Earthworm-based composting offers a low-energy solution to antibiotic resistance

Earthworms could become unexpected allies in the global fight against antibiotic resistance, helping farmers turn manure into safer, high-value organic fertilizer through a process called vermicomposting. The researchers report that this low-energy, nature-based technology can remove antibiotic resistance genes much more consistently than conventional composting, while also improving soil health and supporting sustainable agriculture.

Antibiotic resistance from farm to table

The World Health Organization has named antimicrobial resistance as one of the most serious threats to modern medicine, and livestock production is a major part of the problem. When animals receive antibiotics, resistance genes accumulate in their manure, and if that manure is spread over fields without proper treatment, these genes can move into soil, water, crops, and eventually the human gut. Conventional composting helps, but its performance is erratic and in some cases the basic resistance indicators can even bounce during the composting process.

A living bioreactor under our feet

Vermicomposting uses earthworms and associated microbes to convert raw manure into a stable, friable product known as vermicast. Under carefully controlled moisture, temperature and nutrient conditions, this mesophilic process not only recycles waste into fertilizer but also achieves a multifold reduction in antibiotic resistance genes. Studies summarized in the new review show that vermicomposting can reduce the total abundance of resistance genes by about 70 to 95 percent and mobile genetic elements by up to 68 percent, often outperforming traditional compost piles.

“Earthworms are not just passive decomposers, they are active engineers of a safer microenvironment,” says corresponding author Fengxia Yang of the Agro Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, China. “By reshaping microbial communities and disrupting gene transfer, they help reduce the chain of spread of antibiotic resistance from farms to humans.”

How earthworms disarm resistance genes

The authors describe vermicomposting as an integrated physical, chemical and biological barrier against antibiotic resistance. As earthworms forage and feed, they increase porosity and aeration in the manure, maintaining oxygen-rich conditions that suppress many anaerobic bacteria that often carry resistance genes and support faster breakdown of residual antibiotics. Inside the earthworm gut, mechanical grinding, digestive enzymes and a specialized microbiome further damage resistant bacteria and disrupt both intracellular and extracellular DNA.

A key advantage lies in the way earthworms rebuild the microbial community. Their activity shifts the system away from fast-growing opportunistic bacteria that often harbor resistance genes toward more stable, functionally beneficial groups involved in nitrogen decomposition and fixation. At the same time, vermicomposting reduces the abundance of mobile genetic elements, such as plasmids and intagons, which are the vehicles that transfer resistance genes between bacteria through horizontal gene transfer.

The hidden power of earthworm slime

Beyond the gut, the earthworm’s epidermal mucus and coelomic fluid act as a biochemical interface to the composting mass. This mucus contains carbohydrates, proteins, lipids and bioactive molecules including antimicrobial peptides, lysozymes and DNases that can damage bacterial cell membranes, generate reactive oxygen species and directly degrade resistance genes. Laboratory studies reported in the review show that coelomic fluid can cut multidrug-resistant Escherichia coli populations by several orders of magnitude within hours and remove more than 90 percent of extracellular resistance genes through DNA-cutting activity.

Mucus also alters microbial behavior by interfering with bacterial communication systems and gene expression. In a mechanistic study, exposure to earthworm coelom fluid led to thousands of bacterial genes being up- or down-regulated, disrupting the pathways that bacteria rely on for coordination and conjugation. Network analyzes show that after earthworm treatment, statistical associations between resistance genes and their bacterial hosts weaken, suggesting that vermicomposting ecologically decouples resistance traits from the microbes that carry them.

Increase performance with smart plugins

Performance is further improved when vermicomposting is combined with functional materials such as biochar, zeolite or clay minerals. These additives can adsorb antibiotics and heavy metals, reducing stress on earthworms and microbes, while stabilizing contaminants and reducing selective pressure favoring resistant bacteria. In tests summarized by the authors, combining earthworms with biochar or mineral amendments increased earthworm growth, accelerated organic matter degradation, improved wetting, and increased removal rates for both resistance genes and heavy metal resistance markers.

Together, earthworm activity, mucus-derived biochemistry, and custom additives create a multi-level containment system that works from molecules to entire ecosystems. The result is a stronger, more consistent reduction in antibiotic resistance genes than is typically achieved with conventional composting alone, while producing a high-quality organic fertilizer that can improve soil structure, water retention and plant nutrition.

From promising lab results to reality

Despite these advantages, the authors caution that significant challenges remain before vermicomposting can be widely used as an antibiotic resistance control strategy. Different earthworm species vary in their tolerance to antibiotics and environmental conditions, and key operating parameters such as density, feedstock composition, temperature, and moisture must be fine-tuned for each type of agricultural waste. Large-scale systems must also address the climate sensitivity, reactor design, automation, and logistics of maintaining healthy earthworm populations on an industrial scale.

Another open question is the long-term fate of any resistance genes that remain in the vermicompost once it is applied to fields. The review calls for multi-year field studies and realistic risk assessments to understand whether residual genes can be reactivated under new stresses such as heavy metals or additional antibiotic use. The authors argue that future work should incorporate multi-ohmic tools, artificial intelligence models, and engineered treatment trains that combine thermal pretreatment, vermicomposting, and targeted polishing steps such as enzyme or phage applications.

“Antibiotic resistance is a complex system-wide problem, and no single technology will solve it,” notes Yang. “But by harnessing earthworms and modern biotechnology together, vermicomposting offers a practical path to making manure recycling safer for farmers, consumers and the environment.”