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ABSTRACT: Metagenomics analysis of skin-mucus bacterial microbiota from sea caged Atlantic salmon

PROVIDER: PRJNA552674 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR9644000.fastq.gz	Fastqsanger.gz
	SRR9644010.fastq.gz	Fastqsanger.gz
	SRR9644001.fastq.gz	Fastqsanger.gz
	SRR9644002.fastq.gz	Fastqsanger.gz
	SRR9644003.fastq.gz	Fastqsanger.gz

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Mucus microbiota

Project description:Metagenomic analysis of skin-mucus bacterial microbiota from sea caged Atlantic salmon

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The farmed Atlantic salmon (Salmo salar) skin-mucus proteome

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

Interacting effects of sea louse (Lepeophtheirus salmonis) infection and formalin-killed Aeromonas salmonicida in Atlantic salmon skin transcriptome

Project description:Lepeophtheirus salmonis (sea lice) and bacterial co-infection threatens wild and farmed Atlantic salmon performance and welfare. The present microarray-based study examined the dorsal skin transcriptome response to formalin-killed Aeromonas salmonicida bacterin (ASAL) in pre-adult sea lice-infected and non-infected Atlantic salmon to fill the existing knowledge gap and aid in developing anti-co-infection strategies. To this aim, sea lice-infected and non-infected salmon were intraperitoneally injected with either phosphate-buffered saline (PBS) or ASAL (i.e., 4 injection/infection groups: PBS/no lice, PBS/lice, ASAL/no lice, and ASAL/lice). The analysis of the dorsal skin transcriptome data [Significance Analysis of Microarrays (5% FDR)] identified 345 up-regulated and 2,189 down-regulated DEPs in the comparison PBS/lice vs. PBS/no lice, and 82 up-regulated and 3 down-regulated DEPs in the comparison ASAL/lice vs. ASAL/no lice. The comparison ASAL/lice vs. PBS/lice identified 272 up-regulated and 11 down-regulated DEPs, whereas ASAL/no lice vs. PBS/no lice revealed 27 up-regulated DEPs. The skin transcriptome differences between the co-stimulated salmon (i.e., ASAL/lice) and PBS/no lice salmon accounted for 1,878 up-regulated and 3,120 down-regulated DEPs.

2022-02-28 | GSE186292 | GEO

Keratinocytes Drive the Epithelial Hyperplasia Key to Sea Lice Resistance in Coho Salmon

Project description:Background: Salmonid species have followed markedly divergent evolutionary trajectories in their interactions with sea lice. While sea lice parasitism poses significant economic, environmental, and animal welfare challenges for Atlantic salmon (Salmo salar) aquaculture, coho salmon (Oncorhynchus kisutch) exhibit near-complete resistance to sea lice, achieved through a potent epithelial hyperplasia response leading to rapid louse detachment. The molecular mechanisms underlying these divergent responses to sea lice are unknown. Results: We characterised the cellular and molecular responses of Atlantic salmon and coho salmon to sea lice using single-nuclei RNA sequencing. Juvenile fish were exposed to copepodid sea lice (Lepeophtheirus salmonis), and lice-attached pelvic fin and skin samples were collected 12h, 24h, 36h, 48h, and 60h after exposure, along with control samples. Comparative analysis of control and treatment samples revealed an immune and wound-healing response that was common to both species, but attenuated in Atlantic salmon, potentially reflecting greater sea louse immunomodulation. Our results revealed unique but complementary roles of three layers of keratinocytes in the epithelial hyperplasia response leading to rapid sea lice rejection in coho salmon. Our results suggest that basal keratinocytes direct the expansion and mobility of intermediate and, especially, superficial keratinocytes, which eventually encapsulate the parasite. Conclusions: Our results highlight the key role of keratinocytes in coho salmon’s sea lice resistance, and the diverged biological response of the two salmonid host species when interacting with this parasite. This study has identified key pathways and candidate genes that could be manipulated using various biotechnological solutions to improve Atlantic salmon sea lice resistance.

2024-06-24 | GSE269132 | GEO

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Project description:The present work characterizes the response of co-habited Atlantic (Salmo salar), chum (Oncorhynchus keta) and pink salmon (Oncorhynchus gorbuscha) to sea lice infections. Atlantic and pink salmon anterior kidney samples were profiled at three time points over nine days after the start of an experimental infection. Chum salmon anterior kidney was profiled at day six post infection only. All three species were also profiled at six days post exposure for skin responses of the pectoral fin, typically associated with lice infection.

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2021-04-09 | GSE171693 | GEO

Skin responses in Atlantic salmon post-smolts during exposure to Tenacibaculum finnmarkense

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

Transcriptomic profiling of the adaptive and innate immune responses of Atlantic salmon to Renibacterium salmoninarum infection

Project description:Renibacterium salmoninarum is a Gram-positive, intracellular bacterial pathogen that causes Bacterial Kidney Disease (BKD) in Atlantic salmon (Salmo salar). To identify Atlantic salmon genes responsive to R. salmoninarum pathogen, fish were intraperitoneally injected with R. salmoninarum (BKD) or sterile KDM-2 medium (control). Head kidney samples were collected at 13 days post-infection. Using 44K microarray analysis, transcriptome analysis was performed to identify differentially expressed probes in response to different levels of R. salmoninarum infection.

2020-09-24 | GSE150335 | GEO

Differential expression of miRNAs and mRNAs in Moritella viscosa challenge Atlantic salmon

Project description:Moritella viscosa is a bacterial pathogen causing winter-ulcer disease in Atlantic salmon. The lesions on affected fish lead to increased mortality, decreased fish welfare, and inferior meat quality in farmed salmon. MicroRNAs (miRNAs) are small non-coding RNAs involved in post-transcriptional regulation by guiding the miRNA induced silencing complex to specific mRNA transcripts (target genes). The goal of this study was to identify miRNAs responding to Moritella viscosa in salmon by investigating miRNA expression in head-kidney and the muscle/skin from lesion sites caused by the pathogen. Protein coding gene expression was investigated by microarray analysis in the same materials.

2022-08-14 | GSE211004 | GEO

Profiling the transcriptome response of Atlantic salmon to formalin-killed Renibacterium salmoninarum

Project description:Renibacterium salmoninarum is a Gram-positive, intracellular bacterial pathogen that causes Bacterial Kidney Disease (BKD) in Atlantic salmon (Salmo salar). To identify R. salmoninarum bacterin-responsive genes in Atlantic salmon, fish (n=6) were intraperitoneally injected with a high (5×107 cells/kg; High-Rs) dose of formalin-killed R. salmoninarum or phosphate-buffered saline (PBS control). Head kidney samples were collected at 24 h post-injection. Using 44K microarray analysis, transcriptome analysis was performed to identify differentially expressed probes in response to formalin-killed R. salmoninarum injection.

2020-07-21 | GSE135168 | GEO

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