GEO DataSets

(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; 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; 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

Type:

Methylation profiling by high throughput sequencing

228 related Platforms

237 Samples

Download data: CSV, GFF

(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) 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) 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 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

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

Organism:

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

Type:

Expression profiling by array

Platforms:

GPL7006 GPL1821

48 Samples

Download data: CEL

(Submitter supplied) Bacteroides thetaiotaomicron was grown and transcriptionally profiled on a number of different host mucosal glycans and their component mono- and disaccharides.

Organism:

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

Type:

Expression profiling by array

Platform:

GPL7006

18 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

(Submitter supplied) The probeSequence and CDF files are linked below as supplementary files. Protocol: in situ oligonucleotide synthesis using photolithography

Organism:

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

12 Series

91 Samples

Download data: CDF, TXT