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2014 Swine CAFO Study SE for Agricultural Antibiotic Resistance in Mississippi State, Mississippi

    The purpose of this study was to measure the microbial constituents of swine-sow, -nursery, and -finisher farm manure lagoon wastewater and determine the changes induced by farm management. A total of 37 farms were visited in the Mid-South USA and analyzed for the genes 16S rRNA, spaQ (Salmonella spp.), Camp-16S (Campylobacter spp.), tetA, tetB, ermF, ermA, mecA, and intI using quantitative PCR. Additionally, 16S rRNA sequence libraries were created.

    Vaccination Against Lawsonia intracellularis Decreases Shedding of Salmonella enterica serovar Typhimurium in Co-Infected Pigs and Alters the Gut Microbiome

      *Salmonella enterica* is a leading cause of foodborne illness worldwide and pork can serve a source of infection. In this study, we investigated if vaccinating pigs against L*awsonia intracellularis*, a common pathogen of swine that has previously been shown to favor *Salmonella enterica* infection, confers protection against *Salmonella enterica serovar Typhimurium*. We investigated the underlying changes in the gut microbiome mediated by single *S. Typhiumurium* infection compared to co-infection with *L. intracellularis* as well as the effect of vaccination on the microbiome.

      GenSAS: A Web-Based Platform for Structural and Functional Annotation and Curation of Genomes

        The Genome Sequence Annotation Server (GenSAS) is an online platform that provides a pipeline for whole genome structural and functional annotation. Users can upload genome sequences and select from a variety of tools for repeat masking, prediction of gene models and other structural features as well as functional annotation tools. GenSAS integrates with JBrowse and Apollo to provide visualization and editing.

        Microbial community structure is affected by cropping sequences and poultry litter under long-term no-tillage

          Soil microorganisms play essential roles in soil organic matter dynamics and nutrient cycling in agroecosystems and have been used as soil quality indicators. The response of soil microbial communities to land management is complex and the long-term impacts of cropping systems on soil microbes is largely unknown. Therefore, changes in soil bacterial community composition were assessed in response to cropping sequences and bio-covers at long-term no-tillage sites.

          Data from: Defensive aphid symbiont Hamiltonella defensa effects on Aphelinus glycinis and Aphelinus atriplicis

            *Aphelinus glycinis* was collected in the Peoples Republic of China under a Memorandum of Understanding between their Ministry of Agriculture and the United States Department of Agriculture (USDA). *Aphelinus atriplicis* was collected by employees of the USDA, Agricultural Research Service (ARS), in the Republic of Georgia with the permission of that government. The parasitoids were imported into the USDA, ARS, Beneficial Insect Introductions Research Unit containment facility in Newark, Delaware, under permits from the USDA, Animal and Plant Health Inspection Service (Permit Numbers P526P-08-02142 and P526P-09-01929). No specific permissions were required to collect *Aphis craccivora* or *Acyrthosiphon pisum* because these are cosmopolitan aphids that occur in the field throughout North America. None of the species collected or studied are endangered or protected.