Intestinal contents microorganisms of Atlantic salmon and culture environment microorganisms
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1090561 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR28493902_1.fastq.gz | Fastqsanger.gz | |||
| SRR28493902_2.fastq.gz | Fastqsanger.gz | |||
| SRR28493903_1.fastq.gz | Fastqsanger.gz | |||
| SRR28493903_2.fastq.gz | Fastqsanger.gz | |||
| SRR28493904_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 42 |
Similar Datasets
Project description:Genotype Environment interaction in Salmon
| PRJEB53340 | ENA
Project description:The aquaculture industry has confronted severe economic losses due to infectious diseases in the last years. Piscirickettsiosis or Salmonid Rickettsial Septicaemia (SRS) is the bacterial disease caused by Piscirickettsia salmonis. This Gram-negative, non-motile, cellular pathogen has the ability to infect, survive, replicate, and propagate in salmonid monocytes/macrophages generating a systemic infection characterized by the colonization of several organs including kidney, liver, spleen, intestine, brain, ovary and gills. In this study, we attempted to determine whether global gene expression differences can be detected in different genetic groups of Atlantic salmon as a result of Piscirickettsia salmonis infection. Moreover, we sought to characterize the fish transcriptional response in order to reveal the mechanisms that might confer resistance in Atlantic salmon to an infection with Piscirickettsia salmonis. In doing so, after challenging with Piscirickettsia salmonis, we selected the families with the highest (HS) and the lowest (LS) recorded susceptibility for gene expression analysis using 32K cGRASP microarrays. Our results revealed in LS families expression changes are linked to iron depletion, as well as, low contents of iron in kidney cells and low bacterial load, indicated that the iron-withholding strategy of innate immunity is part of the mechanism of resistance against Piscirickettsia salmonis. This information contributes to elucidate the underlying mechanisms of resistance to Piscirickettsia salmonis infection in Atlantic salmon and to identify new candidate genes for selective breeding programmes.
2013-01-04 | GSE43255 | GEO
Project description:Recirculation systems (RAS), which reduce water consumption and improve pathogen control are increasingly used in Atlantic salmon aquaculture. Performance and adaptation of fish to new farming environment is actively investigated. Here, responses to crowding stress were compared in salmon reared in two systems (RAS with brackish water and flowthrough with full salinity water) at low and high density.
2021-04-27 | GSE173229 | GEO
Project description:Captive rearing programs (hatcheries) are often used in conservation and management efforts for at-risk salmonid fish populations. However, hatcheries typically rear juveniles in environments that contrast starkly with natural conditions, which may lead to phenotypic and/or genetic changes that adversely affect the performance of juveniles upon their release to the wild. Environmental enrichment has been proposed as a mechanism to improve the efficacy of population restoration efforts from captive-rearing programs: in this study, we examine the influence of environmental enrichment during embryo and yolk-sac larval rearing at the level of the transcriptome in Atlantic salmon (Salmo salar). Full siblings were reared in either a M-bM-^@M-^\simpleM-bM-^@M-^] environment devoid of structure or a M-bM-^@M-^\complexM-bM-^@M-^] environment enriched with gravel substrate. At the end of endogenous feeding by juveniles, we examined patterns of gene transcription in head tissues using the cGRASP-designed Agilent 4M-CM-^W44K microarray. Significance analysis of microarrays (SAM) indicated that 808 genes were differentially transcribed between rearing environments and a total of 184 gene ontological (GO) terms were over- or under-represented, several of which are associated with mitosis/cell cycle and muscle and heart development. However, there were also pronounced differences among families in gene transcriptional response to rearing environment, with the number of genes significantly differentially transcribed by juveniles in our independent analyses of each family ranging from zero to 3445 (FDR of 5%). Overall, our results suggest that rearing environment enrichment can profoundly change patterns of gene transcription during salmon development, but that the degree of response depends on genetic background. This was a two-condition experiment in which a total of 30 RNA samples isolated from the heads of developing salmon were analysed: 15 juveniles reared in a traditional hatchery environment and 15 reared in a hatchery environment enriched with gravel substrate.
2014-12-10 | E-GEOD-63982 | biostudies-arrayexpress
Project description:Tenacibaculum finnmarkense is a novel Gram-negative, aerobic bacterial strain causing skin ulcers in Atlantic salmon. This is an emerging pathogen, which may cause serious problems to aquaculture. The study was designed to compare the life stages (smolt and posmolt) and to assess effects of environment (fresh and brackis water) on the course of disease and salmon responses to the pathogen.
2021-04-09 | GSE171699 | GEO
Project description:Captive rearing programs (hatcheries) are often used in conservation and management efforts for at-risk salmonid fish populations. However, hatcheries typically rear juveniles in environments that contrast starkly with natural conditions, which may lead to phenotypic and/or genetic changes that adversely affect the performance of juveniles upon their release to the wild. Environmental enrichment has been proposed as a mechanism to improve the efficacy of population restoration efforts from captive-rearing programs: in this study, we examine the influence of environmental enrichment during embryo and yolk-sac larval rearing at the level of the transcriptome in Atlantic salmon (Salmo salar). Full siblings were reared in either a “simple” environment devoid of structure or a “complex” environment enriched with gravel substrate. At the end of endogenous feeding by juveniles, we examined patterns of gene transcription in head tissues using the cGRASP-designed Agilent 4×44K microarray. Significance analysis of microarrays (SAM) indicated that 808 genes were differentially transcribed between rearing environments and a total of 184 gene ontological (GO) terms were over- or under-represented, several of which are associated with mitosis/cell cycle and muscle and heart development. However, there were also pronounced differences among families in gene transcriptional response to rearing environment, with the number of genes significantly differentially transcribed by juveniles in our independent analyses of each family ranging from zero to 3445 (FDR of 5%). Overall, our results suggest that rearing environment enrichment can profoundly change patterns of gene transcription during salmon development, but that the degree of response depends on genetic background.
2014-12-10 | GSE63982 | GEO
Project description:The aim of this experiment was to explore transcriptomic changes in the distal gut of Altantic salmon fed five experimental and two control diets. The experimental diets were isonitrogenous, isolipidic and isocaloric. They had similar content of fish meal (~22%) and similar total plant protein content (~45%), but differed in the contents of soya protein concentrate (SPC) and bean protein concentrate (BPC). These two ingredients were used to replace each other (either partially or fully) at the levels of incorporation ranging from 0 to 45%, with ~11% increments. As a result, the experimental diets contained either 45% SPC and 0% BPC (S45), 34% SPC and 11% BPC (S34B11), 22% SPC and 22% BPC (S22B22), 11% SPC and 34% BPC (S11B34) or 0% SPC and 45% BPC (B45). The S45 and B45 diets were single plant protein diets, while the others (S34B11, S22B22 and S11B34) were mixed plant protein diets. The control diets were enriched with fish meal (FM diet) or soybean meal (SBM diet) to provide negative and positive controls for gut inflammation (enteritis), respectively. The study was conducted at EWOS Innovation Research Facility in Dirdal (Norway) Atlantic salmon (Salmo salar L.) of the SalmoBreed strain were supplied as fertilized eggs and hatched on site. Mixed-sex juvenile salmon in groups of ~150 fish were transferred to 26 indoor tanks (0.6 x 0.6 x 0.6 m), with ~60 L of freshwater flowing at a rate of 3.9 L/min and continuous aeration. The temperature of water was regulated at 13°C and all animals were exposed to a constant light regime (24 h light/day). Fish were fed a commercial EWOS Start 1 diet and acclimated to the experimental conditions for 2 weeks, after which (at body mass ~1.5 g) they were subjected to a 56-day feeding trial. Tanks were randomly assigned to the dietary treatments, with 4 replicate tanks per each experimental diet (S45, S34B11, S22B22, S11B34 and B45) and 3 replicate tanks per each control diet (FM and SBM diets). Fish were fed to satiation prior to the feeding trial and during the dietary manipulation using automatic band feeders (Holland Technology, Norway). During the feeding trial, all fish in each tank had their biomass recorded on days 0 (start of experiment), 14, 28, 42 and 56 (end of experiment) for evaluation of growth performance.
2016-02-01 | E-MTAB-3613 | biostudies-arrayexpress
Project description:Norway is the largest producer and exporter of farmed Atlantic salmon (Salmo salar) worldwide. Skin disorders correlated with bacterial infections represent an important challenge for fish farmers due to the economic losses caused. Little is known about this topic, thus studying the skin-mucus of Salmo salar and its bacterial community depict a step forward in understanding fish welfare in aquaculture. In this study, we used label free quantitative mass spectrometry to investigate the skin-mucus proteins associated with both Atlantic salmon and bacteria. In addition, the microbial temporal proteome dynamics during 9 days of mucus incubation with sterilized seawater was investigated, in order to evaluate their capacity to utilize mucus components for growth in this environment.
2019-07-15 | PXD008838 | Pride
Project description:The effect of different diets (i.e. fish oil based vs vegetable oil based) on liver transcription profiles over the life history stages (freshwater and marine phases) of cultured Atlantic salmon (Salmo salar) were explored. Two groups of fish were raised from first feeding on different lipid containing diets; a) the standard 100% fish oil based diet, the other enriched with a blend of vegetable oils (75%) + fish oil (25%). Liver samples were taken from fish at four time points: two freshwater phase (as parr 36 weeks post hatch (wph); as pre-smolts, 52 wph) and two marine phase ( as post-smolts 55 wph; and as adult fish , 86 wph). A total of 96 cDNA microarray hybridisations - TRAITS / SGP Atlantic salmon 17k feature cDNA microarray - were performed ( 2 diets x 4 time points x 6 biological replicates x 2 -dye swap) using a comon pooled reference contol design.
2008-08-01 | E-TABM-449 | biostudies-arrayexpress