Gut feeling leads to ground-breaking microbiome research

World-leading experts are uniting to investigate the interaction of the innate immune system with the microbiome and pathogens. New and improved treatments for many serious conditions from inflammatory bowel disease (IBD) to chronic infections could be discovered thanks to a prestigious five-year NHMRC Synergy Grant for microbiome research, awarded to Hudson Institute scientists Professor Paul Hertzog, Professor Elizabeth Hartland and Dr Sam Forster, in collaboration with University of Melbourne’s Professor Christine Wells.

Dr Sam Forster holding a bacterial agar plate showing anaerobic bacteria. 

In an era when antibiotic resistance threatens to limit treatments for bacterial infections, this leading microbiome research will develop alternatives, such as new ways of manipulating our immune systems to fight infections and distinguishing between ‘good’ bacteria and disease-causing ‘bad’ ones.

The pioneering project will explore new medical frontiers to probe how our innate immune system distinguishes ‘friend from foe’, how it interacts with resident microbes differently from pathogens, how these interactions control the immune system, and how the immune system shapes the microbiome—all the microbes, including bacteria, fungi and viruses that live on and inside our bodies.

This will improve our understanding of why an illness develops and how best to treat it.

The multidisciplinary team will use cutting-edge techniques and develop new ones that integrate genome sequencing, sophisticated computer analysis, microchip and microfluidics technology and a unique library of ‘friendly’ bacteria.

“We’ll be generating enough information for thousands of projects,” says Prof Hertzog. “Even though the amount of data to be generated is enormous, we now have computer systems that can actually make sense of it. It’s amazing!”

The research will facilitate the development of new treatments for a range conditions, including infections, inflammatory diseases and cancers affecting the lungs, gastrointestinal and reproductive systems, and urinary tracts.


In a second, separate microbiome research study underway, our researchers are collaborating to identify common protective and inflammation-causing gut bacteria in children diagnosed with IBD, and to identify treatments that target those bacteria.

Up to 10,000 children in Australia suffer from IBD—an incurable lifelong disease that causes inflammation in the colon and rectum. Symptoms can be so severe that some people with the disease need to be hospitalised or undergo surgery.

The disease is currently managed using drugs that suppress the immune system— which become less effective over time and can have significant side effects, such as an increased risk of colorectal cancer and lymphoma.

Dr Sam Forster, Dr Jaclyn Pearson and Dr Edward Giles hope their research will lead to more targeted treatments, including faecal transplants, probiotics or immunomodulators.

“Ultimately, through this work we will find new treatments that will reduce suffering, minimise hospital visits and reduce the need for surgery, optimising growth and psychosocial outcomes for young people,” said Dr Giles.


The human microbiome holds the key to how many ailments develop and play out in our body.

Humans are mostly made up of microbes—more than 100 trillion. Those in the gut, particularly in the large intestine, play an important part in health and disease.

Imbalances in our gut microbiome are known to contribute to complex conditions such as inflammatory bowel disease (IBD), irritable bowel syndrome, allergies and obesity.

“Through our work, we have been at the forefront of understanding these complex communities. At Hudson Institute, we now have one of the most diverse collections of human isolated bacteria in the world,” says Dr Forster.

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