High-throughput 16s amplicon analysis of poultry litter microbial communities and possible links with recurring outbreaks of gangrenous dermatitis in chickens
Date
2010
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Publisher
University of Delaware
Abstract
The production of chicken for their meat (broilers) is a multi-billion dollar industry in which large firms contract the chicken rearing out to individual local farms. Poultry litter, composed of bedding material, chicken excrement and feathers, and spilled feed is often maintained on the floor of the house through many successive growing cycles. The litter generated by this process is used extensively as both feed for other domestic animals and as crop fertilizer. Highthroughput sequencing was chosen as a means to assess the richness and diversity of the poultry litter environment. Samples from under water lines (Wet) and from common areas away from water and feed lines (Dry) were collected from four commercial broiler houses in the Delmarva region. Over 22,000 bacterial 16S rRNA gene sequences were produced using 454 pyrosequencing. All 16S amplicon sequences were assigned to operational taxonomic units (OTUs) at the 95% identity level. 16S OTU clustering by house reveals that the dominant bacterial taxa are not distributed evenly across houses. Furthermore, the distribution of OTUs between Wet and Dry litter samples also reveal dramatic differences. Comparing the most abundant OTUs from each sample type reveals a greater amount of richness and diversity in the Wet litter, with 90% of the total abundance covered across the top 214 OTU clusters. In contrast, the top 50 clusters cover 90% of the total abundance in the Dry litter. This increased diversity is further supported by a number of high abundance OTUs found to be derived entirely from Wet litter sequence. One house, using a modern cooling system, contained the highest number of unique OTU clusters. One of the unique clusters from this house was the sixth largest OTU cluster overall and classified as an Arcobacter sp., a potential human pathogen. Additionally, enumeration of both total virus and bacteria in litter by direct counts found a ten to one hundred-fold greater abundance compared to that found in soils. Two of the broiler houses sampled had experienced recurring outbreaks of the poultry disease gangrenous dermatitis while the other two had no history of the disease. Although the primary pathogenic Clostridial and Staphylococcal species were not found in any house, there were 13 OTUs found primarily in houses affected by recurring GD. These results provide a starting point for future studies aimed at clarifying the relationship between the microbial community of litter and poultry disease.