Strain identifier

BacDive ID: 11115

Type strain: Yes

Species: Nocardioides ganghwensis

Strain Designation: JC2055

Strain history: CIP <- 2004, JCM <- 2003, J. Chun: strain JC2055

NCBI tax ID(s): 252230 (species)

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General

@ref: 6437

BacDive-ID: 11115

DSM-Number: 16411

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

description: Nocardioides ganghwensis JC2055 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from sediment sample of the getbol of Ganghwa island.

NCBI tax id

  • NCBI tax id: 252230
  • Matching level: species

strain history

@refhistory
6437<- J. Chun, IMSNU; JC2055
67770J. Chun JC2055.
67771<- J Chun, Seoul Nat. Univ.
119529CIP <- 2004, JCM <- 2003, J. Chun: strain JC2055

doi: 10.13145/bacdive11115.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Propionibacteriales
  • family: Nocardioidaceae
  • genus: Nocardioides
  • species: Nocardioides ganghwensis
  • full scientific name: Nocardioides ganghwensis Yi and Chun 2004

@ref: 6437

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Nocardioidaceae

genus: Nocardioides

species: Nocardioides ganghwensis

full scientific name: Nocardioides ganghwensis Yi and Chun 2004

strain designation: JC2055

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
30185positive2.7 µm0.45 µmrod-shapedno
67771positive
69480no95.279
69480positive100
119529positiverod-shapedno

colony morphology

  • @ref: 119529

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6437BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)yeshttps://mediadive.dsmz.de/medium/514Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water
34960Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
119529CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperaturerange
6437positivegrowth28mesophilic
18611positiveoptimum28mesophilic
30185positivegrowth30mesophilic
30185positiveoptimum10-40
34960positivegrowth30mesophilic
67770positivegrowth28mesophilic
67771positivegrowth30mesophilic
119529positivegrowth10-41
119529nogrowth45thermophilic

culture pH

@refabilitytypepHPH range
30185positivegrowth6.0-10alkaliphile
30185positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
30185aerobe
67771aerobe
119529obligate aerobe

spore formation

@refspore formationconfidence
30185no
69481no100
69480no98.804

halophily

@refsaltgrowthtested relationconcentration
18611NaClpositivemaximum10 %
30185NaClpositivegrowth0.0-8.0 %
30185NaClpositiveoptimum0.5 %
119529NaClnogrowth0 %
119529NaClnogrowth2 %
119529NaClnogrowth4 %
119529NaClnogrowth6 %
119529NaClnogrowth8 %
119529NaClnogrowth10 %

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1861162968cellulose+
1861116634raffinose+
1861126546rhamnose-
1861128757fructose+
1861129864mannitol+/-
1861117268myo-inositol-
1861118222xylose-
1861117992sucrose+
1861122599arabinose+
1861117234glucose+
3018517057cellobiose+carbon source
3018516947citrate+carbon source
3018528757fructose+carbon source
3018528260galactose+carbon source
3018517234glucose+carbon source
3018517754glycerol+carbon source
3018517716lactose+carbon source
3018529864mannitol+carbon source
3018537684mannose+carbon source
3018516634raffinose+carbon source
3018517814salicin+carbon source
3018553426tween 80+carbon source
3018518222xylose+carbon source
301854853esculin+hydrolysis
3018517632nitrate+reduction
11952916947citrate-carbon source
1195294853esculin-hydrolysis
119529606565hippurate+hydrolysis
11952917632nitrate+reduction
11952916301nitrite-reduction
683794853esculin+hydrolysis
6837916199urea+hydrolysis
683795291gelatin+hydrolysis
6837917992sucrose+fermentation

metabolite production

  • @ref: 119529
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
11952915688acetoin-
11952917234glucose-

enzymes

@refvalueactivityec
30185acid phosphatase+3.1.3.2
30185alkaline phosphatase+3.1.3.1
30185alpha-galactosidase+3.2.1.22
30185catalase+1.11.1.6
30185gelatinase+
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
119529oxidase-
119529beta-galactosidase-3.2.1.23
119529alcohol dehydrogenase-1.1.1.1
119529gelatinase+
119529amylase+
119529caseinase+3.4.21.50
119529catalase+1.11.1.6
119529tween esterase+
119529gamma-glutamyltransferase+2.3.2.2
119529lecithinase-
119529lipase-
119529lysine decarboxylase-4.1.1.18
119529ornithine decarboxylase-4.1.1.17
119529phenylalanine ammonia-lyase+4.3.1.24
119529protease+
119529tryptophan deaminase-
119529urease-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
68382acid phosphatase+3.1.3.2
68382alpha-galactosidase+3.2.1.22
68382beta-galactosidase+3.2.1.23
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
18611--+-++-++++

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
18611+++++++-++++++++---
119529+++-+++--+-++-++----

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
119529++++--++++++++++--+-+++--+-----+-+-+-----------------------++-----------+--+------------+------+--+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
6437sediment sample of the getbol of Ganghwa islandGanghwa islandRepublic of KoreaKORAsia
67770Tidal flat sedimentGanghwa IslandRepublic of KoreaKORAsia
67771Tidal flat sedimentGanghwa IslandRepublic of KoreaKORAsia
119529Environment, Tidal flat sedimentGanghwa islandRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Sediment
#Environmental#Terrestrial#Tidal flat

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
64371Risk group (German classification)
186111Hazard group
1195291Risk group (French classification)

Sequence information

16S sequences

  • @ref: 6437
  • description: Nocardioides ganghwensis strain JC2055 16S ribosomal RNA gene, partial sequence
  • accession: AY423718
  • length: 1438
  • database: ena
  • NCBI tax ID: 252230

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Nocardioides ganghwensis strain CGMCC 4.6875252230.3wgspatric252230
66792Nocardioides ganghwensis CGMCC 4.68752867498717draftimg252230
67770Nocardioides ganghwensis CGMCC 4.6875GCA_004137235contigncbi252230

GC content

@refGC-contentmethod
643772
6777072high performance liquid chromatography (HPLC)
6777172.0high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno96.152yes
gram-positiveyes91.922yes
anaerobicno98.738yes
aerobicyes94.098yes
halophileno91.775yes
spore-formingno84.019yes
glucose-utilyes89.121no
flagellatedno97.916yes
thermophileno98.349yes
glucose-fermentno88.073no

External links

@ref: 6437

culture collection no.: DSM 16411, IMSNU 14028, JCM 12124, KCTC 9920, CGMCC 4.6875, CIP 108507, IAM 15306

straininfo link

  • @ref: 80364
  • straininfo: 132793

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15280305Nocardioides ganghwensis sp. nov., isolated from tidal flat sediment.Yi H, Chun JInt J Syst Evol Microbiol10.1099/ijs.0.03040-02004Actinomycetales/*classification/genetics/*isolation & purification/physiology, Aerobiosis, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/chemistry, DNA, Ribosomal/chemistry, Fatty Acids/analysis, Genes, rRNA, Geologic Sediments/*microbiology, Korea, Molecular Sequence Data, Movement, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Stearic Acids/analysis, Vitamin K 2/analysis, Water MicrobiologyGenetics
Phylogeny16014472Nocardioides oleivorans sp. nov., a novel crude-oil-degrading bacterium.Schippers A, Schumann P, Sproer CInt J Syst Evol Microbiol10.1099/ijs.0.63500-02005Actinomycetales/chemistry/*classification/genetics/physiology, Bacterial Typing Techniques, Biodegradation, Environmental, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Petroleum/*metabolism, Phenotype, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Species SpecificityGenetics
Phylogeny17220437Nocardioides furvisabuli sp. nov., isolated from black sand.Lee SDInt J Syst Evol Microbiol10.1099/ijs.0.64444-02007Actinomycetales/chemistry/*classification/genetics/isolation & purification, Bacterial Typing Techniques, DNA, Bacterial/analysis, Genes, rRNA, Geologic Sediments/*microbiology, Korea, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNAGenetics
Phylogeny18175721Nocardioides hwasunensis sp. nov.Lee SD, Lee DW, Kim JSInt J Syst Evol Microbiol10.1099/ijs.0.65015-02008Actinomycetales/*classification/genetics/isolation & purification/physiology, Bacterial Typing Techniques, Base Composition, DNA Fingerprinting/methods, DNA, Bacterial/analysis, Genes, rRNA, Korea, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S, Seawater/*microbiology, Sequence Analysis, DNA, Species SpecificityGenetics
Phylogeny26442516Nocardioides glacieisoli sp. nov., isolated from a glacier.Liu Q, Liu HC, Zhang JL, Zhou YG, Xin YHInt J Syst Evol Microbiol10.1099/ijsem.0.0006582015Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Ice Cover/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryGenetics
Phylogeny27654931Nocardioides flavus sp. nov., isolated from marine sediment.Wang S, Zhou Y, Zhang GInt J Syst Evol Microbiol10.1099/ijsem.0.0015072016Actinomycetales/*classification/genetics/isolation & purification, Bacteria, Aerobic/classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Pacific Ocean, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/chemistryEnzymology
Phylogeny27902315Nocardioides cavernae sp. nov., an actinobacterium isolated from a karst cave.Han MX, Fang BZ, Tian Y, Zhang WQ, Jiao JY, Liu L, Zhang ZT, Xiao M, Wei DQ, Li WJInt J Syst Evol Microbiol10.1099/ijsem.0.0016762017Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, Caves/*microbiology, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny31135330Nocardioides zhouii sp. nov., isolated from the Hailuogou Glacier in China.Zhang GQ, Liu Q, Liu HC, Zhou YG, Xin YHInt J Syst Evol Microbiol10.1099/ijsem.0.0034712019Actinobacteria/*classification/isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Ice Cover/*microbiology, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny34542392Nocardioides baculatus sp. nov., a novel actinomycete isolated from the rhizosphere of Tagetes patula.Chhetri G, Kim I, Kang M, Kim J, So Y, Seo TInt J Syst Evol Microbiol10.1099/ijsem.0.0050122021*Actinobacteria/genetics, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nocardioides, Phospholipids, Phylogeny, RNA, Ribosomal, 16S/genetics, Rhizosphere, Sequence Analysis, DNA, *TagetesTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
6437Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16411)https://www.dsmz.de/collection/catalogue/details/culture/DSM-16411
18611Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM16411.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
30185Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2653328776041
34960Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6137
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/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
68379Automatically annotated from API Coryne
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)
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
80364Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID132793.1StrainInfo: A central database for resolving microbial strain identifiers
119529Curators of the CIPCollection of Institut Pasteur (CIP 108507)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108507