GEO DataSets

(Submitter supplied) The aim of this RNA-sequencing study is to measure differential gene expression in 4 intestinal bacteria (Bacteroides xylanisolvens, Bacteroides thetaiotaomicron, Subdoligranulum variabile and Roseburia intestinalis). The data highlight the coordinated action of genes within the same locus involved in the degradation of complex carbohydrates. These loci are well characterized in Bacteroidetes species and referred to as polysaccharide utilization loci. more...

Organism:

Bacteroides thetaiotaomicron; Roseburia intestinalis; Subdoligranulum variabile; Bacteroides xylanisolvens

Type:

Expression profiling by high throughput sequencing

4 related Platforms

36 Samples

Download data: CSV

(Submitter supplied) Purpose: Examining the transcriptome of human gut bacteria (Bacteroides xylanisolvens/Bacteroides ovatus) that grow on mucin O-linked glycans as a sole carbon source Methods: Strains were grown on 10 mg/ml mucin O-linked glycans (MOG) or 5 mg/ml glucose as a sole carbon source in vitro. Fold change was calculated as MOG over glucose. Once cells reached an optical density corresponding to mid-log phase growth, RNA was isolated and rRNA depleted. more...

Organism:

Bacteroides ovatus; Bacteroides xylanisolvens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL28983 GPL21072

24 Samples

Download data: XLSX

(Submitter supplied) Purpose: Examining the transcriptome of human gut bacteria that grow on seaweed polysaccharides as a sole carbon source Methods: Strains were grown on 5 mg/ml seaweed polysaccharides (carrageenan, agarose and/or poprhyran respective to strain) or galactose as a sole carbon source in vitro. Fold change was calculated as seaweed polysaccharide over galactose with n=2 biological replicates. Once cells reached an optical density corresponding to mid-log phase growth, RNA was isolated and rRNA depleted. more...

Organism:

Bacteroides thetaiotaomicron; Bacteroides xylanisolvens; Faecalicatena contorta; Faecalicatena fissicatena

Type:

Expression profiling by high throughput sequencing

4 related Platforms

24 Samples

Download data: XLSX

(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; Butyrivibrio fibrisolvens; Ruminococcus flavefaciens; Piromyces communis; Pseudobacteroides cellulosolvens; Eudiplodinium maggii; Segatella bryantii; Acetivibrio clariflavus; uncultured Neocallimastigales; 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; 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) 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) see manufacturer's web site at https://www.genomics.agilent.com/en/Custom-Gene-Expression-Microarrays/Custom-Gene-Expression-Microarrays/?cid=AG-PT-132&tabId=AG-PR-1038

Organism:

Bacteroides fragilis; Bacteroides thetaiotaomicron; Butyrivibrio fibrisolvens; Fibrobacter succinogenes; Xylanibacter ruminicola; Selenomonas ruminantium; Ruminococcus albus; Ruminococcus flavefaciens; Enterococcus faecium; Lactococcus lactis; Clostridium acetobutylicum; Clostridium cellulovorans; Clostridioides difficile; Acetivibrio thermocellus; Clostridium beijerinckii; Ruminiclostridium cellulolyticum; Levilactobacillus brevis; Limosilactobacillus fermentum; Bifidobacterium adolescentis; Cellulomonas fimi; Cellulomonas flavigena; Neocallimastix frontalis; Neocallimastix patriciarum; Piromyces communis; Bifidobacterium animalis; Bacteroides ovatus; Fibrobacter intestinalis; [Eubacterium] cellulosolvens; Bacteroides sp.; Pseudobacteroides cellulosolvens; Lachnospira eligens; Agathobacter rectalis; Ruminococcus sp.; Enterobacter sp.; Piromyces sp.; Epidinium caudatum; Eudiplodinium maggii; Polyplastron multivesiculatum; Orpinomyces joyonii; Piromyces rhizinflatus; Segatella bryantii; Piromyces sp. 'equi'; Roseburia intestinalis; Pseudobutyrivibrio xylanivorans; Butyrivibrio hungatei; Bifidobacterium longum; Acetivibrio clariflavus; Epidinium ecaudatum; Roseburia hominis; uncultured Neocallimastigales; Bacteroides xylanisolvens; Cellulosilyticum ruminicola; Ruminococcus champanellensis; Orpinomyces sp.

1 Series

6 Samples

Download data

(Submitter supplied) see manufacturer's web site at https://www.genomics.agilent.com/en/Custom-Gene-Expression-Microarrays/Custom-Gene-Expression-Microarrays/?cid=AG-PT-132&tabId=AG-PR-1038

Organism:

Bacteroides fragilis; Bacteroides thetaiotaomicron; Butyrivibrio fibrisolvens; Fibrobacter succinogenes; Xylanibacter ruminicola; Selenomonas ruminantium; Ruminococcus albus; Ruminococcus flavefaciens; Enterococcus faecium; Lactococcus lactis; Clostridium acetobutylicum; Clostridium cellulovorans; Clostridioides difficile; Acetivibrio thermocellus; Clostridium beijerinckii; Ruminiclostridium cellulolyticum; Levilactobacillus brevis; Limosilactobacillus fermentum; Bifidobacterium adolescentis; Cellulomonas fimi; Cellulomonas flavigena; Neocallimastix frontalis; Neocallimastix patriciarum; Piromyces communis; Bifidobacterium animalis; Bacteroides ovatus; Fibrobacter intestinalis; [Eubacterium] cellulosolvens; Bacteroides sp.; Pseudobacteroides cellulosolvens; Lachnospira eligens; Agathobacter rectalis; Ruminococcus sp.; Enterobacter sp.; Piromyces sp.; Epidinium caudatum; Eudiplodinium maggii; Polyplastron multivesiculatum; Orpinomyces joyonii; Piromyces rhizinflatus; Segatella bryantii; Piromyces sp. 'equi'; Roseburia intestinalis; Pseudobutyrivibrio xylanivorans; Butyrivibrio hungatei; Bifidobacterium longum; Acetivibrio clariflavus; Epidinium ecaudatum; Roseburia hominis; uncultured Neocallimastigales; Bacteroides xylanisolvens; Cellulosilyticum ruminicola; Ruminococcus champanellensis; Orpinomyces sp.

1 Series

14 Samples

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