Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Fish gut metagenome

ABSTRACT: River and fish-gut associated microbiome in wild brown trout Metagenome

PROVIDER: PRJNA388139 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR6354360_1.fastq.gz	Fastqsanger.gz
	SRR6354360_2.fastq.gz	Fastqsanger.gz
	SRR6354370_1.fastq.gz	Fastqsanger.gz
	SRR6354370_2.fastq.gz	Fastqsanger.gz
	SRR6354380_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 304

Similar Datasets

Transcriptomic profiles of wild brown trout chronically exposed to metals using RNA-seq in a Illumina GAII platform

2014-06-01 | GSE45637 | GEO

Interactions of erythromycin and an antibiotic-mixture to the gut microbiome of juvenile rainbow trout

Project description:Erythromycin (ERY) is a commonly used antibiotic that can be found in wastewater effluents globally. Due to the mechanisms by which they kill and prevent bacterial growth, antibiotics can have significant unwanted impacts on the fish gut microbiome. The overall objective of this project was to assess the effects of erythromycin and an antibiotic mixture on fish gut microbiomes. The project was split into two experiments to assess gut microbiome in response to exposure with ERY alone or in mixture with other common antibiotics. The objectives of experiment 1 were to understand uptake and depuration of ERY in juvenile rainbow trout (RBT) over a 7 d uptake followed by a 7 d depuration period using three concentrations of ERY. Furthermore, throughout the study changes in gut microbiome response were assessed. In experiment 2, a follow-up study was conducted using an identical experimental design to assess the impacts of an antibiotic-mixture (ERY, ampicillin, metronidazole, and ciprofloxacin at 100 µg/g each). Here, three matrices were analyzed, with gut collected for 16s metabarcoding, plasma for untargeted metabolomics, and brain for mRNA-seq analysis. ERY was depurated from the fish relatively quickly and gut microbiome dysbiosis was observed at 7 d after exposure, with a slight recovery after the 7 d depuration period. A greater number of plasma metabolites was dysregulated at 14 d compared to 7 d revealing temporality compared to gut microbiome dysbiosis. Furthermore, several transformation products of antibiotics and biomarker metabolites were observed in plasma due to antibiotic exposure. Brain transcriptome revealed only slight alterations due to antibiotic exposure. The results of these studies will help inform aquaculture practitioners and risk assessors when assessing the potential impacts of antibiotics in fish feed and the environment, with implications for host health.

2024-02-07 | GSE253746 | GEO

Transcriptomic profiles of wild brown trout chronically exposed to metals using RNA-seq in a Illumina GAII platform

Project description:To investigate mechanisms of metal tolerance in the gill, gut, kidney and liver of brown trout inhabiting the river Hayle (highly metal contaminated) compared with a control population from the river Teign. mRNA samples were sequenced (Illumina GAII) from a pooled embryonic sample and 12 multiplexed samples of different tissues from the the Hayle and Teign populations (pooled from 5 and 10 individuals respectively) and used to generate a transcriptome assembly. Expression profiling was then conducted for the gill, gut, kidney and liver samples. Expression profiling results are presented in this Series.

2014-06-01 | E-GEOD-45637 | biostudies-arrayexpress

fish gut microbiome

Project description:fish gut microbiome Genome sequencing

| PRJNA783063 | ENA

Transcription profiling of migratory vs sedentary brown trout (Salmo trutta) and wild vs hatchery Atlantic salmon (Salmo salar)

Project description:A total of 55 individuals were analysed: 15 migratory brown trout (Salmo trutta) individuals from the Redon river, 15 sedentary brown trout (S. trutta) individuals from the Redon river, 15 sedentary brown trout (S. trutta) individuals from the Chevenne river, and 10 Atlantic salmon (S. salar) individuals of a hatchery strain. For each individual, RNA was isolated twice from different parts of the same tissue, independently reverse transcribed into Cy3-labeled cDNA and then probed on two different slides, which leads to total of 110 single slide experiments.

2006-03-27 | E-MEXP-123 | biostudies-arrayexpress

Long-term dietary replacement of fish meal and fish oil in diets for rainbow trout: effects on intestinal and hepatic gene expression

Project description:In the context of replacing fish meal and fish oil in feeds for aquaculture, rainbow trout alevins received from first-feeding onwards, one of the three experimental diets: V (100% plant-based), C (mix of FM-FO & plant ingredients) or M (100% FM-FO based). The long term effects of such dietary replacement on the intestinal (mid gut) and hepatic transcriptome were studied in juveniles after a 7-month feeding trial at 7°C.

2018-02-14 | GSE84985 | GEO

fish gut

Project description:fish gut

| PRJEB15391 | ENA

fish gut metagenome

Project description:Reef fish gut microbiome Raw sequence reads

| PRJNA290348 | ENA

Morphine treatment leads to temporal modulation of the gut microbiome

Project description:Opioid analgesics are frequently prescribed in the United States and worldwide. However, serious side effects such as addiction, immunosuppression and gastrointestinal symptoms limit long term use. In the current study using a chronic morphine-murine model a longitudinal approach was undertaken to investigate the role of morphine modulation of gut microbiome as a mechanism contributing to the negative consequences associated with opioids use. The results revealed a significant shift in the gut microbiome and metabolome within 24 hours following morphine treatment when compared to placebo. Morphine induced gut microbial dysbiosis exhibited distinct characteristic signatures profiles including significant increase in communities associated with pathogenic function, decrease in communities associated with stress tolerance. Collectively, these results reveal opioids-induced distinct alteration of gut microbiome, may contribute to opioids-induced pathogenesis. Therapeutics directed at these targets may prolong the efficacy long term opioid use with fewer side effects.

2018-04-16 | E-MTAB-5550 | biostudies-arrayexpress

Fish gut

Project description:Fish gut Metagenome

| PRJNA846293 | ENA