GEO DataSets

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

Organism:

Bacteroides cellulosilyticus; Bacteroides sp. WH2; Bacteria; Bacteroides ovatus ATCC 8483; Bacteroides uniformis ATCC 8492; Phocaeicola vulgatus ATCC 8482; Parabacteroides distasonis ATCC 8503; Dorea longicatena DSM 13814; [Clostridium] scindens ATCC 35704; Faecalibacterium prausnitzii M21/2; Collinsella aerofaciens ATCC 25986; Thomasclavelia spiroformis DSM 1552; 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:

Bacteria; Bacteroides cellulosilyticus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL17330 GPL17468

116 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:

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; Bacteroides sp. WH2; Bacteroides uniformis ATCC 8492; Phocaeicola vulgatus ATCC 8482; Parabacteroides distasonis ATCC 8503; 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) 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) 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:

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

Type:

Expression profiling by array

Platform:

GPL11169

12 Samples

Download data: CEL

(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 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) 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) Analysis of Bacteroides thetaiotaomicron (BT) from the ceca of ex-germ free Fut2+ or Fut2- mice on polysaccharide rich or glucose rich polysaccharide deficient diet. BT is involved in the breakdown of plant polysaccharides and is also efficiently utilizes host glycans. BT-colonized mice represent a human gut ecosystem model. Results identify genes that may endow flexibility in adapting to dietary changes by mucosal foraging depending on host fucosylation status

Organism:

Bacteroides thetaiotaomicron; Bifidobacterium longum

Type:

Expression profiling by array

Platform:

GPL1821

18 Samples

Download data: CEL

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

Organism:

Mus musculus; Bacteroides thetaiotaomicron VPI-5482; Bacteroides caccae ATCC 43185; Collinsella aerofaciens ATCC 25986; Escherichia coli str. K-12 substr. MG1655; Agathobacter rectalis ATCC 33656; [Clostridium] symbiosum; Bacteroides ovatus ATCC 8483; Desulfovibrio piger GOR1; Marvinbryantia formatexigens DSM 14469

Type:

Expression profiling by high throughput sequencing; Other

7 related Platforms

135 Samples

Download data: TXT

(Submitter supplied) Sulfate-reducing bacteria (SRB) colonize the guts of ~50% of humans. We used genome-wide transposon mutagenesis and insertion-site sequencing (INSeq), RNA-Seq, plus mass spectrometry to characterize genetic and environmental factors that impact the niche of Desulfovibrio piger, the most common SRB in a surveyed cohort of healthy USA adults. Gnotobiotic mice were colonized with an assemblage of sequenced human gut bacterial species with or without D. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

8 Samples

Download data: TXT

(Submitter supplied) Sulfate-reducing bacteria (SRB) colonize the guts of ~50% of humans and produce H2S, a signaling molecule with numerous host effects. We used genome-wide transposon mutagenesis and insertion-site sequencing (INSeq), RNA-Seq, plus mass spectrometry to characterize genetic and environmental factors that impact the niche of Desulfovibrio piger, the most common SRB in a surveyed cohort of healthy USA adults. more...

Organism:

[Clostridium] symbiosum; Bacteroides thetaiotaomicron VPI-5482; Bacteroides ovatus ATCC 8483; Bacteroides caccae ATCC 43185; Agathobacter rectalis ATCC 33656; Desulfovibrio piger GOR1; Collinsella aerofaciens ATCC 25986; Marvinbryantia formatexigens DSM 14469; Escherichia coli str. K-12 substr. MG1655

Type:

Other

6 related Platforms

114 Samples

Download data: TXT

(Submitter supplied) Sulfate-reducing bacteria (SRB) colonize the guts of ~50% of humans and produce H2S, a signaling molecule with numerous host effects. We used genome-wide transposon mutagenesis and insertion-site sequencing (INSeq), RNA-Seq, plus mass spectrometry to characterize genetic and environmental factors that impact the niche of Desulfovibrio piger, the most common SRB in a surveyed cohort of healthy USA adults. more...

Organism:

Collinsella aerofaciens ATCC 25986; Escherichia coli str. K-12 substr. MG1655; [Clostridium] symbiosum; Bacteroides thetaiotaomicron VPI-5482; Bacteroides ovatus ATCC 8483; Bacteroides caccae ATCC 43185; Agathobacter rectalis ATCC 33656; Desulfovibrio piger GOR1; Marvinbryantia formatexigens DSM 14469

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17383

13 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

Download data

(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:

Bacteroides thetaiotaomicron; Bifidobacterium longum

Type:

Expression profiling by array

Platform:

GPL1821

12 Samples

Download data

(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