2012 Annual Report 1a.Objectives (from AD-416): Maintaining gut microbiota in developing chickens is critical for animal health. Gut microbiota plays an important role in innate immunity and disruption in gut normal flora during infectious diseases needs to be better studied in order to understand host-pathogen interaction in necrotic enteritis. Cooperators will access gut microbiota in the intestinal samples which will be collected from experimental disease models developed at ARS. 1b.Approach (from AD-416): Reliable disease models for necrotic enteritis will be developed. Intestinal samples from various parts of the chicken intestine will be collected at different time points following the disease challenge by using an established necrotic enteritis disease model. DNA samples will be prepared and sent to the Cooperator for gut microbiota analysis using pyrosequencing. 3.Progress Report: Avian coccidiosis and necrotic enteritis are among the most economically significant diseases affecting the poultry industry worldwide. Two commercial broiler chickens (C and R) were induced to develop necrotic enteritis using an Eimeria maxima and Clostridium perfringens co-infection model that our laboratory previously developed. Two days post-infection, total genomic DNA was extracted from the ileal contents and sequenced to obtain pooled samples of a specific region (V1 to V3) of a specific gene (16S) for bacterial ribosomal RNA. More than 60,000 partial 16S ribosomal DNA sequences that were obtained from 50 ileal samples are being analyzed using a bioinformatics program to assess the microbial populations.