Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1026909 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR26349805_1.fastq.gz | Fastqsanger.gz | |||
| SRR26349805_2.fastq.gz | Fastqsanger.gz | |||
| SRR26349806_1.fastq.gz | Fastqsanger.gz | |||
| SRR26349806_2.fastq.gz | Fastqsanger.gz | |||
| SRR26349807_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 8 |
Similar Datasets
Project description:Metagenomics of intestinal microbiomes from mice fed different sources of dietary protein
| PRJEB67356 | ENA
Project description:Diet plays a major role in altering the composition and function of the gut microbiota. Previously most studies have focused on the effects of fiber, fat, and different amounts of protein on the gut microbiota. In this study we investigated how different sources of protein affect the gut microbiota of mice. We fed conventional and germ-free C57BL/6J mice a series of defined diets where the source of dietary protein was the key difference, which made up twenty or forty percent of the diet. The dietary protein sources used were purified protein. The diets were fed to the same mice for one week each with a fecal sample collected at the end of each week. The diets were fed in this order: standard chow, 20% soy, 20% casein, 20% rice, 40% soy, 20% yeast, 40% casein, 20% pea, 20% egg white protein, 20% chicken bone broth, and lastly at the end of the experiment half of the mice were fed the 20% soy and half the mice the 20% casein diet again as a control. We did not collect fecal samples for the chicken bone broth diet as the diet was stopped prematurely due to diet intolerance. 12 germ-free mice (6 female, 6 male) in four cages were used. 12 mice with a conventional gut microbiota in four cages were used (6 female, 6 male). One germ-free mouse was found dead after diet 5 (20% yeast) and one conventional mouse was sacrificed after the second diet (20% casein). No sample could be collected from one of the conventional mice after the 20% egg white diet.
2024-12-18 | PXD041586 | Pride
Project description:This study was designed to address key questions concerning the use of alternative protein sources for animal feeds and addresses aspects such as their nutrient composition and impact on gut function, the immune system and systemic physiology. We used casein (CAS), partially delactosed whey powder (DWP), spray dried porcine plasma (SDPP), soybean meal (SBM), wheat gluten meal (WGM) and yellow meal worm (YMW) as protein sources. We investigated the effects of feeding mice during a period of four weeks on semi-synthetic diets containing 30% of six different protein sources. Microarrays were used to detail the global gene expression in the ileal mucosae of mice. Male C57BL/6J mice were stratified according to bodyweight and litter of origin into six dietary treatment groups. These mice were fed for four weeks with semi-synthetic diets containing one of the following protein sources. At the end of four weeks, mice were sacrificed by euthenesia and ileal tissue samples (scrapings) were collected for RNA extraction and hybridization on Affymetrix microarrays. Soybean meal (SBM) diet group served as reference to make comparisons with other experimental diets.
2016-08-24 | E-GEOD-84442 | biostudies-arrayexpress
Project description:Background & Aims: The complex interactions between diet and the microbiota that influence mucosal inflammation and inflammatory bowel disease are poorly understood. Experimental colitis models provide the opportunity to control and systematically perturb diet and the microbiota in parallel to quantify the contributions between multiple dietary ingredients and the microbiota on host physiology and colitis. Methods: To examine the interplay of diet and the gut microbiota on host health and colitis, we fed over 40 different diets with varied macronutrient sources and concentrations to specific pathogen free or germ free mice either in the context of healthy, unchallenged animals or dextran sodium sulfate colitis model. Results: Diet influenced physiology in both health and colitis across all models, with the concentration of protein and psyllium fiber having the most profound effects. Increasing dietary protein elevated gut microbial density and worsened DSS colitis severity. Depleting gut microbial density by using germ-free animals or antibiotics negated the effect of a high protein diet. Psyllium fiber influenced host physiology and attenuated colitis severity through microbiota-dependent and microbiota-independent mechanisms. Combinatorial perturbations to dietary protein and psyllium fiber in parallel explain most variation in gut microbial density, intestinal permeability, and DSS colitis severity, and changes in one ingredient can be offset by changes in the other. Conclusions: Our results demonstrate the importance of examining complex mixtures of nutrients to understand the role of diet in intestinal inflammation. Keywords: IBD; Diet; Microbiota; Mouse Models; Systems Biology
2017-10-30 | GSE104461 | GEO
Project description:We previously observed in mice that Bacteroides thetaiotaomicron (B. theta) significantly increased in abundance in the gut microbiome of mice when mice were fed egg and yeast dietary protein sources. We also observed that B. theta was expressing proteins previously connected to growth on mucin glycans when mice were fed an egg-white diet. To confirm that the bacterium were actually responding to the protein sources, we grew it in vitro using a defined medium, where the sole carbon source was dietary protein, mucin, or glucose. Our controls were glucose and mucin, and our experimental protein sources were soy protein, egg-white protein, and Torula yeast protein. We grew four B. theta cultures per carbon source statically at 37°C in a Coy anaerobic chamber (2.5 % H2 /10 % CO2 /88.5 % N2) in minimal medium (100 mM KH2PO4, 8.5 mM [NH2]4SO4, 15 mM NaCl, 5.8 μM vitamin K3, 1.44 μM FeSO4⋅7H2O, 1 mM MgCl2, 1.9 μM hematin, 0.2 mM L-histidine, 3.69 nM vitamin B12, 208 μM L-cysteine, and 7.2 μM CaCl2⋅2H2O) with one of the above mentioned nutrients added at 0.5% (wt/v) concentration. In order to aid the solubilization of the dietary proteins, we pre-prepared the proteins in 200 mM NaOH at 37°C for four days, the glucose control was also dissolved in 200 mM NaOH. After 8 hours, we enumerated CFUs to confirm growth, and we pelleted cells by centrifuging at 4,000 g for 10 minutes. We then removed the supernatant and froze the pellets at -80°C within 30 minutes.
2024-12-18 | PXD050296 | Pride
Project description:Dietary Methionine restriction (MR) has been demonstrated to induce a set of hepatic responses, including activation of hepatic stress response and suppression of hepatic lipogenesis. In the current study, we used two different protein sources to achieve MR. Casein was used in normal protein (NP, 20% casein) and low protein (LP, 5% casein) diet. Soy protein was used in 20Soy (20% soy), 20Soy+SAA (20% soy, Met and Cys was added back to match their concentration in NP diet), and 10Soy (11.5% soy, the Met concentration matches LP diet). Results show that mice that were fed LP and 10Soy diet have lower body weight and adiposity and increased food and water intake, energy expenditure, and serum FGF21 levels compared to their relative controls. The RNAseq experiment was conducted to compare the effect of MR using these two protein sources on the hepatic transcriptome.
2021-09-01 | GSE168132 | GEO
Project description:Characterized the fecal microbiota of mice fed different dietary protein diets and HFD
| PRJDB7246 | ENA
Project description:We report the application of bulk RNAseq assay in examining the dietary effect on mouse intestinal stem cell (ISC) subpopulation. Lgr5EGFPcreERT2 mice were fed with new western diet 1 (NWD1) or the control AIN76A diet for 3 or 12 months, to investigate differential dietary effect. To examine the reversibility of dietary effect, after 3 months of NWD1 feeding, the mice were switched to AIN feeding, and examined at 6 or 12 months old.
2023-04-12 | GSE186811 | GEO
Project description:This study was designed to address key questions concerning the use of alternative protein sources for animal feeds and addresses aspects such as their nutrient composition and impact on gut function. We used casein (CAS), spray dried porcine plasma (SDPP), soybean meal (SBM), and yellow meal worm (YMW) as protein sources. We have investigated the use of intestinal organoids as a model to test the effects of different protein sources on the intestinal epithelium. Mouse enteroids were exposed to different undigested protein sources (4% w/v, viz. soybean meal, SBM; casein, CAS; spray dried plasma protein, SDPP; and yellow meal worm, YMW) or DMEM as a control. Microarrays were used to detail the global gene expression.
2018-06-19 | GSE98051 | GEO
Project description:Regulatory innovation is central to the evolution of species. Different nutritional sources are one environmental pressure that can select for novel regulatory elements. Dietary composition changes, including exposure to “western” diets with excess fat content, can lead to transcriptional regulatory changes in the liver. In order to investigate how transcriptional regulatory changes in response to a high fat diet diverge across species, we profiled chromatin accessibility, histone modifications and the transcriptome in livers of rhesus macaques and mice fed high fat and normal diets.
2021-04-01 | GSE160247 | GEO