GEO DataSets

(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

(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

(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:

Bacteroides xylanisolvens; Subdoligranulum variabile; Bacteroides thetaiotaomicron; Roseburia intestinalis

Type:

Expression profiling by high throughput sequencing

4 related Platforms

36 Samples

Download data: CSV

(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

(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

(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

(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

(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

(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

(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

(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 cellulosilyticus; Bacteroides intestinalis; Bacteroides oleiciplenus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL29416 GPL29415 GPL29414

12 Samples

Download data: CSV

(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:

Faecalicatena contorta; Faecalicatena fissicatena; Bacteroides xylanisolvens; Bacteroides thetaiotaomicron

Type:

Expression profiling by high throughput sequencing

4 related Platforms

24 Samples

Download data: XLSX

(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

(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

(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

(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

(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

(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

(Submitter supplied) In this study, we studied the fibrolytic potential of the rumen microbiota in the rumen of 6 lambs separated from their dams from 12h of age and artificially fed with milk replacer (MR) and starter feed from d8, in absence (3 lambs) or presence (3 lambs) of a combination of the live yeast Saccharomyces cerevisiae CNCM I-1077 and selected yeast metabolites. The fibrolytic potential of the rumen microbiota of the lambs at 56 days of age was analyzed with a DNA microarray (FibroChip) targeting genes coding for 8 glycoside hydrolase (GH) families.

Organism:

Selenomonas ruminantium; Lactococcus lactis; Clostridioides difficile; Ruminiclostridium cellulolyticum; Limosilactobacillus fermentum; Cellulomonas flavigena; Neocallimastix patriciarum; Bifidobacterium animalis; Agathobacter rectalis; Enterobacter sp.; Orpinomyces joyonii; Piromyces rhizinflatus; Piromyces sp. 'equi'; Pseudobutyrivibrio xylanivorans; Bifidobacterium longum; Butyrivibrio fibrisolvens; Ruminococcus flavefaciens; Piromyces communis; Pseudobacteroides cellulosolvens; Eudiplodinium maggii; Segatella bryantii; Acetivibrio clariflavus; uncultured Neocallimastigales; Bacteroides fragilis; Xylanibacter ruminicola; Ruminococcus albus; Enterococcus faecium; Clostridium acetobutylicum; Acetivibrio thermocellus; Clostridium beijerinckii; Levilactobacillus brevis; Microbiota; Bacteroides ovatus; Fibrobacter intestinalis; Bacteroides sp.; Epidinium caudatum; Polyplastron multivesiculatum; Butyrivibrio hungatei; Epidinium ecaudatum; Bacteroides xylanisolvens; Cellulosilyticum ruminicola; Ruminococcus champanellensis; Orpinomyces sp.; Bacteroides thetaiotaomicron; Fibrobacter succinogenes; Clostridium cellulovorans; Bifidobacterium adolescentis; Cellulomonas fimi; Neocallimastix frontalis; [Eubacterium] cellulosolvens; Lachnospira eligens; Ruminococcus sp.; Piromyces sp.; Roseburia intestinalis; Roseburia hominis

Type:

Genome variation profiling by array

Platform:

GPL25777

6 Samples

Download data: TXT

(Submitter supplied) The goal of this project was to sequence the transcriptome of wild type Bacteroides thetaiotaomicron VPI-5482 grown in minimal media with either glucose or bovine alpha 1 acid glycoprotein (AAGP) as the sole carbon source. Using these data we could then compare relative gene expression levels under each condition and identify genes specifically upregulated during growth on AAGP. Analysis of the spent media indicated that only the N-glycan component of the AAGP had been used by the cells to support growth.

Organism:

Bacteroides thetaiotaomicron VPI-5482

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26482

6 Samples

Download data: TXT