GEO DataSets

(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. 2006. 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) 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:

Butyrivibrio fibrisolvens; Ruminococcus flavefaciens; Piromyces communis; Pseudobacteroides cellulosolvens; Eudiplodinium maggii; Segatella bryantii; Acetivibrio clariflavus; uncultured Neocallimastigales; Bacteroides thetaiotaomicron; Fibrobacter succinogenes; Clostridium cellulovorans; Bifidobacterium adolescentis; Cellulomonas fimi; Neocallimastix frontalis; [Eubacterium] cellulosolvens; Lachnospira eligens; Ruminococcus sp.; Piromyces sp.; Roseburia intestinalis; Roseburia hominis; 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.; 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

Type:

Genome variation profiling by array

Platform:

GPL25777

6 Samples

Download data: TXT

(Submitter supplied) Comparison of transcriptional profile of wild-type and bmoR mutant strains of Bacteroides fragilis grown under anaerobic conditions and after exposure to atmospheric oxygen for 1 hour.

Organism:

Bacteroides fragilis

Type:

Expression profiling by array

Platform:

GPL24065

8 Samples

Download data: CEL, CHP

(Submitter supplied) Ruminants are the most efficient herbivorous animals to transform plant biomass into edible products, principally thanks to the rumen microbiota that produces a large array of enzymes responsible for the hydrolysis of plant cell wall polysaccharides. Several biotic and abiotic factors influence the efficiency of fiber degradation, which can ultimately impact the animal productivity and health. To provide more insight on mechanisms involved in the modulation of fibrolytic activity, a functional DNA microarray targeting genes coding for key enzymes involved in cellulose and hemicellulose degradation by rumen microbiota was designed. more...

Organism:

Ruminococcus flavefaciens; Limosilactobacillus fermentum; Piromyces communis; Pseudobacteroides cellulosolvens; Eudiplodinium maggii; Fibrobacter succinogenes subsp. succinogenes S85; Segatella bryantii; Acetivibrio clariflavus; Bacteroides thetaiotaomicron; Fibrobacter succinogenes; Xylanibacter ruminicola; Clostridium acetobutylicum; Clostridium cellulovorans; Bifidobacterium adolescentis; Cellulomonas fimi; Neocallimastix frontalis; Bacteroides ovatus; [Eubacterium] cellulosolvens; Bacteroides sp.; Lachnospira eligens; Ruminococcus sp.; Piromyces sp.; Roseburia intestinalis; Butyrivibrio hungatei; Roseburia hominis; bovine gut metagenome; Bacteroides xylanisolvens XB1A; Orpinomyces sp.; Bacteroides fragilis; Ruminococcus albus; Enterococcus faecium; Acetivibrio thermocellus; Clostridium beijerinckii; Levilactobacillus brevis; Fibrobacter intestinalis; Epidinium caudatum; Polyplastron multivesiculatum; Orpinomyces joyonii; Piromyces rhizinflatus; Piromyces sp. 'equi'; Epidinium ecaudatum; Bacteroides xylanisolvens; Cellulosilyticum ruminicola; Ruminococcus champanellensis; Butyrivibrio fibrisolvens; Selenomonas ruminantium; Lactococcus lactis; Clostridioides difficile; Ruminiclostridium cellulolyticum; Cellulomonas flavigena; Neocallimastix patriciarum; Bifidobacterium animalis; Agathobacter rectalis; Enterobacter sp.; Escherichia coli K-12; Pseudobutyrivibrio xylanivorans; Bifidobacterium longum; uncultured Neocallimastigales

Type:

Expression profiling by array; Other

Platform:

GPL24327

14 Samples

Download data: TXT

(Submitter supplied) The phylum Bacteroidetes is a major component of the human gut microbiota which has a broad impact on the development and physiology of its host, and a potential role in a wide range of disease syndromes1-3. The predominance of Bacteroidetes and the genus Bacteroides in the distal gut is due in large part to the expansion of paralogous gene clusters, termed Polysaccharide Utilization Loci (PULs), dedicated to the uptake and catabolism of host derived and dietary polysaccharides4,5. more...

Organism:

Bacteroides fragilis 638R

Type:

Expression profiling by array; Third-party reanalysis

Platform:

GPL15788

4 Samples

Download data: CALLS, PAIR, TXT

(Submitter supplied) The phylum Bacteroidetes is a major component of the human gut microbiota which has a broad impact on the development and physiology of its host, and a potential role in a wide range of disease syndromes. The predominance of Bacteroidetes and the genus Bacteroides in the distal gut is due in large part to the expansion of paralogous gene clusters, termed Polysaccharide Utilization Loci (PULs), dedicated to the uptake and catabolism of host derived and dietary polysaccharides. more...

Organism:

Bacteroides fragilis 638R

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21110

2 Samples

Download data: WIG

(Submitter supplied) The human gut microbe Bacteroides fragilis can alter the expression of its surface molecules such as capsular polysaccharides and SusC/SusD family outer membrane proteins through the reversible DNA inversions.　We have revealed that the outer membrane vesicle (OMV) formation in B. fragilis is regulated by BF2766 (tyrosine recombinase)-mediated DNA inversions at two distantly located promoter regions previously designated as class IV regions. more...

Organism:

Bacteroides fragilis YCH46; Bacteroides fragilis

Type:

Expression profiling by array

Platform:

GPL13213

4 Samples

Download data: CALLS, PAIR

(Submitter supplied) Analysis of Clostridium difficile (Cd) from the cecal contents of germ-free mice or Bacteroides thetaiotaomicron (Bt)-monocolonized mice on a standard, polysaccharide rich diet or polysaccharide deficient diet 5 days after infection. Results identify genes that are involved in the Cd response to diet, in vivo colonization and in interactions with Bt.

Organism:

Bacteroides thetaiotaomicron; Clostridioides difficile; Bacteroides fragilis NCTC 9343; Clostridioides difficile 630

Type:

Expression profiling by array

Platform:

GPL19121

20 Samples

Download data: CEL

(Submitter supplied) Compare BF638R gene expression during growth in vivo in a rat tissue cage/artificial abscess model, to cells grown in vitro in minimal defined media with either glucose or mucin glycans as sole carbon/energy source

Organism:

Bacteroides fragilis 638R

Type:

Expression profiling by array

Platform:

GPL15788

11 Samples

Download data: CALLS, PAIR

(Submitter supplied) 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.

Organism:

Bacteroides fragilis; Escherichia coli; Blautia coccoides; [Clostridium] leptum; uncultured bacterium; Lactobacillus acidophilus; human gut metagenome

Type:

Expression profiling by array

Platform:

GPL16731

4 Samples

Download data: TXT

(Submitter supplied) Genome expression study of Bacteroides fragilis strain 638R comparing an ecfO null mutant with an empty vector to a reo (anti-ecfO) null mutant containing the ecfO gene on a plasmid under the control of an IPTG inducible promoter.

Organism:

Bacteroides fragilis 638R

Type:

Expression profiling by array

Platform:

GPL15788

7 Samples

Download data: CALLS, PAIR

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Bacteroides fragilis NCTC 9343; Bacteroides fragilis 638R

Type:

Expression profiling by array

Platforms:

GPL15187 GPL15188

6 Samples

Download data: CALLS, PAIR

(Submitter supplied) Genome expression study of Bacteroides fragilis strain 638R comparing a EcfO/anti-EcfO null mutant with an empty vector to a EcfO/anti-EcfO null mutant containing the EcfO gene on a plasmid under the control of a maltose inducible promoter.

Organism:

Bacteroides fragilis 638R

Type:

Expression profiling by array

Platform:

GPL15188

2 Samples

Download data: CALLS, PAIR

(Submitter supplied) Genome expression study of Bacteroides fragilis strain 638R comparing a EcfO null mutant with an empty vector to a anti-EcfO null mutant containing the EcfO gene on a plasmid under the control of an IPTG inducible promoter.

Organism:

Bacteroides fragilis 638R

Type:

Expression profiling by array

Platform:

GPL15188

2 Samples

Download data: CALLS, PAIR

(Submitter supplied) Genome expression study of Bacteroides fragilis ATCC25285 strain containing the EcfO gene constitutively expressed from plasmid pFD340

Organism:

Bacteroides fragilis NCTC 9343

Type:

Expression profiling by array

Platform:

GPL15187

2 Samples

Download data: CALLS, PAIR

(Submitter supplied) The factors that govern the retention and abundance of specific microbial lineages within a developing intestinal microbiota remain poorly defined. Human milk oligosaccharides consumed by nursing infnats pass undigested to the distal gut where they may be consumed by microbes. We investigated the transcriptional response of Bacterides fragilis, a prominent gut resident, to the presence of HMOs.

Organism:

Bacteroides fragilis NCTC 9343

Type:

Expression profiling by array

Platform:

GPL14584

4 Samples

Download data: CEL

(Submitter supplied) Comparison of transcriptional profiles of the wild-type (WT) and the phoB-mutant strain in B. fragilis strain YCH46 during phosphate (Pi) starvation.

Organism:

Bacteroides fragilis YCH46; Bacteroides fragilis

Type:

Expression profiling by array

Platform:

GPL13213

4 Samples

Download data: CALLS, PAIR

(Submitter supplied) Investigation of whole genome gene expression level changes in a Bacteroides fragilis NCTC 9343 delta-gmd-fcl delta-fkp mutant strain and a Bacteroides fragilis NCTC 9343 delta-lfg mutant strain, each as compared to the wild-type strain. The mutations engineered into these strains interfere with B. fragilis protein glycosylation.

Organism:

Bacteroides fragilis NCTC 9343

Type:

Expression profiling by array

Platform:

GPL7163

9 Samples

Download data: CALLS, PAIR