Strain identifier

BacDive ID: 5823

Type strain: Yes

Species: Geodermatophilus ruber

Strain history: CCM 7619 <-- Y.-Q. Zhang CPCC 201356.

NCBI tax ID(s): 504800 (species)

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General

@ref: 16221

BacDive-ID: 5823

DSM-Number: 45317

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

description: Geodermatophilus ruber DSM 45317 is a mesophilic, Gram-positive, motile bacterium that was isolated from rhizosphere soil of Astragalus membranaceus.

NCBI tax id

  • NCBI tax id: 504800
  • Matching level: species

strain history

@refhistory
16221<- Y.-Q. Zhang, Chinese Academy of Science; CPCC 201356
67770CCM 7619 <-- Y.-Q. Zhang CPCC 201356.

doi: 10.13145/bacdive5823.20230509.8.1

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 ruber
  • full scientific name: Geodermatophilus ruber Zhang et al. 2011

@ref: 16221

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Geodermatophilaceae

genus: Geodermatophilus

species: Geodermatophilus ruber

full scientific name: Geodermatophilus ruber Zhang et al. 2011 emend. Montero-Calasanz et al. 2017

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
29776positivecoccus-shapedyes
69480positive99.999

colony morphology

@refcolony colorincubation periodmedium used
21393Sand yellow (1002)10-14 daysISP 2
2139310-14 daysISP 3
2139310-14 daysISP 4
2139310-14 daysISP 5
21393Orange brown (8023)10-14 daysISP 7
21393Ochre brown (8001)10-14 daysSuter with tyrosine
21393Beige (1001)10-14 daysSuter without tyrosine

multicellular morphology

@refforms multicellular complexmedium name
21393noISP 2
21393noISP 3
21393noISP 4
21393noISP 5
21393noISP 7
21393noSuter with tyrosine
21393noSuter without tyrosine

pigmentation

  • @ref: 29776
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
16221R2A MEDIUM (DSMZ Medium 830)yeshttps://mediadive.dsmz.de/medium/830Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water
16221GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)yeshttps://mediadive.dsmz.de/medium/65Name: 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 water
21393ISP 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
21393ISP 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:
21393ISP 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
21393ISP 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
21393ISP 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
21393Suter with tyrosineyesName: Synthetically suter medium (5337) with and without tyrosine - see Kutzner,H.J., R. M. Kroppensted and F. Korn-Wendisch. (1986) Composition: Glycerol 15.0 g/l Tyrosine 1.0 (optional, see preparation comment) L-arginine 5.0 g/l L-glutamic acid 5.0 g/l L-methionine 0.3 g/l L-isoleucine 0.3 g/l K2HPO4 0.5 g/l MgSO4 x 7 H2O 0.2 g/l Agar 20.0 g/l Trace element solution (5341) 1.0 ml Composition of Trace element solution (5341): CuSO4 x 5 H2O 10.0 g/l CaCl2 x 2 H2O 10.0 g/l FeSO4 x 7 H2O 10.0 g/l ZnSO4 x 7 H2O 10.0 g/l MnSO4 x 7 H2O 40.0 g/l Preparation: Control medium is prepared without tyrosine Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigment Organisms: All Actinomycetes
21393Suter without tyrosineyesName: Synthetically suter medium (5337) with and without tyrosine - see Kutzner,H.J., R. M. Kroppensted and F. Korn-Wendisch. (1986) Composition: Glycerol 15.0 g/l Tyrosine 1.0 (optional, see preparation comment) L-arginine 5.0 g/l L-glutamic acid 5.0 g/l L-methionine 0.3 g/l L-isoleucine 0.3 g/l K2HPO4 0.5 g/l MgSO4 x 7 H2O 0.2 g/l Agar 20.0 g/l Trace element solution (5341) 1.0 ml Composition of Trace element solution (5341): CuSO4 x 5 H2O 10.0 g/l CaCl2 x 2 H2O 10.0 g/l FeSO4 x 7 H2O 10.0 g/l ZnSO4 x 7 H2O 10.0 g/l MnSO4 x 7 H2O 40.0 g/l Preparation: Control medium is prepared without tyrosine Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigment Organisms: All Actinomycetes
16221GPHF-MEDIUM (DSMZ Medium 553)yeshttps://mediadive.dsmz.de/medium/553Name: 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 water

culture temp

@refgrowthtypetemperaturerange
16221positivegrowth28mesophilic
29776positivegrowth10-40
29776positiveoptimum26mesophilic
67770positivegrowth28mesophilic

culture pH

@refabilitytypepH
29776positivegrowth06-08
29776positiveoptimum7.25

Physiology and metabolism

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 98.968

halophily

@refsaltgrowthtested relationconcentration
21393NaClpositivegrowth0 %
29776NaClpositivegrowth<1 %
29776NaClpositiveoptimum0.5 %

observation

  • @ref: 67770
  • observation: quinones: MK-9(H4), MK-9

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2139317234glucose-
2139322599arabinose-
2139317992sucrose-
2139318222xylose-
2139317268myo-inositol-
2139337684mannose+
2139328757fructose+
2139326546rhamnose-
2139316634raffinose-
2139362968cellulose-
2977630089acetate+carbon source
2977628757fructose+carbon source
2977617234glucose+carbon source
2977617596inosine+carbon source
2977625115malate+carbon source
2977637684mannose+carbon source
2977626271proline+carbon source
2977626490quinate+carbon source
2977630031succinate+carbon source
2977617632nitrate+reduction
6837917632nitrate-reduction
683794853esculin-hydrolysis
6837916199urea-hydrolysis
683795291gelatin-hydrolysis
6837917634D-glucose-fermentation
6837916988D-ribose-fermentation
6837965327D-xylose-fermentation
6837916899D-mannitol-fermentation
6837917306maltose-fermentation
6837917716lactose-fermentation
6837917992sucrose-fermentation
6837928087glycogen-fermentation

enzymes

@refvalueactivityec
29776acid phosphatase+3.1.3.2
29776alkaline phosphatase+3.1.3.1
29776catalase+1.11.1.6
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
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase-3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-chymotrypsin-3.4.21.1
68382trypsin-3.4.21.4
68382valine arylamidase-
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)+
68382esterase (C 4)+
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
21393-------------------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
21393+/-++-+-+/---+/-+---+/-----

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinentlatitudelongitude
16221rhizosphere soil of Astragalus membranaceusAstragalus membranaceusQinghai Province, Xining (37° 35' N 101° 49' E; elevation 2800 m)ChinaCHNAsia37.5833101.817
67770rhRizosphere soil of the plant Astragalus membranaceus from XiningAstragalus membranaceusQinghai Province, north-west ChinaChinaCHNAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Soil
#Host#Plants#Herbaceous plants (Grass,Crops)
#Host Body-Site#Plant#Rhizosphere

taxonmaps

  • @ref: 69479
  • File name: preview.99_132563.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_94;96_2039;97_3177;98_36042;99_132563&stattab=map
  • Last taxonomy: Geodermatophilus ruber
  • 16S sequence: EU438905
  • Sequence Identity:
  • Total samples: 1114
  • soil counts: 856
  • aquatic counts: 99
  • animal counts: 27
  • plant counts: 132

Safety information

risk assessment

  • @ref: 16221
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 16221
  • description: Geodermatophilus ruber strain CPCC 201356 16S ribosomal RNA gene, partial sequence
  • accession: EU438905
  • length: 1449
  • database: ena
  • NCBI tax ID: 504800

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Geodermatophilus ruber strain DSM 45317504800.3wgspatric504800
66792Geodermatophilus ruber DSM 453172622736605draftimg504800
67770Geodermatophilus ruber DSM 45317GCA_900114385scaffoldncbi504800

GC content

@refGC-contentmethod
1622172.8high performance liquid chromatography (HPLC)
2977672.8

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes88no
gram-positiveyes91.322no
anaerobicno97.746no
halophileno91.369no
spore-formingno68.929no
glucose-utilyes86.861no
aerobicyes87.886no
thermophileno94.155yes
motileyes79.838yes
flagellatedno94.128no
glucose-fermentno90.866yes

External links

@ref: 16221

culture collection no.: DSM 45317, CCM 7619, CPCC 201356, JCM 17967

straininfo link

  • @ref: 75305
  • straininfo: 404418

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
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

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
16221Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45317)https://www.dsmz.de/collection/catalogue/details/culture/DSM-45317
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
21393Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM45317.pdfCompendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig
29776Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2615628776041
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)
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 updates33211880Nucleic Acids Res. 49: D498-D508 2020
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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)
75305Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID404418.1StrainInfo: A central database for resolving microbial strain identifiers