stool sample in a container. Using a test called shotgun metagenomic testing (the most advanced method available), where the DNA is cut up into tiny fragments. These fragments are then sequenced and pieced back together. This gives us complete insight into your microbiome.
It should help us identify all the microbes living in your gut — the “good” and the “bad.”
Unlike older 16S rRNA tests, it tells us the specific species of bacteria, archaea, yeast, fungi, viruses, and parasites. It also shows which functional genes are present.
The benefit? We can see not just what microbes are present, but also what they can do for you. For example, they can break down fibre, produce vitamins, boost immunity, or carry antimicrobial resistance (AMR) markers.
Other Types of Microbiome Testing
Stool microbiome analysis isn’t the only way to understand your gut. Several other tests also give us the telltale signs of issues not just in your colon but throughout your digestive system. They can identify the effects of dysbiosis (an unbalanced microbiome).
These include:
Hydrogen sulphide breath testing. Can detect if specific hydrogen sulphide-producing bacteria are present.
Hydrogen & methane breath testing. Detects bacterial overgrowth and certain food intolerances (lactose and fructose), often used for diarrhoea, bloating, or gas linked to specific bacteria.
Gut permeability (“leaky gut”) assessments. Checks how well your gut lining is functioning and whether unwanted particles are passing into the bloodstream.
SIBO testing. Identifies bacterial overgrowth in the small intestine, a common cause of bloating, discomfort, and irregular bowel habits.
Gastric acid output test. Measures stomach acid levels to assess for low acid (hypochlorhydria), which can affect digestion and nutrient absorption.
Gut motility and transit studies. Tracks how efficiently food moves through your digestive system, helping diagnose motility issues or constipation-related symptoms.
What Can Microbiome Testing Tell You?
Why bother with microbiome testing? Well, it provides insightful and useful information about your gut microbiome composition.
The most important factor is the balance of “good” and “bad” bacteria. These microbes are categorised based on their links to positive or negative health markers. We know what these microbes like to eat. So, by changing your diet, we can support the good ones, helping them outcompete the bad.
Other useful insights include:
Diversity score. This covers the number of different species. The greater your gut diversity, the healthier you will be.
Pathogen detection. If there are any harmful microorganisms present.
Inflammation markers or dysbiosis indicators. Reveals if your gut environment is inflamed or imbalanced due to an overgrowth of harmful bacteria.
Metabolic pathway analysis. Shows what the microbes are capable of doing, e.g., synthesising vitamins or digesting fibre.
When Should You Consider a Microbiome Test?
Most people never consider their microbiome. But it’s an underappreciated factor in lots of conditions. You should consider a microbiome test if you have:
Persistent bloating, constipation, or diarrhoea
IBS-like symptoms
Skin issues (eczema, acne)
Low mood or anxiety
Unexplained fatigue
Recent antibiotics or a poor diet
Get Your Microbiome Tested Today
Struggling with bloating, digestive problems, food intolerances, or low energy and mood? You’re not alone. The problem might be something you least expect — your gut microbiome.
The Functional Gut Clinic offers a full suite of tests to analyse your microbiome, including advanced DNA sequencing of stool samples. Book your test today to take control of your health and get to the root of your symptoms.
