The body supports a significant bacterial ecosystem whose functions can impact on your health, but did you know that the composition of these microbiomes is unique to you? 

For World Microbiome Day 2021 on 27 June, Senior Lecturer and Infectious Diseases and Immunology Researcher Dr Nic West talks to us about microbiomes, the ‘Aussie Gut’ project and the impact of his research. 

Q & A: 

What is the microbiome? 

The microbiome (or microbiota) is a collection of microorganisms, like viruses, bacteria and fungi, that live in and on our body but are not part of our normal human physiology. These microbiomes can be in the gut or intestinal tract—our area of interest—or in our skin cells. In fact, we’re more bacterial than we are human: for each human cell in our body there are almost 1,000 bacterial cells in our gut! And whilst research suggests that bacterial diversity and the abundance of particular species are important to promote and maintain health, we also know that the composition of microbiomes is not uniform. So, on the one hand, microbiomes can interact with our immune system and with our epithelial cells—our skin cells—to have a protective effect against other microorganisms; but, on the other hand, microbiomes can break down and cause disease or inflammation.  

Microbiomes can have a reputation of being bad but, in general, microbiomes live harmoniously within us. However, microbiomes can turn harmful when something like stress or drugs changes the balance. In fact, 1,500 years ago the idea was that we needed to destroy all bacteria that surrounded us. But now we know that bacteria diversity is essential to promoting and maintaining health and that a lack of diversity can influence your body mass, metabolism, allergies and respiratory infections. There is much yet to learn about—and from—our gut bacteria. 


‘We’re more bacterial than we are human: for each human cell in our body there are almost 1,000 bacterial cells in our gut!’ 


What started you looking at the role of gut bacteria with the ‘Aussie Gut’ project?  

From 2004 to 2008 there was a lot of interest in probiotics and gut health and taking supplements to prevent respiratory illness such as common colds. Studying my PhD at the Australian Institute of Sport, Canberra, enabled me to study athletes, who are an excellent group to research because they tend to follow very structured routines. With athletes you can dictate their stress level, through exhaustion testing or racing, or, if they are doing set workloads, you can measure their immune response to determine the effectiveness of training on their immune system and health. And as it is a controlled training environment, you can give them supplements. As a result, there is a lot less bias or confounding external variables.  

From studying athletes, we moved to the rest of the population and started looking at metabolic disease, eczema, allergies and cancer. The interest this sparked resulted in many people contacting us about our studies and asking about individual microbiome profiles. As this didn’t fit into any of our studies, we trademarked the ‘Aussie Gut’ project. For the cost of lab processing, people can come to a Griffith health clinic, fill out some questionnaires and provide a faecal sample. And whilst we don’t give recommendations about what people should and should not do, the profiles can identify low microbiome diversity and a potential underlying issue of poor health. Most often, the next step is for people to take their profile to a dietician. 

The ‘Aussie Gut’ initiative also allows people in the community to contribute to science. With several hundred participants in different groups, we have started to examine the data more deeply and, as an immunology group, to delve deeper into the relationship between the microbiome and the immune system, particularly relating to allergies or asthma, and dermatitis oncology. 


A smiling Dr Nic West working in a lab, wearing a white lab coat and gloves.

Dr Nic West, Senior Lecturer and Infectious Diseases and Immunology Researcher.


Are microbiomes unique like fingerprints? 

Well, that is an interesting question as whilst no two people are identical, with the exact same microbiome, they can be similar. And this is one of the reasons that there isn’t a huge amount of information about the use of the microbiome for definitive clinical health changes. At this stage, no one worldwide has made strong links between any particular groups of bacteria and an outcome for disease. The exception may be cancer oncology where recently it has been found that certain compositions will improve immunotherapy results. 


‘… whilst no two people are identical, with the exact same microbiome, they can be similar.’ 


Does the idea that microbes can contribute to a sustainable future resonate with you?  

Yes. We know that the diversity and the composition of the microbiome is not stable and has changed over generations. There is a hypothesis that modernity and our lifestyles are having a negative impact on our overall diversity. What is fascinating is that they have found that groups in Kenya living a tribal life have the greatest diversity. So, there is a relationship between our microbiomes and our diseases, such as allergies and asthma—diseases which have increased significantly in the last 50 years. But instead of altering our lifestyle, we are taking all these supplements to try to improve health. And to what degree is taking supplements sustainable?  

What is the impact of your research?  

The impact is in three areas—diagnostics, stratifying and therapeutic targeting.  

With diagnostics it is about the early identification of people who might be trending towards a pathway of disease. Early identification on that microbial composition level can mean early intervention. From diagnostics it is a question of stratification: can the trajectory of disease be altered by administering something like a probiotic to change the composition of the metabolite. For instance, at birth babies are given a vitamin K shot as the microbiome takes several weeks to kick in so hasn’t yet developed enough to produce vitamin K from food. 

Having moved from that diagnostic setting to stratifying people, the next area is therapeutical targeting to change an outcome. Looking at whether an individual’s microbiomes can be altered to change the disease process, to change the interaction with the immune system. With therapeutical targeting we can partner with companies and apply our research to the development of a product to target particular areas involving microbiomes.  


‘Before you start, make sure you have basic data and bioinformatic skills … the data science side of the field is rapidly and continually changing.’   


What advice would you give researchers?  

Take the opportunity to train well in your candidature. Due to technology, the state of the field is moving so quickly that you really don’t get a lot of time to train afterwards. 

Before you start, make sure you have basic data and bioinformatic skills. Week by week there are new methods for analysing samples and data; the data science side of the field is rapidly and continually changing.  

And, ultimately, ensure you have passion for your topic as you are going to spend three years researching it. If at the start you end up doing something you don’t enjoy then halfway through it becomes a real grind. I recommend potential researchers talk to various research groups to figure out what they are interested in—the rest will fall in line afterwards.  

Where do you see your research going in the next 3 to 5 years?  

Our focus is on building the sample sets we have in the obesity metabolism, allergy and atopic space and to identify some well-designed quality trials for the health supplement space. Really, it is about trying to identify the mechanisms of disease in the microbiome that relate to the immune system and then to look for what we call druggable targets—what can we target, either through a drug or supplement lifestyle, that will make a difference to a person’s long-term health. 

Interested in learning more?   

Read more about microbiomes through Dr West’s open access research on Griffith Research Online: