GEO DataSets

(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:

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

Type:

Genome variation profiling by array

Platform:

GPL25777

6 Samples

Download data: TXT

(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:

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.; Ruminococcus flavefaciens; Limosilactobacillus fermentum; Piromyces communis; Pseudobacteroides cellulosolvens; Eudiplodinium maggii; Fibrobacter succinogenes subsp. succinogenes S85; Segatella bryantii; Acetivibrio clariflavus; 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; 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

Type:

Expression profiling by array; Other

Platform:

GPL24327

14 Samples

Download data: TXT

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

Organism:

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

Type:

Expression profiling by high throughput sequencing; Expression profiling by array

Platforms:

GPL7006 GPL19723

22 Samples

Download data: CEL, TXT

(Submitter supplied) Comparisons of gnotobiotic Rag1-/- mice, with and without subcutaneous 260.8 hybridomas, disclosed that this IgA does not affect B. thetaiotaomicron population density or suppress 260.8 epitope production but does affect bacterial gene expression in ways that are emblematic of a diminished host innate immune response.

Organism:

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

Type:

Expression profiling by array

Platform:

GPL7006

12 Samples

Download data: CEL

(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:

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

Type:

Expression profiling by array

Platforms:

GPL7006 GPL1821

12 Samples

Download data: CEL

(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:

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) 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 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) Background: Inflammatory bowel diseases (IBD) may be caused in part by aberrant immune responses to commensal intestinal microbes including Bacteroides thetaiotaomicron (B.theta). Healthy, germ-free HLA-B27 transgenic (Tg) rats develop chronic colitis when colonized with complex gut commensal bacteria whereas non-transgenic (nTg) rats remain disease-free. However, the role of B.theta, a well-characterized anaerobic commensal bacterium, in causing disease in Tg rats is unknown nor is much known about how microbes respond to host inflammation. more...

Organism:

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

Type:

Expression profiling by array

Platform:

GPL7006

6 Samples

Download data: CEL

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

Organism:

Phocaeicola vulgatus; Methanobrevibacter smithii; Methanobrevibacter smithii ATCC 35061; Bacteroides thetaiotaomicron; Agathobacter rectalis; Parabacteroides distasonis; Lachnospira eligens

Type:

Expression profiling by array; Expression profiling by high throughput sequencing

Platforms:

GPL11216 GPL11215 GPL7006

80 Samples

Download data: CEL, 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:

Blautia hydrogenotrophica DSM 10507; Escherichia coli str. K-12 substr. MG1655; Bacteria; [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

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; Methanobrevibacter smithii; Agathobacter rectalis; Bacteroides sp. WH2; 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

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; Bacteroides ovatus; Bacteroides ovatus ATCC 8483; Bacteroides uniformis ATCC 8492; Bacteroides caccae ATCC 43185; Phocaeicola vulgatus ATCC 8482; 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

Type:

Expression profiling by array

Platform:

GPL9803

25 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:

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

Type:

Expression profiling by array

Platform:

GPL7006

14 Samples

Download data: CEL

(Submitter supplied) RNA-sequencing is a powerful tool for exploring expression profiles of microbial species that does not require the production of a custom genechip. We used microarrays to compare our quantitative RNA-sequencing method to the standard expression quantification methods

Organism:

Bacteroides thetaiotaomicron; Lachnospira eligens; Methanobrevibacter smithii; Agathobacter rectalis; Methanobrevibacter smithii ATCC 35061; Phocaeicola vulgatus; Parabacteroides distasonis

Type:

Expression profiling by array

Platform:

GPL7006

4 Samples

Download data: CEL

(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) The adult human gut microbial community is typically dominated by two bacterial phyla (divisions), the Firmicutes and the Bacteroidetes. Little is known about the factors that govern the interactions between their members. Here we examine the niches of representatives of both phyla in vivo. Finished genome sequences were generated from E. rectale and E. eligens, which belong to Clostridium Cluster XIVa, one of the most common gut Firmicute clades. more...

Organism:

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

Type:

Expression profiling by array

Platform:

GPL7006

16 Samples

Download data: CEL

(Submitter supplied) The adult human gut microbial community is typically dominated by two bacterial phyla (divisions), the Firmicutes and the Bacteroidetes. Little is known about the factors that govern the interactions between their members. Here we examine the niches of representatives of both phyla in vivo. Finished genome sequences were generated from E. rectale and E. eligens, which belong to Clostridium Cluster XIVa, one of the most common gut Firmicute clades. more...

Organism:

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

Type:

Expression profiling by array

Platform:

GPL7006

15 Samples

Download data: CEL