The widespread and indiscriminate use of antibiotics has resulted in an era of antibiotic-resistant strains of bacteria that pose a severe threat to public health. Common infections are becoming increasingly challenging to treat with currently available drugs.
The World Health Organization (WHO) has declared antimicrobial resistance (AMR) a global health emergency. A study published in The Lancet estimates that drug-resistant infections could cause 10 million deaths annually by 2050, with western sub-Saharan Africa facing the highest all-age death rate attributable to AMR. This crisis extends beyond human health, affecting animals, pets, and crops, resulting in the global economy’s cumulative loss of trillions.
In the effort to discover new antibiotics, soil microbes emerge as a valuable resource, offering a rich and diverse ecosystem for researchers to explore novel therapeutic compounds.
Rediscovering nature’s pharmacy: the soil microbiome
Soil is a rich and diverse environment that houses many microorganisms, including bacteria, fungi, and actinomycetes. These microorganisms have developed various mechanisms to compete for resources and survive in their ecological niche. As a result, they produce secondary metabolites, including antibiotics, to gain a competitive advantage.
That is why we decided to dig deep into the soil microbiome to find new antibiotics
Most of the antibiotics on the market were isolated from microbes that can be present in soil, says Zeinab Khalil, a research fellow at the Institute for Molecular Bioscience at The University of Queensland.
For example, penicillin, the first widely used antibiotic, was isolated from the fungus Penicillium. Among the microorganisms found in soil, actinomycetes, a type of filamentous bacteria, have been particularly prolific in producing antibiotics. Streptomyces griseus, a genus of actinomycetes, was used to create the first antibiotic effective against tuberculosis.
“That is why we decided to dig deep into the soil microbiome to find new antibiotics,” says Khalil, who presented her work at the Falling Walls Science Summit 2023 held last November in Berlin.
Empowering citizens, inspiring curiosity, and cultivating microbial discoveries
Khalil is one of the researchers behind Soils for Science, the first Australian citizen science project to engage with the public to study microbes in the soil. Citizens who sign up for the project receive a user-friendly kit with a spade, a sachet, a prepaid post bag and labelling instructions. Through a dedicated app, participants can register samples and capture images of collection sites.
This photographic documentation aids in characterising the environmental context, distinguishing between rural and urban settings. Additionally, the researchers have curated a public online gallery showcasing images of the diverse microbes identified in the soil samples. “The science gallery is a reward to the public to thank them for their contribution,” says Khalil. “It also acts as a microscope because people can see what is happening on the plate where the microbes from the soil they collected are.”
The researchers are also planning to install a new robotic system able to process 100 samples a day, rather than the 20 per week they currently have the capacity for. Inside the robot, there will be a camera that will live-stream the sample processing.
The children were surprised to see how many microbes grew on the plane from just one hand.
Soils for Science engages with universities, institutes, schools, aged care centres, childcare facilities, Aboriginal corporations, and other researchers in academia and industry. One heartening aspect of Soils for Science is the active involvement of children. The project incorporates educational initiatives, such as providing children with hands-on experiences, virtual tours, and hosting students in the lab.
“Children are the next generation. As much as we are looking for the next generation of new antibiotics, we need to look after our children and their health,” says Khalil.
She says it brings her immense joy to receive soil samples and heartfelt notes from kids expressing gratitude for the Soils for Science team’s efforts. Teachers have also reached out, highlighting the impact of the science gallery on class discussions, providing a valuable platform for students to explore microbial interactions.
During school visits, after the kids have played with the soil, Khalil asks students to submerge one hand into a petri dish containing the media used to grow microbes in the laboratory. They close the dish’s lid and leave it on a bench until the following day. “The children were surprised to see how many microbes grew on the plane from just one hand.”
A potential antibiotic
From the many samples collected, Khalil and her colleagues could isolate Wollamides, cyclic hexapeptides, from an Australian soil Streptomyces isolate. These molecules show promising in vitro antimicrobial activity against Mycobacterium bovis Bacille Calmette Guérin without being toxic against mammalian cells.
While these potential antibiotics still need to be thoroughly studied and assessed in pre-clinical and clinical trials, Khalil says the result is significant and shows the power of citizens’ collaboration. “It’s very good to work together because we live in the same community, so we need to look after each other.”
Soils for Science extends its impact to agriculture, addressing challenges like crop fungal infections. Fungal pathogens, like Phytophthora, can devastate crops, resulting in substantial economic losses. Soils for Science aims to enhance crop yield and prevent agricultural financial setbacks by generating molecules to inhibit these fungal pathogens. The project also explores the soil for microbes capable of producing new anti-parasitic agents for the animal space.
The project’s reach now extends beyond Australia, inspiring researchers in Canada and Austria to establish their own versions of Soils for Science. The global collaboration seeks to amplify the impact of citizen science in uncovering new antibiotics and addressing the challenge of antimicrobial resistance on a broader scale.
Unveiling the microbial universe in soil
In her speech at the Berlin Summit, Khalil drew a parallel between the dark sky and a handful of soil in a powerful analogy. Just as NASA, with an open telescope shutter, revealed galaxies in a seemingly empty sky, Soils for Science exposes a universe full of potential in a handful of soil.
“You only see the dark earth and mud? We see a universe full of potential. A beacon of hope to safeguard our world from a future silent pandemic.”