0000000001301594
AUTHOR
Jaume Pérez-sánchez
Immunological and pathological status of gilthead sea bream (Sparus aurata L.) under different long-term feeding regimes
The possible influence of the feeding regime (FR) on the immune system and pathological status of gilthead sea bream was studied. Two growth trials were performed starting at different seasons (trial 1 = March; trial 2 = June) under controlled experimental conditions. In both trials, FR-1 groups received a restricted amount of food, whereas FR-2 groups were fed to visual satiety. The pathology study included parasitological and bacteriological examination, and the immunological traits analysed were respiratory burst activity of head kidney leucocytes, serum lysozyme and alternative pathway complement activity (ACH50). The immunological status of gilthead sea bream not only was not impaired …
Genome Sequencing and Transcriptome Analysis Reveal Recent Species-specific Gene Duplications in the Plastic Gilthead Sea Bream
AbstractGilthead sea bream is an economically important fish species that is remarkably well-adapted to farming and changing environments. Understanding the genomic basis of this plasticity will serve to orientate domestication and selective breeding towards more robust and efficient fish. To address this goal, a draft genome assembly was reconstructed combining short- and long-read high-throughput sequencing with genetic linkage maps. The assembled unmasked genome spans 1.24 Gb of an expected 1.59 Gb genome size with 932 scaffolds (∼732 Mb) anchored to 24 chromosomes that are available as a karyotype browser at www.nutrigroup-iats.org/seabreambrowser. Homology-based functional annotation, …
Acting locally - affecting globally: RNA sequencing of gilthead sea bream with a mild Sparicotyle chrysophrii infection reveals effects on apoptosis, immune and hypoxia related genes
[Background] Monogenean flatworms are the main fish ectoparasites inflicting serious economic losses in aquaculture. The polyopisthocotylean Sparicotyle chrysophrii parasitizes the gills of gilthead sea bream (GSB, Sparus aurata) causing anaemia, lamellae fusion and sloughing of epithelial cells, with the consequent hypoxia, emaciation, lethargy and mortality. Currently no preventive or curative measures against this disease exist and therefore information on the host-parasite interaction is crucial to find mitigation solutions for sparicotylosis. The knowledge about gene regulation in monogenean-host models mostly comes from freshwater monopysthocotyleans and almost nothing is known about …
Additional file 4: of Acting locally - affecting globally: RNA sequencing of gilthead sea bream with a mild Sparicotyle chrysophrii infection reveals effects on apoptosis, immune and hypoxia related genes
Exploratory analysis of the samples prior to differential expression study. The FPKM density distributions showed three samples with anomalies (red arrows and red in the legend) that were not included in downstream analyses: gill infected parasitized 1 (A), gill infected non-parasitized 5 (B) and spleen infected 2 (D). All liver samples (C) showed uniform distributions and were included in the analyses. (PDF 292 kb)
Effect of virgin low density polyethylene microplastic ingestion on intestinal histopathology and microbiota of gilthead sea bream
© 2021 The Authors.
Under control: how a dietary additive can restore the gut microbiome and proteomic profile, and improve disease resilience in a marine teleostean fish fed vegetable diets
[Background]: The constant increase of aquaculture production and wealthy seafood consumption has forced the industry to explore alternative and more sustainable raw aquafeed materials, and plant ingredients have been used to replace marine feedstuffs in many farmed fish. The objective of the present study was to assess whether plant-based diets can induce changes in the intestinal mucus proteome, gut autochthonous microbiota and disease susceptibility of fish, and whether these changes could be reversed by the addition of sodium butyrate to the diets. Three different trials were performed using the teleostean gilthead sea bream (Sparus aurata) as model. In a first preliminary short-term tr…
Additional file 3: of Acting locally - affecting globally: RNA sequencing of gilthead sea bream with a mild Sparicotyle chrysophrii infection reveals effects on apoptosis, immune and hypoxia related genes
Pathway classification of DE genes. Bar plots representing the percentage of proteins involved in each broad Reactome pathway. The column labelled Reactome was added as a reference to show the percentage of genes in each category in the database. The other columns represent the percentage of differentially expressed (DE) genes in each category when considering all DE genes in all the tissues of the current experiment (Total) or per tissue, when compared to the control uninfected group. Gill samples are separated in parasitized (P) and non-parasitized (NP) gill sections. (PDF 343 kb)
Additional file 7: Table S2. of Under control: how a dietary additive can restore the gut microbiome and proteomic profile, and improve disease resilience in a marine teleostean fish fed vegetable diets
List of proteins detected in anterior and posterior intestine pooled samples. Data on protein expression are mean ± SEM of 4 pools fed the experimental diets. The number of the contig in the Sea Bream Database ( http://nutrigroup-iats.org/seabreamdb ) is indicated. (PDF 1435 kb)
Additional file 7: Table S2. of Under control: how a dietary additive can restore the gut microbiome and proteomic profile, and improve disease resilience in a marine teleostean fish fed vegetable diets
List of proteins detected in anterior and posterior intestine pooled samples. Data on protein expression are mean ± SEM of 4 pools fed the experimental diets. The number of the contig in the Sea Bream Database ( http://nutrigroup-iats.org/seabreamdb ) is indicated. (PDF 1435 kb)
Virulence and Molecular Typing of Vibrio harveyi Strains Isolated from Cultured Dentex, Gilthead Sea Bream and European Sea Bass
Vibrio harveyi was isolated from internal organs or ulcers of diseased and apparently healthy gilthead sea bream (Sparus aurata) and European sea bass (Dicentrarchus labrax) cultured in several fish farms located on the Spanish Mediterranean coast. The prevalence of the bacterium was significantly higher in European sea bass than in gilthead sea bream, and was closely related to the season in both fish species, occurring almost exclusively on warm months (June to November). After phenotypic characterization, a selection of forty five isolates from gilthead sea bream, sea bass, and several isolates previously obtained from common dentex (Dentex dentex) of the same area, were molecularly type…
Additional file 8: Table S3. of Under control: how a dietary additive can restore the gut microbiome and proteomic profile, and improve disease resilience in a marine teleostean fish fed vegetable diets
List of proteins detected in anterior intestine samples. Data on protein expression are mean ± SEM of 6 fish fed the experimental diets. The number of the contig in the Sea Bream Database ( http://nutrigroup-iats.org/seabreamdb ) is indicated. (PDF 562 kb)
Additional file 1: of Acting locally - affecting globally: RNA sequencing of gilthead sea bream with a mild Sparicotyle chrysophrii infection reveals effects on apoptosis, immune and hypoxia related genes
A) PCR-array results: Mean and SEM of the fold changes of the 45 selected genes in Sparicotyle infected fish (n = 10) calculated relative to the control uninfected group (n = 10) in parasitized gill portions (with parasite presence), non-parasitized gill portions (no parasite present) and spleen. Student’s t test or Mann-Whitney-Wilcoxon test when normality conditions were not met were used to calculate p values comparing expression levels of control and infected animals per gene. Dark red and green indicate significantly up- or down-regulated genes, respectively, with p
Additional file 9: Table S4. of Under control: how a dietary additive can restore the gut microbiome and proteomic profile, and improve disease resilience in a marine teleostean fish fed vegetable diets
List of differentially expressed proteins (P
Reverse-transcribing viruses (Belpaoviridae, Metaviridae, and Pseudoviridae)
Fourth Edition.
Bacteria associated with winter mortalities in laboratory-reared common dentex (Dentex dentex L.)
A pathological study was conducted on laboratory-reared juvenile common dentex (Dentex dentex) suffering trickling and continuous mortalities. During a 3-month period (October-December), water temperature, clinical signs and mortalities were recorded. Moribund or dead fish were examined for bacteria and parasites. Bacteria were isolated from head kidney and external ulcers, and samples from the gills, intestine, stomach, trunk kidney, gall bladder and liver were taken for histology. Cumulative mortality reached 73%, and 80% of fish examined were positive for bacteria (102 isolates). Vibrio splendidus was the most prevalent in head kidney (59.7%) and ulcers (88.9%), and it was frequently iso…
SeqEditor: an application for primer design and sequence analysis with or without GTF/GFF files
[Motivation]: Sequence analyses oriented to investigate specific features, patterns and functions of protein and DNA/RNA sequences usually require tools based on graphic interfaces whose main characteristic is their intuitiveness and interactivity with the user’s expertise, especially when curation or primer design tasks are required. However, interface-based tools usually pose certain computational limitations when managing large sequences or complex datasets, such as genome and transcriptome assemblies. Having these requirments in mind we have developed SeqEditor an interactive software tool for nucleotide and protein sequences’ analysis.
Additional file 9: Table S4. of Under control: how a dietary additive can restore the gut microbiome and proteomic profile, and improve disease resilience in a marine teleostean fish fed vegetable diets
List of differentially expressed proteins (P
Additional file 8: Table S3. of Under control: how a dietary additive can restore the gut microbiome and proteomic profile, and improve disease resilience in a marine teleostean fish fed vegetable diets
List of proteins detected in anterior intestine samples. Data on protein expression are mean ± SEM of 6 fish fed the experimental diets. The number of the contig in the Sea Bream Database ( http://nutrigroup-iats.org/seabreamdb ) is indicated. (PDF 562 kb)
Genome Sequencing and Transcriptome Analysis Reveal Recent Species-Specific Gene Duplications in the Plastic Gilthead Sea Bream (Sparus aurata)
Gilthead sea bream is an economically important fish species that is remarkably well-adapted to farming and changing environments. Understanding the genomic basis of this plasticity will serve to orientate domestication and selective breeding toward more robust and efficient fish. To address this goal, a draft genome assembly was reconstructed combining short- and long-read high-throughput sequencing with genetic linkage maps. The assembled unmasked genome spans 1.24 Gb of an expected 1.59 Gb genome size with 932 scaffolds (~732 Mb) anchored to 24 chromosomes that are available as a karyotype browser at www.nutrigroup-iats.org/seabreamdb. Homology-based functional annotation, supported by R…
Additional file 2: of Acting locally - affecting globally: RNA sequencing of gilthead sea bream with a mild Sparicotyle chrysophrii infection reveals effects on apoptosis, immune and hypoxia related genes
Gene ontology (GO) enrichment analysis based on the number of DE genes per tissue (FDR cutoff 0.05). The Tabs entitled “TISSUE EnrichGO” contain the detailed lists of the enriched GO total, up- and down-regulated sorted by ontology (Biological process (BP), Cellular compartment (CC) and Molecular function (MF)). (XLSX 49 kb)
Additional file 3: Figure S2. of Under control: how a dietary additive can restore the gut microbiome and proteomic profile, and improve disease resilience in a marine teleostean fish fed vegetable diets
Krona visualisation of the relative abundance of intestinal bacterial OTUs identified in fish fed D1. (HTML 238 kb)
Additional file 2: Table S1. of Under control: how a dietary additive can restore the gut microbiome and proteomic profile, and improve disease resilience in a marine teleostean fish fed vegetable diets
Percentage of the different bacterial OTUs identified in intestinal mucus of fish fed different diets. The results can be sorted by Phylum, Family, Genus and Species (OTUs). Numbers represent the mean percentage of four replicate pools. (XLSX 63 kb)
Additional file 6: Figure S5. of Under control: how a dietary additive can restore the gut microbiome and proteomic profile, and improve disease resilience in a marine teleostean fish fed vegetable diets
Krona analysis of the relative abundance of intestinal bacterial OTUs identified in fish fed D4. (HTML 250 kb)
Additional file 6: Figure S5. of Under control: how a dietary additive can restore the gut microbiome and proteomic profile, and improve disease resilience in a marine teleostean fish fed vegetable diets
Krona analysis of the relative abundance of intestinal bacterial OTUs identified in fish fed D4. (HTML 250 kb)
Additional file 2: Table S1. of Under control: how a dietary additive can restore the gut microbiome and proteomic profile, and improve disease resilience in a marine teleostean fish fed vegetable diets
Percentage of the different bacterial OTUs identified in intestinal mucus of fish fed different diets. The results can be sorted by Phylum, Family, Genus and Species (OTUs). Numbers represent the mean percentage of four replicate pools. (XLSX 63 kb)
Additional file 4: Figure S3. of Under control: how a dietary additive can restore the gut microbiome and proteomic profile, and improve disease resilience in a marine teleostean fish fed vegetable diets
Krona analysis of the relative abundance of intestinal bacterial OTUs identified in fish fed D2. (HTML 243 kb)
Additional file 5: Figure S4. of Under control: how a dietary additive can restore the gut microbiome and proteomic profile, and improve disease resilience in a marine teleostean fish fed vegetable diets
Krona analysis of the relative abundance of intestinal bacterial OTUs identified in fish fed D3. (HTML 246 kb)
Additional file 1: Figure S1. of Under control: how a dietary additive can restore the gut microbiome and proteomic profile, and improve disease resilience in a marine teleostean fish fed vegetable diets
Rarefaction curves obtained from the sequencing data of the four different pooled samples per dietary group. (TIFF 437 kb)
Additional file 4: Figure S3. of Under control: how a dietary additive can restore the gut microbiome and proteomic profile, and improve disease resilience in a marine teleostean fish fed vegetable diets
Krona analysis of the relative abundance of intestinal bacterial OTUs identified in fish fed D2. (HTML 243 kb)
Additional file 5: Figure S4. of Under control: how a dietary additive can restore the gut microbiome and proteomic profile, and improve disease resilience in a marine teleostean fish fed vegetable diets
Krona analysis of the relative abundance of intestinal bacterial OTUs identified in fish fed D3. (HTML 246 kb)