The decomposition of manure by anaerobic bacteria produces components that create odor. Over 150 different volatile organic compounds (VOCs) associated with swine manure have been identified, including ammonia, organic acids and alcohols and sulfides. To improve methods for reducing odor associated with swine manure, researchers at the USDA’s National Center for Agricultural Utilization Research have focused on identifying major bacterial species in the swine intestinal tract and swine manure storage pits using molecular and conventional mirobiological analyses. Total DNA was extracted from fecal and manure samples and 16S rDNA genes were amplified using PCR and universal primers. The PCR products were cloned and the 16S rDNA genes sequenced. The sequences were compared to 16S rDNA sequences from known organisms and grouped according to 16S rDNA phylogeny. The majority of sequences obtained were different than, but similar to, those found in known microorganisms. Samples were also diluted, plated onto complex anaerobic media, and colonies from the highest dilutions were isolated for 16S rDNA analysis.  Similarity analyses of the 16S rDNA sequences from total DNA and pure cultures indicated the presence of primarily low G&C, Gram-positive bacteria such as Clostridium sp. and Streptococcus sp.  Additional 16S rDNA sequence analyses of swine waste handling pits using archae-specific primers indicated that the primary archaebacteria present are methanogens. This approach could be used to identify microorganisms that are important in the production of odorous compounds. Probes or PCR primers can also be designed to monitor specific groups of interest (e.g, sulfate reducers or specific pathogens), including the effects of management strategies on odor production. Molecular analyses were also used to identify the presence of erythromycin- and tetracycline- antibiotic resistance genes in bacteria.