Strain identifier

BacDive ID: 7308

Type strain: Yes

Species: Curtobacterium citreum

Strain Designation: 2Y-10

Strain history: CIP <- 1981, IAM <- K. Komagata: strain 2Y-10, Brevibacterium citreum

NCBI tax ID(s): 2036 (species)

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General

@ref: 8895

BacDive-ID: 7308

DSM-Number: 20528

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

description: Curtobacterium citreum 2Y-10 is a mesophilic, Gram-positive bacterium that was isolated from paddy.

NCBI tax id

  • NCBI tax id: 2036
  • Matching level: species

strain history

@refhistory
8895<- IAM <- K. Komagata, 2Y-10 (Brevibacterium citreum)
67770K. Suzuki CNF 026 <-- AJ 1469 <-- IAM 1614 <-- K. Komagata 2Y-10.
118297CIP <- 1981, IAM <- K. Komagata: strain 2Y-10, Brevibacterium citreum

doi: 10.13145/bacdive7308.20230509.8.1

Name and taxonomic classification

LPSN

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

  • synonyms

    • @ref: 20215
    • synonym: Brevibacterium citreum

@ref: 8895

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Microbacteriaceae

genus: Curtobacterium

species: Curtobacterium citreum

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

strain designation: 2Y-10

type strain: yes

Morphology

cell morphology

  • @ref: 69480
  • gram stain: positive
  • confidence: 100

colony morphology

@refcolony colorincubation periodmedium used
18752Maize yellow10-14 daysISP 2
18752Zinc yellow10-14 daysISP 3
18752Light ivory10-14 daysISP 4
18752Oyster white10-14 daysISP 5
1875210-14 daysISP 6
18752Ivory10-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
18752noISP 2
18752noISP 3
18752noISP 4
18752noISP 5
18752noISP 6
18752noISP 7

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
18752ISP 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
18752ISP 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:
18752ISP 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
18752ISP 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
18752ISP 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
18752ISP 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
8895CORYNEBACTERIUM 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
37720MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
118297CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperaturerange
18752positiveoptimum28mesophilic
8895positivegrowth30mesophilic
37720positivegrowth30mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 99.983

halophily

  • @ref: 18752
  • salt: NaCl
  • growth: positive
  • tested relation: maximum
  • concentration: 5 %

murein

  • @ref: 8895
  • 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
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
6836815688acetoinno
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
18752+++-+++++++++-++-++

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
18752+++-+++++++++-++-++

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
18752+----------

Isolation, sampling and environmental information

isolation

@refsample type
8895paddy
67770Chinese paddy
118297Food, Rice

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: X77436
  • 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
88951Risk group (German classification)
187521Hazard group
1182971Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Curtobacterium citreum gene for 16S ribosomal RNA, partial sequence, strain: DSM 20528AB915609946ena2036
20218Curtobacterium citreum partial 16S rRNA gene, type strain DSM 20528AM4106901472ena2036
20218Curtobacterium citreum 16S-23S ribosomal RNA intergenic spacer region, partial sequenceAY191507549ena2036
8895C.citreum (DSM 20528) 16S rRNA geneX774361472ena2036

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Curtobacterium citreum JCM 1345GCA_014646735scaffoldncbi2036
66792Curtobacterium citreum strain DSM 205282036.6wgspatric2036
66792Curtobacterium citreum strain JCM 13452036.7wgspatric2036
66792Curtobacterium citreum DSM 205282806311065draftimg2036
67770Curtobacterium citreum DSM 20528GCA_006715175contigncbi2036

GC content

@refGC-contentmethod
889570.5
6777070.5thermal denaturation, midpoint method (Tm)
6777075.2thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes75no
flagellatedno94.189no
gram-positiveyes91.917no
anaerobicno99.554no
aerobicyes93.545no
halophileno84.337no
spore-formingno93.42no
thermophileno99.489yes
glucose-utilyes87.308no
motileyes50.534no
glucose-fermentno88.956no

External links

@ref: 8895

culture collection no.: DSM 20528, ATCC 15828, CCM 2297, IAM 1614, NCIB 10702, JCM 1345, BCRC 12126, CCUG 12163, CCUG 28999, CGMCC 1.1904, CIP 81.26, IFO 12677, IMET 10359, KCCM 12166, KCTC 9100, LMG 8786, NBRC 12677, NCIMB 10702, NRIC 1859, VKM Ac-2187, VKM B-1207, CCUG 23579

straininfo link

  • @ref: 76758
  • straininfo: 92584

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
Metabolism31442382New Caledonian ultramafic conditions structure the features of Curtobacterium citreum strains that play a role in plant adaptation.Bourles A, Guentas L, Chalkiadakis E, Majorel C, Juillot F, Cavaloc Y, Burtet-Sarramegna V, Medevielle V, Jourand P, Amir HCan J Microbiol10.1139/cjm-2019-02832019Actinomycetales/classification/genetics/metabolism/*physiology, Metals/analysis/metabolism, New Caledonia, *Plant Physiological Phenomena, Plants/metabolism/*microbiology, Polysaccharides, Bacterial/metabolism, Rhizosphere, Soil/*chemistry, *Soil Microbiology, Sorghum/metabolism/microbiology/physiologyPhylogeny

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
8895Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 20528)https://www.dsmz.de/collection/catalogue/details/culture/DSM-20528
18752Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM20528.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
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
37720Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/11185
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)
76758Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID92584.1StrainInfo: A central database for resolving microbial strain identifiers
118297Curators of the CIPCollection of Institut Pasteur (CIP 81.26)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%2081.26