Peck, poop, and PCR: Unveiling entomological and applied insights of pastured poultry systems via DNA metabarcoding

Alternative poultry production systems, including organic and pasture-raised chicken, are gaining global prominence. These systems are often perceived as enabling chickens to live more natural lives, purportedly enhancing their welfare, performance, and nutritional value. Additionally, poultry raised on farms are believed to provide ecosystem services and may potentially suppress insect pests. However, there remains a paucity of research regarding the specific dietary composition of chickens in pasture environments and effective strategies for maximizing pasture utilization. Here, I will discuss ongoing work using diverse metagenetic approaches to explore the ecological connections of, and management strategies for, pastured poultry. We validated DNA metabarcoding diet analysis methods by conducting a proof-of-concept experiment to assess the efficacy of DNA extraction kits and primers for analyzing the dietary composition of backyard chickens as well as persistence of diet DNA in their digestive systems. This validated protocol was applied to investigate the diet composition of pasture-raised chickens in a three year field experiment, thereby informing farm management practices. Follow-up work has shifted the focus of these field trials to the influence of farm characteristics on the diet composition of pasture-raised chickens. Finally, the interaction between diet composition and chicken gut microbiome was also explored. These studies mark a pioneering application of DNA metabarcoding techniques to uncover the specific insects and plants consumed by chickens in pasture environments. The findings will inform strategies for optimizing farm management practices and maximizing profitability, and provide a window into the ecology of small-scale agricultural ecosystems.