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Strain identifier

BacDive ID: 11115

Type strain: Yes

Species: Nocardioides ganghwensis

Strain Designation: JC2055

Strain history: <- J Chun, Seoul Nat. Univ.

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

doi: 10.13145/bacdive11115.20221219.7.1

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
69480positive97.7

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)

culture temp

@refgrowthtypetemperaturerange
6437positivegrowth28mesophilic
18611positiveoptimum28mesophilic
30185positivegrowth30mesophilic
30185positiveoptimum10-40
34960positivegrowth30mesophilic
67770positivegrowth28mesophilic
67771positivegrowth30mesophilic

culture pH

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

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
30185aerobe
67771aerobe

spore formation

@refspore formationconfidence
30185no
69480no91.82

halophily

@refsaltgrowthtested relationconcentrationhalophily levelconfidence
18611NaClpositivemaximum10 %
30185NaClpositivegrowth0.0-8.0 %
30185NaClpositiveoptimum0.5 %
69480non-halophilic96.17

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
6837917992sucrose+fermentation
683795291gelatin+hydrolysis
6837916199urea+hydrolysis
683794853esculin+hydrolysis

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+
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

@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- Fucosidase
18611+++++++-++++++++---

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

isolation source categories

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

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
186111Hazard group
64371Risk group (German 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
66792bacterium W1P31.065GCA_004560755contigpatric1869227

GC content

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

External links

@ref: 6437

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

straininfo link

@refpassport
20218http://www.straininfo.net/strains/381478
20218http://www.straininfo.net/strains/379587
20218http://www.straininfo.net/strains/379589
20218http://www.straininfo.net/strains/379590

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/urltitlejournalpubmedID_cross_reference
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
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
2653310.1099/ijs.0.03040-015280305
30185Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2877604126533
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 updatesNucleic Acids Res. 49: D498-D508 202033211880
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)