Strain identifier

BacDive ID: 7455

Type strain: Yes

Species: Microbacterium ginsengiterrae

Strain history: <- DC Yang, Kyunghee Univ.

NCBI tax ID(s): 546115 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 17780

BacDive-ID: 7455

DSM-Number: 24823

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

description: Microbacterium ginsengiterrae DSM 24823 is an aerobe, spore-forming, mesophilic bacterium that was isolated from soil of ginseng field.

NCBI tax id

  • NCBI tax id: 546115
  • Matching level: species

strain history

@refhistory
17780<- JCM <- <- D.-C. Yang; DCY37
67770D.-C. Yang DCY37.
67771<- DC Yang, Kyunghee Univ.

doi: 10.13145/bacdive7455.20230509.8.1

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 ginsengiterrae
  • full scientific name: Microbacterium ginsengiterrae Kim et al. 2010

@ref: 17780

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Microbacteriaceae

genus: Microbacterium

species: Microbacterium ginsengiterrae

full scientific name: Microbacterium ginsengiterrae Kim et al. 2010

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
29554positive1.5-2 µm0.5-0.7 µmrod-shapedno
67771positive
69480positive100

pigmentation

  • @ref: 29554
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 17780
  • name: R2A MEDIUM (DSMZ Medium 830)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/830
  • composition: Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
17780positivegrowth28mesophilic
29554positivegrowth15-45
29554positiveoptimum30mesophilic
67770positivegrowth28mesophilic
67771positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
29554positivegrowth05-09alkaliphile
29554positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
29554aerobe
67771aerobe

spore formation

@refspore formationconfidence
29554yes
69480no99.828

halophily

@refsaltgrowthtested relationconcentration
29554NaClpositivegrowth01-08 %
29554NaClpositiveoptimum01-08 %

observation

@refobservation
29554aggregates in chains
67770quinones: MK-12, MK-13
67771quinones: MK-12

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
29554161933-hydroxybenzoate+carbon source
29554178794-hydroxybenzoate+carbon source
2955426546rhamnose+carbon source
2955433942ribose+carbon source
2955417992sucrose+carbon source

enzymes

@refvalueactivityec
29554catalase+1.11.1.6
29554cytochrome oxidase+1.9.3.1
29554urease+3.5.1.5

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
17780soil of ginseng fieldRepublic of KoreaKORAsia
67770Soil of a ginseng fieldRepublic of KoreaKORAsia
67771From soil, ginseng fieldRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Engineered#Agriculture#Field
#Environmental#Terrestrial#Soil
#Host#Plants#Herbaceous plants (Grass,Crops)

Safety information

risk assessment

  • @ref: 17780
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
29554Microbacterium ginsengiterrae strain DCY37 16S ribosomal RNA gene, partial sequenceEU873314.11427nuccore546115
17780Microbacterium ginsengiterrae strain DCY37 16S ribosomal RNA gene, partial sequenceEU8733141427ena546115

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Microbacterium ginsengiterrae DSM 24823GCA_014205075contigncbi546115
66792Microbacterium ginsengiterrae JCM 15516GCA_015278215contigncbi546115
66792Microbacterium ginsengiterrae strain DSM 24823546115.4wgspatric546115
66792Microbacterium ginsengiterrae strain JCM 15516546115.5wgspatric546115
66792Microbacterium ginsengiterrae DSM 248232870791180draftimg546115

GC content

@refGC-contentmethod
1778064.5high performance liquid chromatography (HPLC)
2955464.5
6777164.54

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes89no
gram-positiveyes96.322no
anaerobicno99.555yes
halophileno80.699no
spore-formingno85.544yes
glucose-utilyes84.881no
thermophileno99.461yes
aerobicyes94.405no
motileno88.303no
flagellatedno97.6yes
glucose-fermentno89.182no

External links

@ref: 17780

culture collection no.: DSM 24823, JCM 15516, KCTC 19526, DCY 37, NBRC 110802

straininfo link

  • @ref: 76902
  • straininfo: 374135

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny20081025Microbacterium ginsengiterrae sp. nov., a beta-glucosidase-producing bacterium isolated from soil of a ginseng field.Kim YJ, Kim MK, Bui TPN, Kim HB, Srinivasan S, Yang DCInt J Syst Evol Microbiol10.1099/ijs.0.015784-02010Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, Panax/*microbiology, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/chemistry, beta-Glucosidase/metabolismGenetics
Phylogeny25678679Microbacterium shaanxiense sp. nov., isolated from the nodule surface of soybean.Peng S, Dongying L, Bingxin Y, Mingjun L, Gehong WInt J Syst Evol Microbiol10.1099/ijs.0.0001162015Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Glycolipids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Root Nodules, Plant/*microbiology, Sequence Analysis, DNA, *Soil Microbiology, Soybeans/*microbiology, Vitamin K 2/chemistryGenetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
17780Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 24823)https://www.dsmz.de/collection/catalogue/details/culture/DSM-24823
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
29554Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2594928776041
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
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)
76902Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID374135.1StrainInfo: A central database for resolving microbial strain identifiers