The benefits of metagenomic gut microbiome analysis in your clinical practice

Author: Dr Ken McGrath & Krystyna Sullivan

May 2021

Why are integrative health professionals and dietitians uniquely placed to leverage the power of the gut microbiome?

Everyone’s gut microbiome is different. Despite this, a growing body of evidence shows links between the microorganisms in our gut and various health conditions, making now the time to look deeper at these connections and to investigate more personalised interventions for your patients.


What can your patient’s gut microbiome tell you?

The past decade has seen great advancements in gut microbiome analysis technology, led by Microba’s co-founders, Professors Phil Hugenholtz and Gene Tyson, who were able to make world-leading microbiome analysis available to healthcare professionals right here in Australia through, Microba.

Insight™ gut microbiome analysis, powered by Microba’s metagenomic sequencing technology and genome database allows for the most comprehensive and precise identification of over 28,000 microbial species in your patient’s gut and their functional potential1. This powerful platform provides accurate in-depth information empowering you, as a practitioner to:

  • Assess your patient’s Insight™ report to understand their current condition and what challenges they face.
  • Improve your patient’s microbiome health through targeted diet and lifestyle interventions that aim to nurture specific beneficial microbes in their gut.
  • Monitor your patient’s gut microbiome to ensure they are on track and achieving their goals.

Testing your patient’s microbiome will not only inform you of how their microbiome may be influencing their health, but it can also lead to improved efficiency by helping you make evidence-based decisions and managing your patients with more confidence.


How does metagenomic testing compare to other analysis methods?

There are many kinds of stool tests available with each one looking at a different aspect of “gut health”. Examples include the national bowel cancer screening test which detects haemoglobin from blood in the stool, or pathogen screens that search for specific bacteria or parasites, and microscopy which tests for worms and other large organisms. These types of stool tests are integral to healthcare and use methods that give specific answers but do not consider the entire microbial community of the large intestine.

Current research indicates that a patient’s whole microbial population should be considered when assessing the health of their gut, rather than targeting a subset of microorganisms.5 This is done through exploratory tests, powered by DNA sequencing, which look at the community of bacteria living in the gut and what their role is. There are two main types of DNA sequencing tests currently available – 16S sequencing and shotgun-metagenomic sequencing.

16S sequencing looks at a small piece of a single gene found within bacteria and predicts the types of bacteria that may be present. This region is typically >10,000 times smaller than the entire bacterial genome. The resolution attainable using such a small fragment of DNA only provide genus-level identity. This not only limits how much can be understood about the gut microbiome, but it also leaves health professionals unable to discriminate between different species in a sample and unable to accurately measure what these species are doing to potentially impact a patient’s health.



The best way to explore the gut microbiome is through metagenomic sequencing, as this method analyses all the DNA from the microorganisms in a sample. Metagenomics provides the highest-resolution view of the gut microbiome, including detailed information about:

  • Which bacteria are living in a patient’s gut (species)
  • What they are able to do (functional potential)
  • What foods these microbes need as fuel 

In addition, metagenomics can show you how each of these elements are connected to major health systems within the human body. Thus, giving you a fuller, clearer picture of what is going on in your patient’s gut and how it could be impacting their health.


Why use metagenomic testing in your clinic?

Metagenomic gut microbiome analysis is an accurate evaluation of the microbial community in the large intestine and its genetic potential. Insight™ gut microbiome analysis, powered by Microba’s metagenomic platform applies the most recent technologies, research, and understandings of the gut microbiome to better utilise its influence on human health in a clinical setting. We know that each species may have different functions and impacts on a patient’s wellbeing, so it is important to accurately identify each species and what metabolites they may produce, rather than giving a generalised understanding of a bacterial genus and their potential function.  

Interest in what makes a “healthy gut”, and what natural remedies and lifestyle interventions can assist health and wellbeing is rapidly increasing. There has never been a better time to leverage upon this growing interest and utilise gut microbiome analysis to both attract new patients and enhance your offerings for current patients. As a modern practitioner, you are well placed to apply the latest that metagenomic analysis has to offer to assist your patients personally and accurately. Insight™ gut microbiome analysis provides:

  • Superior resolution, which allows for the identification of 25% more of the DNA in a sample than other methods.5 This not only means more species are identified but that they are identified more precisely, giving you the ability to make accurate and evidence-based recommendations.
  • Species-level identification of microorganisms and their functional potential gives you an improved understanding of the microbiome’s associations with your patient’s health status.
  • Actionable recommendations which are based on accurate measurement enables more targeted interventions to promote the growth of beneficial bacteria and encourage a diverse microbiome for your patient.
  • Knowledgeable leadership using the latest technologies and scientific evidence to deliver the most comprehensive gut microbiome analysis available. This gives you the most up-to-date information to refer to when evaluating your patient.
  • Non-invasive sampling with an innovative design that does not require liquid or cold storage for transportation. The small stool amount required makes sample collection quick and simple for your patient and most importantly results in fewer errors and false positives, benefitting your clinical interpretations and recommendations.


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



Where to from here?

There is a vast amount of information that can be applied to clinical practice from an Insight™ microbiome report which is powered by metagenomics, but how can you maximise the value of such a tool? The first step is having a deeper understanding of gut microbiome analysis and interpreting a report. All healthcare professionals who are passionate about using technology in practice and expanding their offerings to patients can do this.

As a member of Microba’s healthcare practitioner network, ongoing training and education is available through exclusive online resources and the Insight™ healthcare team, who aim to ensure that you are informed and supported as a practitioner to apply your expertise to improve patient health outcomes. Your designated Clinical Application Specialist is always available to take you through the report step-by-step, to discuss what is important for you and your patients, and to answer any questions you may have.

Your designated Clinical Application Specialist is always available to take you through the report step-by-step, to discuss what is important for you and your patients, and to answer any questions you may have.


Gain the confidence you need to regularly use gut microbiome analysis in practice. Book a call with the healthcare team.



Access a growing library of clinical reference guides,  video tutorials, and webinars, exclusive to Microba Informed Practitioners. These resources are designed to support your knowledge of the gut microbiome, its associations with overall health and your interpretation of your patients’ reports.


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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.


  1. Donovan H. Parks, Fabio Rigato, Lutz Krause, Kaylyn Tousignant, Alena L. Pribyl, Philip Hugenholtz, Gene W. Tyson, David L.A. Wood. Microba’s Community Profiler enables precise measurement of the gut microbiome. Microba, 2020.
  2. Zhernakova A, Kurilshikov A, Jan Bonder M, et al. Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity. Science, 2016; 352, 565-569.