In early 2020, the University of Queensland’s Institute for Molecular Bioscience launched Soils for Science (S4S), a national citizen science initiative inviting the public to share soil samples from their backyards. From these, we planned to isolate microbes to develop next-generation antibiotics and other life-saving drugs.
The timing of our launch at the start of a global pandemic was challenging, but not as inopportune as we first feared. It worked in our favour that the general public was rapidly acquiring an appreciation of the many threats of infectious viral disease and a thirst to know more about research and innovation that promised solutions.
As the pandemic progressed, there was much relief at the arrival of effective mRNA vaccines and comfort in the knowledge we were all safe again, right? Although the pandemic was winding back, momentum towards another global infectious catastrophe, which had begun decades before, was quietly building.
With a complacency born of a lifetime of ready access to a seeming endless array of reliable antibiotics, most of us view microbial infection as little more than an inconvenience. We expect that a short GP consult and a script (or sometimes a hospital stay to receive ‘better’ antibiotics) will do the job. A few decades ago, these were realistic expectations – but no longer.
When we use antibiotics to treat microbial (bacterial and fungal) infection, we inevitably select in favour of the survival of the very small subpopulation of microbes that are resistant to these antibiotics. With continued exposure to antibiotics, many microbes become resistant to many and even all known antibiotics.
If we liken COVID to a high-speed healthcare car crash, antimicrobial resistance (AMR) is a train wreck in the making – slower but potentially far more devastating. Informed analysts predict that, without urgent action, annual deaths from AMR infections will rise to 10 million by 2050, and continue to rise year on year thereafter – dwarfing the impact of the COVID pandemic.
Since the discovery of the ß-lactam antibiotics (penicillins) from fungi of the genus Penicillium early last century, virtually all commercial antibiotic classes either are or are inspired by the defensive natural products produced by microbes (e.g. cephalosporins, tetracyclines, aminoglycosides, erythromycins, glycopeptides, rifamycins, polymyxins, lipopeptides, polyene macrolides and more), more often than not soil microbes. This should come as no surprise, as microbes have benefited from billions of years of evolution to acquire natural chemical defences that help them survive and prosper in highly complex and competitive microbial communities.
Turning to one microbe for a new antibiotic to fight other microbes is a classic example of the enemy of your enemy being your friend. To exploit this knowledge, we must figure out which handful of the countless millions of microbes in the global microbiome are our friends.
Over many years, my research group has explored the natural products from Australian marine and terrestrial biodiversity, with a particular focus on microbes (bacteria and fungi). In recent years, we have implemented exciting new advances in analytical technologies that have massively enhanced our capacity and capability, allowing us to more rapidly and cost effectively detect and prioritise new over known, and bioactive over non-bioactive natural products. While the traditional scale of our microbial natural products research allowed the assembly and interrogation of libraries of a few thousand microbes, this new and improved capacity/capability could handle so much more – but to do this we needed to think outside the ‘grant funding’ box, and the confines of a single research lab.
Australian soil microbes represent an extraordinarily large and genetically diverse, sustainable natural resource, rich in unexplored chemical diversity that could fuel our research. Significantly, all the existing microbe-inspired commercial antibiotics had been discovered from microbes isolated from substrates (including soils) collected outside Australia. This encouraged the view that the Australian soil microbiome was a valuable and largely unexplored national asset, if only it could be accessed on a scale commensurate with its potential. So the problem became one of how to sample, with limited people and no travel budget, even a modest fraction of the soils of a continent as vast and environmentally diverse as Australia.
A potential answer came from our recent experience with the Cane Toad Challenge citizen science initiative, where we engaged the public, companies and local, state and federal authorities across Queensland, New South Wales, the Northern Territory and Western Australia, empowering them to trial a species-specific tadpole trapping technology to remove toxic cane toads from managed waterways. Thanks in part to citizen science, this cane toad control technology was successfully licenced and is being commercialised by Watergum (bit.ly/3QoZzi9). It was reasoned that, building on the knowledge gained running the Cane Toad Challenge, a new S4S citizen science initiative could inform the public about the threat of AMR, inspire the next generation to take up careers in STEM, demonstrate the benefits of university research, enlist the public to supply backyard soil samples from across Australia and enable assembly of a large library of Australian soil microbes.
As in any research, one of the early challenges was securing funding. We were very fortunate to benefit from generous philanthropic support, which in turn prompted internal support from the University of Queensland and the Institute for Molecular Bioscience. Several elements are critical to success:
- imb.uq.edu.au/soilsforscience has information on AMR and links to key S4S resources, including the option to request a free S4S Soil Kit.
- S4S Soil Kits are shipped free of charge and consist of a small trowel, barcoded soil bags, pre-paid return postage, and instructions (bit.ly/3QlQyGn).
- S4S participants register themselves in the free S4S app (spotteron.com/soilsforscience/auth/login), as well as each soil sample, to ensure they are geotagged and we have some details of the collection site.
- The interactive soilsforsciencegallery.org.au hosts and displays high-resolution digital images of all microbes recovered from individual soil samples, with the option to search against soil samples by barcodes, then zoom, pan and share images on social media.
- Dedicated video clips (such as bit.ly/3QiKP4d) were commissioned and shared, to support national and international print, broadcast and online media.
Public response to the S4S initiative has been humbling. To date, we have shipped more than 4500 S4S Soil Kits to all states across Australia and received more than 11 700 soil samples. Success has prompted an S4S Partners program to offer direct support to multiple schools and colleges, as well as an S4S Teacher-in-Residence to design primary/high school project resources that will dovetail into the science curriculum as of 2024. Along the way, we have been supported by multiple S4S Sponsors, who provide free/discounted services, and S4S Ambassadors, who expand our reach and message across multiple public events. More recently, we have received interest from Canada, Austria and the UK about how to set up parallel S4S initiatives.
So what of our goal to discover next-generation antibiotics? Further to our outreach, we have generated and cryopreserved more than 8000 microbial isolates and subjected their extracts to chemical and biological profiling – with some extremely promising results. The ongoing challenge is to secure sustainable funding to both continue and even expand S4S citizen science engagement, but also support in lab S4S research. S4S has already generated a microbial resource that exceeds our expectations, and will only continue to grow.
If you’re an Australian natural products chemist looking for a collaboration, please feel free to get in touch. We are happy to share, and perhaps together we can apply the brakes to the AMR train.