All You Need To Know About Gut Microbiome Testing - How It Works & What It Can Tell Us
Written by Kate Shore - 31st July, 2024
When it comes to health and well-being, gut health is crucial because a thriving gut microbiome plays an important role in all aspects of health. This includes not only digestion, but also mood regulation, skin health, immune response, as well as cardiovascular and metabolic functions.
In recent years, there has been a growing interest in gut health, and more parents in my clinic are seeking information about gut microbiome testing. In this article, we will break down the benefits of gut health testing, how it works, how to go about getting it done in Australia, and - most importantly - is gut testing necessary?
What is Your Microbiome?
When we talk about gut testing, generally this refers to microbiome testing. Your microbiome is a collection of all the microorganisms - including bacteria, fungi, viruses, and their genes - that live in and on your body. These tiny organisms play a significant role in your health by aiding digestion, producing vitamins, and protecting against pathogens. The gut microbiome, in particular, has been linked to various aspects of health, from digestion and immune function to mood and brain health and cardiovascular and metabolic disorders (1, 2, 3).
Understanding Gut Health Testing
A microbiome test therefore is used to analyse the types and amounts of microorganisms present in the gut. This includes beneficial bacteria, potentially harmful bacteria, viruses, fungi, and other microbes. A comprehensive test with also include a breakdown of key functional markers that provide information on the gut environment in general, such as levels of inflammation, permeability (aka “leaky gut”), digestive function and gluten sensitivity.
When to Consider Microbiome Testing
Most of the time, a thorough case history can reveal clear factors that contribute to gut health issues. Understanding diet, lifestyle, medical history, and symptoms can provide significant insights and guide initial interventions, and gut testing is not always necessary.
However, there are some instances where a microbiome test can help provide a clearer picture and direct more precise treatments. Certain signs and situations where a gut test can be beneficial include:
Persistent Digestive Issues: When there are chronic problems like diarrhea, constipation, or stomach pain that do not resolve with standard treatments, microbiome testing can help identify underlying imbalances or pathogens.
Unexplained Health Problems: For conditions like eczema (7), frequent illnesses, or behavioural changes where traditional approaches have not provided answers, understanding the gut microbiome can offer new insights and potential solutions.
Specific Diagnoses: For those diagnosed with conditions such as irritable bowel syndrome (IBS), inflammatory bowel disease (IBD) (8), allergies, or autism (4, 5, 6) where research consistently shows variations in microbial diversity, microbiome testing can guide targeted and effective treatment plans.
How Does Microbiome Testing Work?
The great thing about gut testing is that it is a relatively easy, non-invasive test that can be completed at home. The step-by-step process includes:
Sample Collection: The process begins with collecting a small stool sample. Most testing kits include detailed instructions and tools to make this process as simple and hygienic as possible.
Laboratory Analysis: Once the sample is collected, it is sent to a laboratory. Here, pathology labs use advanced techniques such as Polymerase Chain Reaction (PCR), shotgun sequencing, or 16S rDNA sequencing to analyse the microbial DNA in the sample.
Results and Interpretation: The lab provides a detailed report showing the various microorganisms present within a sample, along with their relative abundances. This report can reveal imbalances, the presence of pathogens, and other important information about gut health.
Types of Gut Microbiome Tests.
Gut health testing encompasses various methods to analyze the composition and health of the gut microbiome. These tests can differ in their techniques, focus, and the depth of information they provide. Here are the main types of microbiome testing:
Shotgun Sequencing: This advanced technique sequences all the genetic material in a sample, offering a comprehensive view of the gut microbiome. It can identify bacteria, fungi, viruses, and other microbes, providing detailed information about microbial diversity and potential functional capabilities. It is the most thorough but also the most expensive.
PCR testing: PCR-based methods amplify specific DNA sequences to detect and quantify particular microorganisms. This technique is highly sensitive and can be used to identify specific pathogens or microbial groups of interest.
16S rRNA Sequencing: This common method identifies and quantifies bacteria in the gut by analyzing the 16S ribosomal RNA gene, which is unique to bacteria. It provides a broad overview of bacterial composition but is less effective at detecting other microorganisms like fungi and viruses.
What Does a Microbiome Test Tell You?
Gut microbiome testing provides a wealth of information, and identifying imbalances in the gut microbiome can help address issues before they become more serious. Gut tests can provide information on:
Bacterial Composition: This includes a breakdown of the different types of bacterial strains present in the gut, and at what proportion or abundance they occur. Understanding the specific bacterial composition can help identify imbalances that may be linked to symptoms such as anxiety, depression, or ADHD. For instance, an abundance or deficiency of certain bacteria can influence the production of neurotransmitters like serotonin and dopamine, which are crucial for mental health (9).
Pathogens: It can detect harmful bacteria, viruses, and parasites, such as Campylobacter, Dientamoeba fragilis or Clostridium difficile, that contribute to inflammation, gut symptoms such as loose stools or constipation, and neuropsychiatric symptoms.
Imbalances: The test can reveal imbalances in the gut species that can contribute to symptoms such as digestive discomfort, skin issues, or behavioural changes.
In addition to identifying bacteria and pathogens, some microbiome tests measure other important markers, such as:
Calprotectin: An inflammatory marker that can indicate gut inflammation (10).
Zonulin: A marker for intestinal permeability, often referred to as "leaky gut." High levels of zonulin indicate a compromised gut barrier, which allows harmful substances to enter the bloodstream and contribute to a range of symptoms (11, 12)
Short-Chain Fatty Acids (SCFAs): Produced by beneficial bacteria, SCFAs such as butyrate are important for gut health and brain health. They have anti-inflammatory properties and play a role in maintaining the gut barrier. Adequate levels of SCFAs can support brain health by reducing inflammation and promoting a healthy gut-brain axis (13, 14).
Lipopolysaccharides (LPS): A marker for bacterial endotoxins that can exacerbate neuroinflammatory conditions (15). High levels of LPS in the blood can trigger systemic inflammation, which is associated with neuropsychiatric disorders. Reducing LPS levels can help manage these conditions and improve mental health outcomes.
Microbiome Diversity: A measure of the variety of microorganisms in the gut, with higher diversity generally being better. Greater microbial diversity is associated with a more resilient gut microbiome, which can better support health by producing a wider range of beneficial compounds and resisting harmful pathogens (16).
Fibre and Protein Breakdown: Indicates how well the gut microbiome is digesting these nutrients. Efficient breakdown and absorption of fibre and protein are crucial for producing SCFAs and other beneficial metabolites, as well as ensuring optimal absorption of nutrients.
Is There a Way to Test Your Child’s Gut Microbiome?
Yep, absolutely! Identifying imbalances in bacterial breakdown and levels of inflammation is helpful in supporting children’s health, and the benefit of gut testing is that it is a non-invasive test that can be done at home - helpful for little people who might struggle with other tests such as blood tests.
It is, however, important to understand when and why gut testing might be appropriate. Generally, microbiome testing is not recommended for very young children unless there are specific health concerns, as their microbiome is still developing. Testing purely out of curiosity, especially considering the cost, is also often not necessary.
In situations where there are persistent digestive issues, unexplained health problems, or the sudden onset of neuropsychiatric or behavioural symptoms, then microbiome testing can provide valuable insights into what is happening in your child’s gut and help form an individualised treatment plan.
What’s the Best Gut Microbiome Testing in Australia?
When choosing a microbiome test, it's important to select a reliable and comprehensive option and understand the differences in the types of testing available. Understanding the different testing methodologies can help you choose the best gut testing kit.
Within the clinic, I partner with trusted pathology providers and only use the most comprehensive gut microbiome testing Australia currently has available, such as Nutripath and Co-Biome. These providers offer a broad range of gut testing options, from DNA-based microbiome testing to parasite screening, SIBO testing and complete microbiome mapping.
The appropriate test is determined based on individual needs, taking into account specific symptoms, medical history, and health goals. After a thorough case evaluation, we can select the most suitable test to provide detailed insights into your gut health and develop a personalised treatment plan to address any identified issues.
Other important considerations
If you are interested in supporting your child’s gut health and feel like gut testing might be necessary, there are some important considerations to keep in mind,
Look for tests that provide comprehensive reports, and are conducted in accredited labs.
There are a lot of expensive tests online that aren’t necessarily the most up-to-date technology and limited reporting.
Also, consider the interpretation of the information you will receive. There is no point in paying for expensive tests and not understanding the report or knowing what changes to implement for better gut health. This is where arranging testing through an experienced practitioner who can interpret the results for you, will ensure you get the most out of the report.
Commonly asked questions:
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The cost of gut microbiome testing can vary depending on the provider, the type of testing, and the report provided, In Australia, the cost of microbiome testing can range from AUD 150 to AUD 550. Shotgun sequencing tests tend to be on the higher end of this range.
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Considering the impact of gut health on overall well-being, gut microbiome testing can be worth the investment. Having a detailed understanding of what is going on in your child’s gut helps in creating a targeted approach to improving gut health, which can lead to more personalised support and quicker improvements in digestion, immune function and overall improved health.
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Not necessarily. Gut testing conducted by a GP typically focuses on specific concerns such as infections, inflammation, or other digestive disorders. Common tests ordered by a GP might include stool tests for pathogens or blood tests for inflammation markers. These tests are usually aimed at diagnosing particular conditions like infections, coeliac disease, or lactose intolerance.
On the other hand, comprehensive gut microbiome testing analyses the entire spectrum of microorganisms in the gut, providing detailed insights into the balance of beneficial and harmful bacteria, fungi, and viruses. This type of testing often involves advanced techniques like DNA sequencing to map the microbiome's composition.
While both types of testing provide valuable information, they serve different purposes. If you are looking to understand the overall health and balance of your gut microbiome, specialised microbiome testing may be more appropriate.
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Many gut microbiome tests focus on microbial composition and imbalances, and they are not specifically designed to detect intestinal parasites like worms, protozoa, and other pathogens. Although gut tests might detect DNA from parasites, accurate identification typically requires different diagnostic methods or specific testing. Consulting a healthcare provider for appropriate diagnostic tests and treatment is essential.
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Leaky gut, or increased intestinal permeability, occurs when the lining of the small intestine becomes damaged, allowing undigested food particles, toxins, and microbes to leak into the bloodstream. Testing for leaky gut involves measuring intestinal permeability. Common methods include the lactulose-mannitol test, which evaluates the absorption of these two sugars, and blood tests that detect antibodies against zonulin, a protein involved in regulating intestinal tight junctions. Additionally, stool tests can reveal markers of inflammation and gut barrier integrity. While no single test can definitively diagnose leaky gut, a combination of these tests, along with a thorough evaluation of symptoms and medical history by a healthcare provider, can help in assessing intestinal health and identifying potential issues related to leaky gut.
Undoubtedly, gut microbiome testing can provide invaluable insights into health, helping to detect imbalances, identify pathogens, and guide early interventions. If you are concerned about your or your child's gut health or have noticed persistent digestive or health issues, consider microbiome testing as a proactive step towards better health.
Disclaimer: This article is for educational purposes and does not constitute individual health advice. It is important to seek the advice of your primary health practitioner to assess what is right for you and your child. If you have questions of an individual nature, you are welcome to book a free chat here.
More about Kate Shore - Paediatric Naturopath:
Kate Shore is a children’s naturopath with a special interest and clinical focus on gut health, behaviour, and mental health in kids. Kate received her Bachelor of Health Science from Torrens University and has established her practice in North Warrandyte, Melbourne, where she sees clients both in person and via telehealth. Her approach draws heavily on nutrigenomics, microbiome testing, nutritional foundations, and lifestyle support. She works with a range of children and conditions, from anxiety and depression, ADHD and autism, OCD, and PANS/PANDAS.
If you want to get in touch or have any more questions about the above, you are welcome to get in touch here or make an time for a free chat here.
If you want to keep learning, you can keep reading the research here:
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