Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1250844 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR33144914.fastq.gz | Fastqsanger.gz | |||
| SRR33144915.fastq.gz | Fastqsanger.gz | |||
| SRR33144916.fastq.gz | Fastqsanger.gz | |||
| SRR33144917.fastq.gz | Fastqsanger.gz | |||
| SRR33144918.fastq.gz | Fastqsanger.gz |
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Project description:Background: The possible impact of changes in diet composition for the intestinal microbiome is mostly studied after some days of adaptation to the diet of interest. The question arises if few days are enough to reflect the microbial response to the diet by changing the community composition and function. The present study investigated the fecal microbiome of pigs in a time span of four weeks after a dietary change to get an insight of the needed adaptation period. Four different diets were used differing in either protein source (field peas meal vs. soybean meal) or the concentration of calcium and phosphorus (CaP). Results: Twelve pigs were sampled at seven time points within four weeks after the dietary change. Fecal samples were used to sequence the 16S rDNA amplicons, to analyse the microbial proteins via LC-MS/MS and to determine the SCFA production. The analysis of OTU abundances and quantification values of proteins showed a significant separation of three periods of time (p=0.001). Samples from the first day are used to define the ‘Zero phase’, samples of weeks one and two are combined as ‘metabolic phase’ and an ‘equilibrium phase’ was defined based on samples from week three and four. Only in this last phase, a separation according to the supplementation of CaP was significantly detectable (p=0.001). No changes were found based on the corn-soybean meal or corn-field peas administration. The analysis of possible factors causing this significant separation showed only an overall change of bacterial members and functional properties. The metaproteomic approach yields a total of about 9700 proteins, which were used to deduce possible metabolic functions of the bacterialcommunity.
2017-10-26 | PXD006224 | Pride
Project description:Characterization of the fecal (host) proteome in 5 Sarda sheep
2018-01-15 | PXD006145 | Pride
Project description:Dietary supplementation with fish-oil modulates ruminant milk composition towards a healthier fatty acid profile for consumers, but it also causes milk fat depression (MFD). Because the dairy goat industry is mainly oriented towards cheese manufacturing, MFD can elicit economic losses. There is large individual variation in animal susceptibility with goats more (RESPO+) or less (RESPO−) responsive to diet-induced MFD. Thus, we used RNA-Seq to examine gene expression profiles in mammary cells to elucidate mechanisms underlying MFD in goats and individual variation in the extent of diet-induced MFD.
2022-12-11 | E-MTAB-11581 | biostudies-arrayexpress
Project description:Genetic (animal species, breed and genotype) has a considerable effect on milk composition. In particular, goats present a remarkable polymorphism at the alpha-S1-casein (CSN1S1) locus which results in large differences in milk protein content and indirectly in milk fat content and its fatty acids composition. In order to decipher the mammary metabolic pathways involved, we examined the effect of CSN1S1 polymorphism on the expression of 8,379 genes in caprine mammary gland using a bovine oligonucleotide microarray. Six 48-h food-deprived lactating goats were assigned to 2 groups based on their genotype at the CSN1S1 locus: High vs. Low genotype goats carrying, respectively, two reference alleles associated with high CSN1S1 synthesis and two defective alleles associated with low CSN1S1 synthesis. Keywords: Genotype comparison
2008-01-03 | GSE6642 | GEO
Project description:Genetic (animal species, breed and genotype) has a considerable effect on milk composition. In particular, goats present a remarkable polymorphism at the alpha-S1-casein (CSN1S1) locus which results in large differences in milk protein content and indirectly in milk fat content and its fatty acids composition. In order to decipher the mammary metabolic pathways involved, we examined the effect of CSN1S1 polymorphism on the expression of 8,379 genes in caprine mammary gland using a bovine oligonucleotide microarray. Six lactating goats fed ad libitum were assigned to 2 groups based on their genotype at the CSN1S1 locus: High vs. Low genotype goats carrying, respectively, two reference alleles associated with high CSN1S1 synthesis and two defective alleles associated with low CSN1S1 synthesis. Keywords: Genotype comparison
2008-01-03 | GSE6637 | GEO
Project description:Genetic (animal species, breed and genotype) has a considerable effect on milk composition. In particular, goats present a remarkable polymorphism at the alpha-S1-casein (CSN1S1) locus which results in large differences in milk protein content and indirectly in milk fat content and its fatty acids composition. In order to decipher the mammary metabolic pathways involved, we examined the effect of CSN1S1 polymorphism on the expression of 8,379 genes in caprine mammary gland using a bovine oligonucleotide microarray. Six lactating goats fed ad libitum were assigned to 2 groups based on their genotype at the CSN1S1 locus: High vs. Low genotype goats carrying, respectively, two reference alleles associated with high CSN1S1 synthesis and two defective alleles associated with low CSN1S1 synthesis. Keywords: Genotype comparison 6 slides were performed for a total of 3 independent comparisons (Comp1, Comp2, Comp3): each microarray was co-hybridized with one High CSN1S1 genotype goat sample and one Low CSN1S1 genotype goat sample; each hybridization was repeated in a dye-swap manner for a total of 4 spots per oligonucleotide (2 intra- and 2 inter-slides).
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Project description:Genetic (animal species, breed and genotype) has a considerable effect on milk composition. In particular, goats present a remarkable polymorphism at the alpha-S1-casein (CSN1S1) locus which results in large differences in milk protein content and indirectly in milk fat content and its fatty acids composition. In order to decipher the mammary metabolic pathways involved, we examined the effect of CSN1S1 polymorphism on the expression of 8,379 genes in caprine mammary gland using a bovine oligonucleotide microarray. Six 48-h food-deprived lactating goats were assigned to 2 groups based on their genotype at the CSN1S1 locus: High vs. Low genotype goats carrying, respectively, two reference alleles associated with high CSN1S1 synthesis and two defective alleles associated with low CSN1S1 synthesis. Keywords: Genotype comparison 6 slides were performed for a total of 3 independent comparisons (CompA, CompB, CompC): each microarray was co-hybridized with one High CSN1S1 genotype goat sample and one Low CSN1S1 genotype goat sample; each hybridization was repeated in a dye-swap manner for a total of 4 spots per oligonucleotide (2 intra- and 2 inter-slides).
2008-01-02 | E-GEOD-6642 | biostudies-arrayexpress
Project description:An experiment was conducted to investigate the effects of dietary inclusion of rye, a model ingredient to increase gut viscosity, between 14 and 28 days of age on immune competence related parameters and performance of broiler. A total number of 960 one-day-old male Ross 308 chicks were weighed and randomly allocated to 24 pens (40 birds per pen), and the birds in every 8 replicate pens were assigned to one of three experimental diets including graded levels, 0%, 5%, and 10% of rye. Tested immune competence related parameters were composition of the intestinal microbiota, genes expression in gut tissue, and gut morphology. The inclusion of 5% or 10% rye in the diet (d14-28) resulted in decreased performance and litter quality, but in increased villus height and crypt depth in the small intestine (jejunum) of the broilers. Relative bursa and spleen weights were not affected by dietary inclusion of rye. In the jejunum, no effects on number and size of goblet cells, and only trends on microbiota composition in the digesta were observed. Dietary inclusion of rye affected expression of genes involved in cell cycle processes of the jejunal enterocyte cells, thereby influencing cell growth, cell differentiation and cell survival, which in turn were consistent with the observed differences in the morphology of the gut wall. In addition, providing rye-rich diets to broilers affected the complement and coagulation pathways, which are parts of the innate immune system. These pathways are involved in eradicating invasive pathogens. Overall, it can be concluded that inclusion of 5% or 10% rye to the grower diet of broilers had limited effects on performance. Ileal gut morphology, microbiota composition of jejunal digesta, and gene expression profiles of jejunal tissue, however, were affected by dietary rye inclusion level, indicating that rye supplementation to broiler diets might affect immune competence of the birds.
2017-04-19 | GSE94095 | GEO
Project description:The current study was designed to determine if dietary fatty acid concentration and composition affects the development and progression of nonalcoholic fatty liver disease. Male SD rats were overfed diets low (5%) or high (70%) fat diets via total enteral nutrition where the fat source was olive oil (monounsaturated), or corn oil (polyunsaturated). Overfeeding 5% corn oil produced little steatosis relative to feeding 5% olive oil. This was associated with lower fatty acid synthesis and reduced SREBP-c signaling in the 5% corn oil group. Overfeeding 70% fat diets increased steatosis and lead to increased liver necrosis in the 70% corn oil but not olive oil group. Increased injury after feeding polyunsaturated fat diets was linked to peroxidizability of hepatic free fatty acids and triglycerides and appearance of peroxidaized lipid products HETES and HODES previously linked to clinical nonalcoholic steatohepatitis.
2011-10-24 | GSE33166 | GEO