Agricultural insect communities through the eyes of a chicken: DNA metabarcoding diet analysis in pastured poultry systems

Pasture-raised poultry is an increasingly popular production strategy in the United States. Because the open environment encourages birds to move and forage on natural feed, e.g., insects, seeds, snails, etc., this production system is believed to improve bird performance and production yield. Additionally, poultry integrated into crop rotations may help to reduce farm input by providing organic fertilizer, removing crop residue, and potentially regulating insect pest populations. However, there is a lack of quantitative studies on how poultry foraging affects insect communities as well as how ecosystem services and disservices provided by poultry compare in pastured crop rotation settings. Fecal diet analysis using DNA metabarcoding can help to clarify these questions. In this study, we collected fecal samples from chickens that were integrated into crop rotations following various vegetable crops, and used DNA metabarcoding to characterize their diets. We also asked whether farm management strategies, such as stocking density and feed restriction, affect the diet composition of pastured poultry. This study represents the first use of DNA metabarcoding-based diet analysis in pastured poultry systems and will provide valuable insight into both the trophic relationships in rotational integrated farming and proper practice for future farm management.