Ontology highlight
ABSTRACT:
PROVIDER: PRJNA953596 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR24110700_1.fastq.gz | Fastqsanger.gz | |||
| SRR24110700_2.fastq.gz | Fastqsanger.gz | |||
| SRR24110701_1.fastq.gz | Fastqsanger.gz | |||
| SRR24110701_2.fastq.gz | Fastqsanger.gz | |||
| SRR24110702_1.fastq.gz | Fastqsanger.gz |
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Project description:SARST-V1 method was used to asses the effect of live yeast on the microbial population of the rumen of cows fed an acidogenic diet
2013-01-01 | GSE39206 | GEO
Project description:SARST-V1 method was used to asses the effect of live yeast on the microbial population of the rumen of cows fed an acidogenic diet 3 cows were used in 3 by 3 latin-square design with 3 periods. In each period animals received either 0.5g/d of yeast, 5g/d of yeast or none. Rumen microbiota was analysed using the SARST-V1 method for each period.
2013-01-01 | E-GEOD-39206 | biostudies-arrayexpress
Project description:This study provides a clear and accurate dynamic transcriptome profile of mRNAs in rumen, reticulum, omasum and abomasum of yaks. The results include high-quality genomic data and help to elucidate the important roles of these mRNAs in regulation of growth, development and metabolism in yaks, and to further understand the molecular mechanisms underlying metabolic regulation of yak stomach tissues. At the same time, it provided a theoretical basis for age-appropriate weaning and supplementary feeding in yaks.
2023-04-30 | GSE222396 | 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
Project description:Protozoa comprise a major fraction of the microbial biomass in the rumen microbiome, of which the genera Entodinium has been consistently observed to be dominant across a diverse genetic and geographical range of ruminant hosts. Despite the apparent core role that species such as Entodinium caudatum exert, their greater biological and metabolic contributions to rumen function remain largely undescribed. Here, we have leveraged (meta)genome-centric metaproteome datasets from rumen fluid samples originating from both cows and goats fed contrasting diets, to detail the specific metabolic niches that E. caudatum occupies in the context of its bacterial and archaeal co-habitants. Initial proteome estimations via total protein counts and label free quantification highlight that E. caudatum populations comprise an extensive fraction of the total rumen metaproteome. Our analysis also suggested increased microbial predation and volatile fatty acid metabolism by E. caudatum to occur in high methane emitting animals, although with no apparent direct metabolic link to methanogenesis. Despite E. caudatum having a well-established reputation of digesting starch, it was unexpectedly less active 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. Collectively, our results illuminate the substantial metabolic influence under-explored eukaryotic populations have in the rumen, with greater implications towards both digestion and methane metabolism.
2025-11-13 | PXD034544 | Pride
Project description:Protozoa comprise a major fraction of the microbial biomass in the rumen microbiome, of which the genera Entodinium has been consistently observed to be dominant across a diverse genetic and geographical range of ruminant hosts. Despite the apparent core role that species such as Entodinium caudatum exert, their greater biological and metabolic contributions to rumen function remain largely undescribed. Here, we have leveraged (meta)genome-centric metaproteome datasets from rumen fluid samples originating from both cows and goats fed contrasting diets, to detail the specific metabolic niches that E. caudatum occupies in the context of its bacterial and archaeal co-habitants. Initial proteome estimations via total protein counts and label free quantification highlight that E. caudatum populations comprise an extensive fraction of the total rumen metaproteome. Our analysis also suggested increased microbial predation and volatile fatty acid metabolism by E. caudatum to occur in high methane emitting animals, although with no apparent direct metabolic link to methanogenesis. Despite E. caudatum having a well-established reputation of digesting starch, it was unexpectedly less active 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. Collectively, our results illuminate the substantial metabolic influence under-explored eukaryotic populations have in the rumen, with greater implications towards both digestion and methane metabolism.
2025-11-13 | PXD034779 | 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.
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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.
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