Ruminal caprine bacterial epithelial community
Ontology highlight
ABSTRACT:
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR638034.fastq.gz | Fastqsanger.gz | |||
| ERR638035.fastq.gz | Fastqsanger.gz | |||
| ERR638036.fastq.gz | Fastqsanger.gz | |||
| ERR638037.fastq.gz | Fastqsanger.gz | |||
| ERR638038.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:Shifts in the ruminal caprine bacterial epithelial community relative to dietary energy supply
| PRJEB7404 | ENA
Project description:Cattle are often fed high concentrate diets to increase energy intake and improve overall animal performance. Such diets also cause changes in fermentation patterns and epithelial function. However, the molecular mechanisms involved in regulating epithelial function for cattle fed high concentrate diets have not been elucidated. In this study, we aimed to gain a broad overview of the involved molecular mechanisms by detecting differentially expressed genes (DEG) in rumen tissue from dairy cows fed a low concentrate (LC; 8%) compared to a high concentrate (HC; 64%) diet using a bovine-specific microarray platform containing 16,846 unique gene loci and 5,943 ESTs from the bovine genome. Feeding the HC diet increased the total volatile fatty acid concentration and markedly reduced ruminal pH, suggesting that the dietary treatments used did induce changes in ruminal fermentation. In response to changes in the ruminal environment, a total of 5,200 elements were detected as DEG in ruminal tissue with >1.5-fold expression change (P < 0.05) for cows fed HC relative to LC. Of the 5,200 DEG, 2,233 and 2,967 were up- and down-regulated, respectively. The GENECODIS analysis elucidated that relationships among the DEG represented 19 annotations characterized with GO molecular function and KEGG pathways with 26 DEG identified in multiple annotations such as calcium signaling and gap junction pathways. Among those DEG that were identified numerous times, catalytic subunit of cAMP-dependent protein kinase (PRKACB) was down-regulated in ruminal tissue from cows fed HC, suggesting that this gene may have important roles including regulation of cell proliferation and differentiation, and intracellular pH regulation. Two-condition experiment, High concentrate vs. Low concentrate diets. Biological replicates: 5 high concentrate fed, 5 low concentrate, independently grown and harvested. Two replicates per array.
2010-10-02 | E-GEOD-19802 | biostudies-arrayexpress
Project description:Cattle are often fed high concentrate diets to increase energy intake and improve overall animal performance. Such diets also cause changes in fermentation patterns and epithelial function. However, the molecular mechanisms involved in regulating epithelial function for cattle fed high concentrate diets have not been elucidated. In this study, we aimed to gain a broad overview of the involved molecular mechanisms by detecting differentially expressed genes (DEG) in rumen tissue from dairy cows fed a low concentrate (LC; 8%) compared to a high concentrate (HC; 64%) diet using a bovine-specific microarray platform containing 16,846 unique gene loci and 5,943 ESTs from the bovine genome. Feeding the HC diet increased the total volatile fatty acid concentration and markedly reduced ruminal pH, suggesting that the dietary treatments used did induce changes in ruminal fermentation. In response to changes in the ruminal environment, a total of 5,200 elements were detected as DEG in ruminal tissue with >1.5-fold expression change (P < 0.05) for cows fed HC relative to LC. Of the 5,200 DEG, 2,233 and 2,967 were up- and down-regulated, respectively. The GENECODIS analysis elucidated that relationships among the DEG represented 19 annotations characterized with GO molecular function and KEGG pathways with 26 DEG identified in multiple annotations such as calcium signaling and gap junction pathways. Among those DEG that were identified numerous times, catalytic subunit of cAMP-dependent protein kinase (PRKACB) was down-regulated in ruminal tissue from cows fed HC, suggesting that this gene may have important roles including regulation of cell proliferation and differentiation, and intracellular pH regulation.
2010-10-02 | GSE19802 | GEO
Project description:Beef represents a major diet component and one of the major sources of protein in human. The beef industry in the United States is currently undergoing changes and is facing increased demands especially for natural grass-fed beef. The grass-fed beef obtained their nutrients directly from pastures, which contained limited assimilable energy but abundant amount of fiber. On the contrary, the grain-fed steers received a grain-based regime that served as an efficient source of high-digestible energy. Lately, ruminant animals have been accused to be a substantial contributor for the green house effect. Therefore, the concerns from environmentalism, animal welfare and public health have driven consumers to choose grass-fed beef. Rumen is one of the key workshops to digest forage constituting a critical step to supply enough nutrients for animals’ growth and production. We hypothesize that rumen may function differently in grass- and grain-fed regimes. The objective of this study was to find the differentially expressed genes in the ruminal wall of grass-fed and grain-fed steers, and then explore the potential biopathways. In this study, the RNA Sequencing (RNA-Seq) method was used to measure the gene expression level in the ruminal wall. The total number of reads per sample ranged from 24,697,373 to 36,714,704. The analysis detected 342 differentially expressed genes between ruminal wall samples of animals raised under different regimens. The Fisher’s exact test performed in the Ingenuity Pathway Analysis (IPA) software found 16 significant molecular networks. Additionally, 13 significantly enriched pathways were identified, most of which were related to cell development and biosynthesis. Our analysis demonstrated that most of the pathways enriched with the differentially expressed genes were related to cell development and biosynthesis. Our results provided valuable insights into the molecular mechanisms resulting in the phenotype difference between grass-fed and grain-fed cattle. Ruminal wall samples from two randomly chosen animals per group were obtained, totaling four samples. The animals were born, raised and maintained at the Wye Angus farm. This herd, which has been closed for almost 75 years and yielded genetically similar progenies, constitutes an excellent resource to perform transcriptomic analysis. The genetic resemblance among individuals permits us to better control the cause of variation between experimental clusters and individuals. The randomly chosen pairs of animals were part of larger sets of steers that received a particular treatment. All animals received the same diet until weaning. The grain group received conventional diet consisting of corn silage, shelled corn, soy bean and trace minerals. The grass fed steers consumed normally grazed alfalfa; during wintertime, bailage was utilized. The alfalfa has been harvested from land without any fertilizers, pesticides or other chemicals. The steers ate no animal, agricultural or industrial byproducts and never receive any type of grain. Then, the calves were randomly assigned to one diet and exclusively received that regimen until termination. Grain–fed animals reached the market weight around the age of 14 month-old, however, grass-fed steers required approximately 200 additional days to achieve the same weight. Immediately after termination at the Old Line Custom Meat Company (Baltimore, MD) a small piece of ruminal wall was excised, cleaned and preserved at -80°C for posterior processing.
2015-03-31 | E-GEOD-63550 | biostudies-arrayexpress
Project description:Beef represents a major diet component and one of the major sources of protein in human. The beef industry in the United States is currently undergoing changes and is facing increased demands especially for natural grass-fed beef. The grass-fed beef obtained their nutrients directly from pastures, which contained limited assimilable energy but abundant amount of fiber. On the contrary, the grain-fed steers received a grain-based regime that served as an efficient source of high-digestible energy. Lately, ruminant animals have been accused to be a substantial contributor for the green house effect. Therefore, the concerns from environmentalism, animal welfare and public health have driven consumers to choose grass-fed beef. Rumen is one of the key workshops to digest forage constituting a critical step to supply enough nutrients for animals’ growth and production. We hypothesize that rumen may function differently in grass- and grain-fed regimes. The objective of this study was to find the differentially expressed genes in the ruminal wall of grass-fed and grain-fed steers, and then explore the potential biopathways. In this study, the RNA Sequencing (RNA-Seq) method was used to measure the gene expression level in the ruminal wall. The total number of reads per sample ranged from 24,697,373 to 36,714,704. The analysis detected 342 differentially expressed genes between ruminal wall samples of animals raised under different regimens. The Fisher’s exact test performed in the Ingenuity Pathway Analysis (IPA) software found 16 significant molecular networks. Additionally, 13 significantly enriched pathways were identified, most of which were related to cell development and biosynthesis. Our analysis demonstrated that most of the pathways enriched with the differentially expressed genes were related to cell development and biosynthesis. Our results provided valuable insights into the molecular mechanisms resulting in the phenotype difference between grass-fed and grain-fed cattle.
2015-03-31 | GSE63550 | GEO
Project description:The effects of anti-lipopolysaccharide (LPS) antibody on ruminal fermentation, LPS activity, and liver transcriptomes were investigated during the subacute ruminal acidosis (SARA) challenge.
2020-05-15 | GSE150553 | GEO
Project description:An abrupt transition from high forage to high fermentable diet may induce digestive disorders in the rumen. To date, the host mechanisms regulate the adaption to such dietary transition are largely unknown. To understand the molecular mechanisms involved in such phenomena, RNA-sequencing was performed to identify the changes in the transcriptomes of ruminal epithelia during a rapid high grain transition from 3% to 92% grain. In total, the expression of 11,044, 11,322 and 11,282 genes was detected in ruminal epithelia of beef heifers (n=15) fed 3%, 75% and 92% barley grain diet, respectively. When diet was changed from 75% to 92% grain, a significant difference was observed in the mean ruminal pH change among the individuals with five heifers decreased (DG; pH from 6.30 ± 0.09 to 5.87 ± 0.15, P < 0.01) and five other ones increased (UG; pH from 5.84 ± 0.42 to 6.35 ± 0.37, P < 0.05). In the ruminal epithelia of DG animals, the expression of genes involved in ketogenesis (HMGCL, P < 0.1) and lipid synthesis (SREBF2, P < 0.1; FABP4, P < 0.05) was increased, the abundance of genes involved in short chain fatty acid transporters (SMCT1, P < 0.1) and monocarboxylate transporters (MCT4, P < 0.1) was decreased. The function of “Concentration of lipid” was activated after 75% to 92% grain diet transition. Comparing to DG animals, the expression of ketogenesis (ACAT2, P < 0.05; HMGCS P < 0.1) and cholesterol synthesis related genes (HMGC and FDPs, P < 0.1) was deceased, while the expression of proton and cholesterol efflux related genes NHE3 and ABCA1 were increased (P < 0.05), and the function of “Storage of lipid” was inhibited in the ruminal epithelial of UG heifers. In addition, the function of differentially expressed (DE) genes in DG were involved in “T cell receptor signaling” and “complement and coagulation cascades” pathways, while the functions “metabolism of xenobiotics by cytochrome P450” and “p53 signaling pathway” were enriched for DE genes in UG animals. Furthermore, the single nucleotide polymorphisms (SNP) discovery by RNA-seq was performed, and SNP (g.46834311A > G) in FABP4 identified between two groups of animals (P < 0.1). The expression of genes involved in regulating lipid transport and fatty acid metabolism varied between DG and UG heifers during rapid 75% to 92% grain transition. The identified genes and SNP could be potential markers and may account for the varied ruminal pH responses between DG and UG heifers, which can be potentially applied in breeding and selecting beef cattle with more tolerance in dietary transition stress.
2018-02-13 | GSE89874 | GEO