Strain identifier

BacDive ID: 1774

Type strain: Yes

Species: Georgenia thermotolerans

Strain Designation: TT 02-04

Strain history: <- M. Hamada, NBRC <- T. Tamura, IFO; TT 02-04

NCBI tax ID(s): 527326 (species)

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General

@ref: 15680

BacDive-ID: 1774

DSM-Number: 21501

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

description: Georgenia thermotolerans TT 02-04 is a microaerophile, mesophilic, Gram-positive bacterium that was isolated from forest soil.

NCBI tax id

  • NCBI tax id: 527326
  • Matching level: species

strain history

  • @ref: 15680
  • history: <- M. Hamada, NBRC <- T. Tamura, IFO; TT 02-04

doi: 10.13145/bacdive1774.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Bogoriellaceae
  • genus: Georgenia
  • species: Georgenia thermotolerans
  • full scientific name: Georgenia thermotolerans Hamada et al. 2009

@ref: 15680

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Bogoriellaceae

genus: Georgenia

species: Georgenia thermotolerans

full scientific name: Georgenia thermotolerans Hamada et al. 2009

strain designation: TT 02-04

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
29057positive1.5 µm0.6 µmrod-shapedyes
69480positive100

colony morphology

@refcolony colorincubation periodmedium used
18343Broom yellow (1032)10-14 daysISP 2
18343Sulfur yellow (1016)10-14 daysISP 3
18343Beige (1001)10-14 daysISP 4
18343Ivory (1014)10-14 daysISP 5
18343Broom yellow (1032)10-14 daysISP 6
18343Oyster white (1013)10-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
18343noISP 2
18343noISP 3
18343noISP 4
18343noISP 5
18343noISP 6
18343noISP 7

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
15680TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)yeshttps://mediadive.dsmz.de/medium/92Name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Yeast extract 3.0 g/l Distilled water
18343ISP 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
18343ISP 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:
18343ISP 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
18343ISP 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
18343ISP 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
18343ISP 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

culture temp

@refgrowthtypetemperaturerange
18343positiveoptimum28mesophilic
15680positivegrowth28mesophilic
29057positivegrowth25-45
29057positiveoptimum28mesophilic

culture pH

@refabilitytypepHPH range
29057positivegrowth06-09alkaliphile
29057positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 29057
  • oxygen tolerance: microaerophile

spore formation

@refspore formationconfidence
29057no
69481no99
69480no99.991

halophily

@refsaltgrowthtested relationconcentration
29057NaClpositivegrowth<10 %
29057NaClpositiveoptimum0-5 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1834317234glucose-
1834322599arabinose-
1834317992sucrose-
1834318222xylose-
1834317268myo-inositol-
1834329864mannitol-
1834328757fructose+
1834326546rhamnose-
1834316634raffinose-
1834362968cellulose-
2905717057cellobiose+carbon source
2905717234glucose+carbon source
2905717306maltose+carbon source
2905733942ribose+carbon source
2905717814salicin+carbon source
2905717992sucrose+carbon source
2905718222xylose+carbon source
2905717632nitrate+reduction
683794853esculin+hydrolysis
6837916199urea-hydrolysis
683795291gelatin-hydrolysis
6837916899D-mannitol-fermentation
6837917716lactose-fermentation
6837917992sucrose+fermentation
6837928087glycogen-fermentation

enzymes

@refvalueactivityec
29057pyrazinamidase+3.5.1.B15
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
68379gelatinase-
68379urease-3.5.1.5
68379beta-glucosidase+3.2.1.21
68379N-acetyl-beta-glucosaminidase-3.2.1.52
68379alpha-glucosidase+3.2.1.20
68379beta-galactosidase-3.2.1.23
68379beta-glucuronidase+3.2.1.31
68379alkaline phosphatase+3.1.3.1
68379pyrrolidonyl arylamidase+3.4.19.3
68379pyrazinamidase+3.5.1.B15

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
18343+/-++++-+-+--+/-+/-+/--+/--+-

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
18343+++-++---++--+++---

Isolation, sampling and environmental information

isolation

  • @ref: 15680
  • sample type: forest soil
  • geographic location: Iriomote Island, Okinawa
  • country: Japan
  • origin.country: JPN
  • continent: Asia

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Forest
#Environmental#Terrestrial#Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_26111.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_948;97_15848;98_19612;99_26111&stattab=map
  • Last taxonomy: Georgenia
  • 16S sequence: AB436534
  • Sequence Identity:
  • Total samples: 705
  • soil counts: 599
  • aquatic counts: 36
  • animal counts: 20
  • plant counts: 50

Safety information

risk assessment

  • @ref: 15680
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 15680
  • description: Georgenia thermotolerans gene for 16S rRNA, partial sequence
  • accession: AB436534
  • length: 1480
  • database: ena
  • NCBI tax ID: 527326

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Georgenia thermotolerans NBRC 104148GCA_009193185contigncbi527326
66792Georgenia thermotolerans DSM 21501GCA_009299305contigncbi527326
66792Georgenia thermotolerans strain DSM 21501527326.4wgspatric527326
66792Georgenia thermotolerans strain NBRC 104148527326.3wgspatric527326

GC content

@refGC-content
1568073.0
2905773

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno99no
gram-positiveyes91.664yes
anaerobicno97.699no
halophileno72.886yes
spore-formingno91.718yes
glucose-utilyes88.767no
motileyes71.274yes
aerobicyes85.685no
thermophileno98.348yes
flagellatedno93.912no
glucose-fermentno83.673no

External links

@ref: 15680

culture collection no.: DSM 21501, NBRC 104148

straininfo link

  • @ref: 71421
  • straininfo: 400883

literature

  • topic: Phylogeny
  • Pubmed-ID: 19567573
  • title: Georgenia thermotolerans sp. nov., an actinobacterium isolated from forest soil.
  • authors: Hamada M, Tamura T, Ishida Y, Suzuki K
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.005140-0
  • year: 2009
  • mesh: Actinomycetales/chemistry/*classification/genetics/*isolation & purification, Amino Acids/analysis, Bacterial Typing Techniques, Base Composition, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Galactose/analysis, Japan, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Trees, Vitamin K 2/analysis
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
15680Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21501)https://www.dsmz.de/collection/catalogue/details/culture/DSM-21501
18343Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM21501.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
29057Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2548728776041
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)
68379Automatically annotated from API Coryne
68382Automatically annotated from API zym
69479João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich.https://microbeatlas.org/MicrobeAtlas 1.0 beta
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)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
71421Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID400883.1StrainInfo: A central database for resolving microbial strain identifiers