An Assessment of Broiler Litter Bacterial Diversity using Next Generation DNA Sequencing

Broiler chicken farms produce large amounts of litter, comprised mainly of used bedding and bird fecal waste, which is land applied. The regional concentration of broiler farms and land application of litter in the United States is a water quality concern. Geographically concentrated production also increases biosecurity concerns with potential pathogens and high nutrient contents as the litter is moved and land applied. Previous studies have attempted to characterize the bacterial population within litter because of these concerns. To date, this effort has not provided comprehensive information on the bacterial community structure within broiler litter. This lack of knowledge hinders the development of better water quality and biosecurity management efforts. This study characterized the bacterial community structure of broiler litter using Illumina MiSeq sequencing technology, specifically examining whether the litter bacterial community structure changed within in-house litter during a grow-out at one farm (fresh grouping), and whether the long-term stored (LTS) litter bacterial community structure varied in different geographic locations. Actinobacteria was the dominant in the fresh grouping (65.5% ± 10.2%) while only present at 22.2% ± 8% in the LTS. In contrast, the LTS samples were dominated by Firmicutes (77% ± 8%) which was only present at 31.4% ± 10% in the fresh grouping. Within the phylum Firmicutes, Bacillaceae (68% ± 11%) family was dominant in LTS across all of the geographic regions sampled, despite varying moisture content, integrators, and bedding/litter management practices. From ANOSIM, there were statistical differences among comparisons between integrators, and producers while no statistical difference was found among bedding materials. For the in-house comparisons, the bacterial community structure was uniform and dominated by families Brevibacteriaceae (19% ± 5%), Dermabacteraceae (15% ± 4%), Staphylococcaceae (14% ± 7%), and Corynebacteriaceae (13% ± 7%) despite the different times of collection (days 1, 15, and 43). ANOSIM revealed no statistical differences among time of collections (p value > 0.05). Staphylococcus was the only family consistently present in both LTS and fresh samples that contains pathogens of biosecurity concerns. Two dominant bacterial families could be used for the development of broiler litter fecal source tracking: Bacillaceae and Nocardiopsaceae were identified.