Rumen Microbiome
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA945870 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR23918635_1.fastq.gz | Fastqsanger.gz | |||
| SRR23918635_2.fastq.gz | Fastqsanger.gz | |||
| SRR23918636_1.fastq.gz | Fastqsanger.gz | |||
| SRR23918636_2.fastq.gz | Fastqsanger.gz | |||
| SRR23918637_1.fastq.gz | Fastqsanger.gz |
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Project description:The time-resolved impact of monensin on the active rumen microbiome in a rumen-simulating technique (Rusitec) was studied with metaproteomic and metabolomic approaches. Upon monensin treatment, decreased catabolism linked to fiber degradation was observed by the reduced abundance of proteins assigned to fibrolytic bacteria and glycoside hydrolases, sugar transporters and carbohydrate metabolism. Reduced amounts of ammonium as well as branched-chain fatty acids pointed towards a decreased proteolytic activity. The family Prevotellaceae exhibited increased resilience in the presence of monensin, with a switch of metabolism from acetate to succinate production. Prevotella species harbor a membrane bound electron transfer complex, which drives the reduction of fumarate to succinate, the substrate for propionate production in the rumen habitat. Besides the increased succinate production, a concomitant depletion of methane concentration was observed upon monensin exposure. Our study demonstrates that Prevotella sp. shifts its metabolism successfully in response to monensin exposure and Prevotellaceae represents the key bacterial family stabilizing the rumen microbiota during exposure to monensin.
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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
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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- 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 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.
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