Bovine gut metagenome
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA744219 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Fescue toxicosis is a disease of wild and domestic animals grazing on fescue pasture infected with the endophytic fungus, Neotyphodium Coenophialum. Mice, previously selected for increased sensitivity to endophyte-infected fescue seed diets indicated by slow weight gain, were used to study the effects of fescue toxicosis on hepatic gene expression. Liver genes differentially expressed due to fescue toxins were studied using DNA microarray. A two-stage ANOVA of microarray data identified forty differentially expressed genes between mice fed endophyte-infected (E+) and endophyte-free (E-) fescue seeds. Significant Analysis of Microarray (SAM) analysis identified 9 genes as differentially expressed between treatment groups. Hierarchical clustering with the 40 genes identified by ANOVA clearly separate the mice according to their diets, with 100% confidence as computed by bootstrap analysis. Expressions of eleven genes were verified using quantitative real-time PCR (qPCR). The E+ diet resulted in downregulation of genes involved in sex-steroid metabolism pathway, genes involved in cholesterol and lipid metabolism. Keywords = Endophyte Keywords = Fescue Toxicosis Keywords = microarray Keywords: repeat sample
2005-01-26 | GSE2134 | GEO
Project description:Fecal microbiome from angus cattle experiencing fescue toxicosis
| PRJNA476327 | ENA
Project description:The objectives of our study were to identify microRNA (miRNA) present in bovine sperm and to evaluate the effects of fescue toxicosis on sperm miRNA expression.
2014-12-10 | GSE61745 | GEO
Project description:The objective of our study was to assess the effect of fescue toxicosis on the overall transcriptomics profile of liver tissue on growing Angus × Simmental steers and heifers. The susceptibility was determined by the T-snip genetic tests for a total of 42 pregnant cows. At mid-gestation, these animals were randomly assigned to control group which received a based diet and fed endophyte free fescue seeds; a treatment group was fed endophyte-infected tall fescue seeds for 30 days. RNA-seq experiments were performed in liver biopsy samples, and a total of 828 differentially expressed genes were detected.
2023-08-11 | GSE208241 | GEO
Project description:The objectives of our study were to identify microRNA (miRNA) present in bovine sperm and to evaluate the effects of fescue toxicosis on sperm miRNA expression. Angus bulls were assigned to treatments of either toxic or non-toxic fescue seed diets. Semen was collected and subjected to microRNA (miRNA) isolation after 126 days. Three bull's sperm miRNA samples from each treatment group were chosen and pooled for deep sequencing. Sequencing results were used to create a custom microarray for miRNA comparison between groups. LC Sciences was used as a service provider for the sequencing and custom microarray.
2014-12-10 | E-GEOD-61745 | biostudies-arrayexpress
Project description:<p>The study of antimicrobial resistance (AMR) in infectious diarrhea has generally been limited to cultivation, antimicrobial susceptibility testing and targeted PCR assays. When individual strains of significance are identified, whole genome shotgun (WGS) sequencing of important clones and clades is performed. Genes that encode resistance to antibiotics have been detected in environmental, insect, human and animal metagenomes and are known as "resistomes". While metagenomic datasets have been mined to characterize the healthy human gut resistome in the Human Microbiome Project and MetaHIT and in a Yanomani Amerindian cohort, directed metagenomic sequencing has not been used to examine the epidemiology of AMR. Especially in developing countries where sanitation is poor, diarrhea and enteric pathogens likely serve to disseminate antibiotic resistance elements of clinical significance. Unregulated use of antibiotics further exacerbates the problem by selection for acquisition of resistance. This is exemplified by recent reports of multiple antibiotic resistance in Shigella strains in India, in Escherichia coli in India and Pakistan, and in nontyphoidal Salmonella (NTS) in South-East Asia. We propose to use deep metagenomic sequencing and genome level assembly to study the epidemiology of AMR in stools of children suffering from diarrhea. Here the epidemiology component will be surveillance and analysis of the microbial composition (to the bacterial species/strain level where possible) and its constituent antimicrobial resistance genetic elements (such as plasmids, integrons, transposons and other mobile genetic elements, or MGEs) in samples from a cohort where diarrhea is prevalent and antibiotic exposure is endemic. The goal will be to assess whether consortia of specific mobile antimicrobial resistance elements associate with species/strains and whether their presence is enhanced or amplified in diarrheal microbiomes and in the presence of antibiotic exposure. This work could potentially identify clonal complexes of organisms and MGEs with enhanced resistance and the potential to transfer this resistance to other enteric pathogens.</p> <p>We have performed WGS, metagenomic assembly and gene/protein mapping to examine and characterize the types of AMR genes and transfer elements (transposons, integrons, bacteriophage, plasmids) and their distribution in bacterial species and strains assembled from DNA isolated from diarrheal and non-diarrheal stools. The samples were acquired from a cohort of pediatric patients and controls from Colombia, South America where antibiotic use is prevalent. As a control, the distribution and abundance of AMR genes can be compared to published studies where resistome gene lists from healthy cohort sequences were compiled. Our approach is more epidemiologic in nature, as we plan to identify and catalogue antimicrobial elements on MGEs capable of spread through a local population and further we will, where possible, link mobile antimicrobial resistance elements with specific strains within the population.</p>
| phs001260 | dbGaP
Project description:Fescue toxicosis affects wild and domestic animals consuming ergot alkaloids contained in tall fescue forage infected with the endophytic fungus, Neotyphodium coenophialum. , When animals are consuming infected fescue forage during periods of elevated ambient temperatures (summer), a range of phenotypic disorders collectively called summer slump is observed. It is characterized by hyperthermia, with an accompanying decrease in feed intake, growth, milk yield and reproductive fitness. Laboratory mice also exhibit symptoms of fescue toxicosis a thermoneutral temperature, as indicated by reduced growth rate and reproductive fitness. Our goal was to characterize the differences in gene expression in liver of mice exposed to summer-type heat stress (HS) and infected fescue (E+) when compared to mice fed infected fescue at thermoneutral temperature (TN). Mice were fed E+ diet under HS (34 ± 1°C; n = 13; E+HS) or thermoneutral (TN) conditions (24 ± 1°C; n = 14; E+TN) for a period of two weeks between 47 to 60 d of age. Genes differentially expressed between E+HS versus E+TN were identified using DNA microarrays. Forty-one genes were differentially expressed between treatment groups. Expressions of eight genes were measured using quantitative real-time PCR. Genes coding for phase I detoxification enzymes were up-regulated in E+HS mouse liver. This detoxification pathway is known to produce reactive oxidative species. We observed an up-regulation of genes involved in the protection against reactive oxidative species. Key genes involved in de novo lipogenesis and lipid transport were also up-regulated. Finally, genes involved in DNA damage control and unfolded protein responses were down-regulated. Keywords: Stress response
2006-08-29 | GSE5642 | GEO
Project description:Effects of Ceftiofur and Chlortetracycline on the Resistome of Feedlot Cattle
| PRJNA419351 | ENA
Project description:nasal microflora changes of beef cattle Metagenomic assembly
| PRJNA723715 | ENA