Strain identifier

BacDive ID: 7315

Type strain: Yes

Species: Curtobacterium luteum

Strain Designation: 2Y-12

Strain history: CIP <- 1986, NCIB <- K. Yamada: strain 2Y-12, Brevibacterium luteum

NCBI tax ID(s): 33881 (species)

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General

@ref: 8771

BacDive-ID: 7315

DSM-Number: 20542

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

description: Curtobacterium luteum 2Y-12 is an aerobe, Gram-positive bacterium that was isolated from paddy.

NCBI tax id

  • NCBI tax id: 33881
  • Matching level: species

strain history

@refhistory
8771<- CCM <- K. Komagata, 2Y-12 (Brevibacterium luteum)
67770K. Suzuki CNF 188 <-- AJ 1470 <-- IAM 1623 <-- K. Komagata 2Y-12.
120701CIP <- 1986, NCIB <- K. Yamada: strain 2Y-12, Brevibacterium luteum

doi: 10.13145/bacdive7315.20240916.9.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Microbacteriaceae
  • genus: Curtobacterium
  • species: Curtobacterium luteum
  • full scientific name: Curtobacterium luteum (Komagata and Iizuka 1964) Yamada and Komagata 1972 (Approved Lists 1980)

  • synonyms

    • @ref: 20215
    • synonym: Brevibacterium luteum

@ref: 8771

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Microbacteriaceae

genus: Curtobacterium

species: Curtobacterium luteum

full scientific name: Curtobacterium luteum (Komagata and Iizuka 1964) Yamada and Komagata 1972

strain designation: 2Y-12

type strain: yes

Morphology

colony morphology

@refincubation periodmedium usedcolony color
1875710-14 daysISP 2
1875710-14 daysISP 3
1875710-14 daysISP 4Ivory
1875710-14 daysISP 5
1875710-14 daysISP 6Honey yellow
1875710-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
18757noISP 2
18757noISP 3
18757noISP 4
18757noISP 5
18757noISP 6
18757noISP 7

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
18757ISP 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
18757ISP 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:
18757ISP 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
18757ISP 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
18757ISP 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
18757ISP 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
8771CORYNEBACTERIUM AGAR (DSMZ Medium 53)yesName: CORYNEBACTERIUM AGAR (DSMZ Medium 53) Composition: Agar 15.0 g/l Casein peptone 10.0 g/l NaCl 5.0 g/l Glucose 5.0 g/l Yeast extract 5.0 g/l Distilled waterhttps://mediadive.dsmz.de/medium/53
35425MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
120701CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperature
18757positiveoptimum28
8771positivegrowth30
35425positivegrowth30
47859positivegrowth30
67770positivegrowth30

Physiology and metabolism

oxygen tolerance

  • @ref: 47859
  • oxygen tolerance: aerobe

spore formation

  • @ref: 69481
  • spore formation: no
  • confidence: 92

compound production

@refcompound
8771restriction endonuclease BluI
20216Restrictase Blu I
20216Restrictase Blu II

halophily

  • @ref: 18757
  • salt: NaCl
  • growth: positive
  • tested relation: maximum
  • concentration: 5 %

murein

  • @ref: 8771
  • murein short key: B05
  • type: B2ß {Gly} [L-Hsr] D-Glu-D-Orn

observation

  • @ref: 67770
  • observation: quinones: MK-9

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1875762968cellulose-
1875716634raffinose+
1875726546rhamnose-
1875728757fructose-
1875729864mannitol-
1875717268myo-inositol+
1875718222xylose+
1875717992sucrose+
1875722599arabinose+
1875717234glucose+
683685291gelatin-hydrolysis
6836827897tryptophan-energy source
6836816199urea-hydrolysis
6836816947citrate-assimilation
6836818257ornithine-degradation
6836825094lysine-degradation
6836829016arginine-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

metabolite production

@refChebi-IDmetaboliteproduction
6836835581indoleno
6836816136hydrogen sulfideno

metabolite tests

  • @ref: 68368
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

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
68368gelatinase-
68368tryptophan deaminase-4.1.99.1
68368urease-3.5.1.5
68368ornithine decarboxylase-4.1.1.17
68368lysine decarboxylase-4.1.1.18
68368arginine dihydrolase-3.5.3.6
68368beta-galactosidase+3.2.1.23

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
18757+++-+++++++++-+++--

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
18757-++-+++++++++-++++-

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDGEL
18757+---------

Isolation, sampling and environmental information

isolation

@refsample type
8771paddy
47859Paddy
67770Chinese paddy
120701Environment, Paddy

isolation source categories

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

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
87711Risk group (German classification)
187571Hazard group
1207011Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Curtobacterium luteum 16S-23S ribosomal RNA intergenic spacer region, partial sequenceAY191508553nuccore33881
8771C.luteum (DSM20542) 16S rRNA geneX774371472nuccore33881

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Curtobacterium luteum DSM 20542GCA_016907595contigncbi33881
66792Curtobacterium luteum JCM 1480GCA_014646995scaffoldncbi33881
66792Curtobacterium luteum strain ATCC 1583033881.5wgspatric33881
66792Curtobacterium luteum strain DSM 2054233881.7wgspatric33881
66792Curtobacterium luteum strain JCM 148033881.6wgspatric33881
66792Curtobacterium luteum DSM 205422893593147draftimg33881
67770Curtobacterium luteum ATCC 15830GCA_013359885contigncbi33881

GC content

@refGC-contentmethod
877169.8
6777069.8thermal denaturation, midpoint method (Tm)
6777074.9thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69481spore-formingspore-formingAbility to form endo- or exosporesno92no
69480gram-positivegram-positivePositive reaction to Gram-stainingyes87.435no
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no98.666yes
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes85.011yes
69480spore-formingspore-formingAbility to form endo- or exosporesno71.6no
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno97yes
69480flagellatedmotile2+Ability to perform flagellated movementno78.5no

External links

@ref: 8771

culture collection no.: DSM 20542, ATCC 15830, CCM 2298, NCIB 11029, CCUG 23848, IAM 1632, JCM 1480, BCRC 12127, CGMCC 1.1913, CIP 102694, IAM 15150, IAM 1623, IFO 12676, IMET 10360, KCCM 12167, KCTC 3493, LMG 8787, NBRC 12676, NCCB 71046, NCIMB 11029, VKM Ac-2188, VKM B-1210

straininfo link

  • @ref: 76765
  • straininfo: 264341

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny6183393Nucleic acid hybridization studies on Microbacterium, Curtobacterium, Agromyces and related taxa.Dopfer H, Stackebrandt E, Fiedler FJ Gen Microbiol10.1099/00221287-128-8-16971982Actinomycetales/*classification/metabolism, DNA, Bacterial, *Nucleic Acid Hybridization, RNA, Bacterial, RNA, RibosomalMetabolism
Phylogeny18842862Curtobacterium ginsengisoli sp. nov., isolated from soil of a ginseng field.Kim MK, Kim YJ, Kim HB, Kim SY, Yi TH, Yang DCInt J Syst Evol Microbiol10.1099/ijs.0.65591-02008Actinomycetales/chemistry/*classification/*genetics/isolation & purification, Agriculture, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Genes, Bacterial, Genes, rRNA, Korea, Molecular Sequence Data, Panax/*microbiology, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil MicrobiologyGenetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
8771Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 20542)https://www.dsmz.de/collection/catalogue/details/culture/DSM-20542
18757Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM20542.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
20216Curators of the HKIhttp://www.leibniz-hki.de/de/Collection Description Leibniz-Institut für Naturstoff-Forschung und Infektionsbiologie e. V. Hans-Knöll-Institut (HKI)
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
35425Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/14408
47859Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 23848)https://www.ccug.se/strain?id=23848
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)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68368Automatically annotated from API 20E
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)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
76765Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID264341.1StrainInfo: A central database for resolving microbial strain identifiers
120701Curators of the CIPCollection of Institut Pasteur (CIP 102694)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20102694