Abstract
Viral and bacterial pathogens are a significant economic concern to the US broiler industry and the ecological epicenter for poultry pathogens is the mixture of bedding material, chicken excrement and feathers that comprises the litter of a poultry house. This study used high-throughput sequencing to assess the richness and diversity of poultry litter bacterial communities, and to look for connections between these communities and the environmental characteristics of a poultry house including its history of gangrenous dermatitis (GD). Cluster analysis of 16S rRNA gene sequences revealed differences in the distribution of bacterial phylotypes between Wet and Dry litter samples and between houses. Wet litter contained greater diversity with 90% of total bacterial abundance occurring within the top 214 OTU clusters. In contrast, only 50 clusters accounted for 90% of Dry litter bacterial abundance. The sixth largest OTU cluster across all samples classified as an Arcobacter sp., an emerging human pathogen, occurring in only the Wet litter samples of a house with a modern evaporative cooling system. Ironically, the primary pathogenic clostridial and staphylococcal species associated with GD were not found in any house; however, there were thirteen 16S rRNA gene phylotypes of mostly Gram-positive phyla that were unique to GD-affected houses and primarily occurred in Wet litter samples. Overall, the poultry house environment appeared to substantially impact the composition of litter bacterial communities and may play a key role in the emergence of food-borne pathogens.
Highlights
Advances in technology over the last century have greatly increased the scale of both crop and livestock agriculture
In the United States, poultry consumption in 2009 was nearly 21 billion kg of meat produced from 8.2 billion broiler chickens valued at 21 billion US dollars [2]
No study has analyzed bacterial communities of poultry litter using deep sequencing of bacterial 16S rRNA gene amplification products. Previous studies investigating both litter and chicken intestinal microbial communities have employed denaturing gradient gel electrophoresis (DGGE), Sanger sequencing of 16S rRNA gene clone libraries, and cultivation-based assays [29,30,31,32,33]
Summary
Advances in technology over the last century have greatly increased the scale of both crop and livestock agriculture. No study has analyzed bacterial communities of poultry litter using deep sequencing of bacterial 16S rRNA gene amplification products. This house had the highest richness and diversity according to 16S rRNA gene OTU analysis (Fig. 1A&C) and the largest number of unique OTU clusters (i.e., an OTU cluster containing of sequences from only one house) (Table 2).
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