Microbes living in soils in Australia’s coastal areas, inland agricultural regions and vast deserts may hold important links to the next generation of antibiotics for humans and animals.
Dr Zeinab Khalil, a 2024 ARC Future Fellow whose work focuses on “Towards the sustainable discovery and development of new antibiotics” is at the centre of this effort.
Based at the UQ Biosustainability Hub, part of the Australian Institute for Bioengineering and Nanotechnology at The University of Queensland, Dr Khalil is an internationally recognised expert in microbial natural product biodiscovery, medicinal chemistry and metabolomics.
Her work is aimed at countering the growing global threat of antimicrobial resistance in humans, animals and agriculture while doing so in ways that protect ecosystems.
Turning microbial diversity into sustainable solutions
Through her ARC Future Fellowship, Dr Khalil is building BLOOM. BLOOM, which stands for Biosustainable Life Out Of Microbes, is an integrated research platform dedicated to unlocking the potential of microbes collected from diverse environments including soils, marine ecosystems, plants seaweeds and host-associated microbiomes.
“Through our BLOOM program we are turning microbial diversity from nature into practical, sustainable innovations for health, agriculture and the environment,” she says.
BLOOM brings together microbial discovery, chemistry, genomics, protein analysis and metabolomics techniques that allow scientists to identify, characterise and understand the molecules microbes produce to bridge the gap between fundamental scientific discovery and real‑world application, discovering new, useful molecules and developing them at scale.
From citizen science to deep discovery
Dr Khalil previously directed Soils for Science, Australia’s first citizen science program designed to engage the public in studying soil microbes. That experience helped shape both her scientific approach and her commitment to collaboration.
“My ARC Fellowship is enabling me to study microbes at a far more in‑depth level than before, moving from discovery alone to understanding microbial chemistry, genetics and biosynthetic potential in detail,” she says. “Through this integrated, multidisciplinary approach is how we find the next generation of drug leads.”
This deeper level of analysis allows her team to explore not just whether a microbe produces a useful compound, but how stable, scalable and sustainable that production could be.
Why microbes matter across every sector
Microbes have largely been overlooked as a source of future biosustainable solutions, despite historically underpinning many of the most transformative discoveries in medicine and agriculture. Many of the world’s most important antibiotics, antifungals and bioactive compounds including penicillin and streptomycin were originally derived from microorganisms.
“If you look around,” Dr Khalil says, “most antibiotics and many other drugs and natural products all came from microbes. What interests me is biosustainability – beyond soil microbes and in marine environments, plants, animal guts, and even the human gut.”
Many microbes, and the compounds they produce, support human health, regulate immune systems, protect crops, improve soil structure and strengthen ecosystems. For example, soil microbes can suppress plant pathogens and promote healthier crop growth, while microbes in the human gut produce metabolites that influence immunity and overall health. Yet in Australia, one of the world’s most microbially diverse continents, this resource remains largely unexplored.
“Australia spans bushland, deserts, beaches and marine environments,” she says. “Within these lie enormous chemical diversity that could help solve some of the world’s most pressing global concerns, such as antimicrobial resistance to sustainable agriculture and environmental restoration.”
Rethinking agriculture and environmental impact
BLOOM’s work is timely in agriculture, where reliance on synthetic fungicides is increasing resistance, reducing soil biodiversity, polluting waterways and creating resistant pathogens.
“Growers are facing increasing antifungal resistance,” Dr Khalil explains. “Often the approach is to flood environments with chemical agents. Yes, they may kill the target fungus, but they also disrupt soil microbes, accumulate in waterways, and impact aquaculture, fish and even seaweeds.”
Microbe‑based solutions such as biological fertilisers and naturally derived antifungals offer a sustainable alternative.
Collaboration brings complementary strengths
BLOOM brings together academia, industry, community groups and policymakers and their complementary strengths, working together in ways that that accelerate discovery-to-application pipelines, reduce time to market, and enable scalable, real-world solutions.
This work is further strengthened through partnerships with industry leaders such as Agilent Technologies, whose advanced analytical platforms support high-resolution metabolomic profiling and accelerate the identification of novel bioactive compounds. These collaborations ensure that discoveries are not only scientifically robust, but also scalable and ready for translation into practical solutions.
Through the UQ Biosustainability Hub, research teams spanning genomics, microbiology, synthetic biology and chemistry are directly paired with industrial partners to fast-track innovation from early discovery to application and commercialisation.
“We bring all parties together and ask: what real-world problems are you facing?” Dr Khalil says. “Then we design microbial solutions to meet those needs, whether that means discovering new antibiotics, developing sustainable antifungals for agriculture, or identifying beneficial microbes for gut health and functional foods.”
Collaborators range from international universities exploring biodegradable food packaging derived from microbial compounds, to industry partners studying gut microbes for next‑generation functional foods such as weight‑management yoghurt.
In another collaboration, the Capricorn Conservation Council in Rockhampton is working with BLOOM to explore soil microbiomes and their role in water retention.
The partnership includes school visits, community talks and on‑site sample collection, integrating biosustainability education alongside science innovation.
A growing, shared platform
BLOOM is still in its early stages, but it is developing rapidly. The platform already includes around 250 environmental samples, yielding more than 600 microbial strains. Dr Khalil’s vision is to make BLOOM a shared international resource.
“I want BLOOM to be a platform anyone can contribute to and benefit from,” she says. “Drug discovery is just one part. Others might study these microbes for agriculture, environmental repair or new materials.”
For Dr Khalil, Citizen Science Month speaks to the essence of BLOOM’s philosophy: science works best when sectors share knowledge and expertise.
“The more expertise involved … community members and students to farmers, industry and policymakers, the greater the impact we can have, and scale of discoveries we can unearth.”





