Bacteria
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA541392 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR9021430_1.fastq.gz | Fastqsanger.gz | |||
| SRR9021430_2.fastq.gz | Fastqsanger.gz | |||
| SRR9021431_1.fastq.gz | Fastqsanger.gz | |||
| SRR9021431_2.fastq.gz | Fastqsanger.gz | |||
| SRR9021432_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 12 |
Similar Datasets
Project description:Microbiota from rats fed with wheat aleurone and plant omega fatty acids In this study we investigated how an AX-rich WA and ALA from linseed oil (LO) modulate the gut microbiota of rats. Wistar rats were fed a standard diet and received either an iso-energetic control oil (PO), control oil + aleurone (A+PO), linseed oil (LO) or linseed oil + aleurone (A+LO) during 12 weeks. Feacal samples were recovered after the 12 week treatments. DNA extractions were performed using using the Qiagen's DNA Stool Kit (Qiagen, West Sussex, UK). 10ng of DNA template were amplified by PCR (16S gene) and purified using Qiagen's Qiaquick PCR purification kit (Qiagen, West Sussex, UK). 1ug of purified PCR product were labelled with either Cy3 or Cy5 using Genomic DNA ULS Labelling kit (Agilent Technologies, Palo Alto, CA). 250ng of labelled DNA were hybridized on the microarray for 24h at 65M-BM-0C. Washings were performed as recommended by the manufacturer. Microarray scanning was performed on a Surescan Microarray scanner (Agilent Technologies, Palo Alto, CA). Data were extracted using the Feature extraction software (Agilent Technologies, Palo Alto, CA). The retained intensity value for each probe was the ratio between the spotM-bM-^@M-^Ys median intensity signals and the median of background signals. A 13 chip study was realized to analyze the feacal microbiota of rats treated with either an iso-energetic control oil (PO), control oil + aleurone (A+PO), linseed oil (LO) or linseed oil + aleurone (A+LO) during 12 weeks. Each microarray corresponding to hybridization with 250ng of labelled 16S rRNA gene amplicons from 2 rat DNA faecal samples. Microbiota structure and diversity were assessed using the HuGChip (Tottey et al., 2013). Each probe (4441) was synthetized in three replicates. On the same array, 2 different samples were hybridized. One labelled with the Cy3 dye and one with the Cy5 dye. The results were processed as single channel (13 raw data files available on Series records for 25 samples).
2013-05-02 | E-GEOD-46557 | biostudies-arrayexpress
Project description:Oral administration of an extract of compost fermented with thermophiles to pigs reduces the incidence of stillbirth and promotes piglet growth. However, the mechanism by which compost extract modulates the physiological conditions of the animals remains largely unknown. Here, we investigate the effects of compost extract on the gene expression in the intestine of the rat as a mammalian model. Gene expression analyses of the intestine indicated that several immune-related genes were upregulated following compost exposure. Thus, thermophile-fermented compost can contain microbes and/or substances that activate the gut mucosal immune response in the rat. In Male Wistar rats aged 3 weeks, tap water was supplemented with 1.0% (v/v) compost extract for the experimental rats, whereas water only was given to the control rats. The rats received water ad libitum for 12 weeks. Fresh gut samples were collected from individual rats at the end of the feeding test and stored at -80°C. The intestine were separated from the gut and used as samples for the isolation of total RNA. otal RNA was then subjected to microarray experiments using the Whole Rat Genome (4x44k) Oligo Microarray (Agilent Technologies, Inc.)
2012-11-02 | E-GEOD-37732 | biostudies-arrayexpress
Project description:Metagenomic analysis of bacterial diversity from Raw Milk Fermented product Dahi Metagenome
| PRJNA321557 | ENA
Project description:Salmonella enteritidis is suggested to translocate in the small intestine. Previously we identified that prebiotics, fermented in the colon, increased Salmonella translocation in rats, suggesting involvement of the colon in translocation. Effects of Salmonella on colonic gene expression in vivo are largely unknown. The aim of this study was to characterize time dependent Salmonella induced changes of colonic mucosal gene expression in rats using whole genome microarrays. Rats were orally infected with Salmonella enteritidis to mimic a foodbore infection and colonic gene expression was determined at day 1, 3 and 6 post-infection (n=8 per timepoint). Agilent rat whole genome microarray (G4131A Agilent Technologies) were used. Results indicate that colon is clearly a target tissue for Salmonella considering the abundant changes in mucosal gene expression observed. Experiment Overall Design: In the present study, large-scale gene expression analysis was performed to reveal whether Salmonella induced changes of colonic mucosal gene expression in rats. Wistar rats were infected with Salmonella enteritidis. Non-infected control rats were sham-treated. Rats were sacrificed on day 1, 3 or 6 post infection or sham-treatment (n=8 rats per treatment and per time point). RNA was isolated from colonic mucosal scrapings. mRNA samples of 8 rats per group were pooled. Each pooled group-sample was hybridised in duplicate on Agilent rat whole genome microarrays containing 44290 60-mer spots. From the 12 arrays one duplicate array (Colon mucosa non-infected day6) did not pass quality control and was left out from further analysis.
2008-06-15 | E-GEOD-7496 | biostudies-arrayexpress
Project description:Pu-erh tea has attracted increasing attention worldwide because of its special flavor and health effects, but its impact on composition and function of the gut microbiota remains unclear. The aim of this study was to investigate effects of aqueous extracts of fermented (ripe) and non-fermented (raw) Pu-erh teas on the composition and function of intestinal microbiota of rats with diet-induced obesity. We conducted a comparative metagenomic and metaproteomic investigation of the microbial communities in cecal samples taken from obese rats administrated with or without extracts of raw and ripe Pu-erh tea. By analyzing the composition and diversity of 16S rRNA amplicons and expression profiles of 814 distinct proteins, we found that, despite differences in the chemical compositions of the raw and ripe Pu-erh tea, administration of either at two different doses (0.15 and 0.40 g/Kg body weight), significantly (P<0.05) increased community diversity, and changed the composition of the cecal microbiota by increasing the relative abundances of Firmicutes and decreasing those of Bacteroidetes. Community metabolic processes including sucrose metabolism, glycolysis, syntheses of proteins, rRNA and antibiotics were significantly (P<0.05), or had a tendency (0.10<P<0.05) to be, promoted by enriching relevant enzymes. Furthermore, evidences from population, molecular and metabolic levels have shown that polyphenols of raw Pu-erh tea and their metabolites can promote potentially the growth of Akkermansia municiphila by stimulating the type II and III secretion system protein, elongation factor Tu, and glyceraldehyde-3-phosphate dehydrogenase. This study has provided new evidences for the prebiotic effects of Pu-erh tea.
2022-03-03 | PXD010972 | Pride
Project description:A phylogenetic microarray targeting 66 families described in the human gut microbiota has been developped aud used to monitor the gut microbiota's structure and diversity. The microarray format provided by Agilent and used in this study is 8x15K. A study with a total of 4 chips was realized. Arrays 1 and 2: Hybridization with 100ng of labelled 16S rRNA gene amplicons from a mock community sample and 250ng of labelled 16S rRNA gene amplicons from 1 faecal sample. Each Agilent-030618 array probe (4441) was synthetized in three replicates. Arrays 3 and 4: Hybridization with 250ng of labelled 16S rRNA gene amplicons from 2 faecal samples. Each Agilent-40558 array probe (4441) was synthetized in three replicates.
2013-03-01 | E-GEOD-44752 | biostudies-arrayexpress
Project description:Salmonella enteritidis is suggested to translocate in the small intestine. Previously we identified that prebiotics, fermented in the colon, increased Salmonella translocation in rats, suggesting involvement of the colon in translocation. Effects of Salmonella on colonic gene expression in vivo are largely unknown. The aim of this study was to characterize time dependent Salmonella induced changes of colonic mucosal gene expression in rats using whole genome microarrays. Rats were orally infected with Salmonella enteritidis to mimic a foodbore infection and colonic gene expression was determined at day 1, 3 and 6 post-infection (n=8 per timepoint). Agilent rat whole genome microarray (G4131A Agilent Technologies) were used. Results indicate that colon is clearly a target tissue for Salmonella considering the abundant changes in mucosal gene expression observed. Keywords: Time point infection study, colon mucosa, Rat
2007-10-18 | GSE7496 | GEO
Project description:Mounting evidence suggests that long non-coding RNAs (lncRNAs) are involved in the pathogenesis of silicosis. In this study, Wistar rats were treated with an improved intubation method to ferry silicon dioxide (1mL per rat) into lung. Rats in the control group were injected with normal saline solution (1mL per rat). Twenty eight days after exposure, we examined the rats and found the formation of lung fibrosis in rats treated with silica. We then investigated the lncRNAs expression changes in lungs of silica-exposed rats and compared with that of rats in the control group. Treatment of silica leads to 682 lncRNAs differentially expressed including 300 upregulated and 382 down regulated compared to controls.
2021-07-03 | GSE116653 | GEO
Project description:To determine if there exists a consistent gene signature associated with vascular hypertrophy among different rat hypertensive models: treated and untreated Wistar Kyoto (WKY) rats and treated and untreated Spontaneous Hypertensive Rat (SHR) rats. Keywords: strain comparison, treatment vs control
2007-04-11 | GSE7483 | GEO
Project description:5 rats were offered food containing 40mM Li/Kg dry weight for 4 weeks, and 5 control rats obtained standard food. The RNA from the inner medulla of the Li-treated rats was labeled red (channel 1), and from the control rats labeled green (channel 2). The samples from Li-treated rats 1+2 and control rats 1+2 were hybridized to array Li-NDI 1. The samples from Li-treated rats 3+4 and control rats 3+4 were hybridized to array Li-NDI 2. The samples from Li-treated rat 5 and control rat 5 were hybridized to array Li-NDI 3. Keywords: parallel sample
2004-09-01 | GSE1341 | GEO