GEO DataSets

(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) Analysis of B. thetaiotaomicron trans-envelope signaling mutants in ECF-sigma factors, anti-sigma factors and SusC-like transporters.

Organism:

Bacteroides thetaiotaomicron; Bacteroides thetaiotaomicron VPI-5482; Bifidobacterium longum

Type:

Expression profiling by array

Platform:

GPL1821

22 Samples

Download data: CEL

(Submitter supplied) Dietary fiber degradation is a key function of the human gut microbiota. The aim of this study was to increase our knowledge on the degradation of plant cell wall polysaccharide degradation by a prominent human gut bacterial species, Bacteroides xylanisolvens. The transcriptome analysis of B. xylanisolvens XB1AT revealed the existence of six and two genomic loci dedicated to the degradation of pectins and xylan, respectively. more...

Organism:

Bacteroides xylanisolvens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21072

24 Samples

Download data: TXT

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

Organism:

Bacteroides thetaiotaomicron; Lachnospira eligens; Phocaeicola vulgatus; Bifidobacterium longum; Parabacteroides distasonis; Methanobrevibacter smithii; Agathobacter rectalis

Type:

Expression profiling by array

Platforms:

GPL1821 GPL7006

48 Samples

Download data: CEL

(Submitter supplied) Bacteroides thetaiotaomicron was grown and transcriptionally profiled on a number of different host mucosal glycans and their component mono- and disaccharides.

Organism:

Bacteroides thetaiotaomicron; Lachnospira eligens; Phocaeicola vulgatus; Methanobrevibacter smithii; Parabacteroides distasonis; Agathobacter rectalis

Type:

Expression profiling by array

Platform:

GPL7006

18 Samples

Download data: CEL

(Submitter supplied) Growth of isogenic parent ('tdk strain'), 5xECF-sigma factor mutant and complemented mutant strain in the cecum of NMRI inbred mice fed a glycan-restricted, 'simple sugar' diet (35% each glucose and sucrose). Bacteria were collected from mouse distal gut 10 days after colonization.

Organism:

Bacteroides thetaiotaomicron; Bifidobacterium longum

Type:

Expression profiling by array

Platform:

GPL1821

9 Samples

Download data: CEL

(Submitter supplied) Gene expression profiles of Bacteroides thetaiotaomicron in vitro during growth on host mucosal polysaccharides as sole carbon sources. All substrates in this series are derived from porcine gastric mucin and include mucin O-glycans and glycosaminoglycans.

Organism:

Bacteroides thetaiotaomicron; Bifidobacterium longum

Type:

Expression profiling by array

Platform:

GPL1821

21 Samples

Download data: CEL

(Submitter supplied) The human gut microbiota is an important metabolic organ, yet little is known about how its individual species interact, establish dominant positions, and respond to changes in environmental factors such as diet. In this study, gnotobiotic mice were colonized with an artificial microbiota comprising 12 sequenced human gut bacterial species and fed oscillating diets of disparate composition. Rapid, reproducible, and reversible changes in the structure of this assemblage were observed. more...

Organism:

Bacteria; Bacteroides cellulosilyticus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL17330 GPL17468

116 Samples

Download data: TXT

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

Organism:

Dorea longicatena DSM 13814; [Clostridium] scindens ATCC 35704; Faecalibacterium prausnitzii M21/2; Collinsella aerofaciens ATCC 25986; Thomasclavelia spiroformis DSM 1552; Bacteroides cellulosilyticus; Bacteroides sp. WH2; Bacteria; Bacteroides ovatus ATCC 8483; Bacteroides uniformis ATCC 8492; Phocaeicola vulgatus ATCC 8482; Parabacteroides distasonis ATCC 8503; Bacteroides thetaiotaomicron VPI-5482; Blautia obeum ATCC 29174; [Ruminococcus] torques ATCC 27756; Bacteroides caccae ATCC 43185; Agathobacter rectalis ATCC 33656

Type:

Expression profiling by high throughput sequencing; Other; Expression profiling by array

5 related Platforms

895 Samples

Download data: CEL, CHP, TXT

(Submitter supplied) The human gut microbiota is an important metabolic organ, yet little is known about how its individual species interact, establish dominant positions, and respond to changes in environmental factors such as diet. In this study, gnotobiotic mice were colonized with an artificial microbiota comprising 12 sequenced human gut bacterial species and fed oscillating diets of disparate composition. Rapid, reproducible, and reversible changes in the structure of this assemblage were observed. more...

Organism:

Bacteroides sp. WH2; Bacteroides uniformis ATCC 8492; Phocaeicola vulgatus ATCC 8482; Parabacteroides distasonis ATCC 8503; Blautia obeum ATCC 29174; [Clostridium] scindens ATCC 35704; Bacteroides thetaiotaomicron VPI-5482; [Ruminococcus] torques ATCC 27756; Bacteroides caccae ATCC 43185; Thomasclavelia spiroformis DSM 1552; Agathobacter rectalis ATCC 33656; Dorea longicatena DSM 13814; Bacteroides ovatus ATCC 8483; Faecalibacterium prausnitzii M21/2; Collinsella aerofaciens ATCC 25986

Type:

Expression profiling by array

Platform:

GPL9803

168 Samples

Download data: CEL, CHP

(Submitter supplied) The human gut microbiota is an important metabolic organ, yet little is known about how its individual species interact, establish dominant positions, and respond to changes in environmental factors such as diet. In this study, gnotobiotic mice were colonized with an artificial microbiota comprising 12 sequenced human gut bacterial species and fed oscillating diets of disparate composition. Rapid, reproducible, and reversible changes in the structure of this assemblage were observed. more...

Organism:

Bacteria

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL17330 GPL17329 GPL11535

611 Samples

Download data: TXT

(Submitter supplied) We used Affymetrix GeneChips to determine the physiological differences between biofilm and planktonic cells of Bacteroides thetaiotaomicron strain VPI-5482 (ATCC 29148) by comparing gene expression. For this purpose, B. thetaiotaomicron cells were grown in sterile, continuous flow bioreactors fed with tryptone, yeast extract, glucose (TYG) medium. The bioreactors were controlled at a temperature of 37C using a water jacket and a recirculating water heater. more...

Organism:

Phocaeicola vulgatus; Methanobrevibacter smithii; Bacteroides thetaiotaomicron VPI-5482; Parabacteroides distasonis; Bifidobacterium longum; Bacteroides thetaiotaomicron; Lachnospira eligens; Agathobacter rectalis

Type:

Expression profiling by array

Platforms:

GPL1821 GPL7006

12 Samples

Download data: CEL

(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

(Submitter supplied) Laser captured cecal epithelium from gnotobiotic mice colonized with B. thetaiotaomicron or B. longum (mono-association) or B. thetaiotaomicron bi-association with B. longum. Samples were derived from 10d colonizations of NMRI mice fed a standard-chow polysaccharide rich (PR) diet. Keywords: Germ-free vs. Mono-associations or Bi-association, in vivo

Organism:

Mus musculus; Homo sapiens

Type:

Expression profiling by array

Platforms:

GPL1261 GPL1981

16 Samples

Download data

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

Organism:

Bacteroides thetaiotaomicron; Bifidobacterium longum

Type:

Expression profiling by array

Platform:

GPL1821

34 Samples

Download data

(Submitter supplied) Genome wide transcriptional comparison of B. thetaiotaomicron mono-association vs. B. thetaiotaomicron bi-association with B.animalis or L. casei. Cecal populations from 20d colonizations with B6 gnotobiotic mice fed a standard-chow polysaccharide rich (PR) diet (n=5 samples/group) were profiled. Keywords: Mono-association vs. Bi-association, in vivo

Organism:

Bacteroides thetaiotaomicron; Bifidobacterium longum

Type:

Expression profiling by array

Platform:

GPL1821

9 Samples

Download data

(Submitter supplied) Genome wide transcriptional comparison of B. thetaiotaomicron mono-association vs. B. thetaiotaomicron bi-association with B. longum. Cecal populations from 10d colonizations with b6 gnotobiotic mice fed a standard-chow polysaccharide rich (PR) diet (n=5 samples/group) were profiled. Keywords: Mono-association vs. Bi-association, in vivo

Organism:

Bacteroides thetaiotaomicron; Bifidobacterium longum

Type:

Expression profiling by array

Platform:

GPL1821

10 Samples

Download data

(Submitter supplied) Genome wide transcriptional comparison of B. thetaiotaomicron or B. longum mono-association vs. B. thetaiotaomicron bi-association with B. longum. Cecal populations from 10d colonizations with NMRI gnotobiotic mice fed a standard-chow polysaccharide rich (PR) diet (n=5 samples/group) were profiled. Keywords: Mono-association vs. Bi-association, in vivo

Organism:

Bacteroides thetaiotaomicron; Bifidobacterium longum

Type:

Expression profiling by array

Platform:

GPL1821

15 Samples

Download data

(Submitter supplied) Bacteria of the genera Xylanibacter and Segatella are one of the most dominant groups in the rumen microbiota. They are characterized by the ability to utilize different hemicelluloses and pectin of plant cell-wall as well as plant energy storage polysaccharides. The degradation is possible with the use of cell envelope bound multiprotein apparatuses coded in polysaccharide utilization loci (PULs), which have been shown to be substrate specific. more...

Organism:

Segatella bryantii; Xylanibacter ruminicola

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL34343 GPL34344 GPL34345

78 Samples

Download data: TXT