The widespread and indiscriminate use of antibiotics has resulted in an era of antibiotic-resistant bacterial strains that pose a serious threat to public health. Common infections are becoming increasingly difficult to treat with currently available medications.
The World Health Organization (WHO) has declared antimicrobial resistance (AMR) as a global public 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 experiencing the highest mortality rate among all ages attributable to AMR. This crisis extends beyond human health and affects animals, pets and crops, resulting in the cumulative loss of trillions in the global economy.
In the effort to discover new antibiotics, soil microbes are emerging as a valuable resource, providing a rich and diverse ecosystem for researchers to explore new therapeutic compounds.
Rediscovering nature’s pharmacy: the soil microbiome
Soil is a rich and diverse environment that is home to many microorganisms, including bacteria, fungi and actinomycetes. These microorganisms have evolved several 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’s why we decided to dig deep into the soil microbiome to find new antibiotics
Most antibiotics on the market are isolated from microbes that can be present in soil, says Zeinab Khalil, a researcher at the University of Queensland’s Institute for Molecular Bioscience.
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 at producing antibiotics. Streptomyces griseusa genus of actinomycetes, was used to create the first antibiotic effective against tuberculosis.
“That’s 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 in Berlin last November.
Empowering citizens, inspiring curiosity and cultivating microbial discoveries
Khalil is one of the researchers behind Soils for Science, Australia’s first citizen science project to explore microbes in soil with the public. Citizens who sign up for the project will receive an easy-to-use kit that includes a scoop, a bag, a pre-paid mailing bag and labeling instructions. Participants can register samples and take images of collection locations via a special app.
This photographic documentation helps characterize the environmental context, distinguishing between rural and urban environments. In addition, the researchers have put together a public online gallery with images of the various microbes identified in the soil samples. “The science gallery is a reward for the public to thank them for their contribution,” says Khalil. “It also works like a microscope because people can see what’s happening on the plate where the soil microbes they collected are.”
The researchers also plan to install a new robotic system that can process 100 samples per day, instead of the 20 samples per week they currently have the capacity for. The robot will contain a camera that will stream the sample processing live.
The children were amazed to see how many microbes grew on the plane with just one hand.
Soils for Science works with universities, institutes, schools, aged care centres, childcare facilities, Aboriginal businesses and other researchers in academia and industry. An encouraging aspect of Soils for Science is the active involvement of children. The project includes educational initiatives such as providing children with hands-on experiences, virtual tours and hosting students in the laboratory.
“Children are the next generation. As much as we look for the next generation of new antibiotics, we have to take care of our children and their health,” says Khalil.
She says it brings her immense joy to receive soil samples and heartfelt notes from children expressing their gratitude for the efforts of the Soils for Science team. Teachers have also reached out and highlighted the impact of the science gallery on classroom discussions, providing a valuable platform for students to explore microbial interactions.
During school visits, after the children have played with the soil, Khalil asks the students to dip one hand into a petri dish containing the media used to grow microbes in the laboratory. They close the lid of the bowl and leave it on a bench until the next day. “The children were surprised to see how many microbes grew on the plane with just one hand.”
A potential antibiotic
From the many samples collected, Khalil and her colleagues were able to isolate Wollamidescyclic hexapeptides, from Australian soil Streptomyces isolate. These molecules are promising in vitro antimicrobial activity against Mycobacterium bovis Bacille Calmette Guérin without being toxic to mammalian cells.
While these potential antibiotics still need to be thoroughly studied and assessed in preclinical and clinical trials, Khalil says the result is significant and demonstrates the power of citizen collaboration. “It’s very good to work together because we live in the same community, so we have to take care of each other.”
Soils for Science extends its impact to agriculture and tackles challenges such as fungal infections in crops. Fungal pathogens, such as Phytophthora, can destroy crops, causing significant economic losses. Soils for Science aims to improve crop yields and prevent financial setbacks in agriculture by generating molecules that inhibit these fungal pathogens. The project also examines soil in search of microbes that could produce new antiparasitic agents for the animal space.
The project’s reach now extends beyond Australia, inspiring researchers in Canada and Austria to set up their own versions of Soils for Science. The global collaboration aims to increase the impact of citizen science in uncovering new antibiotics and tackling the challenge of antimicrobial resistance more broadly.
Revealing the soil microbial universe
In her speech at the Berlin Summit, Khalil drew a powerful analogy between the dark sky and a handful of soil. Just as NASA revealed galaxies in a seemingly empty sky with an open telescope shutter, Soils for Science reveals a universe full of potential in a handful of Earth.
‘You only see the dark earth and mud? We see a universe full of potential. A beacon of hope to protect our world from a future silent pandemic.”