Project description:Microbiome DNA from the adhering fraction of a sheep rumen. The RSTs were generated using an improved version of SARST (referred to as iSARST) from the microbiome DNA extracted from the adhering fraction of the rumen content taken from a sheep. The iSARST method is going to be submitted to Nature Biotechnology for publication. Keywords: other
Project description:Microbiome DNA from the adhering fraction of a sheep rumen. The RSTs were generated using an improved version of SARST (referred to as iSARST) from the microbiome DNA extracted from the adhering fraction of the rumen content taken from a sheep. The iSARST method is going to be submitted to Nature Biotechnology for publication. Keywords: other
2004-10-15 | GSE1842 | GEO
Project description:Assessing saliva microbiome collection and processing methods
Project description:Rumen epithelial parakeratosis, a common disease in ruminants caused by abnormalities in the ruminal stratified squamous epithelial keratinization process, negatively impacts ruminant health and performance. While we still lack a comprehensive perception of the underlying mechanisms and the predisposing factors for this disorder.Here, we investigated rumen epithelial cell heterogeneity, differentiation trajectories, and cornification to clarify the rumen epithelial keratinization process
Project description:As the unique organ, rumen plays vital roles in providing products for humans, however, the underlying cell composition and interactions with epithelium-attached microbes remain largely unknown. Herein, we performed an integrated analysis in single-cell transcriptome, epithelial microbiome, and metabolome of rumen tissues to explore the differences of microbiota-host crosstalk between newborn and adult cattle models. We found that fewer epithelial cell subtypes and more abundant immune cells (e.g., Th17 cells) in the rumen tissue of adult cattle. Metabolism-related functions and oxidation-reduction process were significantly upregulated in the adult rumen epithelial cell subtypes. The epithelial Desulfovibrio was significantly enriched in the adult cattle. To further clarify the role of Desulfovibrio in host’s oxidation-reduction process, we performed metabolomics analysis of rumen tissues and found that Desulfovibrio showed a high co-occurrence probability with the pyridoxal in the adult cattle compared with newborn ones. The adult rumen epithelial cell subtypes also showed stronger ability of pyridoxal binding. These indicates that Desulfovibrio and pyridoxal likely play important roles in maintaining redox balance in adult rumen. The integrated analysis provides novel insights into the understanding of rumen function and facilitate the future precision improvement of rumen function and milk/meat production in cattle.
Project description:Microbiome sample-material model is a Named Entity Recognition (NER) model that identifies and annotates the material of microbiome samples in texts. This is the final model version used to annotate metagenomics publications in Europe PMC and enrich metagenomics studies in MGnify with sample-material metadata from literature.
For more information, please refer to the following blogs:
http://blog.europepmc.org/2020/11/europe-pmc-publications-metagenomics-annotations.html
https://www.ebi.ac.uk/about/news/service-news/enriched-metadata-fields-mgnify-based-text-mining-associated-publications
Project description:A total of 14 samples were used, 12 paired rumen and colon samples, and two rumen only samples. DNA was extracted from each sample, and PCR amplified using universal bacterial primers 27F and 1492R. Trends between anatomical location, age and sex were considered.
Project description:Emerging data has highlighted the importance of short-chain fatty acids (SCFAs), particularly butyrate, in regulating ruminal homeostasis in vivo isolated epithelial cells. However, little is known about other SCFAs like acetate or propionate, and the interaction between rumen microbes and epithelial immunity are rarely reported. Here, we firstly combined infusion of three SCFAs, to study their different roles in ruminal development, antioxidant capacity, barrier functions, and immunity, as well as cross-talk with ruminal microbiome (16S rRNA sequencing data of rumen digesta) and derived transcriptome (RNA-Seq) and metabolism using an in vivo goat model.
Project description:Emerging data has highlighted the importance of short-chain fatty acids (SCFAs), particularly butyrate, in regulating ruminal homeostasis in vivo isolated epithelial cells. However, little is known about other SCFAs like acetate or propionate, and the interaction between rumen microbes and epithelial immunity are rarely reported. Here, we firstly combined infusion of three SCFAs, to study their different roles in ruminal development, antioxidant capacity, barrier functions, and immunity, as well as cross-talk with ruminal microbiome (16S rRNA sequencing data of rumen digesta) and derived transcriptome (RNA-Seq) and metabolism using an in vivo goat model.
