Impacts of Poultry House Environment on Poultry Litter Bacterial Community Composition Michael D. Dumas 1 , Shawn W. Polson 1,3,7 , Don Ritter 4 , Jacques Ravel 5 , Jack Gelb Jr. 6 , Robin Morgan 6 , K. Eric Wommack 1,2,3 * 1 Department of Biological Sciences, University of Delaware, Newark, Delaware, United States of America, 2 Department of Plant and Soil Sciences, University of Delaware, Newark, Delaware, United States of America, 3 Delaware Biotechnology Institute, University of Delaware, Newark, Delaware, United States of America, 4 Mountaire Farms Inc., Millsboro, Delaware, United States of America, 5 Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America, 6 Department of Animal and Food Sciences, University of Delaware, Newark, Delaware, United States of America, 7 Center for Bioinformatics and Computational Biology, University of Delaware, Newark, Delaware, United States of America 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. Citation: Dumas MD, Polson SW, Ritter D, Ravel J, Gelb J Jr, et al. (2011) Impacts of Poultry House Environment on Poultry Litter Bacterial Community Composition. PLoS ONE 6(9): e24785. doi:10.1371/journal.pone.0024785 Editor: Jack Anthony Gilbert, Argonne National Laboratory, United States of America Received April 30, 2011; Accepted August 17, 2011; Published September 16, 2011 Copyright: ß 2011 Dumas et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Funding: The authors gratefully acknowledge the support of the University of Delaware, Avian Biosciences Center (http://ag.udel.edu/abc/). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing Interests: The authors have declared that no competing interests exist. * E-mail: wommack@dbi.udel.edu Introduction Advances in technology over the last century have greatly increased the scale of both crop and livestock agriculture. In the past 50 years, poultry production and consumption of broiler meat has increased by approximately 4% per year [1]. 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]. Steady production increases have resulted from industry moves to ever-larger poultry houses with most containing more than 20,000 birds. Despite its economic benefit, the high stocking density of birds in a house has spawned numerous health issues for both birds and humans [3]. In part, these issues arise from the volume of litter produced in a poultry house. Plant-based bedding material along with chicken excrement, feathers, and spilled feed are the principal components of litter. Typically, in United States broiler houses, a layer of new bedding material is deposited between each new flock and over the course of several years; dozens of flocks will be raised on a single bed of layered litter. Thus, poultry litter likely maintains the microbiological record of every past flock and is believed to be a reservoir of disease-causing microorganisms. Previous molecular genetic studies detected a diverse range of antibiotic resistance genes [4] and both human and avian pathogens [5] within poultry litter samples. However, none of these studies has investigated possible links between the compo- sition of litter microbial communities and the incidence of disease within a poultry house. One emerging disease of concern in the poultry industry is gangrenous dermatitis (GD), an avian disease that demonstrates links in its occurrence to environmental factors [6]. This low morbidity, high mortality disease progresses rapidly and begins with redness or swollen areas on the skin which quickly progress to large gangrenous lesions of dead and dying tissue [7]. Once the first symptoms occur, infected individuals die within 24– 72 hours. The primary pathogens associated this disease are Clostridium perfringens, Clostridium septicum, and Staphylococcus aureus [8,9,10],. However, there is no consensus on how the disease is spread or why some poultry houses exhibit chronic recurring outbreaks while other houses nearby never experience an outbreak. Moreover, in the US, GD incidence is most prevalent during the late spring/early summer in the Delmarva growing region of the mid-Atlantic, with other geographic regions experiencing little to no incidence of the disease [6]. Because affected and unaffected houses all receive the same bedding PLoS ONE | www.plosone.org 1 September 2011 | Volume 6 | Issue 9 | e24785