Strain identifier

BacDive ID: 10606

Type strain: Yes

Species: Gordonia sihwensis

Strain Designation: KAIST

Strain history: CIP <- 2003, DSMZ <- K.K. Kim: strain SPR2 <- C.S. Lee, KAIST

NCBI tax ID(s): 1223544 (strain), 173559 (species)

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General

@ref: 11873

BacDive-ID: 10606

DSM-Number: 44576

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

description: Gordonia sihwensis KAIST is an obligate aerobe, mesophilic, Gram-positive bacterium that was isolated from sulphur particle.

NCBI tax id

NCBI tax idMatching level
173559species
1223544strain

strain history

@refhistory
11873<- K. K. Kim; SPR2 <- C. S. Lee; KAIST
67770IFM 10619 <-- DSM 44576 <-- K. K. Kim SPR2 <-- C. S. Lee.
122603CIP <- 2003, DSMZ <- K.K. Kim: strain SPR2 <- C.S. Lee, KAIST

doi: 10.13145/bacdive10606.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Mycobacteriales
  • family: Gordoniaceae
  • genus: Gordonia
  • species: Gordonia sihwensis
  • full scientific name: Gordonia sihwensis Kim et al. 2003

@ref: 11873

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Gordoniaceae

genus: Gordonia

species: Gordonia sihwensis

full scientific name: Gordonia sihwensis Kim et al. 2003

strain designation: KAIST

type strain: yes

Morphology

cell morphology

  • @ref: 122603
  • gram stain: positive
  • cell shape: rod-shaped
  • motility: no

colony morphology

@refcolony colorincubation periodmedium used
20074Beige (1001)10-14 daysISP 2
20074Beige (1001)10-14 daysISP 3
20074Beige (1001)10-14 daysISP 4
20074Beige (1001)10-14 daysISP 5
20074Beige (1001)10-14 daysISP 6
20074Beige (1001)10-14 daysISP 7
122603

multicellular morphology

@refforms multicellular complexmedium name
20074noISP 2
20074noISP 3
20074noISP 4
20074noISP 5
20074noISP 6
20074noISP 7

multimedia

  • @ref: 11873
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_44576.jpg
  • caption: Medium 535 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11873TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)yeshttps://mediadive.dsmz.de/medium/535Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water
20074ISP 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
20074ISP 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:
20074ISP 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
20074ISP 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
20074ISP 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
20074ISP 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
33896MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
122603CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
20074positiveoptimum28mesophilic
11873positivegrowth28mesophilic
33896positivegrowth30mesophilic
67770positivegrowth28mesophilic
122603positivegrowth25-45
122603nogrowth10psychrophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 122603
  • oxygen tolerance: obligate aerobe

halophily

@refsaltgrowthtested relationconcentration
122603NaClpositivegrowth0-4 %
122603NaClnogrowth6 %
122603NaClnogrowth8 %
122603NaClnogrowth10 %

observation

  • @ref: 67770
  • observation: quinones: MK-9(H2), MK-8(H2)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2007417234glucose+
2007422599arabinose-
2007417992sucrose+
2007418222xylose-
2007417268myo-inositol-
2007429864mannitol+
2007428757fructose-
2007426546rhamnose-
2007416634raffinose-
2007462968cellulose-
12260316947citrate-carbon source
1226034853esculin-hydrolysis
122603606565hippurate+hydrolysis
12260317632nitrate+reduction
12260316301nitrite-reduction
12260317632nitrate-respiration
683794853esculin-hydrolysis
6837916199urea-hydrolysis
683795291gelatin-hydrolysis
6837917992sucrose+fermentation

antibiotic resistance

  • @ref: 122603
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

  • @ref: 122603
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12260315688acetoin-
12260317234glucose-

enzymes

@refvalueactivityec
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
122603oxidase-
122603beta-galactosidase-3.2.1.23
122603alcohol dehydrogenase-1.1.1.1
122603gelatinase-
122603amylase-
122603DNase+
122603caseinase-3.4.21.50
122603catalase+1.11.1.6
122603tween esterase+
122603gamma-glutamyltransferase-2.3.2.2
122603lecithinase-
122603lipase-
122603lysine decarboxylase-4.1.1.18
122603ornithine decarboxylase-4.1.1.17
122603phenylalanine ammonia-lyase-4.3.1.24
122603protease-
122603tryptophan deaminase-
122603urease-3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382leucine arylamidase+3.4.11.1
68382valine arylamidase+
68382cystine arylamidase+3.4.11.3
68382trypsin-3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase-3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase+3.2.1.20
68382beta-glucosidase+3.2.1.21
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API coryne

@refPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELSAC
20074-++--+----+

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
20074+++-+++--++---++---
122603+++++++--++---++----

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
122603++-+---+---------------------------+-----------------+-----+----------------------------+-+-----+--

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
11873sulphur particleKoreaRepublic of KoreaKORAsia
67770Wastewater-treatment bioreactor, the lake of SihwaRepublic of KoreaKORAsia
122603Environment, From a sulphur-oxidizing, autotrophic denitrification reactor used for advanced treatment of wastewaterLake of SihwaRepublic of KoreaKORAsia

isolation source categories

  • Cat1: #Condition
  • Cat2: #Sulfuric

taxonmaps

  • @ref: 69479
  • File name: preview.99_2948.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_85;97_1820;98_2276;99_2948&stattab=map
  • Last taxonomy: Gordonia
  • 16S sequence: AJ416151
  • Sequence Identity:
  • Total samples: 1008
  • soil counts: 85
  • aquatic counts: 620
  • animal counts: 263
  • plant counts: 40

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
118731Risk group (German classification)
200741German classification
1226031Risk group (French classification)

Sequence information

16S sequences

  • @ref: 11873
  • description: Gordonia sihwaniensis 16S rRNA gene, strain DSM 44576
  • accession: AJ416151
  • length: 1499
  • database: ena
  • NCBI tax ID: 173559

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Gordonia sihwensis NBRC 1082361223544.3wgspatric1223544
66792Gordonia sihwensis NBRC 1082362523231046draftimg1223544
67770Gordonia sihwensis NBRC 108236GCA_000333035contigncbi1223544

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno96.7no
gram-positiveyes91.605no
anaerobicno99.513no
aerobicyes91.048no
halophileno87.853no
spore-formingno87.703no
glucose-utilyes90.411yes
flagellatedno98.707no
thermophileno98.288yes
glucose-fermentno85.467no

External links

@ref: 11873

culture collection no.: DSM 44576, CIP 108158, NRRL B-24155, SPR 2, JCM 13435, BCRC 16380, IFM 10619, NBRC 108236

straininfo link

  • @ref: 79880
  • straininfo: 87979

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny13130028Gordonia sihwensis sp. nov., a novel nitrate-reducing bacterium isolated from a wastewater-treatment bioreactor.Kim KK, Lee CS, Kroppenstedt RM, Stackebrandt E, Lee STInt J Syst Evol Microbiol10.1099/ijs.0.02224-02003Bioreactors, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/analysis, Gordonia Bacterium/classification/genetics/*isolation & purification/*metabolism, Korea, Molecular Sequence Data, Mycolic Acids/analysis, Nitrates/metabolism, Oxidation-Reduction, Phenotype, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Waste Disposal, FluidMetabolism
Phylogeny17329793Gordonia shandongensis sp. nov., isolated from soil in China.Luo H, Gu Q, Xie J, Hu C, Liu Z, Huang YInt J Syst Evol Microbiol10.1099/ijs.0.64536-02007China, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Gordonia Bacterium/chemistry/*classification/genetics/isolation & purification, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, *Soil MicrobiologyGenetics

Reference

@idauthorscataloguedoi/urltitle
11873Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44576)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44576
20074Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM44576.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
33896Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5749
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/
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
79880Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID87979.1StrainInfo: A central database for resolving microbial strain identifiers
122603Curators of the CIPCollection of Institut Pasteur (CIP 108158)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108158