Ontology highlight
ABSTRACT:
PROVIDER: PRJNA809425 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR18105800_1.fastq.gz | Fastqsanger.gz | |||
| SRR18105800_2.fastq.gz | Fastqsanger.gz | |||
| SRR18105801_1.fastq.gz | Fastqsanger.gz | |||
| SRR18105801_2.fastq.gz | Fastqsanger.gz | |||
| SRR18105802_1.fastq.gz | Fastqsanger.gz |
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Project description:Long-term dietary intake influences the structure and activity of the trillions of microorganisms residing in the human gut, but it remains unclear how rapidly and reproducibly the human gut microbiome responds to short-term macronutrient change. Here we show that the short-term consumption of diets composed entirely of animal or plant products alters microbial community structure and overwhelms inter-individual differences in microbial gene expression. The animal-based diet increased the abundance of bile-tolerant microorganisms (Alistipes, Bilophila and Bacteroides) and decreased the levels of Firmicutes that metabolize dietary plant polysaccharides (Roseburia, Eubacterium rectale and Ruminococcus bromii). Microbial activity mirrored differences between herbivorous and carnivorous mammals, reflecting trade-offs between carbohydrate and protein fermentation. Foodborne microbes from both diets transiently colonized the gut, including bacteria, fungi and even viruses. Finally, increases in the abundance and activity of Bilophila wadsworthia on the animal-based diet support a link between dietary fat, bile acids and the outgrowth of microorganisms capable of triggering inflammatory bowel disease. In concert, these results demonstrate that the gut microbiome can rapidly respond to altered diet, potentially facilitating the diversity of human dietary lifestyles. RNA-Seq analysis of the human gut microbiome during consumption of a plant- or animal-based diet.
2013-12-05 | E-GEOD-46761 | biostudies-arrayexpress
Project description:Long-term dietary intake influences the structure and activity of the trillions of microorganisms residing in the human gut, but it remains unclear how rapidly and reproducibly the human gut microbiome responds to short-term macronutrient change. Here we show that the short-term consumption of diets composed entirely of animal or plant products alters microbial community structure and overwhelms inter-individual differences in microbial gene expression. The animal-based diet increased the abundance of bile-tolerant microorganisms (Alistipes, Bilophila and Bacteroides) and decreased the levels of Firmicutes that metabolize dietary plant polysaccharides (Roseburia, Eubacterium rectale and Ruminococcus bromii). Microbial activity mirrored differences between herbivorous and carnivorous mammals, reflecting trade-offs between carbohydrate and protein fermentation. Foodborne microbes from both diets transiently colonized the gut, including bacteria, fungi and even viruses. Finally, increases in the abundance and activity of Bilophila wadsworthia on the animal-based diet support a link between dietary fat, bile acids and the outgrowth of microorganisms capable of triggering inflammatory bowel disease. In concert, these results demonstrate that the gut microbiome can rapidly respond to altered diet, potentially facilitating the diversity of human dietary lifestyles.
2013-12-05 | GSE46761 | GEO
Project description:Herbivorous fish gut metagenome sequencing and assembly
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Project description:Gut bacteria of herbivorous fish and their comparison
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Project description:The effects of ambient temperature and dietary plant toxins on differential gene expression in the liver were compared in herbivorous rodents (woodrats, genus Neotoma) using microarrays custom-designed for woodrats. Expression profiles revealed a greater number of up-egulated genes at 22C comapred to a thermoneutral temperature (27C). Genes and pathways up-regulated at 22C were related to growth and biosynthesis, suggesting the liver could be in a building state at this temperature. Conversely, genes associated with gluconeogenesis, apoptosis and protein misfolding, which likely reflected a more stressed state for the liver. Taken together, these results highlighted the important role of temperature on gene expression profiles in the desert woodrat. As crucial players in many ecosystems, understanding how herbivorous mammals will respond to climate change is imperative to accurately predict repercussions and aid in conservation efforts.
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Project description:Plant-based protein sources play an important role in aquaculture by dwindling fish meal to sustainable levels. However, the use of such feedstuffs requires nutrient supplementation to fulfil fish nutritional requirements. This work addressed the response in the liver of farmed fish to dietary methionine (Met), assessing at the same time the growth performance. Fish were fed at suboptimal levels of dietary Met (0.77% w/w; M0.65 diet), within (1% w/w Met; M0.85 diet)and above(1.36 % w/w Met (M1.25 diet); 1.66% w/w Met(M1.5 diet)) the estimated requirement for this species, in a total of four tested conditions. The impact of dietary methionine supplementation in seabass juvenile’s performance was assessed through 85 days of trial, between May and August of 2018. Fish were reared in triplicate tanks and three liver samples/tank (9 per treatment) were collected for liver proteome analysis at the end of the trial i.e., after 85 days of feeding.
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Project description:Fish oil, olive oil, and coconut oil dietary supplementation have several cardioprotective benefits, but it is not established if they can protect against air pollution-induced adverse effects. We hypothesized that these dietary supplements would attenuate ozone-induced systemic and pulmonary effects. Male Wistar Kyoto rats were fed either a normal diet, or a diet enriched with fish, olive, or coconut oil starting at 4 weeks of age for 8 weeks. Animals were then exposed to air or ozone (0.8 ppm), 4h/day for 2 consecutive days. The fish oil diet completely abolished phenylephrine-induced vasoconstriction that was increased following ozone exposure in the animals fed all other diets. Only the fish oil diet increased baseline levels of bronchoalveolar lavage fluid (BALF) markers of lung injury and inflammation. Ozone-induced pulmonary injury/inflammation were comparable in rats on normal, coconut oil, and olive oil diets with altered expression of markers in animals fed the fish oil diet. Fish oil, regardless of exposure, led to enlarged, foamy macrophages in the BALF that coincided with decreased mRNA expression of cholesterol transporters, cholesterol receptors, and nuclear receptors in the lung. Serum miRNA profile was assessed using small RNA-sequencing in normal and fish oil groups and demonstrated marked depletion of a variety of miRNAs, several of which were of splenic origin. No ozone-specific changes were noted. Collectively, these data indicate that while fish oil offered protection from ozone-induced aortic vasoconstriction, it increased pulmonary injury/inflammation and impaired lipid transport mechanisms resulting in foamy macrophage accumulation, demonstrating the need to be cognizant of potential off-target pulmonary effects that might offset the overall benefit of this vasoprotective dietary supplement.
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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.
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Project description:Plant-based protein sources play an important role in aquaculture by dwindling fish meal to sustainable levels. However, the use of such feedstuffs requires nutrient supplementation to fulfil fish nutritional requirements. This work addressed the response in the liver of farmed fish to dietary methionine (Met), assessing at the same time the growth performance. Fish were fed at suboptimal levels of dietary Met (0.77% w/w; M0.65 diet), within (1% w/w Met; M0.85 diet)and above(1.36 % w/w Met (M1.25 diet); 1.66% w/w Met(M1.5 diet)) the estimated requirement for this species, in a total of four tested conditions. The impact of dietary methionine supplementation in seabass juvenile’s performance was assessed through 85 days of trial, between May and August of 2018. Fish were reared in triplicate tanks and three liver samples/tank (9 per treatment) were collected for liver proteome analysis at the beginning and at the end of the trial i.e., after 18 and 85 days offeeding, correspondingly. This dataset refers to the 18th day of sampling.
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