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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.

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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.

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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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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.

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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

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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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Transcriptional changes in Atlantic salmon (Salmo salar) after embryonic exposure to road salt (NaCl)

Project description:The present study aimed to identify the persistent molecular changes occurring in Atlantic Salmon salmon (Salmo salar) eggs after 24h exposure to high concentrations (5000 mg/L) of road salt at fertilization.

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Morphology and transcriptome of Atlantic salmon skin after seawater transfer, comparison of a semi-closed containment system and open net-pen

Project description:Development of semi-closed containment systems is a promising strategy to further expand Atlantic salmon production. The technology operates with higher production intensities where skin integrity is recognized as a central factor for animal health and welfare. This study investigate the skin development and its immune status in healthy Atlantic salmon growers reared in a semi-closed containment system and a traditional open net-pen system (control).

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