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Microbiome Assessment: How We Can Measure Our Microbiome

By Dr Brad Leech

In recent years, the gut microbiome has emerged as a focal point of scientific research, revolutionising our understanding of human health and disease. This complex ecosystem of microorganisms residing within our gastrointestinal tract plays a pivotal role in various physiological processes, from digestion to immune regulation. With advancements in technology, measuring the gut microbiome has become more accessible, offering profound insights into individual health and wellbeing.

Understanding the Gut Microbiome: A Complex Ecosystem

To comprehend the significance of gut microbiome testing, it’s essential to first grasp the intricate dynamics of this microbial community. The gastrointestinal tract, comprising the mouth, oesophagus, stomach, small intestine, and large intestine, provides diverse environments that support distinct microbial populations. While the small intestine boasts acidity and oxygen levels conducive to fast-growing bacteria, the large intestine fosters dense populations capable of processing undigested food without oxygen.

In the quest to measure the gut microbiome, researchers primarily rely on stool samples. However, it’s crucial to recognise that stool microbiome analysis captures microbes residing in the lumen of the large intestine, overlooking those inhabiting the mucus layer. This distinction underscores the complexity of the gut microbiome and the challenges associated with comprehensive measurement.

The Gut Microbiome and Its Influence on Health

Mounting evidence suggests a profound link between gut microbiome composition and overall health. Studies have revealed distinct microbial signatures associated with various physical and mental disorders, highlighting the potential of microbiome analysis as a diagnostic tool. Moreover, healthy individuals tend to exhibit greater microbial diversity, underscoring the importance of a balanced gut ecosystem.

But what exactly can microbiome testing unveil? Through metagenomic analysis, individuals gain insights into microbial diversity, nutrient breakdown potential, and gene expression within their gut microbiome. Such information not only offers a snapshot of current health status but also holds promise for personalised interventions aimed at optimising gut health.

The Promise of Microbiome Testing

Thanks to remarkable advancements in medical technology, microbiome testing has become more accessible, efficient, and detailed than ever before. Today, individuals can access world-leading insights into their gut microbiome from the comfort of their own homes. Despite lingering questions surrounding the utility of microbiome testing, its potential benefits are undeniable.

By understanding the functions of their gut microbiome, individuals can assess its role in maintaining health and preventing disease. Microbiome testing enables the identification of microbial imbalances or deficiencies, paving the way for targeted interventions to restore gut equilibrium. From optimising nutrient breakdown to modulating immune responses, the insights gleaned from microbiome testing hold tremendous potential for enhancing overall wellbeing.

Butyrate: The Gut Microbiome’s Secret Weapon

Among the myriad compounds produced by gut bacteria, butyrate stands out for its diverse physiological effects. As a short-chain fatty acid, butyrate plays a crucial role in nourishing gut cells, modulating immune responses, and regulating metabolic processes. Its ability to support gastrointestinal health and protect against inflammation-based diseases underscores its significance in gut microbiome function.

However, inadequate production of butyrate can have far-reaching implications for health. Low levels of butyrate have been associated with gastrointestinal issues, inflammation, and metabolic disorders such as diabetes. Addressing deficiencies in butyrate production requires a multifaceted approach, encompassing dietary interventions, microbial diversity enhancement, and personalised clinical interventions.

Clinical Interventions for Butyrate Enhancement

For healthcare professionals, supporting clients in enhancing butyrate production involves tailored strategies informed by individual microbiome composition and clinical history. Promoting microbial diversity through dietary interventions and increasing intake of resistant starch—a key precursor of butyrate—can bolster gut health and mitigate associated risks.

Resistant starch, found in various plant-based foods such as barley, oats, and legumes, serves as a vital substrate for butyrate-producing bacteria. While its role in gut disorders like Irritable Bowel Syndrome (IBS) remains debated, its potential benefits underscore the importance of personalised approaches to gut health. By leveraging the synergistic relationship between specific bacteria and dietary substrates, individuals can optimise butyrate production and support overall wellbeing.

Personalised Approaches to Gut Health

In navigating the complexities of gut microbiome health, personalised care is paramount. Healthcare professionals must consider each client’s unique microbiome composition, dietary habits, and clinical history when formulating interventions. Referral to qualified specialists may be warranted in cases where dietary restrictions or underlying health conditions necessitate expert guidance.


The gut microbiome represents a dynamic ecosystem with profound implications for human health. Through microbiome testing and targeted interventions, individuals can gain valuable insights into their gut health and take proactive steps towards optimising wellbeing. By embracing personalised approaches informed by the latest research, we can unlock the full potential of the gut microbiome in promoting health and vitality.

More about the author

Dr Brad Leech

Dr Brad Leech is a PhD-qualified Clinical Nutritionist and Herbalist specialising in chronic autoimmune conditions and complex gastrointestinal disorders. He provides complete and personalised care to his patients using functional nutrition, integrative medicine and holistic wellness. 

After entering the profession in 2008, Brad has taught and developed subjects at leading universities and conducted research on intestinal permeability, autoimmune disease management and food-based probiotics.

Brad is the Lead Clinical Educator at Co-Biome by Microba where his expertise in gastrointestinal healthcare enables him to translate the latest science on the gut microbiome into practical clinical applications. 

In addition to being an Adjunct Fellow at the National Centre for Naturopathic Medicine, Brad offers practitioner support through his multiple mentoring programs.