Earthworms turn manure into a powerful tool against antibiotic resistance
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Mechanisms and challenges in reducing antibiotic resistance genes by vermicomposting
view moreCredit: Bowen Li, Yuanye Zeng, Zhonghan Li, Simeng Cheng, Siyi Hu & Fengxia Yang
Earthworms could become unexpected allies in the global fight against antibiotic resistance, by helping farmers turn manure into safer, high-value organic fertilizer through a process called vermicomposting. Researchers report that this low energy, nature-based technology can remove antibiotic resistance genes far 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 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 on fields without proper treatment, those genes can move into soil, water, crops and eventually the human gut. Conventional composting helps, but its performance is unstable and in some cases key resistance markers can even rebound during the composting process.
A living bioreactor under our feet
Vermicomposting uses earthworms and their associated microbes to transform raw manure into a stable, crumbly product known as vermicast. Under carefully controlled moisture, temperature and nutrient conditions, this mesophilic process not only recycles waste into fertilizer but also achieves multi pathway reduction of antibiotic resistance genes. Studies summarized in the new review show that vermicomposting can reduce the total abundance of resistance genes by roughly 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 cut the chain of antibiotic resistance spread from farms to people.”
How earthworms disarm resistance genes
The authors describe vermicomposting as an integrated physical, chemical and biological barrier against antibiotic resistance. As earthworms burrow 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 disturb both intracellular and extracellular DNA.
A key advantage lies in how earthworms restructure the microbial community. Their activity shifts the system away from fast growing opportunistic bacteria that frequently host resistance genes toward more stable, functionally beneficial groups involved in decomposition and nitrogen fixation. At the same time, vermicomposting lowers the abundance of mobile genetic elements such as plasmids and integrons, which are the vehicles that shuttle resistance genes between bacteria through horizontal gene transfer.
The hidden power of earthworm mucus
Beyond the gut, earthworm epidermal mucus and coelomic fluid act as a biochemical interface in 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 cited in the review show that coelomic fluid can cut multidrug resistant Escherichia coli populations by several orders of magnitude within hours and remove over 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 one mechanistic study, exposure to earthworm coelomic fluid led to thousands of bacterial genes being up or down regulated, disrupting pathways that bacteria rely on for coordination and conjugation. Network analyses indicate that after earthworm processing, the statistical links between resistance genes and their bacterial hosts weaken, suggesting that vermicomposting ecologically decouples resistance traits from the microbes that carry them.
Boosting performance with smart additives
Performance improves further when vermicomposting is combined with functional materials such as biochar, zeolite or clay minerals. These additives can adsorb antibiotics and heavy metals, easing stress on earthworms and microbes while stabilizing pollutants and reducing the selective pressure that favors resistant bacteria. In trials summarized by the authors, pairing earthworms with biochar or mineral amendments increased earthworm growth, accelerated organic matter degradation, improved humification and raised removal rates for both resistance genes and heavy metal resistance markers.
Together, earthworm activity, mucus derived biochemistry and tailored additives create a multi level containment system that acts from molecules to whole ecosystems. The result is a more robust, stable reduction of antibiotic resistance genes than is typically achieved in 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 field reality
Despite these advantages, the authors caution that significant challenges remain before vermicomposting can be deployed widely as an antibiotic resistance control strategy. Different earthworm species vary in their tolerance to antibiotics and environmental conditions, and key operating parameters such as stocking density, feedstock composition, temperature and moisture must be fine tuned for each type of agricultural waste. Large scale systems must also address climate sensitivity, reactor design, automation and the logistics of maintaining healthy earthworm populations at industrial scale.
Another open question is the long term fate of any resistance genes that remain in 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 integrate multi omics 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,” Yang notes. “But by harnessing earthworms and modern biotechnology together, vermicomposting offers a practical pathway to make manure recycling safer for farmers, consumers and the environment.”
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Journal reference: Li B, Zeng Y, Li Z, Cheng S, Hu S, et al. 2025. Mechanisms and challenges in reducing antibiotic resistance genes by vermicomposting. Biocontaminant 1: e024
https://www.maxapress.com/article/doi/10.48130/biocontam-0025-0021
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Method of Research
Literature review
Subject of Research
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Article Title
Mechanisms and challenges in reducing antibiotic resistance genes by vermicomposting
