Strain identifier

BacDive ID: 7429

Type strain: Yes

Species: Microbacterium ginsengisoli

Strain history: <- ST Lee, KAIST

NCBI tax ID(s): 400772 (species)

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General

@ref: 7642

BacDive-ID: 7429

DSM-Number: 18659

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

description: Microbacterium ginsengisoli DSM 18659 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from soil, ginseng field.

NCBI tax id

  • NCBI tax id: 400772
  • Matching level: species

strain history

@refhistory
7642<- Sung-Taik Lee <- Wan-Taek Im; Gsoil 259
67770KCTC 19189 <-- D.-C. Yang Gsoil 259.
67771<- ST Lee, KAIST

doi: 10.13145/bacdive7429.20230509.8.1

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 ginsengisoli
  • full scientific name: Microbacterium ginsengisoli Park et al. 2008

@ref: 7642

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Microbacteriaceae

genus: Microbacterium

species: Microbacterium ginsengisoli

full scientific name: Microbacterium ginsengisoli Park et al. 2008

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
32265positive0.7 µm0.35 µmrod-shapedno
67771positive

colony morphology

@refcolony colorincubation periodmedium used
19768Rapeseed yellow (1021)10-14 daysISP 2
19768Rapeseed yellow (1021)10-14 daysISP 3
1976810-14 daysISP 4
1976810-14 daysISP 5
19768Rapeseed yellow (1021)10-14 daysISP 6
19768Beige (1001)10-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
19768noISP 2
19768noISP 3
19768noISP 4
19768noISP 5
19768noISP 6
19768noISP 7

pigmentation

  • @ref: 32265
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7642TRYPTICASE 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
19768ISP 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
19768ISP 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:
19768ISP 4yesName: ISP 4; DSM 547 Solution I: Difco soluble starch, 10.0 g. Make a paste of the starch with a small amount of cold distilled water and bring to a volume of 500 ml. Solution II: CaCO3 2.0 g K2HPO4 (anhydrous) 1.0 g MgSO4 x 7 H2O 1.0 g NaCl 1.0 g (NH4)2SO4 2.0 g Distilled water 500.0 ml Trace salt solution (see below) 1.0 ml The pH should be between 7.0 and 7.4. Do not adjust if it is within this range. Mix solutions I and II together. Add 20.0 g agar. Liquify agar by steaming at 100°C for 10 to 20 min. Trace element solution: FeSO4 x 7 H2O 0.1 g MnCl2 x 4 H2O 0.1 g ZnSO4 x 7 H2O 0.1 g Distilled water 100.0 ml
19768ISP 5yesName: ISP 5 (5323) Composition L-Asparagine 1.0 g/l Glycerol 10.0 g/l K2HPO4 1.0 g/l Salt solution (see preparation) 1.0 ml/l Agar 20.0 g/l Preparation: Salt solution 1.0 g FeSO4 x 7 H2O 1.0 g MnCl2 x 4 H2O 1.0 g ZNSO4 x 7 H2O in 100 ml water Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.2 Usage: Maintenance and taxonomy Organisms: All Actinomycetes
19768ISP 6yesName: ISP 6 (5318) Composition Peptone 15.0 g/l Proteose peptose 5.0 g/l Ferric ammonium citrate 0.5 g/l Sodium glycerophosphate 1.0 g/l Sodium thiosulfate 0.08 g/l Yeast extract 1.0 g/l Agar 15.0 g/l Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigments Organisms: All Actinomycetes
19768ISP 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
7642positivegrowth28mesophilic
19768positiveoptimum28mesophilic
32265positivegrowth18-30
67770positivegrowth28mesophilic
67771positivegrowth30mesophilic

culture pH

  • @ref: 32265
  • ability: positive
  • type: growth
  • pH: 05-09
  • PH range: alkaliphile

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
32265aerobe
67771aerobe

halophily

  • @ref: 32265
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: <4 %

observation

  • @ref: 67770
  • observation: quinones: MK-12, MK-11

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
32265370543-hydroxybutyrate+carbon source
3226530089acetate+carbon source
3226516449alanine+carbon source
3226524265gluconate+carbon source
3226517234glucose+carbon source
3226525115malate+carbon source
3226517306maltose+carbon source
3226529864mannitol+carbon source
3226537684mannose+carbon source
3226526271proline+carbon source
3226517272propionate+carbon source
3226526546rhamnose+carbon source
3226517822serine+carbon source
3226517992sucrose+carbon source
3226531011valerate+carbon source
322654853esculin+hydrolysis
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

enzymes

@refvalueactivityec
32265acid phosphatase+3.1.3.2
32265catalase+1.11.1.6
32265cytochrome oxidase+1.9.3.1
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
19768------+--+-------+-

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
19768--++++-++++---+----

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
7642soil, ginseng fieldDaejonRepublic of KoreaKORAsia
67770Soil from a ginseng fieldPocheonRepublic 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

@refbiosafety levelbiosafety level comment
76421Risk group (German classification)
197681Risk group (German classification)

Sequence information

16S sequences

  • @ref: 7642
  • description: Microbacterium ginsengisoli gene for 16S rRNA, partial sequence
  • accession: AB271048
  • length: 1458
  • database: ena
  • NCBI tax ID: 400772

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Microbacterium ginsengisoli strain DSM 18659400772.4wgspatric400772
66792Microbacterium ginsengisoli DSM 186592671180799draftimg400772
67770Microbacterium ginsengisoli DSM 18659GCA_000956535contigncbi400772

GC content

@refGC-contentmethod
764269.4
6777069.4high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
gram-positiveyes92.507yes
anaerobicno99.45yes
halophileno90.609no
spore-formingno94.032no
glucose-utilyes87.378no
aerobicyes89.903no
motileno90.36no
flagellatedno97.956yes
thermophileno98.33yes
glucose-fermentno90.449yes

External links

@ref: 7642

culture collection no.: DSM 18659, KCTC 19189, Gsoil 259, JCM 15304

straininfo link

  • @ref: 76878
  • straininfo: 292548

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny18218944Microbacterium ginsengisoli sp. nov., a beta-glucosidase-producing bacterium isolated from soil of a ginseng field.Park MJ, Kim MK, Kim HB, Im WT, Yi TH, Kim SY, Soung NK, Yang DCInt J Syst Evol Microbiol10.1099/ijs.0.65226-02008Actinomycetales/*classification/*enzymology/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/analysis, Fatty Acids/analysis, Genes, rRNA, Molecular Sequence Data, Panax/*growth & development, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Species Specificity, beta-Glucosidase/*biosynthesisEnzymology
Phylogeny26296337Microbacterium rhizomatis sp. nov., a beta-glucosidase-producing bacterium isolated from rhizome of Korean mountain ginseng.Hoang VA, Kim YJ, Nguyen NL, Kang CH, Kang JP, Singh P, Farh ME, Yang DU, Yang DCInt J Syst Evol Microbiol10.1099/ijsem.0.0003992015*Actinomycetales/classification, Bacterial Typing Techniques, Base Composition, Cellulases/genetics, DNA, Bacterial/genetics, Fatty Acids/chemistry, Genotype, Glucosidases, Glycolipids/chemistry, Lipids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization/genetics, Panax/microbiology, Peptidoglycan/chemistry, Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Rhizome, Sequence Analysis, DNA, Soil MicrobiologyGenetics
Phylogeny26757723Microbacterium horti sp. nov., a bacterium isolated from Cucurbita maxima cultivating soil.Akter S, Park JH, Yin CSArch Microbiol10.1007/s00203-015-1183-32016Actinomycetales/chemistry/*classification/genetics/metabolism, Base Composition, Cucurbita, Fatty Acids/analysis, Molecular Sequence Data, Peptidoglycan/metabolism, *Phylogeny, RNA, Ribosomal, 16S/genetics, *Soil Microbiology, Species Specificity, Vitamin K 2/metabolismMetabolism
Phylogeny27692033Huakuichenia soli gen. nov., sp. nov., a new member of the family Microbacteriaceae, isolated from contaminated soil.Zhang L, Chen XL, Hu Q, Ruan ZP, Chen K, Li SP, Jiang JDInt J Syst Evol Microbiol10.1099/ijsem.0.0015312016Actinomycetales/*classification/genetics/isolation & purification, Aminobutyrates/chemistry, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, China, DNA, Bacterial/genetics, Environmental Pollution, Fatty Acids/chemistry, Glycolipids/chemistry, Peptidoglycan/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Soil/chemistry, *Soil MicrobiologyTranscriptome
Phylogeny33502309Microbacterium caowuchunii sp. nov. and Microbacterium lushaniae sp. nov., isolated from plateau pika (Ochotona curzoniae) on the Qinghai-Tibet Plateau of PR China.Tian Z, Yang J, Lai XH, Pu J, Jin D, Luo X, Huang Y, Li J, Zhang G, Wang S, Xu JInt J Syst Evol Microbiol10.1099/ijsem.0.0046622021Animals, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Gastrointestinal Contents/microbiology, Lagomorpha/*microbiology, Microbacterium/*classification/isolation & purification, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Tibet, Vitamin K 2/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
7642Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18659)https://www.dsmz.de/collection/catalogue/details/culture/DSM-18659
19768Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM18659.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
32265Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2850628776041
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
76878Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID292548.1StrainInfo: A central database for resolving microbial strain identifiers