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; 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.; 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:

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; 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) Expression profile of wild-type S. ovata and methanol-adapted strain grown autotrophically with H2 as the source of electron.

Organism:

Sporomusa ovata DSM 2662

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19818

6 Samples

Download data: TXT

(Submitter supplied) DNA methylation is an important regulator of genome function in the eukaryotes, but it is currently unclear if the same is true in prokaryotes. While regulatory functions have been demonstrated for a small number of bacteria, there have been no large-scale studies of prokaryotic methylomes and the full repertoire of targets and biological functions of DNA methylation remains unclear. Here we applied single-molecule, real-time sequencing to directly study the methylomes of 232 phylogenetically diverse prokaryotes. more...

Organism:

Lactococcus lactis subsp. lactis; Lactiplantibacillus plantarum; Lachnobacterium bovis; Clostridium perfringens ATCC 13124; Methanocaldococcus jannaschii DSM 2661; Methylorubrum extorquens AM1; Thermoplasma volcanium GSS1; Acidobacteriaceae bacterium TAA 166; Mycoplasmopsis bovis PG45; Methanospirillum hungatei JF-1; Actinobacillus succinogenes 130Z; Fervidobacterium nodosum Rt17-B1; Bifidobacterium longum subsp. infantis ATCC 15697 = JCM 1222 = DSM 20088; Staphylothermus marinus F1; Thermoanaerobacter sp. X514; Xenorhabdus nematophila ATCC 19061; Galbibacter orientalis; Dyadobacter fermentans DSM 18053; Streptosporangium roseum DSM 43021; Pedobacter heparinus DSM 2366; Rhizobium etli CIAT 652; Meiothermus ruber DSM 1279; Planctopirus limnophila DSM 3776; Methanothermus fervidus DSM 2088; Sebaldella termitidis ATCC 33386; Methanohalophilus mahii DSM 5219; Aminobacterium colombiense DSM 12261; Acidobacteriaceae bacterium KBS 146; Pontibacter actiniarum DSM 19842; Thermobacillus composti KWC4; Marinithermus hydrothermalis DSM 14884; Bernardetia litoralis DSM 6794; Desulfobacca acetoxidans DSM 11109; Rikenella microfusus DSM 15922; Echinicola vietnamensis DSM 17526; Orenia marismortui DSM 5156; Sporocytophaga myxococcoides DSM 11118; Niabella soli DSM 19437; Sinorhizobium medicae WSM1115; Hippea alviniae EP5-r; Hippea sp. KM1; Sphingomonas melonis C3; Methylophilaceae bacterium 11; Thioalkalivibrio sp. ARh3; Thiomonas sp. FB-6; Oxalobacteraceae bacterium AB_14; Solidesulfovibrio cf. magneticus IFRC170; Desulfotignum balticum DSM 7044; Methylobacterium sp. EUR3 AL-11; Kallotenue papyrolyticum; Bryobacter aggregatus MPL3; Ruminococcus albus AD2013; Eubacterium sp. AB3007; Ruminococcaceae bacterium AE2021; Lachnospiraceae bacterium AC2031; Selenomonas ruminantium AC2024; Selenomonas sp. AB3002; Peptostreptococcaceae bacterium VA2; Ruminococcus sp. HUN007; Streptococcus equinus; Salmonella enterica subsp. arizonae serovar 62:z4,z23:-; Xylella fastidiosa Temecula1; Acetivibrio thermocellus ATCC 27405; Rhodopseudomonas palustris CGA009; Neisseria meningitidis FAM18; Thermoplasma acidophilum DSM 1728; Hydrogenovibrio crunogenus XCL-2; Chloroflexus aggregans DSM 9485; Thermosipho melanesiensis BI429; Shewanella woodyi ATCC 51908; Bradyrhizobium elkanii USDA 76; Dinoroseobacter shibae DFL 12 = DSM 16493; Parabacteroides distasonis ATCC 8503; Anoxybacillus flavithermus WK1; Escherichia coli str. K-12 substr. MG1655; Capnocytophaga ochracea DSM 7271; Haloterrigena turkmenica DSM 5511; Palaeococcus ferrophilus DSM 13482; Acetivibrio thermocellus DSM 1313; Gracilinema caldarium DSM 7334; Treponema succinifaciens DSM 2489; Caldithrix abyssi DSM 13497; Calidithermus chliarophilus DSM 9957; Cohnella panacarvi Gsoil 349; Methylobacterium sp. 10; Xanthobacter sp. 91; Geopsychrobacter electrodiphilus DSM 16401; Hydrogenovibrio marinus DSM 11271; Nocardia sp. BMG111209; Klebsiella oxytoca BRL6-2; Polaribacter sp. Hel_I_88; Methylohalobius crimeensis 10Ki; Streptomyces sp. WMMB 714; Ruminiclostridium josui JCM 17888; Alteromonas sp. ALT199; Aminiphilus circumscriptus DSM 16581; Caldicoprobacter oshimai DSM 21659; Microbacterium sp. KROCY2; Thermogemmatispora carboxidivorans; Ruminococcus flavefaciens AE3010; Butyrivibrio sp. FCS014; Polycyclovorans algicola TG408; Clostridium sp. KNHs205; Lachnospiraceae bacterium AC2029; Enterococcus faecalis 68A; Butyrivibrio sp. AE3004; Teredinibacter purpureus; Enterococcus gallinarum; Clostridium algidicarnis; Pyrococcus horikoshii OT3; Methylocystis sp. LW5; Agrobacterium fabrum str. C58; Persephonella; Mastigocladopsis repens PCC 10914; Neisseria gonorrhoeae FA 1090; Clostridioides difficile 630; Thiobacillus denitrificans ATCC 25259; Salmonella enterica subsp. enterica serovar Paratyphi A str. ATCC 9150; Sulfurimonas denitrificans DSM 1251; Sulfolobus acidocaldarius DSM 639; Flavobacterium psychrophilum JIP02/86; Methanocorpusculum labreanum Z; Cronobacter; Pseudarthrobacter chlorophenolicus A6; Saccharomonospora viridis DSM 43017; Verrucomicrobia bacterium LP2A; Thermanaerovibrio acidaminovorans DSM 6589; Corynebacterium aurimucosum ATCC 700975; Zymomonas mobilis subsp. pomaceae ATCC 29192; Klebsiella aerogenes FGI35; Cellulophaga algicola DSM 14237; Flexistipes sinusarabici DSM 4947; Sulfurospirillum barnesii SES-3; Gillisia limnaea DSM 15749; Spirochaeta thermophila DSM 6578; Ruminococcus sp. NK3A76; Spirochaeta africana DSM 8902; Holophaga foetida DSM 6591; Salmonella enterica subsp. enterica serovar Paratyphi B str. SPB7; Acetivibrio clariflavus 4-2a; Thermacetogenium phaeum DSM 12270; Methylophilus sp. 5; Arthrobacter sp. 31Y; Methylophilus sp. 42; Methylotenera versatilis 79; Psychrilyobacter atlanticus DSM 19335; Prevotella sp. 10(H); Methylotenera sp. 73s; Acidovorax sp. JHL-3; Gillisia sp. JM1; Cellulomonas sp. KRMCY2; Clostridium sp. ASBs410; Limisalsivibrio acetivorans; Polaromonas sp. EUR3 1.2.1; Levilactobacillus brevis AG48; Pediococcus acidilactici AGR20; Exiguobacterium chiriqhucha; Prevotella sp. HUN102; Flavimarina sp. Hel_I_48; Lachnospiraceae bacterium AC2012; Clostridioides mangenotii LM2; Exiguobacterium aurantiacum DSM 6208; Exiguobacterium acetylicum DSM 20416; Exiguobacterium oxidotolerans JCM 12280; Exiguobacterium antarcticum DSM 14480; Methylobacter tundripaludum 21/22; Lachnoclostridium phytofermentans KNHs2132; Staphylococcus epidermidis AG42; Butyrivibrio sp. AE3003; Teredinibacter turnerae; Escherichia coli CFT073; Salmonella bongori NCTC 12419; Treponema denticola ATCC 35405; Akkermansia muciniphila ATCC BAA-835; Phaeobacter inhibens DSM 17395; Actinosynnema mirum DSM 43827; Staphylococcus aureus subsp. aureus USA300_TCH1516; Sphaerobacter thermophilus DSM 20745; Veillonella parvula DSM 2008; Streptobacillus moniliformis DSM 12112; Allomeiothermus silvanus DSM 9946; Sedimentitalea nanhaiensis DSM 24252; Sediminispirochaeta smaragdinae DSM 11293; Hirschia baltica ATCC 49814; Coraliomargarita akajimensis DSM 45221; Syntrophothermus lipocalidus DSM 12680; Stutzerimonas stutzeri RCH2; Syntrophobotulus glycolicus DSM 8271; Bacillus spizizenii str. W23; Phocaeicola salanitronis DSM 18170; Pseudofrankia sp. DC12; Nitratifractor salsuginis DSM 16511; Cellulophaga lytica DSM 7489; Asinibacterium sp. OR53; Solitalea canadensis DSM 3403; Patulibacter minatonensis DSM 18081; Acetobacterium woodii DSM 1030; Nocardia sp. BMG51109; Halomicrobium katesii DSM 19301; Nitriliruptor alkaliphilus DSM 45188; Methylophilus sp. 1; Pseudomonas aeruginosa NCAIM B.001380; Kangiella aquimarina DSM 16071; Pelobacter seleniigenes DSM 18267; Thiomicrospira pelophila DSM 1534; Desulfurobacterium sp. TC5-1; Bacteroides sp. 14(A); Clostridium sp. 12(A); Hydrogenovibrio kuenenii DSM 12350; Leptolyngbya sp. PCC 6406; Maribacter sp. Hel_I_7; Desulfospira joergensenii DSM 10085; Tolumonas lignilytica; Cellvibrionaceae bacterium 1162T.S.0a.05; Lacrimispora indolis SR3; Lacrimispora indolis DSM 755; Desulforegula conservatrix Mb1Pa; Oceanicola sp. HL-35; Algoriphagus marincola HL-49; Desulfohalovibrio reitneri; Alicyclobacillus macrosporangiidus CPP55; Pseudacidobacterium ailaaui; Mediterraneibacter gnavus AGR2154; Sediminibacter sp. Hel_I_10; Hydrogenovibrio sp. MA2-6; Pseudobutyrivibrio ruminis HUN009; Lachnoclostridium phytofermentans KNHs212; Robinsoniella sp. KNHs210

Type:

Methylation profiling by high throughput sequencing

228 related Platforms

237 Samples

Download data: CSV, GFF

(Submitter supplied) We investigated the specific interactions of the most dominant bacterial CF-pathogen, Pseudomonas aeruginosa, and the anaerobic bacterium Veilllonella parvula, that has been recovered at comparable cell numbers in the respiratory tract of CF patients. We used our recently established in-vivo murine tumor model to investigate mutual influences of the two pathogens during a biofilm-associated infection process. more...

Organism:

Mus musculus; Pseudomonas aeruginosa PA14; Veillonella parvula DSM 2008

Type:

Expression profiling by high throughput sequencing

4 related Platforms

12 Samples

Download data: TXT

(Submitter supplied) Differental gene expression of three consortia: Dhc195/DVH with exogenous cobalamin, Dhc195/DVH/PF with exogenous cobalamin, Dhc195/DVH/PF without exogenous cobalamin Acronyms: Dhc195: Dehalococcoides mccartyi strain 195; DVH: Desulfovibrio vulgaris Hildenborough; PF: Pelosinus fermentans strain R7

Organism:

Dehalococcoides mccartyi VS; Nitratidesulfovibrio vulgaris str. Hildenborough; Dehalococcoides mccartyi CBDB1; Pelosinus fermentans DSM 17108; Dehalococcoides mccartyi BAV1; Dehalococcoides mccartyi 195

Type:

Expression profiling by array

Platform:

GPL10838

9 Samples

Download data: CEL

(Submitter supplied) Increasing atmospheric CO2 concentrations are causing decreased pH over vast expanses of the ocean. This decreasing pH may alter biogeochemical cycling of carbon and nitrogen via the microbial process of nitrification, a key process that couples these cycles in the ocean, but which is often sensitive to acidic conditions. Recent reports indicate a decrease in oceanic nitrification rates under experimentally lowered pH. more...

Organism:

environmental samples; environmental samples; environmental samples; environmental samples; synthetic construct; environmental samples; environmental samples

Type:

Other

Platforms:

GPL17583 GPL17584

24 Samples

Download data: TXT

(Submitter supplied) A prototype oligonucleotide microarray was designed to detect and identify viable bacterial species with the potential to grow of common beer spoilage microorganisms from the genera Lactobacillus, Megasphaera, Pediococcus and Pectinatus. Probes targeted the intergenic spacer regions (ISR) between 16S and 23S rRNA, which were amplified in a combination of reverse transcriptase (RT) and polymerase chain reaction (PCR) prior to hybridization. more...

Organism:

Loigolactobacillus coryniformis; Schleiferilactobacillus perolens; Pediococcus inopinatus; Pectinatus cerevisiiphilus; Pectinatus frisingensis; Levilactobacillus brevis; Pediococcus damnosus; Lacticaseibacillus casei; Megasphaera cerevisiae

Type:

Expression profiling by array

Platforms:

GPL5157 GPL5158

12 Samples

Download data: GPR

(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

(Submitter supplied) Each oligonucleotide species-specific probe was spotted in 70 replicate spots on the microarray. Nine single beer spoilage bacteria species were detected with the developed prototype oligonucleotide microarray and also three mixes of two different beer spoilage bacteria species. Protocol: Standard glass microscope slides were coated with a poly-L-lysine solution and stored for several weeks to allow the surface to become sufficiently hydrophobic. more...

Organism:

Pectinatus frisingensis; Levilactobacillus brevis; Lacticaseibacillus casei; Loigolactobacillus coryniformis; Megasphaera cerevisiae; Pediococcus damnosus; Pectinatus cerevisiiphilus; Schleiferilactobacillus perolens; Pediococcus inopinatus

1 Series

4 Samples

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(Submitter supplied) Each oligonucleotide species-specific probe was spotted in 70 replicate spots on the microarray. Nine single beer spoilage bacteria species were detected with the developed prototype oligonucleotide microarray and also three mixes of two different beer spoilage bacteria species. Protocol: Standard glass microscope slides were coated with a poly-L-lysine solution and stored for several weeks to allow the surface to become sufficiently hydrophobic. more...

Organism:

Pectinatus frisingensis; Levilactobacillus brevis; Lacticaseibacillus casei; Loigolactobacillus coryniformis; Megasphaera cerevisiae; Pediococcus damnosus; Pectinatus cerevisiiphilus; Schleiferilactobacillus perolens; Pediococcus inopinatus

1 Series

8 Samples

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