microbiome | Ag Data Commons

Data from: C-section increases cecal abundance of the archetypal bile acid and glucocorticoid modifying Lachnoclostridium [Clostridium] scindens in mice

Statistics summary of cecal microbiota taxa patterns, derived from cecal contents of 3 wk old male and female mice.

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The effects of different feed additives on bird performance and the gastrointestinal microbiome of Salmonella-challenged broilers

This dataset contain raw sequence data for 16S amplicon microbiome profiling of broilers challenged with Salmonella and fed several different intervention strategies. Files are tar archives containing zipped fastq raw data files for each sample.

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A consistent and predictable commercial broiler chicken bacterial microbiome in antibiotic-free production displays strong correlations with performance

This dataset includes forward and reverse raw sequencing reads for 2,309 broiler chicken gut, respiratory, and litter samples surveyed using 16S amplicon profiling.

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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.

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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.

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Data from: Metagenomic and near full-length 16S rRNA sequence data in support of the phylogenetic analysis of the rumen bacterial community in steers

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Data from: Assessment of bacterial diversity in the cattle tick Rhipicephalus (Boophilus) microplus through tag-encoded pyrosequencing

The objective of this study was to explore the R. microplus microbiome by applying the bacterial 16S tag-encoded FLX-titanium amplicon pyrosequencing (bTEFAP) technique to characterize its bacterial diversity.

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Data from: Pyrosequencing-Based Analysis of the Microbiome Associated with the Horn Fly, Haematobia irritans

The bacterial 16S tag-encoded FLX-titanium amplicon pyrosequencing (bTEFAP) method was used to carry out the classification analysis of bacterial flora in adult female and male horn flies and horn fly eggs. The bTEFAP method identified 16S rDNA sequences in our samples which allowed the identification of various prokaryotic taxa associated with the life stage examined. This is the first comprehensive report of bacterial flora associated with the horn fly using a culture-independent method. Several rumen, environmental, symbiotic and pathogenic bacteria associated with the horn fly were identified and quantified. This is the first report of the presence of Wolbachia in horn flies of USA origin and is the first report of the presence of Rikenella in an obligatory blood feeding insect.

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