Strain identifier

BacDive ID: 5815

Type strain: Yes

Species: Geodermatophilus obscurus

Strain Designation: G-20

Strain history: <- TK Oh <- IFO <- KCC A-0152 <- GM Luedemann G-20

NCBI tax ID(s): 526225 (strain), 1861 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 8.1 (current version)

General

@ref: 10828

BacDive-ID: 5815

DSM-Number: 43160

keywords: genome sequence, 16S sequence, Bacteria, microaerophile, mesophilic, Gram-positive

description: Geodermatophilus obscurus G-20 is a microaerophile, mesophilic, Gram-positive bacterium that was isolated from soil.

NCBI tax id

NCBI tax idMatching level
1861species
526225strain

strain history

@refhistory
10828<- KCC <- G.M. Luedemann, G-20
67770KCC A-0152 <-- G. M. Luedemann G-20.
67771<- TK Oh <- IFO <- KCC A-0152 <- GM Luedemann G-20

doi: 10.13145/bacdive5815.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Geodermatophilales
  • family: Geodermatophilaceae
  • genus: Geodermatophilus
  • species: Geodermatophilus obscurus
  • full scientific name: Geodermatophilus obscurus Luedemann 1968 (Approved Lists 1980)

@ref: 10828

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Geodermatophilaceae

genus: Geodermatophilus

species: Geodermatophilus obscurus

full scientific name: Geodermatophilus obscurus Luedemann 1968 emend. Montero-Calasanz et al. 2017

strain designation: G-20

type strain: yes

Morphology

cell morphology

@refgram stainconfidence
67771positive
69480positive100

colony morphology

@refcolony colorincubation periodmedium used
19943Fir green (6009)10-14 daysISP 2
19943Fir green (6009)10-14 daysISP 3
19943Fir green (6009)10-14 daysISP 4
19943Fir green (6009)10-14 daysISP 5
19943Fir green (6009)10-14 daysISP 6
19943Fir green (6009)10-14 daysISP 7
627357 days

multicellular morphology

@refforms multicellular complexmedium name
19943noISP 2
19943noISP 3
19943noISP 4
19943noISP 5
19943noISP 6
19943noISP 7

multimedia

@refmultimedia contentcaptionintellectual property rights
10828https://www.dsmz.de/microorganisms/photos/DSM_43160.jpgMedium 65 28°C© Leibniz-Institut DSMZ
66793EM_DSM_43160_1.jpgelectron microscopic image© HZI/Manfred Rohde

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
19943ISP 2yesName: ISP 2 / Yeast Malt Agar (5265); 5265 Composition Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l Agar 15.0 g/l Preparation: Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.0 Usage: Maintenance and Taxonomy Organisms: All Actinomycetes
19943ISP 3yesName: ISP 3; 5315 Composition Dog oat flakes 20.0 g/l Trace element solution (5314) 2.5 ml/l Agar 18.0 g/l Preparation: Oat flakes are cooked for 20 minutes, trace element solution and agar are added (in the case of non rolled oat flakes the suspension has to bee filtrated). Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.8 Usage: Maintenance and taxonomy (e.g. SEM As liquid medium for metabolite production) Organisms: All Actinomycetes Trace element solution 5314 Name: Trace element solution 5314; 5314 Composition CaCl2 x H2O 3.0 g/l Fe-III-citrate 1.0 g/l MnSO4 0.2 g/l ZnCl2 0.1 g/l CuSO4 x 5 H2O 0.025 g/l Sodium tetra borate 0.2 g/l CoCl2 x 6 H2O 0.004 g/l Sodium molybdate 0.01 g/l Preparation: Use double destillated water. Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Trace element solution for different media Organisms:
19943ISP 4yesName: ISP 4; DSM 547 Solution I: Difco soluble starch, 10.0 g. Make a paste of the starch with a small amount of cold distilled water and bring to a volume of 500 ml. Solution II: CaCO3 2.0 g K2HPO4 (anhydrous) 1.0 g MgSO4 x 7 H2O 1.0 g NaCl 1.0 g (NH4)2SO4 2.0 g Distilled water 500.0 ml Trace salt solution (see below) 1.0 ml The pH should be between 7.0 and 7.4. Do not adjust if it is within this range. Mix solutions I and II together. Add 20.0 g agar. Liquify agar by steaming at 100°C for 10 to 20 min. Trace element solution: FeSO4 x 7 H2O 0.1 g MnCl2 x 4 H2O 0.1 g ZnSO4 x 7 H2O 0.1 g Distilled water 100.0 ml
19943ISP 5yesName: ISP 5 (5323) Composition L-Asparagine 1.0 g/l Glycerol 10.0 g/l K2HPO4 1.0 g/l Salt solution (see preparation) 1.0 ml/l Agar 20.0 g/l Preparation: Salt solution 1.0 g FeSO4 x 7 H2O 1.0 g MnCl2 x 4 H2O 1.0 g ZNSO4 x 7 H2O in 100 ml water Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.2 Usage: Maintenance and taxonomy Organisms: All Actinomycetes
19943ISP 6yesName: ISP 6 (5318) Composition Peptone 15.0 g/l Proteose peptose 5.0 g/l Ferric ammonium citrate 0.5 g/l Sodium glycerophosphate 1.0 g/l Sodium thiosulfate 0.08 g/l Yeast extract 1.0 g/l Agar 15.0 g/l Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigments Organisms: All Actinomycetes
19943ISP 7yesName: ISP 7 (5322) Composition Glycerol 15.0 g/l L-Tyrosine 0.5 g/l L-Asparagine 1.0 g/l K2HPO4 0.5 g/l NaCl 0.5 g/l FeSO4 x 7 H2O 0.01 g/l Trace element solution 5343 1.0 ml/l Agar 20.0 Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.3 Usage: Production of melanoid pigments Organisms: All Actinomycetes
10828GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)yesName: GYM STREPTOMYCES MEDIUM (DSMZ Medium 65) Composition: Agar 18.0 g/l Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l CaCO3 2.0 g/l Distilled waterhttps://mediadive.dsmz.de/medium/65
10828GPHF-MEDIUM (DSMZ Medium 553)yesName: GPHF-MEDIUM (DSMZ Medium 553) Composition: Agar 20.0 g/l Glucose 10.0 g/l Beef extract 5.0 g/l Yeast extract 5.0 g/l Casein peptone 5.0 g/l CaCl2 x 2 H2O 0.74 g/l Distilled waterhttps://mediadive.dsmz.de/medium/553
10828CZAPEK PEPTONE AGAR (DSMZ Medium 83)yesName: CZAPEK PEPTONE AGAR (DSMZ Medium 83) Composition: Sucrose 30.0 g/l Agar 20.0 g/l Peptone 5.0 g/l NaNO3 3.0 g/l Yeast extract 2.0 g/l K2HPO4 1.0 g/l MgSO4 x 7 H2O 0.5 g/l KCl 0.5 g/l FeSO4 x 7 H2O 0.01 g/l Distilled waterhttps://mediadive.dsmz.de/medium/83

culture temp

@refgrowthtypetemperaturerange
19943positiveoptimum30mesophilic
10828positivegrowth28mesophilic
62735positivegrowth37mesophilic
67770positivegrowth28mesophilic
67771positivegrowth28mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
62735microaerophile
67771aerobe

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 95.608

halophily

  • @ref: 19943
  • salt: NaCl
  • growth: positive
  • tested relation: maximum
  • concentration: 2.5 %

observation

@refobservation
67770quinones: MK-9(H4)
67771quinones: MK-9(H_4_)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1994362968cellulose+
1994316634raffinose+
1994326546rhamnose+
1994328757fructose+
1994329864mannitol+
1994317268myo-inositol+
1994318222xylose+
1994317992sucrose+
1994322599arabinose+
1994317234glucose+
683685291gelatin-hydrolysis
6836827897tryptophan-energy source
6836816199urea+hydrolysis
6836816947citrate+assimilation
6836818257ornithine+degradation
6836825094lysine+degradation
6836829016arginine+hydrolysis

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinyes
6836835581indoleno
6836816136hydrogen sulfideno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole test
6836815688acetoin+
6836835581indole-

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucosidase-3.2.1.21
68382alpha-glucosidase+3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase-3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase-
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin+3.4.21.1
68382trypsin+3.4.21.4
68382cystine arylamidase-3.4.11.3
68382valine arylamidase+
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)+
68382esterase (C 4)+
68382alkaline phosphatase+3.1.3.1
68368gelatinase-
68368tryptophan deaminase-4.1.99.1
68368urease+3.5.1.5
68368ornithine decarboxylase+4.1.1.17
68368lysine decarboxylase+4.1.1.18
68368arginine dihydrolase+3.5.3.6
68368beta-galactosidase-3.2.1.23

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
19943+++-++-+++----+----

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
19943-++++-+--+-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
10828soildesert of Nevada, AmargosUSAUSANorth America
62735SoilNevada,Amargosa DesertUSAUSANorth America
67770Soil, Amargosa DesertNVUSAUSANorth America
67771From soilAmargosa desert, NevadaUSAUSANorth America

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Soil

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
199431German classification
108281Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Geodermatophilus obscurus DSM 43160 16S ribosomal RNA gene, partial sequenceJQ899243646ena526225
20218G.obscurus 16S ribosomal RNA (strain DSM43160)X923561482ena526225
67771Geodermatophilus obscurus obscurus 16S ribosomal RNA (16S rRNA) geneL406201416ena1861

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Geodermatophilus obscurus DSM 43160GCA_000025345completencbi526225
66792Geodermatophilus obscurus DSM 43160526225.7completepatric526225
66792Geodermatophilus obscurus G-20, DSM 43160646311931completeimg526225

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes76no
motileyes75.043no
flagellatedno90.763no
gram-positiveyes93.314yes
anaerobicno98.644no
aerobicyes91.649no
halophileno82.055no
spore-formingno59.926no
thermophileno97.697yes
glucose-utilyes88.353yes
glucose-fermentno87.345no

External links

@ref: 10828

culture collection no.: CCUG 61914, KCTC 9177, DSM 43160, ATCC 25078, CBS 237.69, IAM 14282, IFO 13315, JCM 3152, KCC A-0152, NBRC 13315, IMSNU 21280, NRRL B-3577, RIA 944, VKM Ac-658

straininfo link

  • @ref: 75297
  • straininfo: 38343

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny20190022Geodermatophilus ruber sp. nov., isolated from rhizosphere soil of a medicinal plant.Zhang YQ, Chen J, Liu HY, Zhang YQ, Li WJ, Yu LYInt J Syst Evol Microbiol10.1099/ijs.0.020610-02010Actinomycetales/*classification/genetics/*isolation & purification/physiology, Astragalus propinquus/*microbiology, Base Composition, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Diaminopimelic Acid/analysis, Fatty Acids/analysis, Hydrogen-Ion Concentration, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, *Rhizosphere, Sequence Analysis, DNA, Sodium Chloride/metabolism, *Soil Microbiology, Temperature, Vitamin K 2/analysisGenetics
Genetics21304698Complete genome sequence of Geodermatophilus obscurus type strain (G-20).Ivanova N, Sikorski J, Jando M, Munk C, Lapidus A, Glavina Del Rio T, Copeland A, Tice H, Cheng JF, Lucas S, Chen F, Nolan M, Bruce D, Goodwin L, Pitluck S, Mavromatis K, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Meincke L, Brettin T, Detter JC, Rohde M, Goker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HPStand Genomic Sci10.4056/sigs.7113112010
Phylogeny22273761Geodermatophilus nigrescens sp. nov., isolated from a dry-hot valley.Nie GX, Ming H, Li S, Zhou EM, Cheng J, Yu TT, Zhang J, Feng HG, Tang SK, Li WJAntonie Van Leeuwenhoek10.1007/s10482-012-9696-02012Actinomycetales/*classification/genetics/*isolation & purification/physiology, Bacterial Typing Techniques, Base Composition, Carbohydrates/analysis, China, Cluster Analysis, Culture Media/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Diaminopimelic Acid/analysis, Fatty Acids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phylogeny, Pigments, Biological/metabolism, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analysisGenetics
Phylogeny23159748Geodermatophilus telluris sp. nov., an actinomycete isolated from Saharan desert sand.Montero-Calasanz MDC, Goker M, Potter G, Rohde M, Sproer C, Schumann P, Klenk HP, Gorbushina AAInt J Syst Evol Microbiol10.1099/ijs.0.046888-02012Actinomycetales/*classification/genetics/isolation & purification, Africa, Northern, Bacterial Typing Techniques, Base Composition, Chad, DNA, Bacterial/genetics, Fatty Acids/analysis, Molecular Sequence Data, Peptidoglycan/analysis, Phospholipids/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Silicon Dioxide, *Soil Microbiology, Vitamin K 2/analogs & derivatives/analysisGenetics
Metabolism27671711Degradation of carbonyl sulfide by Actinomycetes and detection of clade D of beta-class carbonic anhydrase.Ogawa T, Kato H, Higashide M, Nishimiya M, Katayama YFEMS Microbiol Lett10.1093/femsle/fnw2232016
Phylogeny29789182Geodermatophilus chilensis sp. nov., from soil of the Yungay core-region of the Atacama Desert, Chile.Castro JF, Nouioui I, Sangal V, Trujillo ME, Montero-Calasanz MDC, Rahmani T, Bull AT, Asenjo JA, Andrews BA, Goodfellow MSyst Appl Microbiol10.1016/j.syapm.2018.03.0052018Actinobacteria/chemistry/*classification/*genetics/physiology, Chile, DNA, Bacterial/genetics, *Desert Climate, Genes, Bacterial, Genome, Bacterial/genetics, Multigene Family, Phenotype, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Species SpecificityGenetics
Phylogeny31418670Geodermatophilus marinus sp. nov., isolated from the marine sponge Leucetta chagosensis.Li L, Zhang D, Tang WZ, Lin HW, Lu YHInt J Syst Evol Microbiol10.1099/ijsem.0.0034782019Actinobacteria/*classification/isolation & purification, Animals, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Multilocus Sequence Typing, Nucleic Acid Hybridization, Oceans and Seas, Phospholipids/chemistry, *Phylogeny, Pigmentation, Porifera/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
10828Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 43160)https://www.dsmz.de/collection/catalogue/details/culture/DSM-43160
19943Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM43160.pdfCompendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
62735Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 61914)https://www.ccug.se/strain?id=61914
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
66793Mukherjee et al.10.1038/nbt.3886GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life 35: 676-683 201728604660
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
68368Automatically annotated from API 20E
68382Automatically annotated from API zym
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
75297Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID38343.1StrainInfo: A central database for resolving microbial strain identifiers