N-227. Microbial Community Structure of Feedlot Cattle Feces

L. M. Durso, G. P. Harhay, M. L. Clawson, W. W. Laegreid, J. L. Bono, J. E. Keen, T. P. L. Smith;
USDA/ARS, Clay Center, NE.

Background: Cattle feces are a reservoir of Shiga-toxigenic Escherichia coli O157:H7 (STEC O157), an important food-borne pathogen. Although STEC O157 is often studied in isolation, the STEC O157 fecal habitat consists of many different kinds of bacteria, and STEC O157 is part of a complex microbial community that has not been fully characterized. Microbial identification by DNA sequence variation within the 16S ribosomal gene (16S rDNA) is now commonly used to study microbial community structure, and we used these tools to characterize the bacterial population structure of feedlot cattle feces. Methods: Fecal samples were collected from six animals. DNA was isolated from each sample and 16S rDNA was amplified using "universal" 16S primers. The amplicons were cloned into TOPO4 vectors and sequenced bi-directionally using an ABI 3730 XL. Chimeric sequences were identified by Bellepheron3 and removed from the study. Adequate sequencing coverage of the fecal samples was determined by rarefaction curves generated in DOTUR. Microbes represented by the 16S rDNA sequences were determined using multiple tools, including the classifier tool available through the Ribosomal Database Project and BLAST searches using the NCBI database. Results: Over 11,000 full-length 16S rDNA sequences were generated in this study. Bacteroidetes were the predominant phyla in every sample, followed by the Firmicutes and Proteobacteria. At the genus level, all samples contained sequences associated with feces, such as Bacteroides and Coprobacillus, as well as sequences of rumen-associated bacteria such as Ruminococcus. However, many of the bacterial 16S sequences recovered show low homology with known organisms. Conclusion: Cattle feces contain 16S rDNA sequences that represent a diverse spectrum of microbes. These results expand our understanding of fecal microbial populations and may lead to intervention strategies in the control of STEC O157.