Strain identifier

BacDive ID: 7317

Type strain: Yes

Species: Curtobacterium pusillum

Strain Designation: 100

Strain history: CIP <- 1981, IAM <- H. Iizuka: strain 100, Brevibacterium pusillum

NCBI tax ID(s): 69373 (species)

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General

@ref: 8894

BacDive-ID: 7317

DSM-Number: 20527

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

description: Curtobacterium pusillum 100 is a mesophilic, Gram-positive bacterium that was isolated from oil brine.

NCBI tax id

  • NCBI tax id: 69373
  • Matching level: species

strain history

@refhistory
8894<- IAM <- K. Komagata, 100 (Brevibacterium pusillum)
67770K. Suzuki CNF 106 <-- IAM 1479 <-- K. Komagata 100.
122066CIP <- 1981, IAM <- H. Iizuka: strain 100, Brevibacterium pusillum

doi: 10.13145/bacdive7317.20230509.8.1

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 pusillum
  • full scientific name: Curtobacterium pusillum (Iizuka and Komagata 1965) Yamada and Komagata 1972 (Approved Lists 1980)

  • synonyms

    • @ref: 20215
    • synonym: Brevibacterium pusillum

@ref: 8894

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Microbacteriaceae

genus: Curtobacterium

species: Curtobacterium pusillum

full scientific name: Curtobacterium pusillum (Iizuka and Komagata 1965) Yamada and Komagata 1972

strain designation: 100

type strain: yes

Morphology

cell morphology

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

colony morphology

@refcolony colorincubation periodmedium used
18446Ivory (1014)10-14 daysISP 2
18446Light ivory (1015)10-14 daysISP 3
18446Colorless10-14 daysISP 4
18446Colorless10-14 daysISP 5
18446Colorless10-14 daysISP 6
18446Light ivory (1015)10-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
18446noISP 2
18446noISP 3
18446noISP 4
18446noISP 5
18446noISP 6
18446noISP 7

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
18446ISP 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
18446ISP 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:
18446ISP 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
18446ISP 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
18446ISP 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
18446ISP 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
8894CORYNEBACTERIUM 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
37719MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
122066CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperaturerange
18446positiveoptimum28mesophilic
8894positivegrowth30mesophilic
37719positivegrowth30mesophilic
67770positivegrowth30mesophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481no94
69480no99.898

halophily

  • @ref: 18446
  • salt: NaCl
  • growth: positive
  • tested relation: maximum
  • concentration: 7.5 %

murein

  • @ref: 8894
  • murein short key: B05
  • type: B2ß {Gly} [L-Hsr] D-Glu-D-Orn

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1844617234glucose+
1844622599arabinose+
1844617992sucrose+
1844618222xylose+
1844617268myo-inositol+
1844629864mannitol-
1844628757fructose-
1844626546rhamnose+
1844616634raffinose+
1844662968cellulose-
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
18446-++++++++----------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
18446+++-++++-++++-+++++

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
18446+----------

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentgeographic location
8894oil brine
67770Oil-brine in Yabase oil-field in Akita Pref.JapanJPNAsia
122066Oil brineJapanJPNAsiaAkita

isolation source categories

Cat1Cat2Cat3
#Engineered#Contamination#Oil (Fuel)
#Condition#Saline
#Engineered#Food production#Oil (Food)

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: LN681569
  • 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
88941Risk group (German classification)
184461
1220661Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Curtobacterium pusillum 16S-23S ribosomal RNA intergenic spacer region, partial sequenceAY191510634ena69373
20218Curtobacterium pusillum 16S rRNA gene, type strain DSM 20527AJ7844001509ena69373
20218Curtobacterium sp. IFO 12674T gene for 16S rRNA, partial sequenceAB0463641506ena133417
8894Curtobacterium pusillum partial 16S rRNA gene, type strain DSM 20527TLN6815691474ena69373

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Curtobacterium pusillum strain ATCC 1909669373.17wgspatric69373
67770Curtobacterium pusillum ATCC 19096GCA_013359865contigncbi69373

GC content

@refGC-contentmethod
889469.0
6777074.2thermal denaturation, midpoint method (Tm)
6777069thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno94no
gram-positiveyes92.662no
anaerobicno99.282no
halophileno90.833no
spore-formingno93.443no
glucose-utilyes87.56yes
thermophileno99.236yes
flagellatedno93.766no
motileyes54.081no
aerobicyes91.402no
glucose-fermentno87.635yes

External links

@ref: 8894

culture collection no.: DSM 20527, ATCC 19096, IAM 1479, NCIB 10354, JCM 1350, BCRC 10376, CGMCC 1.1905, CIP 81.24, IFO 12674, IMET 11077, KCCM 12168, KCTC 3492, LMG 8788, NBRC 12674, NCIMB 10354, VKM Ac-1413, VKM Ac-2099

straininfo link

  • @ref: 76767
  • straininfo: 10472

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
8894Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 20527)https://www.dsmz.de/collection/catalogue/details/culture/DSM-20527
18446Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM20527.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
37719Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/11183
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
76767Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID10472.1StrainInfo: A central database for resolving microbial strain identifiers
122066Curators of the CIPCollection of Institut Pasteur (CIP 81.24)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%2081.24