Could Australia's microbiome contain new antibiotics?

Industry and academia are coming together in a three-year, $6.9 million quest to search for new antibiotics in 500,000 species of Australian microbes.

Dr Heng Chooi, an ARC Future Fellow at The University of Western Australia (UWA), is one of the lead researchers of the project, headed by biopharmaceutical company Microbial Screening Technologies (MST), ARC Future Fellow Dr Andrew Piggott from Macquarie University and industry partner Advanced Veterinary Therapeutics (AVT). Dr Chooi is an emerging leader in molecular and genomic research of antibiotic production by microorganisms, harnessing molecular genetic approaches to unlock the hidden potential of microbes to produce new drug molecules.

“Genome sequencing has revealed that microorganisms, especially bacteria and fungi, harbour vast genetic potential for production of diverse bioactive molecules,” Dr Chooi said. “Their abilities were previously underestimated, as microbes tend to produce only a small subset of the molecules encoded in their genomes in standard laboratory growth conditions.”

The three-year project, ‘BioAustralis, towards the future’, will harness MST’s collection as a source of next-generation antibiotics capable of overcoming microbial resistance. The project will also provide these new actives, and a library of other unique microbial metabolites, in a ready-to-use format gratis for Australian researchers during the period of the grant.

“We have samples of over 500,000 Australian microbes,” said Dr Ernest Lacey, Managing Director of MST and the leader of the project.

“We’ve collected them from the soil in backyards, in paddocks and forests. We’ve collected them from insects, plants and animals. We’ve gone everywhere to find Australia’s unique microbiome.”

Building on MST’s microbial library, the UWA-led team will use molecular and genomics tools to accelerate the discovery of new drug molecules as well as the rediscovery of lost antibiotics to combat drug-resistant bacterial pathogens and develop next-generation pharmaceuticals.

“Lost antibiotics are molecules with interesting antimicrobial properties that were investigated decades ago but stalled in clinical development,” Dr Lacey explained. “Some of the producing microbial strains were completely lost and, to effectively combat drug-resistant bacteria, these ‘old’ molecules needed to be reinvestigated under new light.”

MST has been the sole supplier of some of these lost antibiotics to researchers worldwide and has been evaluating the potential of these molecules as treatment with AVT. The project will further expand the library of ‘old’ and new drug molecules for advancing antimicrobial research and drug discovery with the aid of cutting-edge molecular and genomics research at UWA and Macquarie University.

“Each microbe contains a unique cocktail of metabolites,” Dr Lacey said. “When we find an interesting new molecule, we’ll be relying on Macquarie University researcher Dr Andrew Piggott and his team to help us to work out its structure and mode of action.

“Then Dr Heng Chooi from UWA will use genomics to unravel how the microbes assemble these metabolites and then boost their productivity.

“Advanced Veterinary Therapeutics (AVT) is led by Dr Stephen Page and will focus on animal health potential.”

The $6.9 million project has just secured $3 million in federal government funding through the Cooperative Research Centre Project (CRC-P) Program, announced by Assistant Minister for Science, Jobs and Innovation Zed Seselja. The remaining $3.9 million comes in the form of cash and in-kind contributions from participating universities and industry partners.

“The project collaborators have a long and successful track record of unlocking the hidden biosynthetic potential of microbes,” Dr Lacey said. “As well as identifying new antibiotics, this grant will enable MST to move faster, stronger and more broadly in the development of a unique global niche in the fine chemical market.”

Image credit: ©stock.adobe.com/au/peshkova