Dr Zeinab Khalil: Unlocking the hidden chemistry of microbes

Dr Zeinab Khalil is prepared to go to the moon and back to make an impact on human health and sustainability.

She is intent on finding new products from microbes, even analysing bacteria growing at zero gravity to see what they do differently.

Working at AIBN has given her the opportunity to work with industry partners to see her research have real world impact.

Collaborating with the UQ Biosustainability Hub has given her access to facilities to elevate her research to another level.

An ambitious and dedicated researcher, if she isn’t remembered for her discoveries, she wants the legacy she leaves to be a well-supported next generation of leaders and scientists to continue her journey.

The quest

Dr Khalil is on a quest to deepen our understanding of microbial ecosystems and discover new molecules from microbes.

These could be antibiotics, antifungals, pesticides or new drug leads for diseases.

“Microbes live together in a community and when we isolate them from a sample, for example soil, we observe chemical interactions between bacteria and fungi which we can use for our benefit,” she said.

“These chemicals could be communication signals or fighting mechanisms to kill other species – and they may be the next antibiotic or anti-cancer drug.”

Dr Khalil’s team has already discovered several new microbial molecules made by microbes that can kill or disarm harmful bacteria, fungi and parasites, including some of the toughest drug-resistant strains.

Translation with AIBN

Dr Khalil’s ambition to expand her capabilities led her to AIBN’s door where she has recently been appointed.

“What we do in the lab is really amazing, but I wanted to focus on translational outcomes – I enjoy working with others to turn our research into real-world benefits.”

Working with industry

Her move to AIBN has created new opportunities across a range of industry-aligned projects, spanning agriculture, food and environmental applications.

These include collaborations focused on developing microbial solutions for crop protection, sustainable agriculture and foods that provide extra health benefits.

“Every partner is different, and that is what is so exciting,” she said,

“We work closely with stakeholders to understand their challenges and translate our research into practical, real-world solutions.”

“It's still microbes, it's still chemistry, but now it's translation.”

Digging deep with the UQ Biosustainability Hub

Working at the Biosustainability Hub has enabled Dr Khalil to expand her study of microbe molecules by combining metabolomics (study of metabolites) with genomics (study of genetic material). 

“I’m not looking to rediscover what we already know, I want to uncover rare and entirely new chemistry that has never been seen before.”

Finding locked chemistry

Previously, Dr Khalil grew microbial communities up from samples (plant, soil, marine etc.) in the lab, then analysed their extracts for antibacterial, antifungal and cytotoxic properties.

“But we were only seeing chemicals produced under normal lab conditions – less than 1 per cent of what is possible.

We were barely scratching the surface,” she said.

“By doing full genome sequencing, we get access to ‘locked chemistry’ – we are now finding silent genes and also chemical cues that activate these silent genes.

“It gives us access to a large array of different molecules, the hidden 99 per cent.”

Scaling up

The Biosustainability Hub has given a vital boost to one of Dr Khalil’s projects to tackle antimicrobial resistance, providing training and use of the biofermenters to enable scale up.

Dr Khalil has found new compounds that inhibit the cell wall formation in Gram-negative bacteria, such as E.coli and Pseudomonas.

The cell wall of these increasingly drug-resistant bacteria acts as an extra shield against antibiotics.

“For our experiments, we need to grow large volumes of bacteria – it takes around 1000 agar plates to produce only 2 milligrams.

“Using the biofermenters to grow large quantities is a gamechanger, enabling us to accelerate our research.”

“This is the beautiful thing about collaboration and working in the Biohub – it’s easy to reach out, we can ask for advice and give advice.”

Reaching to the moon

After discovering that when bacteria grow without gravity, they have a completely different chemistry, Dr Khalil has turned her attention to how bacteria operate in space.

“Once I found out that antibiotics don’t fight microbial infections for astronauts in space, I was intrigued.”

In collaboration with UQ’s School of Agriculture and Food Sciences, Dr Khalil is developing tools to explore how gravity changes the way microbes behave and produce chemicals by recreating microgravity on Earth.

“I want to know how gravity is affecting these bacteria and with new technologies, we are able to analyse bacteria grown in zero gravity conditions and plan experiments in space.”

This to Zeinab is a rare opportunity to discover another set of new molecules.

Supporting young researchers

In Dr Khalil’s team, you imagine that her passion, enthusiasm and energy must be infectious.

“I want my team to come to work feeling excited about the work and what adventure they are embarking on that day – this is the environment I'm trying to provide.

Acknowledging that a research career can be a difficult road, she wants to ensure everyone in her team is supported.

“I say to my team that I want you to develop and move forward, so when you leave here, you do so with new skills and new capabilities.”

“I will be happy that I left behind a new generation of leaders and scientists who can continue my journey.”

Looking ahead, her vision is to build a globally connected platform for microbial biodiscovery bridging fundamental science with real-world impact across health, agriculture and the environment.

Dr Khalil is an ARC Future Fellow at AIBN.
She leads the BLOOM (Biosustainable Life Out Of Microbes) program.