GEO DataSets

(Submitter supplied) The large-scale application of genomic and metagenomic sequencing technologies has yielded a number of insights about the metabolic potential of symbiotic human gut microbes. Bacteria that colonize the mucosal layer that overlies the gut epithelium have access to highly-sulfated polysaccharides (i.e., mucin oligosaccharides and glycosaminoglycans), which they could potentially forage as nutrient sources. more...

Organism:

Bacteroides thetaiotaomicron; Streptococcus thermophilus; Lacticaseibacillus casei; Bifidobacterium animalis; Agathobacter rectalis; Bifidobacterium longum; Lactobacillus delbrueckii

Type:

Expression profiling by array

Platform:

GPL11169

12 Samples

Download data: CEL

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

Organism:

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

Type:

Expression profiling by array

Platforms:

GPL7006 GPL1821

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:

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

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:

Bifidobacterium longum; Bacteroides thetaiotaomicron

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:

Bifidobacterium longum; Bacteroides thetaiotaomicron

Type:

Expression profiling by array

Platform:

GPL1821

21 Samples

Download data: CEL

(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:

Homo sapiens; Mus musculus

Type:

Expression profiling by array

Platforms:

GPL1981 GPL1261

16 Samples

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

Organism:

Bifidobacterium longum; Bacteroides thetaiotaomicron

Type:

Expression profiling by array

Platform:

GPL1821

34 Samples

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(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

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(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

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(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

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(Submitter supplied) Transcriptional profiling of Bacteroides thetaiotaomicron was performed on samples taken from (i) chemostat cultures (in vitro) and (ii) from the ceca of gnotobiotic monoassociated NMRI mice (in vivo). In vitro profiles were obtained from biological duplicate cultures taken at five timepoints from log to stationary phase in three types of media: (i) minimal media glucose (MM-G), (ii) minimal media maltotriose (MM-M), and (iii) rich media (TYG). more...

Organism:

Bacteroides thetaiotaomicron; Bifidobacterium longum

Type:

Expression profiling by array

Dataset:

GDS1849

Platform:

GPL1821

42 Samples

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Analysis of Bacteroides thetaiotaomicron (BT) from the ceca of mice on polysaccharide or simple sugar diets. BT is involved in the breakdown of plant polysaccharides. BT-colonized mice is a human gut ecosystem model. Results identify genes that may endow flexibility in adapting to dietary changes.

Organism:

Bacteroides thetaiotaomicron; Bifidobacterium longum

Type:

Expression profiling by array, count, 5 growth protocol, 2 protocol, 16 time sets

Platform:

GPL1821

Series:

GSE2231

42 Samples

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(Submitter supplied) The human gut microbiota is a metabolic organ whose cellular composition is determined by a dynamic process of selection and competition. To identify microbial genes required for establishment of human symbionts in the gut, we developed an approach (insertion-sequencing, or INSeq) based on a mutagenic transposon that allows capture of adjacent chromosomal DNA to define its genomic location. We used massively parallel sequencing to monitor the relative abundance of tens of thousands of transposon mutants of a saccharolytic human gut bacterium, Bacteroides thetaiotaomicron, as they established themselves in wild-type and immunodeficient gnotobiotic mice, in the presence or absence of other human gut commensals. more...

Organism:

Bacteroides thetaiotaomicron

Type:

Other

Platforms:

GPL9055 GPL9054

59 Samples

Download data: 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:

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:

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

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:

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

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) This SuperSeries is composed of the SubSeries listed below.

Organism:

Bacteroides thetaiotaomicron; Bifidobacterium longum

Type:

Expression profiling by array

Platform:

GPL1821

28 Samples

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(Submitter supplied) Gnotobiotic NMRI mice were colonized at birth with B. thetaiotaomicron. Mice were sacrificed at P17 or P30, cecal contents were harvested and used for transcriptional profiling. Keywords: developmental timepoints, in vivo

Organism:

Bifidobacterium longum; Bacteroides thetaiotaomicron

Type:

Expression profiling by array

Platform:

GPL1821

12 Samples

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(Submitter supplied) Genome wide trascriptional comparison of B. thetaiotaomicron wild-type vs. an isogenic mutant (BT3172::pGERM). Cecal populations of wt or BT3172::pGERM monoassociated 10d with NMRI gnotobiotic mice fed a standard-chow polysaccharide rich (PR) diet (n=5 samples/group) were profiled. Keywords: Wild-type versus Knockout, in vivo

Organism:

Bacteroides thetaiotaomicron; Bifidobacterium longum

Type:

Expression profiling by array

Platform:

GPL1821

23 Samples

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