Hydrocarbon metagenome
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA209397 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR921501.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 1 of 1 |
Similar Datasets
Project description:Metagenome data from soil samples were collected at 0 to 10cm deep from 2 avocado orchards in Channybearup, Western Australia, in 2024. Amplicon sequence variant (ASV) tables were constructed based on the DADA2 pipeline with default parameters.
2025-06-15 | GSE298403 | GEO
Project description:Petroleum hydrocarbons are recalcitrant contaminants, which has caused most serious environmental problems. Acinetobacter calcoaceticus Aca13 was isolated from petroleum polluted soil for petroleum biodegradation. Hexadecane and naphthalene were used to incubate with Acinetobacter calcoaceticus Aca13. After incubation, the whole transcriptome was obtained from treated groups and control groups, and then used for RNA sequence and analysis. Obtained data in this project will help us understand the biodegradation mechanism of hexadecane and naphthalene, and will be helpful for the bioremediation of petroleum hydrocarbons.
2024-06-30 | GSE235642 | GEO
Project description:Petroleum substances are complex mixtures of hydrocarbons with vast structural diversity, posing significant challenges for toxicity assessment. To evaluate their safety under the REACH legislation, in vivo toxicological tests, particularly prenatal developmental toxicity assessments, are mandated. However, these tests are resource-intensive. Given the substantial number of compositionally and biologically similar petroleum substances, a more efficient approach is essential to meet regulatory requirements while supporting the industry's competitiveness and innovation. Petroleum substance toxicity is frequently attributed to the presence of polycyclic aromatic hydrocarbons (PAHs). PAHs’ underlying mechanism of action involves the aryl hydrocarbon receptor (AhR) activation as a molecular initiating event followed by cytochrome P450 induction, which in turn catalyzes the transformation of PAH to epoxide-containing reactive metabolites. To evaluate the dependence of this adverse outcome pathway, an AhR-knockout (AhR-KO) rat model was orally exposed to Benzo[a]Pyrene (BaP), a prototypical PAH. This study offers valuable insights into the AhR-dependent and -independent maternal toxicity and fetal developmental effects of BaP exposure, employing transcriptomic assessments to enhance the comprehension of the underlying mechanisms across four distinct tissues: blood, kidney, liver, and thymus. This research contributes toward a more efficient approach to assessing the safety of diverse petroleum substances, in alignment with regulatory objectives and the interests of the industry.
2025-06-29 | E-MTAB-13996 | biostudies-arrayexpress
Project description:Dietary intake of fruits and vegetables (FV) has been inversely associated with lower risk of ulcerative colitis. A pig model was used to evaluate the impact of feeding FV on the host response to dextran sulfate sodium (DSS)-induced colitis. Methods: Six-week-old pigs were fed a grower diet alone or supplemented with lyophilized FV equivalent to the half (half-FV) or full (full-FV) daily levels recommended for humans by the Dietary Guidelines for Americans (DGA). Pigs were fed a 1) grower diet alone (negative control), 2) grower diet and orally treated with 4% DSS for 10 days to induce colitis (positive control), 3) half-FV diet treated with 4% DSS or 4) full-FV diet treated with 4% DSS. Pigs were monitored for the development of clinical signs of colitis. Proximal colon (PC) contents and mucosa (PCM) were collected for gut metagenome, tissue transcriptome and histopathological analysis. Results: Pigs fed the full-FV diet did not exhibit diarrhea, showed less fecal occult blood (FOB), PCM crypt hyperplasia but with no differential expressed genes (DEG) or changes in PC microbiome diversity (p < 0.05). Pigs within the half-FV group exhibited increased group FOB and DEG associated with tissue remodeling, crypt and goblet cell hyperplasia in the PCM and no changes in PC microbiome diversity and two pigs exhibiting diarrhea (p < 0.05). Pigs within the DSS positive control group exhibited a reduced DEG involved with intestinal immune response and PC microbiome diversity with altered metagenome, increased group PCM erosion and FOB with persistent diarrhea in one pig (p < 0.05) Conclusions: Overall, our results showed that pigs fed a three-week full-FV supplemented diet, were resistant to DSS-induced colitis with a differential dose-dependent protective effect on host intestinal tissue and gut metagenome when exposed to an inflammatory challenge.
2026-04-01 | GSE317287 | GEO
Project description:hydrocarbon metagenome Genome sequencing and assembly
| PRJNA301899 | ENA
Project description:Traditional biomarkers for hydrocarbon exposure are not induced by all petroleum substances. The objective of this study was to determine if exposure to a crude oil and different refined oils would generate a common hydrocarbon-specific response in gene expression profiles that could be used as generic biomarkers of hydrocarbon exposure. Juvenile rainbow trout (Oncorhynchus mykiss) were exposed to the water accommodated fraction (WAF) of either kerosene, gas oil, heavy fuel oil, or crude oil for 96 hours. Tissue was collected for RNA extraction and microarray analysis. Exposure to each WAF resulted in a different list of differentially regulated genes, with few genes in common across treatments. Exposure to crude oil WAF changed the expression of genes including CYP1A and GST with known roles in detoxification pathways. These gene expression profiles were compared to others from previous experiments which used a diverse suite of toxicants. Clustering algorithms successfully i dentified gene expression profiles resulting from hydrocarbon exposure. These preliminary analyses highlight the difficulties of using single genes as diagnostic of petroleum hydrocarbon exposures. Further work is needed to determine if multivariate transcriptomic-based biomarkers may be a more effective tool than single gene studies for exposure monitoring of different oils.
2009-12-15 | GSE19483 | GEO
Project description:Petroleum hydrocarbon-contaminated ecopiles Raw sequence reads
| PRJNA925022 | ENA
Project description:16S pyrotag sequences from the Hydrocarbon Metagenomics Project
| PRJNA181037 | ENA
Project description:16S pyrotag sequences from the Hydrocarbon Metagenomics Project 2012
| PRJNA235891 | ENA