This repository contains the MiSeq sequencing data for fungal communities in a study on biofilters. The BioFilter.zip folder contains 42 FASTQ files. The project run summary report specifies additional information on how the FASTQ data were produced for the "Jason" fungal community samples.
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 Lawsonia 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.
This study recruited experts from production, harvest, retail, and allied pork industries to assess 30 common pork supply movements for their industry criticality. Movements spanned five categories: equipment, live animal production, genetics, harvest, and people. Experts were recruited via email to the American Association of Swine Veterinarians (AASV) mailing list and their assessments were collected via an online survey. The Data.csv file contains the raw survey responses.
Changes in the Porcine Intestinal Microbiome in Response to Infection with Salmonella Enterica and Lawsonia Intracellularis
Salmonella enterica is a leading cause of food borne illness. Recent studies have shown that S. enterica is a pathogen capable of causing alterations to the composition of the intestinal microbiome. A recent prospective cross-sectional study of French pork production farms found a statistically significant association between Lawsonia intracellularis and carriage of S. enterica. The ZIP file includes 51 sequence files (FASTA format) and 1 Excel file describing the species, age, sampled tissue, treatment condition, and sample name corresponding to the different file names. The Excel file is converted to a csv for archival purposes. The Readme.txt file describes the context of how the data was created and any codes used in the spreadsheet.
Feed and Ingredient Information is presented as Tables of chemical composition and nutritional value for an extensive list of feed nutrient constituents. The tables include Nutrient, Mean, Number of Samples (n), Standard Deviation (SD), Coefficient of Variation (CV), and Min / Max values for Main…
This database contains functional information on genes commonly studied in humans, pigs, and rodents, including more than 2,300 sequenced at DGIL. Each entry has been manually-annotated and is linked to other porcine databases as well as Homologene, InnateDb and Gene Ontology.
The Animal Quantitative Trait Loci (QTL) Database (Animal QTLdb) strives to collect all publicly available trait mapping data, i.e. QTL (phenotype/expression, eQTL), candidate gene and association data (GWAS), and copy number variations (CNV) mapped to livestock animal genomes, in order to facilitate locating and comparing discoveries within and between species. New data and database tools are continually developed to align various trait mapping data to map-based genome features such as annotated genes.
NASS Data Visualization provides a dynamic web query interface supporting searches by Commodity (e.g. Cotton, Corn, Farms & Land, Grapefruit, Hogs, Oranges, Soybeans, Wheat), Statistic type (automatically refreshed based upon choice of Commodity - e.g. Inventory, Head, Acres Planted, Acres Harvested, Production, Yield) to generate chart, table, and map visualizations by year (2001-2016), as well as a link to download the resulting data in CSV format compatible for updating databases and spreadsheets.