Bridging the gap between researchers and practitioners: A look at the research and technologies behind clinical microbiome testing

Authors: Hayley Parcell, Dr Kylie Ellis, Sahana Rajashekar 

July 2021



While our understanding of the microbiome continues to advance through research carried out across the globe, clinicians may be left wondering what do these research-based discoveries mean for their patients’ health and management?

Healthcare practitioners often struggle to keep up with the latest microbiome science to assist their patients. At Microba, we support global microbiome research and have the unique opportunity to translate this fast-evolving evidence to practitioners utilising microbiome testing in clinical practice. 

Read on to learn more about the various research projects we are involved in which aim to inform clinicians and how they practice. Also, discover how research quality methods can assist healthcare practitioners in making more targeted clinical decisions.


Guiding practitioners through scientific discovery

Both Microba’s internal research and external research projects that we service have led to some of the strongest associations between the microbiome and health conditions. Many of these discoveries are coming from novel species that can only be identified using Microba’s unique analysis platform1. As our metagenomic-powered research continues, we compile this information about novel species and provide these findings to practitioners through the Insight™ report.



What are Microba’s internal research programs discovering?

Microba researches specific disease states and their associations with the gut microbiome. Ultimately, insights gleaned from these programs are aimed at improving patient outcomes by providing healthcare practitioners with disease-relevant biomarkers to drive new therapeutic and diagnostic opportunities which may be used in clinic. 

Microba’s Inflammatory Bowel Disease (IBD) Research and Development Program is one of our major therapeutic programs currently underway to develop novel therapeutics derived from the gut microbiome to keep IBD patients in remission for longer and to prevent flare-ups. So far, we have identified dozens of bacterial species associated with IBD and isolated the top 20 commonly found in healthy individuals but rarely detected in those with Crohn’s and/or Ulcerative Colitis. We are now in pre-clinical studies and aim to continue to translate these discoveries into effective biotherapeutics, with a phase 1 study in 2022.  

Microba’s Non-alcoholic Steatohepatitis (NASH) Non-invasive Diagnostic Test Program is looking for new biomarkers to power a diagnostic tool for earlier prediction of non-alcoholic fatty liver disease (NAFLD). This program aims to achieve preventative health outcomes for patients by providing the opportunity for early intervention.


What are some of the external research projects discovering?

Microba also services external research partners to identify microbiome health associations and develop various clinical interventions and practitioner products, such as prebiotics, probiotics, and functional foods. 

Testing to investigate the role of the microbiome in the development, progression and management of diseases such as Parkinson’s disease, cardiovascular disease, autism spectrum disorder (ASD), irritable bowel syndrome (IBS), and depression is how several research partners are utilising Microba’s precision microbiome analysis tools. Microba’s partnership with the University of Queensland (UQ) to investigate if treating gut dysbiosis can ease the non-motor symptom of constipation, often associated with early-stage Parkinson’s disease is one such research study. These studies open the possibility for gut microbiome testing to serve as a life-saving diagnostic tool for a wide-range of diseases, and for alleviation of symptoms through modulation of the gut. 

Testing the maternal and infant microbiome is an area of research that is also rapidly gaining interest, with many aiming to pioneer predictive and preventive prenatal and postnatal healthcare. There is substantial evidence that the microbiota has a critical role to play in the overall wellbeing of a child and into adulthood. Microba have partnered with the Hunter Medical Research Institute (HMRI), the University of Newcastle, and Hunter New England Health in the NEW1000 Family Study. This study will investigate the human microbiome in pregnant women, fathers, and their children to determine the role of the microbiome in the developmental origins of health and disease.


Interested to know more or to join the study? Find out here.



Testing to improve the evidence base around products has become a more frequent use of microbiome research with many groups exploring the impact their nutraceutical and other products have on the gut microbiome, as a likely mechanism of action. This allows for practitioners to choose products best suited for their patients from a wide range of options backed by high-quality and accurate scientific data, enabling personalised care and evidence-based practice.     

Testing for dietary or food-based associations is another common use of Microba’s analysis platform. For example, Microba is working with Unilever to investigate the link between the gut microbiome, sleep, and diet. Through identifying potential microbial drivers for good sleep, the research not only helps us better understand the functions of the gut-brain axis, but also establishes evidence around the relationship between dietary habits and sleep quality. Practitioners can provide sound dietary advice based on information from such research. This also provides potential for the development of foods or supplements that can be used by practitioners in clinic.


Interested to know more? Find out here.



So lets address the elephant in the lumen: Are microbiome research technologies ready for clinical use? 

Microba’s leading sequencing method provides the critical piece to enable the latest microbiome research and make these groundbreaking discoveries possible. 

Our wholemicrobiome sequencing method – Shotgun Metagenomics – is a key differentiator from other microbiome sequencing methods and is now “bridging the gap” between researchers and clinicians1. One of the incredible benefits of Shotgun Metagenomics is that it is revealing the unknown, and opening the research up to not only see more clearly which microbes inhabit a microbial community but to identify the “function” of those microbes.



Previously, research technologies were unable to accurately identify microbial species or functions, creating challenges in translating the evidence into clinically useful information. However, it is with the advancements in detection of microbial metabolite production, and the improved accuracy of detection, that this technology has become ready for clinical use.  

Healthcare practitioners can now predict how microbes can behave and whether an individual’s microbiome can adequately perform essential functions to keep them healthy or perform functions that may hinder their health. Examples of these functions include an individual’s ability to produce:

  • Short Chain Fatty Acids (SCFAs) to support gut health2,
  • Hexa-Lipopolysaccharide (Hexa-LPS) which can contribute to systemic inflammation3, or
  • Trimethylamine (TMA) which has been linked to cardiovascular disease4, to name a few. 

With this functional microbiome knowledge at hand, clinicians can be guided to specific dietary and lifestyle interventions to tailor a patient’s treatment plan.


Microba’s state-of-the-art sample collection methods better assist practitioners and patients.

Unfortunately, many collection methods developed for culture and PCR testing do not adequately stabilise a sample, allowing large changes in the microbial community composition while a sample is in transit to the lab. This happens by either reducing or completely eliminating certain microbial communities while also allowing other microbes to flourish. These fluctuations can result in the under-or over-representation of certain microbes. Therefore, these collection method challenges can impact how a clinician chooses to guide their patient interventions. 

Microba uses a swab sampling method that reliably stabilises a sample, a critical component to achieving accurate study outcomes5,6. The swab device has been developed to stabilise a sample quickly without messy liquids or any cold storage.



Translated into clinical practice, this advanced collection method not only makes sample collection for patients simple and non-invasive but also accurately preserves their sample and microbial community, which is essential for a clinician to base their decisions.



When it comes to the gut microbiome there is a lot to learn and the research Microba is embarking on, both internally and with our partners, is helping us make sense of the complexities of this fascinating microbial community.  

Excitingly, Microba’s unique analysis platform is enabling some of the strongest associations between the microbiome and health conditions, thus bringing the work of researchers and clinicians closer together, both aligning more with individualised patient outcomes.   

As Microba is at the forefront of gut microbiome research, by focusing on making new discoveries in this area of study, we can share these findings directly with practitioners through Insight™. Ultimately, we can support healthcare practitioners and their patients in clinical practice through reliable measurement and credible results.

About the author


Hayley Parcell

Hayley is an experienced nutritionist and the Head of Healthcare for Insight™ with more than nine years of specialist healthcare knowledge. She has a Bachelor of Health Science (Nutritional Medicine) from Endeavour College of Natural Health. At Microba, Hayley aims to help practitioners and their patients by driving clinical understanding and implementation of gut microbiome analysis.

Dr Kylie Ellis

Dr Kylie Ellis is the Head of Research Partnerships at Microba with a strong scientific research background that allows her to leverage knowledge for project design and management. She has a PhD in neuroscience and regenerative medicine from The University of Adelaide and a background in research commercialisation at two Group of Eight Universities. Dr Ellis is a specialist in project design to develop bespoke solutions for research clients and identify global partnership opportunities.

Sahana Rajashekar

Sahana is a biotech engineer and Research Project Coordinator at Microba. She has a master’s degree in biotechnology and has previously worked in the functional neuromodulation and novel therapeutics lab at the Queensland Brain Institute where she investigated the role of the gut-brain axis in anxiety and depression. Sahana leverages her excellent project management skills and passion for research to ensure the highest quality research outcomes are delivered.


  1. Parks D, Rigato F, Krause L, et alMicroba’s Community Profiler enables precise measurement of the gut microbiome. Microba, 2020.  
  1. Koh, A., De Vadder, F., Kovatcheva-Datchary, P. & Bäckhed, F. From Dietary Fiber to Host Physiology: Short-Chain Fatty Acids as Key Bacterial Metabolites. Cell, 2016;165(6):1332-1345. doi:  
  1. Lyte JM, Gabler NK, Hollis JH. Postprandial serum endotoxin in healthy humans is modulated by dietary fat in a randomized, controlled, cross-over study. Lipids Health Dis, 2016;15(1):186.      
  1. Heianza, Y., Ma, W., Manson, J., Rexrode, K, & Qi, L. Gut microbiota metabolites and risk of major adverse cardiovascular disease events and death: A systematic review and meta‐analysis of prospective studiesJournal of the American Heart Association, 2017.  
  1. Pribyl A,  Tousignant K, Parks D, et al. Benchmarking Microba’s sample collection device. Microba, 2020.  
  1. Pribyl A, Parks D, Angel N, et al. Critical evaluation of faecal microbiome preservation using metagenomic analysisISME COMMUN, 2021;1(14).