Goat rumen epithelium microbiome and meta-transcriptome
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA594390 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR10664941_1.fastq.gz | Fastqsanger.gz | |||
| SRR10664941_2.fastq.gz | Fastqsanger.gz | |||
| SRR10664942_1.fastq.gz | Fastqsanger.gz | |||
| SRR10664942_2.fastq.gz | Fastqsanger.gz | |||
| SRR10664943_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 70 |
Similar Datasets
Project description:Investigation of whole genome gene expression level changes in rumen epithelium of dairy cattle at different stages of rumen development and on different diets.
2009-11-01 | GSE18382 | GEO
Project description:Rumen epithelium plays a central role in absorbing, transporting, and metabolizing of short-chain fatty acids. For diary calve, the growth of rumen papillae greatly enhances the rumen surface area to absorb nutrients. However, the molecular mechanism underlying diary calve rumen postnatal development remains rarely understood. Here, we firstly performed a shotgun approach and bioinformatics analyses were used to investigate and compare proteomic profiles of Holstein calve rumen epithelium on day 0, 30, 60 and 90 of age. Then,a total of 4372 proteins were identified, in which we found 852, 342, 164 and 95 differentially expressed proteins (DEPs) between D0 and D30, between D30 and D60, between D60 and D90, respectively. Finally, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed to provide a comprehensive proteomic landscape of diary calve rumen development at tissue level.To conclude, our data indicated that keratinocyte differentiation, mitochondrion formation, the establishment of urea transport and innate immune system play central roles during rumen epithelium development. BH4 presents an important role in rumen epithelial keratinization. The biological processes of BH4 biosynthesis and molecular function of NADP binding participate in mitochondrial cristae formation. The proposed datasets provide a useful basis for future studies to better comprehend diary calve rumen epithelial development.
2022-10-25 | PXD037396 | Pride
Project description:rumen fluid from goat Raw sequence reads
| PRJNA510909 | ENA
Project description:a shotgun approach and bioinformatics analyses to investigate and compare proteomic profile of sheep rumen epithelium tissue on day 0, 15, 30, 45 and 60 of age.
2023-03-11 | PXD034787 | Pride
Project description:Ruminant livestock are one of the major contributors to carbon emission contributing the global warming issue. Methane (CH4) produced from enteric microbial fermentation of feed in the reticulo-rumen are known to differ between sheep with different digestive function and fermentation products such as metabolites. However, the molecular mechanism underpinning differences in methane emission remains to be fully elucidated. We extracted a membrane and cytosolic protein fraction of rumen epithelium proteins from both high (H) and low (L) CH4 emitting sheep. Protein abundance differences between the phenotypes were quantified using SWATH-mass spectrometry. We identified 92 proteins annotated as cell surface transporters, of which only solute carrier family (SLC) 40A1 had a greater fold change of protein expression in the high methane emission phenotype. The main difference in protein abundance we found were related to the metabolism of glucose, lactate and processes of cell defence against microbes in the epithelium of sheep in each group. To best of our knowledge, this represents one of the most comprehensive proteomes of ovine rumen epithelium to date.
2023-03-11 | PXD026538 | Pride
Project description:Protozoa comprise a major fraction of the microbial biomass in the rumen microbiome, of which the entodiniomorphs (order: Entodiniomorphida) and holotrichs (order: Vestibuliferida) are consistently observed to be dominant across a diverse genetic and geographical range of ruminant hosts. Despite the apparent core role that protozoal species exert, their major biological and metabolic contributions to rumen function remain largely undescribed in vivo. Here, we have leveraged (meta)genome27 centric metaproteomes from rumen fluid samples originating from both cattle and goats fed diets with varying inclusion levels of lipids and starch, to detail the specific metabolic niches that protozoa occupy in the context of their microbial co-habitants. Initial proteome estimations via total protein counts and label-free quantification highlight that entodiniomorph species Entodinium and Epidinium as well as the holotrichs Dasytricha and Isotricha comprises an extensive fraction of the total rumen metaproteome. Proteomic detection of protozoal metabolism such as hydrogenases (Dasytricha, Isotricha, Epidinium, Enoploplastron), carbohydrate-active enzymes (Epidinium, Diplodinium, Enoploplastron, Polyplastron), microbial predation (Entodinium) and volatile fatty acid production (Entodinium and Epidinium) was observed at increased levels in high methane-emitting animals. Despite certain protozoal species having well-established reputations for digesting starch, they were unexpectedly less detectable in low methane emitting-animals fed high starch diets, which were instead dominated by propionate/succinate-producing bacterial populations suspected of being resistant to predation irrespective of host. Finally, we reaffirmed our abovementioned observations in geographically independent datasets, thus illuminating the substantial metabolic influence that under-explored eukaryotic populations have in the rumen, with greater implications for both digestion and methane metabolism.
2023-04-19 | PXD040454 | Pride
Project description:Protozoa comprise a major fraction of the microbial biomass in the rumen microbiome, of which the entodiniomorphs (order: Entodiniomorphida) and holotrichs (order: Vestibuliferida) are consistently observed to be dominant across a diverse genetic and geographical range of ruminant hosts. Despite the apparent core role that protozoal species exert, their major biological and metabolic contributions to rumen function remain largely undescribed in vivo. Here, we have leveraged (meta)genome27 centric metaproteomes from rumen fluid samples originating from both cattle and goats fed diets with varying inclusion levels of lipids and starch, to detail the specific metabolic niches that protozoa occupy in the context of their microbial co-habitants. Initial proteome estimations via total protein counts and label-free quantification highlight that entodiniomorph species Entodinium and Epidinium as well as the holotrichs Dasytricha and Isotricha comprises an extensive fraction of the total rumen metaproteome. Proteomic detection of protozoal metabolism such as hydrogenases (Dasytricha, Isotricha, Epidinium, Enoploplastron), carbohydrate-active enzymes (Epidinium, Diplodinium, Enoploplastron, Polyplastron), microbial predation (Entodinium) and volatile fatty acid production (Entodinium and Epidinium) was observed at increased levels in high methane-emitting animals. Despite certain protozoal species having well-established reputations for digesting starch, they were unexpectedly less detectable in low methane emitting- 37 animals fed high starch diets, which were instead dominated by propionate/succinate-producing bacterial populations suspected of being resistant to predation irrespective of host. Finally, we reaffirmed our abovementioned observations in geographically independent datasets, thus illuminating the substantial metabolic influence that under-explored eukaryotic populations have in the rumen, with greater implications for both digestion and methane metabolism.
2023-04-19 | PXD040467 | Pride
Project description:We performed single-cell RNA-sequencing on the rumen epithelium of dairy cows to construct an epithelial single-cell map of the rumen.
2021-10-21 | GSE175652 | GEO