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ABSTRACT: Gut metagenome of Atlantic salmon, shotgun sequencing study

PROVIDER: PRJEB60591 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR11011119_1.fastq.gz	Fastqsanger.gz
	ERR11011119_2.fastq.gz	Fastqsanger.gz
	ERR11011037_1.fastq.gz	Fastqsanger.gz
	ERR11011037_2.fastq.gz	Fastqsanger.gz
	ERR11011038_1.fastq.gz	Fastqsanger.gz

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Project description:Salmon gut metagenome, 16S ribosomal RNA study

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Dietary supplementation to a plant-based diet for Atlantic salmon

Project description:The study evaluated effects of dietary cholesterol (CH), taurocholate (TC), choline (CN) and taurine (TA) in Atlantic salmon fed a plant based diet for 77 days. The additives did not affect growth or organ weights of Atlantic salmon, but promoted induction of cholesterol and plant sterol efflux in the intestine, whereas sterol uptake was suppressed. Microarray analyses in the liver indicated decreased cholesterol biosynthesis and enhanced conversion to bile acids. The marked effect of cholesterol on bile acid synthesis suggests that dietary cholesterol can be used to stimulate bile acid synthesis in fish. The study clearly demonstrated how Atlantic salmon adjusted metabolic functions in response to the dietary load of cholesterol, and has expanded our understanding of sterol metabolism and turnover that adds to the knowledge of these processes in fish. Feed supplementation with choline improved lipid absorption and suppressed abnormal accumulation of fat in the gut.

2013-10-31 | GSE51887 | GEO

Enniatin B and beauvericin prevailing in fish feed affect intestinal cell function and hematological processes in Atlantic salmon (Salmo salar) after acute exposure

Project description:Unintentional use of mold-infested plant-based feed ingredients are sources of mycotoxins in fish feeds. The presence of the emerging mycotoxins ENNB and BEA in Norwegian commercial fish feeds and plant-based feed ingredients has raised concerns regarding the health effects on farmed Atlantic salmon (Salmon salar). Atlantic salmon pre-smolts were exposed to a non-lethal single-dose of BEA and ENNB, and total RNA sequencing of the intestine and liver was carried out to evaluate gut health and identify possible hepatological changes after a single-dose dietary exposure. ENNB and BEA did not give acute toxicity, however ENNB caused the onset of pathways linked to acute intestinal inflammation and BEA exposures caused the onset of hepatic hematological disruption. The prevalence and concentration of ENNB found in today's commercial feed could affect the fish health if consumed over a longer time-period.

2022-12-01 | GSE213817 | GEO

Enhanced transcriptomic responses in the Pacific salmon louse Lepeophtheirus salmonis oncorhynchi to the non-native Atlantic Salmon Salmo salar suggests increased parasite fitness

Project description:This study investigates host-specific gene expression of the Pacific salmon lice, Lepeophtheirus salmonis oncorhynchii, while parasitizing a resistant host (Coho salmon), two susceptible hosts (Atlantic salmon, Sockeye salmon), and a population with-held hosts (starved), over 48 hrs.

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Fermented sunflower meal in diets for Atlantic salmon

Project description:The increasing aquaculture production volumes have caused an escalating demand for alternative protein feed ingredients. Agro-industrial by-products such as sunflower meal are relatively abundant and cheap, but the inclusion levels are limited due to the presence of antinutritional factors and fiber. Solid state fermentation is a processing method with the aim of reducing the content of fiber and antinutritional factors and improving nutritional value in plant protein raw materials. In this study, Atlantic salmon (Salmo salar) at two commercial-like fish farms were fed diets containing 5% non-fermented sunflower meal (as a control diet) and two experimental diets with 5% or 10% fermented sunflower meal. The field trial lasted for eight and 11 months in a coastal and fjord location, respectively with the aim of comparing the effect of fermented diets on growth performance, gut microbiota, distal intestine histology and gene expression of Atlantic salmon under different environmental conditions. The findings revealed that diets with fermented sunflower meal sustained growth performance, improved intestinal health by reducing the prevalence of prominent inflammation and ectopic goblet cells and promoted gut lactic acid bacteria Lactiplantibacillus and Lactobaccilaceae after long-term feeding. Our results suggest that fermented sunflower meal is suitable as a protein source for Atlantic salmon when included at a level of up to 10% in the diet.

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Gene expression in Atlantic salmon cell culture in response to infectious salmon anaemia virus (ISAV) and polyinosinic-polycytidylic acid - poly(I:C)

Project description:ISAV is one of the most dangerous pathogens causing high mortality of farmed Atlantic salmon. In this study, transcriptome responses to the virus were examined in vitro in Atlantic salmon head kidney cells culture (ASK). Poly(I:C), synthetic double-stranded RNA stimulating antiviral responses was used as a positive control.

2021-09-03 | GSE183265 | GEO

From a cells model to a fish trial: Characterization of the immunomodulatory effects of Heat-killed Lactiplantibacillus plantarum as a functional ingredient in aquafeeds for salmonids

Project description:RNA-seq analysis showed that HK L-137 was able to modulate the gene expression of pathways related to molecular function, biological process and cellular component in DI, without compromising fish performance and gut microbiota. Considering these data, our study has shown that HK L-137 can modulate the physiological response of Atlantic salmon, making fish more robust and possibly more able to cope better under stress factors during production.

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Zakhartsev2022 - Constraint-based model of metabolism of Atlantic salmon (Salmo salar)

Project description:SALARECON links the Atlantic salmon genome to metabolic fluxes and growth, focusing on energy, amino acid, and nucleotide metabolism.

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Host-gut microbiota interactions shape parasite infections in farmed Atlantic salmon

Project description:Animals and their associated microbiota share long evolutionary histories. However, it is not always clear how host genotype and microbiota interact to affect phenotype. We applied a hologenomic approach to explore how host-microbiota interactions shape lifetime growth and parasite infection in farmed Atlantic salmon (Salmo salar). Multi-omics data sets were generated from the guts of 460 salmon, 82% of which were naturally infected with an intestinal cestode. A single Mycoplasma bacterial strain, MAG01, dominated the gut metagenome of large, non-parasitized fish, consistent with previous studies showing high levels of Mycoplasma in the gut microbiota of healthy salmon. While small and/or parasitized salmon also had high abundance of MAG01, we observed increased alpha diversity in these individuals, driven by increased frequency of low-abundance Vibrionaceae and other Mycoplasma species that carried known virulence genes. Colonization by one of these cestode-associated Mycoplasma strains was associated with host individual genomic variation in long non-coding RNAs. Integrating the multi-omic data sets revealed coordinated changes in the salmon gut mRNA transcriptome and metabolome that correlated with shifts in the microbiota of smaller, parasitized fish. Our results suggest that the gut microbiota of small and/or parasitized fish is in a state of dysbiosis that partly depends on the host genotype, highlighting the value of using a hologenomic approach to incorporate the microbiota into the study of host-parasite dynamics.

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