RNA-seq of stomach and pyloric caeca from Atlantic salmon (Salmo salar) fed diets containing chitin from shrimp and black soldier fly larvae
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Illumina HiSeq 4000
ORGANISM(S): Salmo salar
SUBMITTER: Matilde Holen
PROVIDER: E-MTAB-10594 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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Project description:Facing a bottleneck in the growth of aquaculture, and a gap in the supply and demand of the highly beneficial omega-3 (n-3) long-chain polyunsaturated fatty acids (LC-PUFA), sustainable alternatives to the traditional feeds are much needed. Therefore, in this trial, an oil extracted from newly designed plant, Camelina sativa, was tested for its n-3 replacement capabilities, using three different groups of post-smolt Atlantic salmon (Salmo salar) which were fed for 12 weeks three experimental diets; a control diet containing a blend of fish oil (5 %) and rapeseed oil (15 %) (FO), a wild-type Camelina (20 %) (WCO) and the transgenic Camelina oil (20 %) (DCO), all of them having the same basal composition. By comparing them, an overall evaluation of fish performance, fatty acid profile, feeds digestibility and gene expression was done. In the context of the new transgenic diet, there were no negative effects on the growth, survival rate or health of the fish. The whole fish n-3 levels were highest in the DCO-fed fish with EPA+DHA levels almost double compared to FO-fed fish and more than double when compared to WCO-fed ones, clearly suggesting the efficiency of the Camelina oil in providing competitive levels of n-3 LC-PUFA compared to the commercial “gold standard”.
2019-11-30 | E-MTAB-6228 | biostudies-arrayexpress
Project description:Plant-based protein sources play an important role in aquaculture by dwindling fish meal to sustainable levels. However, the use of such feedstuffs requires nutrient supplementation to fulfil fish nutritional requirements. This work addressed the response in the liver of farmed fish to dietary methionine (Met), assessing at the same time the growth performance. Fish were fed at suboptimal levels of dietary Met (0.77% w/w; M0.65 diet), within (1% w/w Met; M0.85 diet)and above(1.36 % w/w Met (M1.25 diet); 1.66% w/w Met(M1.5 diet)) the estimated requirement for this species, in a total of four tested conditions. The impact of dietary methionine supplementation in seabass juvenile’s performance was assessed through 85 days of trial, between May and August of 2018. Fish were reared in triplicate tanks and three liver samples/tank (9 per treatment) were collected for liver proteome analysis at the end of the trial i.e., after 85 days of feeding.
2020-11-25 | PXD019622 | Pride
Project description:Farmed and wild Atlantic salmon was given either vegetable oil (low DHA and EPA) feed or fish oil (high in DHA and EPA) feed or phospholipid (high in phospholipid) feed from start of feeding. We sampled and RNAseq two tissues (pyloric caeca and liver) on day 0, day 48, day 65 and day 94 after initial feeding.
2019-10-30 | E-MTAB-8306 | biostudies-arrayexpress
Project description:Plant-based protein sources play an important role in aquaculture by dwindling fish meal to sustainable levels. However, the use of such feedstuffs requires nutrient supplementation to fulfil fish nutritional requirements. This work addressed the response in the liver of farmed fish to dietary methionine (Met), assessing at the same time the growth performance. Fish were fed at suboptimal levels of dietary Met (0.77% w/w; M0.65 diet), within (1% w/w Met; M0.85 diet)and above(1.36 % w/w Met (M1.25 diet); 1.66% w/w Met(M1.5 diet)) the estimated requirement for this species, in a total of four tested conditions. The impact of dietary methionine supplementation in seabass juvenile’s performance was assessed through 85 days of trial, between May and August of 2018. Fish were reared in triplicate tanks and three liver samples/tank (9 per treatment) were collected for liver proteome analysis at the beginning and at the end of the trial i.e., after 18 and 85 days offeeding, correspondingly. This dataset refers to the 18th day of sampling.
2020-12-02 | PXD019610 | Pride
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.
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Project description:Background: Enteromyxosis caused by the intestinal myxozoan parasite Enteromyxum scophthalmi is a serious threat for turbot (Scophthalmus maximus, L.) aquaculture, causing severe catarrhal enteritis leading to a cachectic syndrome, with no therapeutic options available. There are still many aspects of host-parasite interaction and disease pathogenesis that are yet to be elucidated, and to date, no analysis of the transcriptomic changes induced by E. scophthalmi in turbot organs has been conducted. In this study, RNA-seq technology was applied to head kidney, spleen and pyloric caeca of severely infected turbot with the aim of furthering our understanding of the pathogenetic mechanisms and turbot immune response against enteromyxosis. Results: A huge amount of information was generated with more than 23,000 identified genes in the three organs, amongst which 4,762 were differently expressed (DE) between infected and control fish. Associate gene functions were studied based on gene ontology terms and available literature, and the most interesting DE genes were classified into five categories: 1) immune and defence response; 2) apoptosis and cell proliferation; 3) iron metabolism and erythropoiesis; 4) cytoskeleton and extracellular matrix and 5) metabolism and digestive function. The analysis of down-regulated genes of the first category revealed evidences of a connexion failure between innate and adaptive immune response, especially represented by a high number of DE interferon-related genes in the three organs. Furthermore, we found an intense activation of local immune response at intestinal level that appeared exacerbated, whereas in kidney and spleen genes involved in adaptive immune response were mainly down-regulated. The apoptotic machinery was only clearly activated in pyloric caeca, while kidney and spleen showed a marked depression of genes related to erythropoiesis, probably related to disorders in iron homeostasis. The genetic signature of the causes and consequences of cachexia was also demonstrated by the down-regulation of the genes encoding structural proteins and those involved in the digestive metabolism. Conclusions: This transcriptomic study has enabled us to gain a better understanding of the pathogenesis of enteromyxosis and identify a large number of DE target genes that bring us closer to the development of strategies designed to effectively combat this pathogen. Four samples per organ (kidney, spleen and pyloric caeca) were sequenced by Illumina HiSeq 2000 as 100bp paired-end reads. For each organ, three samples were taken from Enteromyxum severely infected turbot and the remaining one was a pool of three control turbot.
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