Biodiversity and the Natural Suppression of Human Pathogens

Restoring livestock to mixed-vegetable farms allows on-farm fertilizer production and the sale of high-value meat products.  Likewise, diversifying farms with native plants provides habitat for pest-killing birds and predatory insects. Unfortunately, both practices carry the risk of unintentional contamination of produce by human pathogens (e.g., E. coli O157:H7), transmitted through livestock feces or those of vertebrate wildlife drawn to native plantings. Currently, the only way to manage this risk is to remove all natural vegetation from the farm, which disrupts natural pest control, or to install deer-fencing around the entire farm perimeter, which is expensive and cannot exclude all vertebrate carriers of human pathogens. Arthropods and microbes that eat feces likely reduce this risk, but little is known about coprophage biodiversity, impacts, or conservation. Working on farms varying in their levels of livestock integration, we propose to: (1) Quantify biodiversity of feces-feeding arthropods (e.g., dung beetles, flies) through intensive field sampling; (2) Assess functional-genetic diversity of soil microbes using next-generation sequencing approaches, focusing on genes likely to be active in feces digestion; and (3) Relate biodiversity among coprophagous arthropods and microbes to rates of feces removal and E. coli suppression. Our ultimate goal is to provide vegetable growers with practical ways to reduce the risk of harboring human pathogens on their farms, by conserving and augmenting beneficial coprophagous insects and microbes. We address BIOAg goals by developing “biologically-intensive approaches to sustainable management of soil quality, whole farm food systems, livestock and animal health, and organic wastes.”

Grant Information

  • Project ID: 135
  • Project Status: Complete


  • Principal Investigator(s): Snyder, W.
  • Investigator(s): Besser, T., Reganold, J.
  • Grant Amount: $39,193
  • 2014 Progress Report (PDF)


Jones, M.S., Z. Fu, J.P. Reganold, D.S. Karp, T.E. Besser, J.M. Tylianakis, W.E. Snyder. 2019. Organic farming promotes biotic resistance to foodborne human pathogens. Journal of Applied Ecology.

Additional Funds Leveraged

1. Bill Snyder is PD, with Tom Besser and John Reganold as Co-PDs: USDA-NIFA-ORG, “A natural
approach to human-pathogen suppression: Can biodiversity fill the GAPs?” ($498,235 over 3 years).
2. Project PhD student Matt Jones has just been awarded a Fulbright Fellowship to expand this research
into New Zealand.


Short-Term: The central goal of our project is to provide organic mixed-vegetable farmers, including
those that integrate livestock into their farming operations, with an ecological approach to reducing
their food safety risks. Our project already is providing evidence that on-farm populations of
coprophagous insects are contributing to rapid feces removal. Work in upcoming years of the project
will focus on microbial degradation of feces, and the combined impacts of coprophagous arthropods and
microbes on pathogenic E. coli.
Intermediate-Term: Organic growers are under increasing pressure to conform to regulations often
presented under the heading of “Good Agricultural Practices” (GAP), which include practices designed to
reduce food-safety risks. Harmful strains of E. coli and several other human pathogens are thought to be
brought onto farms, at least in part, by livestock and vertebrate wildlife. To reduce these perceived risks,
GAP regulations often mandate the complete removal of hedgerows and other non-crop vegetation
from farms, with unknown harm to beneficial predatory insects, pollinators, and other species that rely
on these habitats as refuges. Our project seeks to demonstrate that many of the more draconian GAP
mandates are unnecessary, allowing growers to retain natural vegetation on their farms along with the
many environmental benefits that these habitats provide.
Long-Term: The ultimate goal of our project is to provide new, transitioning organic growers with a
roadmap for how to build naturally-pathogen-resistant farms. However, our project may also suggest to
long-time organic vegetable growers that they could benefit from a second transition, moving towards
livestock integration or the adoption of other practices found to build coprophage biodiversity.