How can gut microbiome testing change the way you practice?

Author: Dr Ken McGrath & Krystyna Sullivan

May 2021

As a healthcare professional, you already appreciate the power of information and the value of testing to better understand your patients’ health presentation.

Now, after a decade of seeing great advancements in gut microbiome analysis technology, led by Microba’s co-founders, Professors Phil Hugenholtz and Gene Tyson, it has led to broader availability of the latest scientific evidence right here in Australia.

With access to more microbiome insights than ever before, science is showing that guiding your patient’s health journey using a more tailored approach is key and delving into their unique gut microbiome using the latest analysis technology is a valuable skill that can further assist your clinical decision-making.

Research shows that the gut microbiome of individuals with various health conditions is different compared to those of healthy people.1 Therefore, testing microbiome biomarkers such as microbial diversity, the presence of certain microbial species, and the production of certain metabolites (functional potential)2,3 using shotgun metagenomics, can be a very useful clinical tool.

So, how are practitioners using metagenomic testing in clinic?


Interested to discuss metagenomic gut microbiome analysis further? Contact the healthcare team.



The clinical application of metagenomic testing

From looking at what metabolites your patient’s gut microbiome is producing, to which prebiotics will best fuel health-promoting gut bacteria, meaningful insights such as these are found in the Insight™ microbiome report and can better inform your patient evaluations and clinical recommendations. 

Examples of valuable report insights include:

  • Microbial diversity level or the Shannon Diversity Index is the standard measurement of both the different types of species in your patient’s gut and how evenly they are distributed.  Microbial diversity is an important biomarker for microbiome health, where low diversity has been associated with various health conditions, including inflammatory bowel disease, type 1 diabetes, obesity, and more4-7. Discover whether your patient’s diversity could be contributing to their health presentation, or whether there are any microbial overgrowths.  You can then use this information to inform lifestyle and dietary interventions, such as recommending more diverse eating habits to boost microbial diversity8.
  • Human DNA abundance is typically at low levels in healthy stool. If human DNA is showing at elevated levels, it may be an indicator of gut inflammation or more serious GI concerns. You may wish to consider further investigation for inflammatory markers or exploratory testing and review potential microbial metabolites that may contribute to GI inflammation, such as ammonia.
  • Fibre digestion potential is an important function of the gut microbiome, as it is directly linked to the growth of beneficial fibre-degrading bacteria9. A similar or high potential to break down fibre compared to our ‘healthy cohort’ is considered beneficial to support the production of short chain fatty acids (SCFAs), such as butyrate. Your patient’s ability to digest fibre can inform dietary interventions and may be an indicator of whether fibre intake may be inadequate.
  • The food frequency questionnaire (FFQ) is a valuable practitioner tool, developed by Microba microbiome experts and is unique to Insight™. Your patient’s FFQ results summary can assist your evaluation of their eating habits by providing an overview of their dietary history and how they are fuelling their microbiome. Through these insights, you can identify the beneficial patterns your patient already has in place, as well as areas they can improve to promote optimal microbiome health and general wellbeing.


Discuss important report insights with a Clinical Application Specilist. Book Now.


Another key aspect of your patient’s Insight™ report is understanding their microbiome’s functional potential or ability to produce metabolites. These microbially produced substances can interact with the immune, metabolic, and nervous systems and have been linked to various health conditions10. Some metabolites promote good health while others promote inflammation and disease. 

Examples of key metabolites in the Insight™ report include:

  • Lipopolysaccharide (LPS), a pro-inflammatory compound, can trigger immune activation and contribute to systemic inflammation11. The hexa form of LPS known as Hexa-Lipopolysaccharide (Hexa-LPS), is most noted to have strong immunostimulatory potential by binding to TLR4 immune cells and activating the inflammatory cascade12. Hexa-LPS absorption is increased in the presence of saturated fats. Therefore, a high potential to produce Hexa-LPS can inform dietary interventions, such as recommending your patient decrease saturated fat intake and maximise their omega-3 fatty acid and fibre intake13,14.

Find out more about Hexa-LPS in our Hexa-LPS Clinical Reference Guide.



  • Butyrate, a key Short Chain Fatty Acid (SCFA) which is required for regular gut cell function. A low potential to produce butyrate is considered unhealthy and can contribute to inflammation, poor gut barrier integrity and other negative health consequences. This insight can inform dietary interventions, such as recommending your patient increase their resistant starch and pectin intake, which are precursors for butyrate production14,15.
  • Trimethylamine (TMA), when produced at high levels, is linked to cardiometabolic diseases and may indicate an increased risk of several health conditions including cardiovascular disease, type 2 diabetes, inflammation, and hypertension16. This insight can inform dietary interventions, such as recommending your patient decrease their red meat intake or increase their cruciferous vegetable intake17-19.

Find out more about TMA in our TMA Clinical Reference Guide.




As an integrative health professional and/or dietitian you are well placed to utilise gut microbiome analysis in clinic because you can understand the importance of gut health in your patient’s presentation. You also have the tools to support your patient with key dietary and lifestyle changes tailored to improve their unique microbiome.

Metagenomic gut microbiome analysis provides a holistic view of the gut microbiome, not merely the presence of specific bacteria. With gut microbiome diversity being viewed as a key indicator of health and disease prevention, a detailed understanding of your patient’s microbiome can assist with your recommendations for supporting the diversity of their gut. 

Assessment of the functional potential of your patient’s microbiome allows you, as a practitioner, to have a targeted and personalised approach by addressing key metabolites that may contribute to your patient’s health concerns. Metagenomic gut microbiome analysis delivers insights into potentially harmful metabolites, how to address the effects of these and encourage beneficial metabolites associated with positive health outcomes and disease prevention.

About the author


Dr Ken McGrath

Dr Ken McGrath is the Clinical Solutions Manager with Microba. He has a PhD in Molecular Pathology from the University of Queensland, with a research background in microbial community genomics, including human and environmental microbiomes and metagenomics analysis. Ken has also been a part of several international microbiome research projects.



Krystyna Sullivan

Krystyna Sullivan is a naturopath with a background in the health, wellness and fitness industries. She has a Master’s Degree in Public Health from Monash University and a Bachelor of Naturopathy from Southern Cross University. With nearly a decade of experience, Krystyna brings a deep understanding of the integrated health arena to her role as a Clinical Application Specialist with the Insight™ team. She has a strong interest in public health and a passion for supporting other practitioners to use gut microbiome analysis in clinical practice.


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