GEO DataSets

(Submitter supplied) Approximately 15% of US adults have circulating levels of uric acid above its solubility limit, which is causally linked to the inflammatory disease gout. In most mammals, uric acid elimination is facilitated by the enzyme uricase. However, human uricase is a pseudogene, having been inactivated early in hominid evolution. Though it has long been known that a substantial amount of uric acid is eliminated in the gut, the role of the gut microbiota in hyperuricemia has not been studied. more...

Organism:

Clostridium sporogenes ATCC 15579; [Clostridium] saccharolyticum WM1; Collinsella aerofaciens ATCC 25986

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL32367 GPL32369 GPL32368

18 Samples

Download data: TXT

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

Organism:

Bacteroides cellulosilyticus; Bacteroides sp. WH2; 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; 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; 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; 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) This SuperSeries is composed of the SubSeries listed below.

Organism:

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

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 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; Marvinbryantia formatexigens DSM 14469; 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

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:

[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; Collinsella aerofaciens ATCC 25986; Escherichia coli str. K-12 substr. MG1655

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17383

13 Samples

Download data: TXT

(Submitter supplied) The interrelationships between our diets and the structure and operations of our gut microbial communities are poorly understood. A model microbial community of ten sequenced human gut bacteria was introduced into gnotobiotic mice and changes in the abundance of each species were measured in response to randomized perturbations of four defined ingredients in the host diet. From the responses, we developed a statistical model that predicted over 50% of the variation in species abundance in response to the diet perturbations and were able to identify which factors in the diet best explained the changes seen for each community member. more...

Organism:

Bacteria; [Clostridium] symbiosum; Bacteroides thetaiotaomicron VPI-5482; Bacteroides ovatus ATCC 8483; Bacteroides caccae ATCC 43185; Agathobacter rectalis ATCC 33656; Desulfovibrio piger GOR1; Blautia hydrogenotrophica DSM 10507; Escherichia coli str. K-12 substr. MG1655; Collinsella aerofaciens ATCC 25986; Marvinbryantia formatexigens DSM 14469

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL11535

490 Samples

Download data: TXT

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

Organism:

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

Type:

Expression profiling by array

Platforms:

GPL9803 GPL7006

39 Samples

Download data: CEL

(Submitter supplied) Symbiotic bacteria inhabiting the distal human gut have evolved under intense pressure to utilize complex carbohydrates, predominantly plant cell wall glycans abundant in our diets. These substrates are recalcitrant to depolymerization by digestive enzymes encoded in the human genome, but are efficiently targeted by some of the ~103-104 bacterial species that inhabit this niche. These species augment our comparatively narrow carbohydrate digestive capacity by unlocking otherwise unusable sugars and fermenting them into host-absorbable forms, such as short-chain fatty acids. more...

Organism:

Bacteroides sp. WH2; 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; Parabacteroides distasonis ATCC 8503; Agathobacter rectalis ATCC 33656; Bacteroides ovatus; Bacteroides ovatus ATCC 8483; Bacteroides uniformis ATCC 8492; Bacteroides caccae ATCC 43185; Phocaeicola vulgatus ATCC 8482

Type:

Expression profiling by array

Platform:

GPL9803

25 Samples

Download data: CEL

(Submitter supplied) In situ oligonucleotide synthesis using photolithography.

Organism:

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

4 Series

193 Samples

Download data: CDF, TXT