Strain identifier

BacDive ID: 7307

Type strain: Yes

Species: Curtobacterium albidum

Strain Designation: Y-3-2

Strain history: CIP <- 1986, NCIB <- K. Komagata: strain Y-3-2, Brevibacterium albidum

NCBI tax ID(s): 50728 (species)

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General

@ref: 8861

BacDive-ID: 7307

DSM-Number: 20512

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

description: Curtobacterium albidum Y-3-2 is a Gram-positive bacterium that was isolated from paddy.

NCBI tax id

  • NCBI tax id: 50728
  • Matching level: species

strain history

@refhistory
8861<- IAM <- K. Komagata, Y-3-2 (Brevibacterium albidum)
67770K. Suzuki CNF 028 <-- AJ 1472 <-- IAM 1631 <-- K. Komagata Y-3-2.
116189CIP <- 1986, NCIB <- K. Komagata: strain Y-3-2, Brevibacterium albidum

doi: 10.13145/bacdive7307.20240916.9.1

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 albidum
  • full scientific name: Curtobacterium albidum (Komagata and Iizuka 1964) Yamada and Komagata 1972 (Approved Lists 1980)

  • synonyms

    • @ref: 20215
    • synonym: Brevibacterium albidum

@ref: 8861

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Microbacteriaceae

genus: Curtobacterium

species: Curtobacterium albidum

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

strain designation: Y-3-2

type strain: yes

Morphology

colony morphology

@refcolony colorincubation periodmedium used
18443Saffron yellow (1017)10-14 daysISP 2
18443Saffron yellow (1017)10-14 daysISP 3
18443Colorless10-14 daysISP 4
18443Colorless10-14 daysISP 6
18443Light ivory (1015)10-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
18443no
18443noISP 2
18443noISP 3
18443noISP 4
18443noISP 6
18443noISP 7

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
18443ISP 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
18443ISP 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:
18443ISP 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
18443ISP 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
18443ISP 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
8861CORYNEBACTERIUM 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
40447MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
116189CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperature
18443positiveoptimum28
8861positivegrowth30
40447positivegrowth30
67770positivegrowth28

Physiology and metabolism

compound production

@refcompound
8861restriction endonuclease BalI
20216Endonuclease Bal I

halophily

  • @ref: 18443
  • salt: NaCl
  • growth: positive
  • tested relation: maximum
  • concentration: 5 %

murein

  • @ref: 8861
  • murein short key: B06
  • type: B2ß {Gly} [L-Hsr] D-Glu(Hyg)-Gly-D-Orn

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1844317234glucose+
1844322599arabinose+
1844317992sucrose+
1844318222xylose+
1844317268myo-inositol+
1844329864mannitol-
1844328757fructose+
1844326546rhamnose+
1844316634raffinose+
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
6836815688acetoinyes
6836835581indoleno
6836816136hydrogen sulfideno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole test
6836815688acetoin+
6836835581indole-

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
18443-++-+----++--+---+-

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
18443+++-+----++--+-----

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
18443------+--+-

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
8861paddy
67770Chinese paddy
116189Environment, Chinese paddyChinaCHNAsia

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_614.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_387;97_436;98_498;99_614&stattab=map
  • Last taxonomy: Curtobacterium
  • 16S sequence: LC110196
  • Sequence Identity:
  • Total samples: 48823
  • soil counts: 11124
  • aquatic counts: 6793
  • animal counts: 21247
  • plant counts: 9659

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
88611Risk group (German classification)
184431German classification
1161891Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Curtobacterium albidum 16S-23S ribosomal RNA intergenic spacer region, partial sequenceAY191509520nuccore50728
20218Curtobacterium albidum 16S rRNA gene, strain DSM 20512AM0426921443nuccore50728
20218Curtobacterium albidum partial 16S rRNA gene, type strain DSM 20512AM4106911504nuccore50728
20218Curtobacterium albidum gene for 16S rRNA, partial sequenceAB0463631504nuccore50728
67770Curtobacterium albidum gene for 16S ribosomal RNA, partial sequence, strain: JCM 1344LC1101951407nuccore50728
67770Curtobacterium albidum gene for 16S ribosomal RNA, partial sequence, strain: IAM 1631 = JCM 20229LC1101961456nuccore50728

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Curtobacterium albidum strain DSM 2051250728.3wgspatric50728
67770Curtobacterium albidum DSM 20512GCA_013359825contigncbi50728

GC content

@refGC-contentmethod
886170.0
6777072thermal denaturation, midpoint method (Tm)
6777070thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69481spore-formingspore-formingAbility to form endo- or exosporesno86no
69480gram-positivegram-positivePositive reaction to Gram-stainingyes88.096no
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no95.854no
69480spore-formingspore-formingAbility to form endo- or exosporesno75.286no
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes84.95no
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno98yes
69480flagellatedmotile2+Ability to perform flagellated movementno78.5no

External links

@ref: 8861

culture collection no.: DSM 20512, ATCC 15831, CCM 2296, IAM 1631, NCIB 11030, JCM 1344, AJ 1472, BCRC 12116, CGMCC 1.1650, CGMCC 1.1903, CIP 102693, HAMBI 2039, IAM 12367, IFO 15078, JCM 20229, KCTC 3491, NBIMCC 1100, NBRC 15078, NCIMB 11030, VKM Ac-2186, VKM B-1206

straininfo link

  • @ref: 76757
  • straininfo: 36514

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Enzymology2946296Cloning of the lambda resistant genes from Brevibacterium albidum and Proteus vulgaris into Escherichia coli.Chae KS, Yoo OJBiochem Biophys Res Commun10.1016/0006-291x(86)90748-51986Bacterial Outer Membrane Proteins, Bacteriophage lambda/*physiology, Brevibacterium/*genetics, Cloning, Molecular, Escherichia coli/genetics, *Genes, Bacterial, Phenotype, Porins, Proteus vulgaris/*genetics, Receptors, Virus/*genetics, *Transformation, BacterialPhenotype
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
8861Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 20512)https://www.dsmz.de/collection/catalogue/details/culture/DSM-20512
18443Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM20512.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
40447Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/14407
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
69479João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich.https://microbeatlas.org/MicrobeAtlas 1.0 beta
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
76757Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID36514.1StrainInfo: A central database for resolving microbial strain identifiers
116189Curators of the CIPCollection of Institut Pasteur (CIP 102693)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20102693