Strain identifier

BacDive ID: 7428

Type strain: Yes

Species: Microbacterium koreense

Strain Designation: JS53-2

Strain history: CIP <- 2005, KCTC <- J.S. Lee, KRIBB: strain JS53-2

NCBI tax ID(s): 323761 (species)

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General

@ref: 7509

BacDive-ID: 7428

DSM-Number: 18332

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

description: Microbacterium koreense JS53-2 is an aerobe, spore-forming, mesophilic bacterium that was isolated from seawater.

NCBI tax id

  • NCBI tax id: 323761
  • Matching level: species

strain history

@refhistory
7509<- CIP <- KCTC
67770KCTC 19074 <-- J.-S. Lee JS53-2.
67771<- JS Lee, KRIBB
120468CIP <- 2005, KCTC <- J.S. Lee, KRIBB: strain JS53-2

doi: 10.13145/bacdive7428.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Microbacteriaceae
  • genus: Microbacterium
  • species: Microbacterium koreense
  • full scientific name: Microbacterium koreense Lee et al. 2006

@ref: 7509

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Microbacteriaceae

genus: Microbacterium

species: Microbacterium koreense

full scientific name: Microbacterium koreense Lee et al. 2006

strain designation: JS53-2

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
31585positive03-04 µm0.7 µmrod-shapedno
67771positive
120468positiverod-shapedyes

colony morphology

  • @ref: 120468
  • hemolysis ability: 1

pigmentation

  • @ref: 31585
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7509TRYPTICASE 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
38289MEDIUM 29- Brain heart agaryesDistilled water make up to (1000.000 ml);Brain heart infusion agar (52.000 g)
120468CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72
120468CIP Medium 29yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=29

culture temp

@refgrowthtypetemperaturerange
7509positivegrowth28mesophilic
31585positivegrowth20-37
31585positiveoptimum30mesophilic
38289positivegrowth30mesophilic
58974positivegrowth30-37mesophilic
67770positivegrowth28mesophilic
67771positivegrowth30mesophilic
120468positivegrowth15-37
120468nogrowth10psychrophilic
120468nogrowth41thermophilic
120468nogrowth45thermophilic

culture pH

@refabilitytypepH
31585positivegrowth06-08
31585positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31585aerobe
58974aerobe
67771aerobe
120468obligate aerobe

spore formation

  • @ref: 31585
  • spore formation: yes

halophily

@refsaltgrowthtested relationconcentration
31585NaClpositivegrowth0-10 %
120468NaClpositivegrowth0-10 %

observation

@refobservation
31585aggregates in chains
67770quinones: MK-11, MK-12
67771quinones: MK-11, MK-12

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3158517057cellobiose+carbon source
3158528757fructose+carbon source
3158517306maltose+carbon source
3158529864mannitol+carbon source
3158537684mannose+carbon source
31585506227N-acetylglucosamine+carbon source
3158526546rhamnose+carbon source
3158517992sucrose+carbon source
315854853esculin+hydrolysis
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
6837124265gluconate-builds acid from
6837118403L-arabitol-builds acid from
6837118333D-arabitol-builds acid from
6837118287L-fucose-builds acid from
6837128847D-fucose-builds acid from
6837162318D-lyxose-builds acid from
6837132528turanose+builds acid from
6837117151xylitol-builds acid from
6837128087glycogen-builds acid from
6837116634raffinose-builds acid from
683716731melezitose-builds acid from
6837115443inulin-builds acid from
6837127082trehalose+builds acid from
6837117992sucrose+builds acid from
6837128053melibiose-builds acid from
6837117306maltose+builds acid from
6837117057cellobiose+builds acid from
683714853esculin+builds acid from
6837159640N-acetylglucosamine+builds acid from
6837117924D-sorbitol-builds acid from
6837116899D-mannitol+builds acid from
6837117268myo-inositol-builds acid from
6837116813galactitol-builds acid from
6837117266L-sorbose-builds acid from
6837116024D-mannose+builds acid from
6837115824D-fructose+builds acid from
6837117634D-glucose+builds acid from
6837174863methyl beta-D-xylopyranoside-builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837165327D-xylose+builds acid from
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from
12046816947citrate-carbon source
1204684853esculin+hydrolysis
120468606565hippurate+hydrolysis
12046817632nitrate-reduction
12046816301nitrite-reduction
12046817632nitrate-respiration

metabolite production

  • @ref: 120468
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12046815688acetoin+
12046817234glucose+

enzymes

@refvalueactivityec
31585catalase+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
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
120468oxidase-
120468beta-galactosidase+3.2.1.23
120468alcohol dehydrogenase-1.1.1.1
120468gelatinase+/-
120468amylase+
120468DNase+
120468caseinase-3.4.21.50
120468catalase+1.11.1.6
120468tween esterase-
120468gamma-glutamyltransferase-2.3.2.2
120468lecithinase-
120468lipase-
120468lysine decarboxylase-4.1.1.18
120468ornithine decarboxylase-4.1.1.17
120468phenylalanine ammonia-lyase-4.3.1.24
120468protease-
120468tryptophan deaminase-
120468urease-3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
120468-+++-++-+-++---+-++-

API 50CHac

@refQGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
7509------+---++++-+--+---+--+-++--++---+---+---------
120468+--+++---+/-+++----+-+/-+/-++/-++++++/--++------++-+-------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
120468+++++-+++++---++++++++--------++-+++--+--+-+-----+++-+-----++---+--------+----+++-+---+--+++++----+

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentsampling dategeographic location
7509seawaterRepublic of KoreaKORAsia
58974SeawaterRepublic of KoreaKORAsia2002the South sea
67770SeawaterRepublic of KoreaKORAsia
67771From seawaterRepublic of KoreaKORAsiaSouth sea
120468Environment, SeawaterRepublic of KoreaKORAsiaSouth sea

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Aquatic
  • Cat3: #Marine

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
75091Risk group (German classification)
1204681Risk group (French classification)

Sequence information

16S sequences

  • @ref: 7509
  • description: Microbacterium koreense strain JS53-2 16S ribosomal RNA gene, partial sequence
  • accession: AY962574
  • length: 1436
  • database: ena
  • NCBI tax ID: 323761

GC content

@refGC-contentmethod
750968
6777068high performance liquid chromatography (HPLC)
6777168.0

External links

@ref: 7509

culture collection no.: DSM 18332, CCUG 50754, CIP 108696, KCTC 19074, JCM 15305, NBRC 110803, NRRL B-24570

straininfo link

  • @ref: 76877
  • straininfo: 214735

literature

  • topic: Phylogeny
  • Pubmed-ID: 16449451
  • title: Microbacterium koreense sp. nov., from sea water in the South Sea of Korea.
  • authors: Lee JS, Lee KC, Park YH
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.63854-0
  • year: 2006
  • mesh: Actinomycetales/chemistry/*classification/genetics/*isolation & purification, Bacterial Typing Techniques, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Genes, rRNA, Korea, Molecular Sequence Data, Nucleic Acid Hybridization, Oceans and Seas, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
7509Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18332)https://www.dsmz.de/collection/catalogue/details/culture/DSM-18332
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
31585Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2787428776041
38289Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6354
58974Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 50754)https://www.ccug.se/strain?id=50754
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
68371Automatically annotated from API 50CH acid
68382Automatically annotated from API zym
76877Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID214735.1StrainInfo: A central database for resolving microbial strain identifiers
120468Curators of the CIPCollection of Institut Pasteur (CIP 108696)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108696