Ontology highlight
ABSTRACT:
PROVIDER: PRJNA764499 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR15974000.fastq.gz | Fastqsanger.gz | |||
| SRR15974100.fastq.gz | Fastqsanger.gz | |||
| SRR15974001.fastq.gz | Fastqsanger.gz | |||
| SRR15974101.fastq.gz | Fastqsanger.gz | |||
| SRR15974002.fastq.gz | Fastqsanger.gz |
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Project description:Bacteriophage – host dynamics and interactions are important for microbial community composition and ecosystem function. Nonetheless, empirical evidence in engineered environment is scarce. Here, we examined phage and prokaryotic community composition of four anaerobic digestors in full-scale wastewater treatment plants (WWTPs) across China. Despite relatively stable process performance in biogas production, both phage and prokaryotic groups fluctuated monthly over a year of study period. Nonetheless, there were significant correlations in their α- and β-diversities between phage and prokaryotes. Phages explained 40.6% of total prokaryotic community composition, much higher than the explainable power by abiotic factors (14.5%). Consequently, phages were significantly (P<0.010) linked to parameters related to process performance including biogas production and volatile solid concentrations. Association network analyses showed that phage-prokaryote pairs were deeply rooted, and two network modules were exclusively comprised of phages, suggesting a possibility of co-infection. Those results collectively demonstrate phages as a major biotic factor in controlling bacterial composition. Therefore, phages may play a larger role in shaping prokaryotic dynamics and process performance of WWTPs than currently appreciated, enabling reliable prediction of microbial communities across time and space.
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Project description:RNA sequencing (RNA-Seq) was performed on rumen papillae from 16 steers with variation in gain and feed intake. Sixteen rumen papillae samples were sequenced by Cofactor Genomics (St.Louis, MO).
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Project description:Metaproteomic studies of the rumen microbiota are challenged by the need of optimized sample preparation protocols in order to retrieve an enhanced amount of prokaryotic instead of plant and bovine derived cells before protein extraction and subsequent LC-MS/MS analysis. The present study evaluates three different protocols applied to the rumen microbiota either attached to plant fibres or present as planktonic cells. The findings of our work suggest the integration of cheesecloth-gauze filtration in sample preparation to achieve a better protein identification ratio.
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Project description:AIMS: To explore and validate the utility of rumen endoscopy for collection of rumen papillae for gene expression measurement. METHODS: Four adult Coopworth ewes were fasted for either 4 or 24 hours. Animals were sedated, placed in a dorsally recumbent position at 45 degrees with the head upright, and an endoscope inserted via a tube inserted into the mouth. Biopsies of rumen papillae were taken from the ventral surface of the rumen atrium under visual guidance. Two biopsies were collected from one of the animals that had been fasted for 4 hours, and three from one of the animals that had been fasted for 24 hours. Video of the rumen atrium and reticulum was also collected. The animals recovered uneventfully. Biopsies were subsequently used for extraction and sequencing of mRNA. RESULTS: The ventral surface of the rumen atrium was accessible after 4 hours off pasture, but a larger region was accessible after 24 hours of fasting. Sedation allowed access for endoscope use for around 5 to 10 minutes after which increased saliva flow was noted. Rumen papillae biopsies were easily collected, with samples from a variety of sites collected in the ∼10 minute time window. High quality RNA was obtained for stranded mRNA sequencing. Of the resulting reads, 69–70% mapped uniquely to version 3.1 of the ovine genome, and 48–49% to a known gene. The rumen mRNA profiles were consistent with a previously reported study. CONCLUSIONS: This method for obtaining rumenal tissue was found to be rapid and resulted in no apparent short or long term effects on the animal. High quality RNA was successfully extracted and amplified from the rumen papillae biopsies, indicating that this technique could be used for future gene expression studies. The use of rumen endoscopy could be extended to collection of a variety of rumen and reticulum anatomical measurements and deposition and retrieval of small sensors from the rumen. Rumen endoscopy offers an attractive and cost effective approach to repeated rumen biopsies compared with serial slaughter or use of cannulated animals.
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