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Items: 1 to 20 of 1994

1.

The global RNA-binding protein RbpB is a regulator of polysaccharide utilization in Bacteroides thetaiotaomicron

(Submitter supplied) Paramount to human health, symbiotic bacteria in the gastrointestinal tract rely on the breakdown of complex polysaccharides to thrive in this sugar-deprived environment. Gut Bacteroides are metabolic generalists and deploy dozens of polysaccharide utilization loci (PULs) to forage diverse dietary and host-derived glycans. The expression of the multi-protein PUL complexes is tightly regulated at the transcriptional level. more...
Organism:
Bacteroides thetaiotaomicron
Type:
Expression profiling by high throughput sequencing
Platform:
GPL28094
4 Samples
Download data: WIG
Series
Accession:
GSE244816
ID:
200244816
2.

Bacteroides expand the functional versatility of a universal transcription factor and transcribed DNA to program capsule diversity

(Submitter supplied) Human gut Bacteroides species encode numerous (eight or more) tightly regulated capsular polysaccharides (CPS). Specialized paralogs of the universal transcription elongation factor NusG, called UpxY (Y), and an anti-Y UpxZ (Z) are encoded by the first two genes of each CPS operon. The Y-Z regulators combine with promoter inversions to limit CPS transcription to a single operon in most cells. Y enhances transcript elongation whereas Z inhibits noncognate Ys. more...
Organism:
Bacteroides fragilis NCTC 9343
Type:
Other
Platform:
GPL35091
1 Sample
Download data: TXT
Series
Accession:
GSE281607
ID:
200281607
3.

Antibiotic Susceptibility Influenced by Carbon Source in Bacteroides thetaiotaomicron

(Submitter supplied) Antibiotic therapy causes changes in bacterial abundance and metabolism within the gut microbiome. These changes can lead to complications in the host such as microbiome dysbiosis and opportunistic infections. Additionally, increasing multidrug resistance causes significant morbidity and mortality in patients with bacterial infections. Bacteroides thetaiotaomicron (Bth) is both a normal commensal in the gut and an opportunistic pathogen in other body sites. more...
Organism:
Bacteroides thetaiotaomicron VPI-5482
Type:
Expression profiling by high throughput sequencing
Platform:
GPL34028
64 Samples
Download data: TXT
Series
Accession:
GSE251676
ID:
200251676
4.

An expanded transcriptome atlas for Bacteroides thetaiotaomicron reveals a small RNA that modulates tetracycline sensitivity

(Submitter supplied) Gene expression plasticity allows bacteria to adapt to diverse environments, tie their metabolism to available nutrients, and cope with stress. This is particularly relevant in a niche as dynamic and hostile as the human intestinal tract, yet transcriptional networks remain largely unknown in gut Bacteroides spp. Here, we map transcriptional units and profile their expression levels in Bacteroides thetaiotaomicron over a suite of 15 defined experimental conditions that are relevant in vivo, such as variation of temperature, pH, and oxygen tension, exposure to antibiotic stress, and growth on simple carbohydrates or on host mucin-derived glycans. more...
Organism:
Bacteroides thetaiotaomicron
Type:
Expression profiling by high throughput sequencing
Platform:
GPL28094
40 Samples
Download data: CSV, XLSX
Series
Accession:
GSE234958
ID:
200234958
5.

Effect of supplementation of a minimal culture medium with inulin, corn fiber and pectin, compared with a glucose condition, on the gene expression of a set of bacteria of the intestinal microbiota

(Submitter supplied) The aim of this RNA-sequencing study is to measure differential gene expression in 4 intestinal bacteria (Bacteroides xylanisolvens, Bacteroides thetaiotaomicron, Subdoligranulum variabile and Roseburia intestinalis). The data highlight the coordinated action of genes within the same locus involved in the degradation of complex carbohydrates. These loci are well characterized in Bacteroidetes species and referred to as polysaccharide utilization loci. more...
Organism:
Subdoligranulum variabile; Bacteroides thetaiotaomicron; Roseburia intestinalis; Bacteroides xylanisolvens
Type:
Expression profiling by high throughput sequencing
4 related Platforms
36 Samples
Download data: CSV
Series
Accession:
GSE237111
ID:
200237111
6.

New functions of pirin proteins and a 2-ketoglutarate: Ferredoxin oxidoreductase ortholog in Bacteroides fragilis metabolism and their impact on antimicrobial susceptibility to metronidazole and amixicile

(Submitter supplied) Genome expression study of Bacteroides fragilis strain 638R comparing a fur deletion mutant with the wild-type strain grown in minimal defined media with iron-replete or iron-limiting conditions following oxygen exposure. The construction of the fur mutant analyzed in this study was described in Robertson KP, Smith CJ, Gough AM, Rocha ER. Characterization of Bacteroides fragilis hemolysins and regulation and synergistic interactions of HlyA and HlyB. more...
Organism:
Bacteroides fragilis 638R
Type:
Expression profiling by array
Platform:
GPL15788
10 Samples
Download data: PAIR, TXT
Series
Accession:
GSE241676
ID:
200241676
7.

New functions of pirin proteins and a 2-ketoglutarate: Ferredoxin oxidoreductase ortholog in Bacteroides fragilis metabolism and their impact on antimicrobial susceptibility to metronidazole and amixicile

(Submitter supplied) Genome expression study of Bacteroides fragilis strain 638R comparing an fur deletion mutant with the wild-type strain grown in minimal defined media with iron-replete, iron-limiting, heme-replete and heme-limiting conditions. The construction of the fur mutant analyzed in this study was described in Robertson KP, Smith CJ, Gough AM, Rocha ER. Characterization of Bacteroides fragilis hemolysins and regulation and synergistic interactions of HlyA and HlyB. more...
Organism:
Bacteroides fragilis 638R
Type:
Expression profiling by array
Platform:
GPL15788
12 Samples
Download data: CALLS, PAIR, TXT
Series
Accession:
GSE241210
ID:
200241210
8.

Measuring the effect of deoxycholate on Bacteroides fragilis gene expression

(Submitter supplied) We used RNAseq as an approach to assess the B. fragilis strain p207 response to the bile salt, deoxycholic acid (DC). A 6min DC exposure dramatically remodeled the transcriptome with approximately 20% of transcripts exhibiting significant changes. Chaperones and efflux systems were among the most highly induced genes, while protein synthesis genes were strongly repressed by DC.
Organism:
Bacteroides fragilis
Type:
Expression profiling by high throughput sequencing
Platform:
GPL32937
9 Samples
Download data: TXT
Series
Accession:
GSE220692
ID:
200220692
9.

CRISPR-based screening of small RNA modulators of bile susceptibility in Bacteroides thetaiotaomicron

(Submitter supplied) Microbiota-centric interventions are limited by our incomplete understanding of the gene functions of many of its constituent species. This applies in particular to small RNAs (sRNAs), which are emerging as important regulators in microbiota species yet tend to be missed by traditional functional genomics approaches. Here, we establish CRISPR interference (CRISPRi) in the abundant microbiota member Bac-teroides thetaiotaomicron for genome-wide sRNA screens. more...
Organism:
Bacteroides thetaiotaomicron
Type:
Other
Platforms:
GPL33520 GPL28094
9 Samples
Download data: FASTA, TXT
Series
Accession:
GSE235620
ID:
200235620
10.

Role of OxyR and iron in gene regulation in Bacteroides thetaiotaomicron

(Submitter supplied) Role of OxyR and iron in gene regulation in Bacteroides thetaiotaomicron
Organism:
Bacteroides thetaiotaomicron
Type:
Expression profiling by high throughput sequencing
Platform:
GPL26901
16 Samples
Download data: XLSX
Series
Accession:
GSE169260
ID:
200169260
11.

Transcriptomic analysis of Bacteroides thetaiotaomicron inositol lipid knockout strains

(Submitter supplied) We report next generation sequencing RNA-seq data of human gut commensal Bacteroides thetaiotaomicron strains deficient in inositol lipid synthesis, including dBT_1522 (phosphoinositol dihydroceramide synthase knockout) and its wild-type background strain, and iSPTdBT_1526 (myo-inositol-phosphate synthase) knockout with its background strain ("iSPT," inducible serine palmitoyltransferase).
Organism:
Bacteroides thetaiotaomicron
Type:
Expression profiling by high throughput sequencing
Platform:
GPL31230
8 Samples
Download data: TXT
Series
Accession:
GSE193734
ID:
200193734
12.

RNA-seq of human gut Bacteroides xylanisolvens and Bacteroides ovatus isolates grown on mucin O-linked glycans compared to glucose

(Submitter supplied) Purpose: Examining the transcriptome of human gut bacteria (Bacteroides xylanisolvens/Bacteroides ovatus) that grow on mucin O-linked glycans as a sole carbon source Methods: Strains were grown on 10 mg/ml mucin O-linked glycans (MOG) or 5 mg/ml glucose as a sole carbon source in vitro. Fold change was calculated as MOG over glucose. Once cells reached an optical density corresponding to mid-log phase growth, RNA was isolated and rRNA depleted. more...
Organism:
Bacteroides ovatus; Bacteroides xylanisolvens
Type:
Expression profiling by high throughput sequencing
Platforms:
GPL28983 GPL21072
24 Samples
Download data: XLSX
Series
Accession:
GSE155869
ID:
200155869
13.

Next generation sequencing (NGS) allows identification of differentially regulated genes during Bacteroides growth on xylose:arabinose and insoluble wheat arabinoxylan

(Submitter supplied) Purpose: Identify differentially regulated genes in three Bacteroides species (B. intestinalis, B. cellulosylitycus, and B. oleiciplenus) under xylose:arabinose growth compared to insoluble wheat arabinoxylan Methods: Bacterial mRNA profiles of mid-log cultures were generated by deep sequencing using Illumina 4000, in duplicates. The sequences were trimmed based on quality scores using Trimmomatic.
Organism:
Bacteroides intestinalis; Bacteroides oleiciplenus; Bacteroides cellulosilyticus
Type:
Expression profiling by high throughput sequencing
Platforms:
GPL29416 GPL29414 GPL29415
12 Samples
Download data: CSV
Series
Accession:
GSE161471
ID:
200161471
14.

RNA-seq of human gut bacterial isolates grown on seaweed polysaccharides

(Submitter supplied) Purpose: Examining the transcriptome of human gut bacteria that grow on seaweed polysaccharides as a sole carbon source Methods: Strains were grown on 5 mg/ml seaweed polysaccharides (carrageenan, agarose and/or poprhyran respective to strain) or galactose as a sole carbon source in vitro. Fold change was calculated as seaweed polysaccharide over galactose with n=2 biological replicates. Once cells reached an optical density corresponding to mid-log phase growth, RNA was isolated and rRNA depleted. more...
Organism:
Bacteroides thetaiotaomicron; Bacteroides xylanisolvens; Faecalicatena contorta; Faecalicatena fissicatena
Type:
Expression profiling by high throughput sequencing
4 related Platforms
24 Samples
Download data: XLSX
Series
Accession:
GSE149357
ID:
200149357
15.

High-resolution view at the coding transcriptome and noncoding RNAs of major gut microbe Bacteroides thetaiotaomicron

(Submitter supplied) Gram-negative, obligate anaerobic Bacteroides thetaiotaomicron is emerging as the model organism for gut microbiota research. Colonization of its host niche within the human colon depends to large parts on the extensive metabolic capacity encoded in the Bacteroides genome, but little is known about how its transcription is organized. Here, we transferred differential RNA-seq (dRNA-seq) to B. thetaiotaomicron type strain VPI-5482 to globally map transcription start sites (TSSs). more...
Organism:
Bacteroides thetaiotaomicron
Type:
Expression profiling by high throughput sequencing
Platform:
GPL28094
24 Samples
Download data: WIG, XLSX
Series
Accession:
GSE144492
ID:
200144492
16.

Improved bacterial RNA-seq by Cas9-based depletion of ribosomal RNA reads

(Submitter supplied) A major challenge for RNA-seq analysis of gene expression is to achieve sufficient coverage of informative non-ribosomal transcripts. In eukaryotic samples, this is typically achieved by selective oligo(dT)-priming of messenger RNAs to exclude ribosomal RNA (rRNA) during cDNA synthesis. However, this strategy is not compatible with prokaryotes in which functional transcripts are generally not polyadenylated. more...
Organism:
Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344; Bacteroides thetaiotaomicron VPI-5482
Type:
Expression profiling by high throughput sequencing
Platforms:
GPL28278 GPL20056
40 Samples
Download data: CSV, WIG
Series
Accession:
GSE147155
ID:
200147155
17.

Genome-wide RNA-seq of Bacteroides thetaiotaomicron VPI-5482 with Bacteroides phage challenge

(Submitter supplied) Purpose: Examining the transcriptome of Bacteroides thetaiotaomicron VPI-5482 challenged with Bacteroides phage to assess surface molecule expression changes Methods: Bacteroides thetaiotaomicron was grown in BPRM in vitro or Germ-Free mice were monocolonized with Bacteroides thetaiotaomicron and gavaged with ARB25 phage. Fold change was calculated as live phage versus heat-killed phage treated samples with n=3 biological replicates. more...
Organism:
Bacteroides thetaiotaomicron VPI-5482
Type:
Expression profiling by high throughput sequencing
Platforms:
GPL28279 GPL28278
36 Samples
Download data: XLSX
Series
Accession:
GSE147071
ID:
200147071
18.

Genome-wide RNA-seq of Bacteroides thetaiotaomicron VPI-5482 grown on ribose

(Submitter supplied) Purpose: Examining the transcriptome of Bacteroides thetaiotaomicron VPI-5482 grown on ribose to look at global changes in regulation in vitro on the defined monosaccharide, ribose as a sole carbon source. Methods: Bacteroides thetaiotaomicron was grown on 5 mg/ml ribose or glucose as a sole carbon source in vitro. Fold change was calculated as ribose over glucose with n=3 biological replicates. Once cells reached an optical density corresponding to mid-log phase growth (absorbance between 0.6-0.8), RNA was isolated and rRNA depleted. more...
Organism:
Bacteroides thetaiotaomicron
Type:
Expression profiling by high throughput sequencing
Platform:
GPL19723
6 Samples
Download data: TXT
Series
Accession:
GSE137571
ID:
200137571
19.

Elucidating BT4338 binding in Bacteroides thetaiotaomicron following 10 minutes of carbon starvation.

(Submitter supplied) Use ChIPseq to elucidate BT4338 binding in Bacteroides thetaiotaomicron following 10 minutes of carbon starvation.
Organism:
Bacteroides thetaiotaomicron
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL26901
6 Samples
Download data: BIGWIG
Series
Accession:
GSE134116
ID:
200134116
20.

Elucidating the BT4338 regulon

(Submitter supplied) RNAseq to define BT4338-dependent gene expression changes in B. thetaiotaomicron
Organism:
Bacteroides thetaiotaomicron
Type:
Expression profiling by high throughput sequencing
Platform:
GPL26901
12 Samples
Download data: XLSX
Series
Accession:
GSE134115
ID:
200134115

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