Project description:A custom high density oligo-microarray (8 x 15K) was designed and printed by means of the eArray web tool (Agilent) to analyze the transcriptome of the three intestinal sections of Euroipan sea bass (Dicentrarchus labrax). Naïve stock juveniles sea bass, maintained under intensive rearing conditions in the indoor experimental facilities of IATS, were sampled after overnight fasting for anterior, middle and posterior sections of intestine. The array comprised 60-oligomer sequences for 14,147 different sea bass annotated sequences. Total RNA (150ng) from individual fish were labelled with cyanine 3-CTP and 1,000ng of each labelled cRNA were hybridized to microarray slides. Analysis of the scanned data, including principal component analysis and unpaired t-test with Benjamini-Hochberg multiple testing correction, was carried out with GeneSpring GX software (Agilent). Pathway analysis of differentially expressed sequences was performed using the Ingenuity Pathway Analysis (IPA) software.
Project description:Comparison of the hepatic transcriptomes for two half-sib-families of European sea bass fed on vegetable and fish diet. These two half-sib-families exhibit similar growth on fish diet while significantly different on vegetable diet. The aim of the study is to point out the large panel of metabolic and physiological effects induced by total substitution of both fish meal and fish oil in the diets of European sea bass and to reveal physiological characteristics associated to the two half-sib-families.
Project description:Gut microbiome research is rapidly moving towards the functional characterization of the microbiota by means of shotgun meta-omics. Here, we selected a cohort of healthy subjects from an indigenous and monitored Sardinian population to analyze their gut microbiota using both shotgun metagenomics and shotgun metaproteomics. We found a considerable divergence between genetic potential and functional activity of the human healthy gut microbiota, in spite of a quite comparable taxonomic structure revealed by the two approaches. Investigation of inter-individual variability of taxonomic features revealed Bacteroides and Akkermansia as remarkably conserved and variable in abundance within the population, respectively. Firmicutes-driven butyrogenesis (mainly due to Faecalibacterium spp.) was shown to be the functional activity with the higher expression rate and the lower inter-individual variability in the study cohort, highlighting the key importance of the biosynthesis of this microbial by-product for the gut homeostasis. The taxon-specific contribution to functional activities and metabolic tasks was also examined, giving insights into the peculiar role of several gut microbiota members in carbohydrate metabolism (including polysaccharide degradation, glycan transport, glycolysis and short-chain fatty acid production). In conclusion, our results provide useful indications regarding the main functions actively exerted by the gut microbiota members of a healthy human cohort, and support metaproteomics as a valuable approach to investigate the functional role of the gut microbiota in health and disease.
Project description:Comparison of the hepatic transcriptomes for two half-sib-families of European sea bass fed on vegetable and fish diet. These two half-sib-families exhibit similar growth on fish diet while significantly different on vegetable diet. The aim of the study is to point out the large panel of metabolic and physiological effects induced by total substitution of both fish meal and fish oil in the diets of European sea bass and to reveal physiological characteristics associated to the two half-sib-families. Fish from both two half-sib-families (G and g) were fed a a fish diet (FD) or a vegetable diet (VD) diet for 9 months. Five to eight independent experiments were performed for each experimental groups (G-FD; G-VD; g-FD; g-VD) using different fishes for each experiment.
Project description:Previous works in the framework of EU ARRAINA Project evidenced a pro-inflammatory condition in gilthead sea bream (Sparus aurata) fed extremely low fish meal/fish oil diets, and this effect was mostly reversed by butyrate supplementation. The hypothesis of work is that these nutritionally-mediated changes can be extensive to intestinal mucus proteome and gut microbiota, which in turn could modify disease outcome.s If so, the prevalence and progression of the disease might be also modified by diet composition and feed additives. Gilthead sea bream fingerlings were fed with control and experimental diets formulated by BioMar until two year-old. FM was added at 25% in the control diet (D1) and at 5% in the other three diets (D2-D4). Added oil was either FO (D1 control diet) or a blend of vegetable oils, replacing the 58% (D2) and the 84% (D3-D4 diets) of FO. A commercial sodium butyrate preparation (NOREL, BP70) was added to the D4 diet at 0.4%. At month 20, 6 fish per each dietary treatment were sampled for iTRAQ profiling and fingerprinting of intestinal mucus proteome. Mucus collected from anterior and posterior intestine segments was trypsin digested, labelled with iTRAQ reagents, isoelectrofocused and resolved by LC-MS/MS. More than 1000 proteins were unequivocally annotated and principal component analysis clearly separated anterior and posterior segments. The diet effect with changes in the abundance of approximately 120 proteins was restricted to anterior section with a reversion of the pattern of the extreme diet (D3 fish) with dietary butyrate supplementation. Butyrate supplementation also reversed the decrease of microbiotay diversity associated with D3 feeding, and led to a improvement the disease outcomes in fish challenged with Photobacterium damselae and the intestinal parasite Enteromyxum leei.
Project description:A sea bass oligo microarray platform was used to profile gene expression in whole heads of 38 days-old sea bass affected by prognathism, a skeletal malformation that strongly affects sea bass production. Two different conditions: i) prognathous individuals, and ii) normal individuals were analyzed. For each condition, total RNA was extracted from three (3) independent biological replicates, each consisting of pools of five (5) heads.
