Aquatic metagenome
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA356261 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:We aimed at obtaining a reference transcriptome for the European seabass. We characterized by Illumina paired-ends RNA-seq the D. labrax transcriptome for two targeted organs, using a diversity of conditions, animal stages and genotypes to warranty the widest variety of reconstructed transcripts. The brain (including pineal gland and pituitary) and liver were chosen as they are complementary and at a crossroads of many key neuroendocrine, metabolic and behavioral regulations. Dicentrarchus labrax_2 targeted organs (liver and brain) with two technical replicates each (using two different fragment sizes) half a GAIIX run total. We used two flow cells per organ and each was corresponding to a different fragment size. The expected sizes were 350 and 500bp.
2014-02-01 | E-MTAB-1867 | biostudies-arrayexpress
Project description:Transcriptomic profiling of egg quality in seabass (Dicentrarchus labrax)
| PRJNA329662 | ENA
Project description:The aim of the project was to identify differently expressed genes in eggs of European seabass (Dicentrarchus labrax) characterized by different quality. In this way it was expected to identify genes possibly being a molecular indicator of egg quality in this species, which was never studied to date. For the study microarray analysis of over 26 thousand genes in 16 egg batches was performed. Additionally, for each egg batch biological quality was determined, what allowed to compare the gene expression profile with overall egg quality (divided into two groups representing ‘high’ and ‘low’ egg quality). The analysis allowed to identify 39 differently expressed genes between the two groups representing ‘high’ and ‘low’ egg quality. From those genes, expression level of 7 were verified by real-time qPCR which confirmed significant difference in expression in 5 of them.
2016-12-31 | GSE84559 | GEO
Project description:Fish respond to stressors by means of an array of changes that involve many biological compartments including molecular, cellular, metabolic, physiological and behavioral acclimation. Among these changes, the immune system also experiences significant alterations that are characterized by an induction of the innate non-specific responses and changes in the acquired specific response. The present investigation was undertaken to check whether the innate response of the complement system is affected after a combination of an immune challenge and a husbandry stressor. In European seabass, two different transcripts of the complement C3 protein, which correspond to two tissue-specific isoforms, have been detected in liver. They may come from post-transcriptional modifications at the pre-mRNA level or from alternative splicing in order to generate a diversified repertoire of protein isoforms in some fish species according to the tissue were they are located. After cloning the hepatic C3, the quantification of seabass isoforms showed specific responses, thus confirming the possible specialized roles of the C3 different isoforms in terms of defence immunity. On one hand, a stronger esbC3_2 expression was observed in front to the viral challenge, suggesting a specific participation of this molecule in front to viruses. This observation is in agreement with previous studies in trout macrophages in our lab, demonstrating that the immune response to viral infections was stronger than to bacterial ones. On the other hand, the esbC3_1 expression appeared stronger after bacterial challenge, especially under high density conditions. Our results confirm the hypothesis of an immune-activation of specific isoforms of the C3 protein of the complement system as a non-specific response in front to either immune or other type of stressors. In order to confirm our hypothesis, we created an oligonucleotide microarray (Agilent Technologies) containing 6275 annotated transcripts, each with x3 specific probes, and 4516 ESTs with 1 probe/target sequence. Gene expression profiles obtained from the livers of fish held under high density culture conditions highlighted a significant contrast in the liver response. In total, 54 transcripts were differentially expressed (GDE; fold change FC >2) in treatment over the control (p<0.01)/201 (p<0.05). Oligonucleotide probes were used to construct a high-density seabass microarray based on the Agilent 4 × 44 K design format (http://www.agilent.com/), which covers 13,199 unique transcripts of Dicentrarchus labrax. Oligonucleotides, 60-mer plus a “linker”, are synthesized directly on glass slides using the Agilent’s SurePrint Tecnology; oligo design was carried out by Agilent and three or more non-overlapping probes were designed for each EST cluster. The number of transcripts represented by three is 6,275, while 6,924 targets EST have only one probe.
2011-04-23 | E-GEOD-28812 | biostudies-arrayexpress
Project description:<p>Dietary glycerol supplementation in aquaculture feed is seen as an alternative and inexpensive way to fuel fish metabolism, attenuate metabolic utilization of dietary proteins and, subsequently reduce nitrogen excretion. In this study, we evaluated the impact of dietary glycerol supplementation has on nitrogen excretion of European seabass (Dicentrarchus labrax) and its effects on metabolite profile and bacterial community composition of gut digesta. These effects were evaluated in a 60-day trial with fish fed diets supplemented with 0, 2.5 or 5% (w/w) refined glycerol. Nuclear magnetic resonance spectroscopy and high-throughput 16S rRNA sequencing characterized the effects of glycerol supplementation of digesta metabolite and bacterial community composition of 6h postprandial fish. Our results showed ammonia excretion was not altered by dietary glycerol supplementation and the highest glycerol dosage was associated with significant increases in amino acids and a significant decrease of ergogenic creatine in digesta metabolome. Concomitantly, significant decreases in putative amino acid degradation pathways were detected in the predicted metagenome analysis, suggesting a metabolic shift. Taxon-specific analysis revealed significant increases in abundance of some specific genera (e.g. Burkholderia and Vibrio) and bacterial diversity. Overall, our results indicate glycerol supplementation may decrease amino acid catabolism without adversely affecting fish gut bacterial communities.</p>
2020-07-30 | MTBLS870 | MetaboLights
Project description:Fresh fish are highly perishable food products and their short shelf-life limits their commercial exploitation, leads to waste and has a negative impact on aquaculture sustainability. New non-thermal food processing methods, such as High pressure (HP), are being investigated to prolong shelf-life while assuring high food quality. We applied several tools to evaluate the impacts of HP processing on European sea bass (Dicentrarchus labrax) fillets quality and shelf life. The data here presented includes visual and physical measurements of flesh quality and the microbiome and proteome profiles of control and HP-processed sea bass fillets (600MPa, 25ºC, 5min), after isothermal storage (2°C) for different periods ranging from 1 to 67 days. Color (L-, a- and b- values) change and texture (hardness, cohesiveness and adhesiveness) parameters were obtained by using appropriate colorimeter and texture analyser, respectively, during refrigerated storage. Bacterial diversity was analysed by Illumina high-throughput sequencing of the 16S rRNA gene in five pooled DNAs from control or HP-processed fillets after 1, 11 or 67 days and the raw reads were deposited in the NCBI-SRA database with accession number PRJNA517618. In addition, high-throughput sequencing of the internal transcribed spacer (ITS) region targeting yeast and moulds was run for control or HP-processed fillets at the end of storage (11 or 67 days, respectively), being deposited under SRA accession PRJNA517779. Quantitative label-free proteomics profiles were analysed by SWATH-MS (Sequential Windowed data independent Acquisition of the Total High-resolution-Mass Spectra) in myofibrillar or sarcoplasmic enriched protein extracts pooled for control or HP-processed filets after short (1d) or long-term (11-67 days) storage. These data support the findings reported in “High pressure processing of European sea bass (Dicentrarchus labrax) fillets and tools for flesh quality and shelf life monitoring” (Tsironi et al. 2019).
2019-11-06 | PXD012737 | Pride
Project description:The sustainable growth of fish aquaculture will require the procurement of non-marine feed sources. Glycerol is a potential feed supplement whose metabolism may spare the catabolism of dietary amino acids, thereby extending the use of the feed protein to other physiological functions such as growth. In the present study, the effects of dietary glycerol supplementation on the muscle and liver metabolomes of rainbow trout (Oncorhynchus mykiss) and European seabass (Dicentrarchus labrax) were evaluated. Fish juveniles were fed diets with 0%, 2.5%, and 5% glycerol. Muscle and liver aqueous fractions were extracted and 1H NMR spectra were acquired. Metabolite profiles derived from the 1H NMR signals were assessed using univariate and multivariate statistical analyses. The adenylate energy charge was determined in the muscle. For both species, the muscle metabolite profile showed more variability compared to that of the liver and was most perturbed by the 5.0% glycerol diet. For the liver metabolite profile, rainbow trout showed fewer differences compared to European seabass. No differences were observed in energy charge between experimental groups for either species. Thus, rainbow trout appeared to be less susceptible to tissue metabolite perturbations, compared to seabass, when the diet was supplemented with up to 5% glycerol.
2020-02-24 | MTBLS832 | MetaboLights
Project description:Dicentrarchus labrax genome 2021
| PRJEB43042 | ENA