Calicophoron daubneyi
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA396008 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR5877444_1.fastq.gz | Fastqsanger.gz | |||
| SRR5877444_2.fastq.gz | Fastqsanger.gz | |||
| SRR5877445_1.fastq.gz | Fastqsanger.gz | |||
| SRR5877445_2.fastq.gz | Fastqsanger.gz | |||
| SRR5877446_1.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:Diseases caused by parasitic flatworms of rumen tissues (paramphistomosis) are a significant threat to global food security as a cause of morbidity and mortality in ruminant livestock in subtropical and tropical climates. Calicophoron daubneyi is currently the only paramphistome species commonly infecting livestock species in temperate European climates. However, recorded incidences of C. daubneyi infection in European livestock have been increasing over the last decade. Whilst clinical paramphistomosis caused by adult worms is currently uncommon in Europe, fatalities have been reported in association with severe haemorrhagic enteritis resulting from the migration of immature paramphistomes. Large numbers of mature adults can reside in the rumen, yet to date, the impact on rumen fermentation, and consequently in productivity and economic management of infected livestock have not been resolved. Limited public available nucleotide and protein sequences for C. daubneyi underpin this lack of biological and economic understanding. Here we present for the first time a de novo assembled transcriptome, with functional annotations, for adult C. daubneyi, which provides a reference database for protein and nucleotide sequence identification to facilitate fundamental biology, anthelmintic, vaccine and diagnostics discoveries. This dataset identifies a number of genes potentially unique to C. daubneyi and, by comparison to an existing transcriptome for the related Paramphistomum cervi, identifies novel genes which may be unique to the paramphistome group of platyhelminthes. Additionally, we present the first coverage of the excretory/secretory and soluble somatic proteome profiles for adult C. daubneyi and identify the release of extracellular vesicles from adult C. daubneyi parasites during in vitro, ex-host culture. Finally, we have performed the first analysis of rumen fluke impacting upon rumen fermentation parameters using an in vitro gas production study resulting in a significant increase in propionate production.
2019-11-12 | PXD007772 | Pride
Project description:Generating transcriptome resources for the rumen fluke, Calicophoron daubneyi.
| PRJEB28150 | ENA
Project description:A healthy rumen is crucial for normal growth and improved production performance of ruminant animals. Rumen microbes participate in and regulate rumen epithelial function, and the diverse metabolites produced by rumen microbes are important participants in rumen microbe-host interactions. SCFAs, as metabolites of rumen microbes, have been widely studied, and propionate and butyrate have been proven to promote rumen epithelial cell proliferation. Succinate, as an intermediate metabolite in the citric acid cycle, is a final product in the metabolism of certain rumen microbes, and is also an intermediate product in the microbial synthesis pathway of propionate. However, its effect on rumen microbes and rumen epithelial function has not been studied. It is unclear whether succinate can stimulate rumen epithelial development. Therefore, in this experiment, Chinese Tan sheep were used as experimental animals to conduct a comprehensive analysis of the rumen microbiota community structure and rumen epithelial transcriptome, to explore the role of adding succinate to the diet in the interaction between the rumen microbiota and host.
2023-06-12 | GSE233696 | GEO
Project description:The Calicophoron daubneyi (rumen fluke) draft genome assembly
| PRJEB76148 | ENA
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.
2022-11-17 | GSE183285 | GEO
Project description:Experiment to understand relationships between sheep rumen wall transcriptome and microbial methane emissions
2017-12-30 | GSE81847 | GEO
Project description:Helminth parasites secrete molecules in soluble form (i.e the secretome) or packaged into extracellular vesicles (EVs) as a means of exporting effector molecules into the host microenvironment. Once released, the parasite-derived molecules can trigger a range of biological effects including modulation of host immunity. While the secretome and molecular cargo of EVs have been characterised in many parasites, little is known about the molecules released by the rumen fluke, Calicophoron daubneyi – an emerging infection of livestock in Western Europe. Here we used a mass spectrometry-based proteomics approach to characterise the secretome of the infective newly-excysted juvenile (NEJ) stage and adult flukes. We also profile the proteome of two sub-populations of EVs (termed 15K and 120K EVs) released by the adult flukes.
2021-02-16 | PXD014550 | Pride
Project description:The transcriptome of Escherichia coli K-12 has been widely studied over a variety of conditions for the past decade while such studies involving E. coli O157:H7, its pathogenic cousin, are just now being conducted. To better understand the impact of rumen fluid on E. coli O157:H7, global transcript levels of strain EDL933 cells resuspended in heat clarified rumen fluid for 15 min were compared to cells resuspended in fresh LB using microarrays. Seven independent RNA samples from rumen fluid treated cultures were paired with seven independent RNA samples from control cultures for hybridization to seven two-color microarrays. For three arrays, the control RNA sample was labeled with Cy3 dye and the experimental RNA sample was labeled with Cy5 dye, the dyes were reversed for the other four arrays to overcome dye bias.
2010-12-01 | E-GEOD-16747 | biostudies-arrayexpress
Project description:Hanwoo cattle are a Korean breed renowned for their cultural significance and high-quality beef, characterized by low cholesterol and high unsaturated fat ratio. Growth is divided into a growing phase focused on development and a fattening phase for marbling. Proper feed management, considering genetic and environmental factors, is vital for maximizing growth potential. The rumen plays a crucial role in digestion and gene expression regulation, with rumen fermentation being central to nutrient absorption and cattle health. In this study, we conduct transcriptome analysis of the rumen at eight timepoints. Our goal is to identify genetic factors that influence the growth of Hanwoo steers to enhance our understanding of the rumen’s functions and roles during their growth. In this RNA-sequencing analysis of Hanwoo steer rumen, differential gene expression was examined over eight timepoints, highlighting significant genetic changes, particularly between 12 and 26 months. Weighted gene co-expression network analysis identified and organized as three modules: turquoise, blue, and yellow. The turquoise module, linked to immune response, showed down-regulation in genes at 30 months. The blue module, associated with steroid metabolism, was notably up-regulated at 26 months. The yellow module’s genes showed a consistent increase in expression with growth. These modules and their functional annotations provide a deeper understanding of the biological processes during Hanwoo growth, highlighting the intricate relationship between gene expression and cattle development. The growth stages of Hanwoo steers were explored in our investigation utilizing rumen transcriptome data. The rumen plays critical role in their development, particularly during the growing and fattening phases. Proper feed management, considering the rumen’s function, is essential for optimal growth. Transcriptome analysis helps identify genes associated with growth and provides insights for cattle breeding and management practices. Understanding the complex connection between gene expression and Hanwoo development is essential for maximizing productivity and health.
2024-06-02 | GSE267733 | GEO
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).
2015-07-22 | E-GEOD-71153 | biostudies-arrayexpress