Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1218914 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR32218800_1.fastq.gz | Fastqsanger.gz | |||
| SRR32218800_2.fastq.gz | Fastqsanger.gz | |||
| SRR32218753_1.fastq.gz | Fastqsanger.gz | |||
| SRR32218753_2.fastq.gz | Fastqsanger.gz | |||
| SRR32218754_1.fastq.gz | Fastqsanger.gz |
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Project description:hindgut microbiomes in grazing lambs
| PRJEB93828 | ENA
Project description:To investigate the potential effect of grazing movement on miRNA circulation in cattle, here we profiled miRNA expression in centrifugally prepared exosomes from the plasma of both grazing and housed Japanese Shorthorn cattle. Microarray analysis of the c-miRNAs resulted in detection of a total of 231 bovine exosomal miRNAs in the plasma, with a constant expression level of let-7g across the duration and cattle groups. Expression of muscle-specific miRNAs such as miR-1, miR-133a, miR-206, miR-208a/b, and miR-499 were undetectable, suggesting the mildness of grazing movement as exercise.
2016-01-01 | GSE69717 | GEO
Project description:By comparing transcriptomes of tolerant and intolerant plants of sickle alfalfa subject to intensive animal grazing, we identified pathways involved in nutrient-responsive signaling, light and wound response, cell wall formation, and energy metabolism. In these pathways, grazing suppressed 39 genes, but less severe in the tolerant plant, and activated 5 genes all carrying polymorphisms in their homologous transcripts between the tolerant and intolerant plants. These genes and pathways - responsive to grazing and differentially expressed between the tolerant and intolerant plants â?? underline a defense mechanism in alfalfa against grazing stresses. We examined transcriptomes of 3 alfalfa plants: grazing tolerant and grazed, grazing tolerant and not grazed, grazing intolerant and grazed, all at single replicate each.
2016-08-24 | E-GEOD-50430 | biostudies-arrayexpress
Project description:By comparing transcriptomes of tolerant and intolerant plants of sickle alfalfa subject to intensive animal grazing, we identified pathways involved in nutrient-responsive signaling, light and wound response, cell wall formation, and energy metabolism. In these pathways, grazing suppressed 39 genes, but less severe in the tolerant plant, and activated 5 genes all carrying polymorphisms in their homologous transcripts between the tolerant and intolerant plants. These genes and pathways - responsive to grazing and differentially expressed between the tolerant and intolerant plants – underline a defense mechanism in alfalfa against grazing stresses.
2016-08-24 | GSE50430 | GEO
Project description:The clinical importance of microbiomes to the chronicity of wounds is widely appreciated, yet little is understood about patient-specific processes shaping wound microbiome composition. Here, a two-cohort microbiome-genome wide association study is presented through which patient genomic loci associated with chronic wound microbiome diversity were identified. Further investigation revealed that alternative TLN2 and ZNF521 genotypes explained significant inter-patient variation in relative abundance of two key pathogens, Pseudomonas aeruginosa and Staphylococcus epidermidis. Wound diversity was lowest in Pseudomonas aeruginosa infected wounds, and decreasing wound diversity had a significant negative linear relationship with healing rate. In addition to microbiome characteristics, age, diabetic status, and genetic ancestry all significantly influenced healing. Using structural equation modeling to identify common variance among SNPs, six loci were sufficient to explain 53% of variation in wound microbiome diversity, which was a 10% increase over traditional multiple regression. Focusing on TLN2, genotype at rs8031916 explained expression differences of alternative transcripts that differ in inclusion of important focal adhesion binding domains. Such differences are hypothesized to relate to wound microbiomes and healing through effects on bacterial exploitation of focal adhesions and/or cellular migration. Related, other associated loci were functionally enriched, often with roles in cytoskeletal dynamics. This study, being the first to identify patient genetic determinants for wound microbiomes and healing, implicates genetic variation determining cellular adhesion phenotypes as important drivers of infection type. The identification of predictive biomarkers for chronic wound microbiomes may serve as risk factors and guide treatment by informing patient-specific tendencies of infection.
2020-04-25 | GSE149314 | GEO
Project description:<p>BACKGROUND: Grazing yearly on pasture is a traditional practice for yaks, which cannot meet the requirements of yak production since the insufficient forage supplied in the cold season results in a long production cycle. An intensive feeding system increasing production efficiency has been selected for beef and dairy cattle. However, its impacts on yaks are less studied, and it is unclear how the rumen microbiome, rumen metabolites and the host metabolome respond to an intensive feeding system and contribute to yak growth. Here, multi-omics, including rumen metagenomics, rumen and plasma metabolomics, were performed to classify the effects and regulatory mechanisms of intensive feeding system on yaks. </p><p>RESULTS: In our results, increased growth performance and rumen volatile fatty acid (VFA) concentration were observed in yaks under the intensive feeding system compared to yaks grazing on pastures. Metagenomics of the rumen microbiome revealed that species of Clostridium and Methanobrevibacter as well as Piromyces sp. E2 and Anaeromyces robustus were increased in the rumen of intensively fed yaks, interacting and contributing to amino acid and carbohydrate metabolism. The rumen of yaks grazing on pasture had more cellulolytic microbes, such as Bacteroides and Fibrobacter species. Moreover, yaks under the intensive feeding system had lower methanogens and increased methane degradation functions, suggesting that the methane emission of these yaks may be decreased. These abundant microbiomes were correlated with the pathways of 'Alanine aspartate and glutamate metabolism' and 'Pyruvate metabolism'. Similar with rumen VFA results, metabolomics found that intensively fed yaks had greater concentrations of metabolites related to carbohydrates. The methyl metabolites associated with methane production were greater in the rumen of yak grazing on pasture. Additionally, these changed rumen microbiomes and their metabolites resulted in changes in plasma metabolome, finally influencing yaks’ growth. </p><p>CONCLUSIONS: This study compressively classifies the mechanism that an intensive feeding system benefits yak growth and reveals the importance of the rumen microbiome for host metabolism and performance. These findings evidence that an intensive feeding system could be used for the yak industry.</p>
2024-10-01 | MTBLS10450 | MetaboLights
Project description:<p>Background: Grazing yearly on pasture is a traditional practice for yaks, which cannot meet the requirements of yak products since the insufficient forage supplied in the cold season results in a long production cycle. An intensive feeding system increasing production efficiency has been selected for beef and dairy cattle. However, its impacts on yaks are less studied, and it is unclear how the rumen microbiome, rumen metabolites and the host metabolome respond to an intensive feeding system and contribute to yak growth. Here, multi-omics, including rumen metagenomics, rumen and plasma metabolomics, were performed to classify the effects and regulatory mechanisms of intensive feeding system.</p><p>Results: In our results, increased growth performance and rumen volatile fatty acid (VFA) concentration were observed in yaks under the intensive feeding system compared to yaks grazing on pastures. Metagenomics of the rumen microbiome revealed that species of Clostridium and Methanobrevibacter as well as Piromyces sp. E2 and Anaeromyces robustus were increased in the rumen of intensively fed yaks, interacting and contributing to amino acid and carbohydrate metabolism. The rumen of yaks grazing on pasture had more cellulolytic microbes, such as Bacteroides and Fibrobacter species. Moreover, yaks under the intensive feeding system had lower methanogen and increased methane degradation functions, suggesting that the methane emission of these yaks may be decreased. These abundant microbiomes were correlated with the pathways of “Alanine aspartate and glutamate metabolism” and “Pyruvate metabolism”. Similar with rumen VFA results, metabolomics found that intensively fed yaks had greater concentrations of metabolites related to carbohydrates. The methyl metabolites associated with methane production were greater in the rumen of yak grazing on pasture. Additionally, these changed rumen microbiomes and their metabolites resulted in changes in plasma metabolome, finally affecting yaks’ growth.</p><p>Conclusions: This study compressively classifies the mechanism that an intensive feeding system benefits yak production and reveals the importance of the rumen microbiome for host metabolism and performance. These findings evidence that an intensive feeding system could be used for the yak industry.</p>
2024-10-01 | MTBLS10856 | MetaboLights