By Professor Ashley Franks, Pro Vice-Chancellor (Research Capability)
As a microbiologist, who has dedicated the last decade to understanding the structure and function of microbiomes, the growing interest of industry, academia and the community in the influence and impact of the microbiome has been inspiring to witness.
Having spent my career working across a large range of environments, including plant rhizospheres, soils, electrogenic microbes and aquatic systems, the complexity and multiple drivers of mammalian microbiomes come as no surprise.
We’ve always known that microbiome research uses a systems approach, which is essential to ensure we don’t think what occurs within the microbiome does not affect, nor is not affected, by what is happening with the host.
Our initial investigations into microbiomes occurred by investigating beneficial bacterial-plant interactions. Through the production of several metabolites, through reduction of pathogenic microbes, and the choice of beneficial traits, we discovered we could improve several aspects of growth, yield and resistance for a number of crops.
Another one of the most surprising early findings we encountered was that some plant varieties were controlling the microbes at the molecular level to produce the compounds the plant required. However, in some instances, the beneficial microbes did not persist in a system as expected but still provided long-term benefits through the engineering of the plant rhizosphere to contain more beneficial microbes.
We first worked on mammalian microbiomes with Professor Elisa Hill, RMIT University, by working on an autism mouse model. Through this collaborative research partnership, I was quite surprised to discover that a single point mutation in the brain had a significant influence on the development and composition of the mouse microbiome.
This initial work has led our laboratories to a long, mutually beneficial research collaboration. It has seen us track the microbiome response to antidepressants and the different responses seen in males and females, to the spatial and temporal development of microbiomes in calves before birth, as well as investigate ways to influence and engineer the microbiome for beneficial outcomes.
Together, we have developed the importance of the microbial community being treated as a functional system and not just a grouping of individual microorganisms.
Our work has led us to be able to isolate new probiotics, test microbiome interventions, use evolution to improve strains, incorporate phage into our systems understanding and provide industry services both nationally and internationally.
The question that we keep discussing is what are our next major steps in microbiome research?
The answer to this is health and well-being in humans and animals.
Understanding and maintaining the microbiome provides resilience, health, mental longevity and many other benefits.
The other big question is what is a healthy microbiome?
We know what it looks like and what happens when other ecosystems such as a rainforest or coral reef are healthy, but we’re still unable to take a snapshot of an individual microbiome and draw a conclusion on how things are tracking. What we do know from our own studies, is that a personalised approach to microbiome health is required due to the influence of the host's own genome, as well as the environment and food intake.
To overcome these limitations, we are now combining several areas of research for functional outcomes.
Starting with food and production, we are connecting how production and nutrition help or hinder our microbiome health. How does the loss or gain of function shift microbiomes over time? How can we pair our understanding of the host genome with the microbiome? And then, how do we use this knowledge to improve quality of life?
In this work we are now looking at the atemporal and spatial location of the microbiome along the gut, the interaction with several neurological disorders and the microbiome. Even now, we’re using spiders to study how space travel will affect the microbiome for potential trips to Mars.
Overall, our ability to now understand microbial communities at a system level is providing an unparalleled ability to predict and produce functional outcomes in microbiome research.
From the transfer of genes through the individual microbe to the microbiome/host system. Our work is going from the paddock to gut, looking at the impact of changing environments and systems, how to restore and improve as well as validate our own predictions.
La Trobe Industry Communications and Media Enquiries: industry.engagement@latrobe.edu.au
