Strain identifier

BacDive ID: 1773

Type strain: Yes

Species: Georgenia ruanii

Strain history: <- WJ Li, Yunnan Univ, China

NCBI tax ID(s): 348442 (species)

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General

@ref: 6997

BacDive-ID: 1773

DSM-Number: 17458

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

description: Georgenia ruanii DSM 17458 is an aerobe, chemoorganotroph, mesophilic bacterium that was isolated from forest soil.

NCBI tax id

  • NCBI tax id: 348442
  • Matching level: species

strain history

@refhistory
6997<- Wen-Jun Li, YIM 004
67770C.-L. Jiang YIM 004.
67771<- WJ Li, Yunnan Univ, China

doi: 10.13145/bacdive1773.20230509.8.1

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 ruanii
  • full scientific name: Georgenia ruanii Li et al. 2007

@ref: 6997

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Bogoriellaceae

genus: Georgenia

species: Georgenia ruanii

full scientific name: Georgenia ruanii Li et al. 2007

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
23157positive1.4-2.0 µm0.5-0.8 µmrod-shapedyes
67771positive
69480positive100

colony morphology

@refcolony colorincubation periodmedium usedcolony sizecolony shape
19749Lemon yellow (1012)10-14 daysISP 2
19749Lemon yellow (1012)10-14 daysISP 3
23157white-yellow to straw-colouredISP 2 agar1.1-1.2 mmcircular

multicellular morphology

@refforms multicellular complexmedium name
19749noISP 2
19749noISP 3

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6997TRYPTICASE 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
19749ISP 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
19749ISP 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:
23157ISP 2 agaryes

culture temp

@refgrowthtypetemperaturerange
19749positiveoptimum28mesophilic
6997positivegrowth28mesophilic
23157positivemaximum37mesophilic
23157positiveminimum10psychrophilic
23157positiveoptimum28-30mesophilic
67770positivegrowth28mesophilic
67771positivegrowth28mesophilic

culture pH

@refabilitytypepHPH range
23157positiveminimum6.5
23157positivemaximum10.0alkaliphile
23157positiveoptimum7.0

Physiology and metabolism

oxygen tolerance

  • @ref: 67771
  • oxygen tolerance: aerobe

nutrition type

  • @ref: 23157
  • type: chemoorganotroph

spore formation

@refspore formationconfidence
69481no98
69480no99.987

halophily

  • @ref: 23157
  • salt: NaCl
  • growth: no
  • tested relation: growth
  • concentration: >5 %

murein

@refmurein short keytype
6997A11.35A4alpha L-Lys-L-Ala-L-Glu
23157A4alpha L-Lys-L-Ala-L-Glu

observation

@refobservation
67770quinones: MK-8(H4)
67771quinones: MK-8(H4)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2315716199urea-degradation
2315717632nitrate-reduction
2315728757fructose+builds acid from
2315728260galactose+builds acid from
2315717234glucose+builds acid from
2315717716lactose+builds acid from
2315729864mannitol+builds acid from
2315737684mannose+builds acid from
2315733942ribose+builds acid from
2315717992sucrose+builds acid from
2315718222xylose+builds acid from
2315715963ribitol+carbon source
2315722599arabinose+carbon source
2315722605arabinitol+carbon source
2315717057cellobiose+carbon source
2315723652dextrin+carbon source
2315716813galactitol+carbon source
2315728757fructose+carbon source
2315728260galactose+carbon source
2315724175galacturonate+carbon source
2315717234glucose+carbon source
2315717268myo-inositol+carbon source
2315717716lactose+carbon source
2315717306maltose+carbon source
2315729864mannitol+carbon source
2315737684mannose+carbon source
231576731melezitose+carbon source
2315728053melibiose+carbon source
2315716634raffinose+carbon source
2315726546rhamnose+carbon source
2315733942ribose+carbon source
2315717814salicin+carbon source
2315730911sorbitol+carbon source
2315727922sorbose+carbon source
2315717992sucrose+carbon source
2315732528turanose+carbon source
2315717151xylitol+carbon source
2315727856acetamide+degradation
2315717368hypoxanthine+degradation
2315753424tween 20+degradation
2315753426tween 80+degradation
2315715318xanthine+degradation
2315715963ribitol+energy source
2315722599arabinose+energy source
2315722605arabinitol+energy source
2315717057cellobiose+energy source
2315723652dextrin+energy source
2315716813galactitol+energy source
2315728757fructose+energy source
2315728260galactose+energy source
2315724175galacturonate+energy source
2315717234glucose+energy source
2315717268myo-inositol+energy source
2315717716lactose+energy source
2315717306maltose+energy source
2315729864mannitol+energy source
2315737684mannose+energy source
231576731melezitose+energy source
2315728053melibiose+energy source
2315716634raffinose+energy source
2315726546rhamnose+energy source
2315733942ribose+energy source
2315717814salicin+energy source
2315730911sorbitol+energy source
2315727922sorbose+energy source
2315717992sucrose+energy source
2315727897tryptophan+energy source
2315732528turanose+energy source
2315717151xylitol+energy source
231574853esculin+hydrolysis
2315728017starch+hydrolysis
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

antibiotic resistance

@refChEBImetaboliteis antibioticis resistant
2315717698chloramphenicolyesyes
2315727644chlortetracyclinyesyes
2315717833gentamicinyesyes
2315728368novobiocinyesyes
2315716869oleandomycinyesyes
2315717076streptomycinyesyes
2315727902tetracyclineyesyes

metabolite production

  • @ref: 23157
  • Chebi-ID: 35581
  • metabolite: indole
  • production: yes

metabolite tests

  • @ref: 23157
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: +

enzymes

@refvalueactivityec
23157alpha-galactosidase-3.2.1.22
23157arginine dihydrolase-3.5.3.6
23157beta-galactosidase+3.2.1.23
23157beta-glucosidase+3.2.1.21
23157beta-glucuronidase-3.2.1.31
23157L-aspartate arylamidase+3.4.11.21
23157lysine decarboxylase+4.1.1.18
23157N-acetyl-beta-glucosaminidase+3.2.1.52
23157ornithine decarboxylase-4.1.1.17
23157tryptophan deaminase+4.1.99.1
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
19749++--+-+--+-----+---

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
19749----+----++--++-+--

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
6997forest soilYunnan ProvinceChinaCHNAsia
67770SoilLijiang, Yunnan ProvinceChinaCHNAsia
67771From soilYunnan ProvinceChinaCHNAsia

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: DQ203185
  • Sequence Identity:
  • Total samples: 705
  • soil counts: 599
  • aquatic counts: 36
  • animal counts: 20
  • plant counts: 50

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
69971Risk group (German classification)
197491Risk group (German classification)

Sequence information

16S sequences

  • @ref: 6997
  • description: Georgenia ruanii strain YIM 004 16S ribosomal RNA gene, partial sequence
  • accession: DQ203185
  • length: 1516
  • database: ena
  • NCBI tax ID: 348442

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Georgenia ruanii strain JCM 15130348442.3wgspatric348442
66792Georgenia ruanii strain JCM 15130348442.4wgspatric348442
67770Georgenia ruanii JCM 15130GCA_009193175contigncbi348442
67770Georgenia ruanii JCM 15130GCA_009362295contigncbi348442

GC content

@refGC-contentmethod
699772.9
6777172.9high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno98no
gram-positiveyes90.602yes
anaerobicno98.336no
halophileno87.289no
spore-formingno90.165no
glucose-utilyes88.455yes
motileyes74.168no
flagellatedno93.498no
thermophileno98.562yes
aerobicyes83.661yes
glucose-fermentno87.969yes

External links

@ref: 6997

culture collection no.: DSM 17458, CCTCC AB 204065, KCTC 19029, NBRC 103883, YIM 004, JCM 15130

straininfo link

  • @ref: 71420
  • straininfo: 232152

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny17625169Georgenia ruanii sp. nov., a novel actinobacterium isolated from forest soil in Yunnan (China), and emended description of the genus Georgenia.Li WJ, Xu P, Schumann P, Zhang YQ, Pukall R, Xu LH, Stackebrandt E, Jiang CLInt J Syst Evol Microbiol10.1099/ijs.0.64749-02007Actinomycetales/chemistry/*classification/*isolation & purification/physiology, Base Composition, Cell Wall/chemistry, China, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Genes, rRNA/genetics, Locomotion, Lysine/analysis, Molecular Sequence Data, Peptidoglycan/analysis, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, *Soil Microbiology, Trees, Vitamin K 2/analysisGenetics
Phylogeny19667374Georgenia halophila sp. nov., a halophilic actinobacterium isolated from a salt lake.Tang SK, Wang Y, Lee JC, Lou K, Park DJ, Kim CJ, Li WJInt J Syst Evol Microbiol10.1099/ijs.0.014993-02009Actinobacteria/classification/*genetics/growth & development/*isolation & purification, Alanine/analysis, China, DNA, Bacterial/genetics, Esterases/analysis, Fresh Water/microbiology, Glutamine/analysis, Glycoside Hydrolases/analysis, Lysine/analysis, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Bacterial/chemistry/genetics, RNA, Ribosomal, 16S/chemistry/genetics, Sodium Chloride/pharmacology, Soil MicrobiologyGenetics
Phylogeny21930682Georgenia daeguensis sp. nov., isolated from 4-chlorophenol enrichment culture.Woo SG, Cui Y, Kang MS, Jin L, Kim KK, Lee ST, Lee M, Park JInt J Syst Evol Microbiol10.1099/ijs.0.033217-02011Actinomycetales/*classification/genetics/*isolation & purification/metabolism, Bacterial Typing Techniques, Base Composition, Carbohydrates/analysis, Chlorophenols/*metabolism, Cluster Analysis, Culture Media/chemistry, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/analysis, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sewage/*microbiologyMetabolism
Phylogeny23811137Georgenia sediminis sp. nov., a moderately thermophilic actinobacterium isolated from sediment.You ZQ, Li J, Qin S, Tian XP, Wang FZ, Zhang SInt J Syst Evol Microbiol10.1099/ijs.0.051714-02013Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Molecular Sequence Data, Peptidoglycan/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryGenetics
Phylogeny26303654Georgenia subflava sp. nov., isolated from a deep-sea sediment.Wang S, Xu X, Wang L, Jiao K, Zhang GInt J Syst Evol Microbiol10.1099/ijsem.0.0005532015Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Pacific Ocean, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
6997Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17458)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17458
19749Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM17458.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
23157Wen-Jun Li, Ping Xu, Peter Schumann, Yu-Qin Zhang, Rüdiger Pukall, Li-Hua Xu, Erko Stackebrandt,Cheng-Lin Jiang10.1099/ijs.0.64749-0Georgenia ruanii sp. nov., a novel actinobacterium isolated from forest soil in Yunnan (China), and emended description of the genus GeorgeniaIJSEM 57: 1424-1428 200717625169
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)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
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
71420Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID232152.1StrainInfo: A central database for resolving microbial strain identifiers