Flavobacterium sequencing in salmonid fish
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ABSTRACT:
PROVIDER: PRJEB27605 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:In a context of fast development of aquaculture, infections by Flavobacterium psychrophilum, a member of the family Flavobacteriaceae, are a major sanitary concern for the salmonid farming industry worldwide. Several phenotypic traits related to pathogenesis have been documented for this bacterium, but molecular factors involved remain poorly characterized. Here, we conducted a global study of adaptation to outside- and within-host environments using a combination of in vitro transcriptomic and computational approaches. The repertoire of transcription start sites and transcriptional units was established using 5’-end and global RNA-Seq. Responses to environmental conditions were explored by expression profiling across conditions, including host-related stresses, exposure to fish mucus and plasma, growth on blood, osmotic changes or freshwater. Analysis of these data allowed to identify many new regulatory elements including alternative sigma-factors promoters, 5’ cis-encoded and trans-acting RNAs. It also revealed interconnected regulations linked to specific environmental conditions for a wide range of biological processes: proteolytic activity, iron acquisition, fatty acids metabolism, respiration under low-oxygen concentration, protein secretion and folding, efflux pumps as well as adhesion and spreading. Results reported here constitute an important resource for guiding basic and applied research on this important pathogen, and a dedicated website is provided to facilitate their exploration.
2022-01-12 | GSE163842 | GEO
Project description:In a context of fast development of aquaculture, infections by Flavobacterium psychrophilum, a member of the family Flavobacteriaceae, are a major sanitary concern for the salmonid farming industry worldwide. Several phenotypic traits related to pathogenesis have been documented for this bacterium, but molecular factors involved remain poorly characterized. Here, we conducted a global study of adaptation to outside- and within-host environments using a combination of in vitro transcriptomic and computational approaches. The repertoire of transcription start sites and transcriptional units was established using 5’-end and global RNA-Seq. Responses to environmental conditions were explored by expression profiling across conditions, including host-related stresses, exposure to fish mucus and plasma, growth on blood, osmotic changes or freshwater. Analysis of these data allowed to identify many new regulatory elements including alternative sigma-factors promoters, 5’ cis-encoded and trans-acting RNAs. It also revealed interconnected regulations linked to specific environmental conditions for a wide range of biological processes: proteolytic activity, iron acquisition, fatty acids metabolism, respiration under low-oxygen concentration, protein secretion and folding, efflux pumps as well as adhesion and spreading. Results reported here constitute an important resource for guiding basic and applied research on this important pathogen, and a dedicated website is provided to facilitate their exploration.
2022-01-12 | GSE164190 | GEO
Project description:In a context of fast development of aquaculture, infections by Flavobacterium psychrophilum, a member of the family Flavobacteriaceae, are a major sanitary concern for the salmonid farming industry worldwide. Several phenotypic traits related to pathogenesis have been documented for this bacterium, but molecular factors involved remain poorly characterized. Here, we conducted a global study of adaptation to outside- and within-host environments using a combination of in vitro transcriptomic and computational approaches. The repertoire of transcription start sites and transcriptional units was established using 5’-end and global RNA-Seq. Responses to environmental conditions were explored by expression profiling across conditions, including host-related stresses, exposure to fish mucus and plasma, growth on blood, osmotic changes or freshwater. Analysis of these data allowed to identify many new regulatory elements including alternative sigma-factors promoters, 5’ cis-encoded and trans-acting RNAs. It also revealed interconnected regulations linked to specific environmental conditions for a wide range of biological processes: proteolytic activity, iron acquisition, fatty acids metabolism, respiration under low-oxygen concentration, protein secretion and folding, efflux pumps as well as adhesion and spreading. Results reported here constitute an important resource for guiding basic and applied research on this important pathogen, and a dedicated website is provided to facilitate their exploration.
2022-01-12 | GSE164189 | GEO
Project description:Clinical Flavobacterium columnare ATCC 49512 was grown on Flavobacterium columnare growth medium (FCGM). Bacteria from four colonies at mid-exponential phase were harvested, total proteins were isolated, and identified using 2-DE MALDI TOF/TOF MS and 2-D LC ESI MS/MS analyses. The MS/MS spectra for all peptides were analyzed using sequest algorithm
2016-03-11 | PRD000810 | Pride
Project description:Rainbow trout (1000 fish) was exposed to the bacterial pathogen F. psychrophilum by simple bath challenge without any pre-treatment with hydrogen peroxide. Samples (fin clip for Affymetrix QTL analysis) were taken from 167 moribund fish during the course of infection. When mortality/morbidity ended (day 40) we euthanized a total of 197 specimens of the remaining fish and took samples for DNA (QTL analysis) and assigned the status: Survivor. For gene expression analysis we took samples from gill, spleen and liver between day 11 and 15 from fish with clinical signs (CS) and no clinical signs (NCS), whereas samples from survivors were taken at day 40.
2023-11-01 | GSE216505 | GEO
Project description:Flavobacterium psychrophilum overview
| PRJNA36217 | ENA
Project description:Flavobacterium psychrophilum Genome sequencing
| PRJNA645884 | ENA
Project description:Flavobacterium psychrophilum Genome sequencing
| PRJNA253698 | ENA
Project description:Genomic diversity and evolution of the fish pathogen Flavobacterium psychrophilum
| PRJEB21067 | ENA
Project description:Transcriptome architecture and regulation at environmental transitions of the fish pathogen Flavobacterium psychrophilum
| PRJNA687747 | ENA