Strain identifier

BacDive ID: 7442

Type strain: Yes

Species: Microbacterium kribbense

Strain history: <- CJ Kim, KRIBB

NCBI tax ID(s): 433645 (species)

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General

@ref: 7914

BacDive-ID: 7442

DSM-Number: 19265

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

description: Microbacterium kribbense DSM 19265 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from soil.

NCBI tax id

  • NCBI tax id: 433645
  • Matching level: species

strain history

@refhistory
7914<- Chang-Jin Kim; MSL 04
67770KCTC 19269 <-- C.-J. Kim MSL-04.
67771<- CJ Kim, KRIBB

doi: 10.13145/bacdive7442.20230509.8.1

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 kribbense
  • full scientific name: Microbacterium kribbense Dastager et al. 2008

@ref: 7914

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Microbacteriaceae

genus: Microbacterium

species: Microbacterium kribbense

full scientific name: Microbacterium kribbense Dastager et al. 2008

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
31204positive0.5-0.8 µm0.4-0.6 µmrod-shapedno
67771positive

colony morphology

@refcolony colorincubation periodmedium used
18332Colourless10-14 daysISP 2
1833210-14 daysISP 3
1833210-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
18332noISP 2
18332noISP 3
18332noISP 7

pigmentation

  • @ref: 31204
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7914TRYPTICASE 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
18332ISP 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
18332ISP 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:
18332ISP 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

culture temp

@refgrowthtypetemperaturerange
7914positivegrowth28mesophilic
18332positiveoptimum28mesophilic
31204positivegrowth20-37
31204positiveoptimum28mesophilic
67770positivegrowth28mesophilic
67771positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
31204positivegrowth07-11alkaliphile
31204positiveoptimum7.2-7.4

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31204aerobe
67771aerobe

halophily

@refsaltgrowthtested relationconcentration
31204NaClpositivegrowth0-3 %
31204NaClpositiveoptimum0-3 %

murein

  • @ref: 7914
  • murein short key: B06
  • type: B2ß {Gly} [L-Hsr] D-Glu(Hyg)-Gly-D-Orn

observation

@refobservation
31204aggregates in chains
67770quinones: MK-11, MK-12

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3120422599arabinose+carbon source
3120428260galactose+carbon source
3120417234glucose+carbon source
3120417306maltose+carbon source
3120429864mannitol+carbon source
3120437684mannose+carbon source
3120428053melibiose+carbon source
3120416634raffinose+carbon source
3120426546rhamnose+carbon source
3120417992sucrose+carbon source
3120427082trehalose+carbon source
312044853esculin+hydrolysis
3120417632nitrate+reduction
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

metabolite production

  • @ref: 31204
  • Chebi-ID: 16136
  • metabolite: hydrogen sulfide
  • production: yes

enzymes

@refvalueactivityec
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
18332----+-+++--------+-

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
18332-++-++-+-+-+-+++++-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
7914soilBigeum IslandRepublic of KoreaKORAsia
67770Soil from Bigeum IslandRepublic of KoreaKORAsia
67771From farming fieldBikeum islandRepublic of KoreaKORAsia

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Soil

Safety information

risk assessment

  • @ref: 7914
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 7914
  • description: Microbacterium kribbense strain MSL 04 16S ribosomal RNA gene, partial sequence
  • accession: EF466125
  • length: 1428
  • database: ena
  • NCBI tax ID: 433645

GC content

@refGC-contentmethod
791471.0thermal denaturation, midpoint method (Tm)
3120471
6777071thermal denaturation, midpoint method (Tm)

External links

@ref: 7914

culture collection no.: DSM 19265, KCTC 19269, MSL 04, JCM 16950

straininfo link

  • @ref: 76890
  • straininfo: 398019

literature

  • topic: Phylogeny
  • Pubmed-ID: 18984689
  • title: Microbacterium kribbense sp. nov., isolated from soil.
  • authors: Dastager SG, Lee JC, Ju YJ, Park DJ, Kim CJ
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.2008/001222-0
  • year: 2008
  • mesh: Actinomycetales/*classification/genetics/isolation & purification/physiology, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Genes, rRNA, Genotype, Korea, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Species Specificity
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
7914Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19265)https://www.dsmz.de/collection/catalogue/details/culture/DSM-19265
18332Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM19265.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
31204Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2753128776041
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
76890Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID398019.1StrainInfo: A central database for resolving microbial strain identifiers