GEO DataSets

(Submitter supplied) mRNA sequencing in bacteria is challenging due to the abundance of ribosomal rRNA that cannot be easily removed prior to sequencing. While commercially available kits target specific rRNA sequences found in defined lists of common bacterial species, they are frequently inefficient when applied to other divergent species, including those from environmental isolates. Similar to the commercial kits, other common techniques for rRNA depletion typically employ large probe sets that tile full-length rRNA sequences; however, such approaches are both time consuming and expensive when applied to multiple species or complex consortia of non-model microbes. more...

Organism:

Escherichia coli; Fibrobacter succinogenes; Geobacter metallireducens; Anaeromyces robustus; Caecomyces churrovis

Type:

Expression profiling by high throughput sequencing

10 related Platforms

65 Samples

Download data: TXT

(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:

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

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:

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

Type:

Expression profiling by array; Other

Platform:

GPL24327

14 Samples

Download data: TXT

(Submitter supplied) Microorganisms are key components for plant biomass breakdown within rumen environments. Gram negative Fibrobacter succinogenes have been identified as being active and dominant cellulolytic members of the rumen. In this study, F. succinogenes type strain S85 was adapted for steady state growth in continuous culture at pH 5.75 and confirmed to grow in the range of pH 5.60-5.65, which is lower than has been reported previously. more...

Organism:

Fibrobacter succinogenes subsp. succinogenes S85

Type:

Expression profiling by high throughput sequencing

Platform:

GPL22970

10 Samples

Download data: CSV, 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

Download data