Strain identifier

BacDive ID: 3124

Type strain: Yes

Species: Corynebacterium variabile

Strain Designation: FK 31

Strain history: CIP <- 1989, ATCC, Caseobacter polymorphus <- G. Müller: strain FK 31, Arthrobacter variabilis

NCBI tax ID(s): 1727 (species)

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General

@ref: 8557

BacDive-ID: 3124

DSM-Number: 20132

keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, mesophilic

description: Corynebacterium variabile FK 31 is an obligate aerobe, mesophilic bacterium that was isolated from food.

NCBI tax id

  • NCBI tax id: 1727
  • Matching level: species

strain history

@refhistory
8557<- ATCC <- G. Miller, FK 31
67770IAM 12346 <-- CCM 1565 <-- G. Müller FK31.
123795CIP <- 1989, ATCC, Caseobacter polymorphus <- G. Müller: strain FK 31, Arthrobacter variabilis

doi: 10.13145/bacdive3124.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Mycobacteriales
  • family: Corynebacteriaceae
  • genus: Corynebacterium
  • species: Corynebacterium variabile
  • full scientific name: Corynebacterium variabile corrig. (Müller 1961) Collins 1987

  • synonyms

    @refsynonym
    20215Caseobacter polymorphus
    20215Arthrobacter variabilis
    20215Corynebacterium mooreparkense
    20215Corynebacterium variabilis

@ref: 8557

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Corynebacteriaceae

genus: Corynebacterium

species: Corynebacterium variabile

full scientific name: Corynebacterium variabile (Müller 1961) Collins 1987

strain designation: FK 31

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480no95.047
69480100positive
123795nopositiverod-shaped

colony morphology

@refcolony colorincubation periodmedium used
18626Light ivory (1015)10-14 daysISP 2
18626Oyster white (1013)10-14 daysISP 3
18626Colorless10-14 daysISP 4
18626Colorless10-14 daysISP 5
18626Oyster white (1013)10-14 daysISP 6
18626Colorless10-14 daysISP 7
123795

multicellular morphology

@refforms multicellular complexmedium name
18626noISP 2
18626noISP 3
18626noISP 4
18626noISP 5
18626noISP 6
18626noISP 7

multimedia

@refmultimedia contentintellectual property rightscaption
8557https://www.dsmz.de/microorganisms/photos/DSM_20132-1.jpg© Leibniz-Institut DSMZ
8557https://www.dsmz.de/microorganisms/photos/DSM_20132.jpg© Leibniz-Institut DSMZMedium 535a 37°C

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
18626ISP 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
18626ISP 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:
18626ISP 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
18626ISP 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
18626ISP 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
18626ISP 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
8557COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)yesName: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar basehttps://mediadive.dsmz.de/medium/693
8557TRYPTICASE SOY BROTH AGAR+BLOOD (DSMZ Medium 535a)yesName: TRYPTICASE SOY BROTH AGAR+BLOOD (DSMZ Medium 535a) Composition: None 50.0 g/l Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled waterhttps://mediadive.dsmz.de/medium/535a
38093MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
123795CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
18626positiveoptimum28mesophilic
8557positivegrowth37mesophilic
38093positivegrowth30mesophilic
67770positivegrowth30mesophilic
123795positivegrowth15-30
123795nogrowth10psychrophilic
123795nogrowth37mesophilic
123795nogrowth41thermophilic
123795nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 123795
  • oxygen tolerance: obligate aerobe

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 99.999

halophily

@refsaltgrowthtested relationconcentration
18626NaClpositivemaximum2.5 %
123795NaClpositivegrowth0-10 %

murein

  • @ref: 8557
  • murein short key: A31
  • type: A1gamma m-Dpm-direct

observation

  • @ref: 67770
  • observation: quinones: MK-9(H2)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1862662968cellulose-
1862616634raffinose-
1862626546rhamnose-
1862628757fructose+
1862629864mannitol-
1862617268myo-inositol-
1862618222xylose-
1862617992sucrose-
1862622599arabinose-
1862617234glucose+
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
6837124265gluconate-builds acid from
6837118403L-arabitol-builds acid from
6837118333D-arabitol-builds acid from
6837118287L-fucose-builds acid from
6837128847D-fucose-builds acid from
6837116443D-tagatose-builds acid from
6837162318D-lyxose-builds acid from
6837132528turanose-builds acid from
6837128066gentiobiose-builds acid from
6837117151xylitol-builds acid from
6837128087glycogen-builds acid from
6837128017starch-builds acid from
6837116634raffinose-builds acid from
683716731melezitose-builds acid from
6837115443inulin-builds acid from
6837127082trehalose-builds acid from
6837117992sucrose-builds acid from
6837128053melibiose-builds acid from
6837117716lactose-builds acid from
6837117306maltose-builds acid from
6837117057cellobiose-builds acid from
6837127613amygdalin-builds acid from
6837159640N-acetylglucosamine-builds acid from
68371320061methyl alpha-D-glucopyranoside-builds acid from
6837143943methyl alpha-D-mannoside-builds acid from
6837117924D-sorbitol-builds acid from
6837116899D-mannitol-builds acid from
6837117268myo-inositol-builds acid from
6837116813galactitol-builds acid from
6837162345L-rhamnose-builds acid from
6837117266L-sorbose-builds acid from
6837112936D-galactose-builds acid from
6837174863methyl beta-D-xylopyranoside-builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837165327D-xylose-builds acid from
6837116988D-ribose-builds acid from
6837130849L-arabinose-builds acid from
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from
6837117754glycerol-builds acid from
683685291gelatin-hydrolysis
6836827897tryptophan-energy source
6836816199urea+hydrolysis
6836816947citrate+assimilation
6836818257ornithine-degradation
6836825094lysine-degradation
6836829016arginine-hydrolysis
12379516947citrate-carbon source
1237954853esculin+hydrolysis
123795606565hippurate-hydrolysis
12379517632nitrate-reduction
12379516301nitrite-reduction
12379517632nitrate-respiration
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

antibiotic resistance

  • @ref: 123795
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinyes
6836835581indoleno
6836816136hydrogen sulfideno
12379535581indoleno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole testmethylred-test
6836815688acetoin+
6836835581indole-
12379515688acetoin-
12379517234glucose-

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
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)+
68382esterase (C 4)+
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
123795oxidase-
123795beta-galactosidase-3.2.1.23
123795alcohol dehydrogenase-1.1.1.1
123795gelatinase-
123795amylase-
123795DNase-
123795caseinase-3.4.21.50
123795catalase+1.11.1.6
123795tween esterase+
123795gamma-glutamyltransferase-2.3.2.2
123795lecithinase-
123795lipase-
123795lysine decarboxylase-4.1.1.18
123795ornithine decarboxylase-4.1.1.17
123795phenylalanine ammonia-lyase-4.3.1.24
123795protease-
123795tryptophan deaminase-
123795urease+3.5.1.5

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
18626-++-+++--++---++-+-

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
18626+++-+++--++---++---
123795-++-+-+--++---++----

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
18626----+-+--+-

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
123795----------+/-+/-+/-----------+/-+/-+/------------------------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
123795++--+-------------+-------+----------------------++--+---------------------+-+-+++-+------------+--

Isolation, sampling and environmental information

isolation

@refsample type
8557food
67770Food
123795Food

isolation source categories

  • Cat1: #Engineered
  • Cat2: #Food production
  • Cat3: #Food

taxonmaps

  • @ref: 69479
  • File name: preview.99_425.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_288;97_318;98_353;99_425&stattab=map
  • Last taxonomy: Corynebacterium
  • 16S sequence: AJ222815
  • Sequence Identity:
  • Total samples: 16580
  • soil counts: 1425
  • aquatic counts: 2885
  • animal counts: 11599
  • plant counts: 671

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
186261German classification
85571Risk group (German classification)
1237952Risk group (French classification)

Sequence information

16S sequences

  • @ref: 20218
  • description: Corynebacterium variabilis (strain DSM 20132) 16S rRNA gene
  • accession: AJ222815
  • length: 1436
  • database: ena
  • NCBI tax ID: 1727

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Corynebacterium variabile strain NBRC 152861727.16wgspatric1727
67770Corynebacterium variabile NBRC 15286GCA_006539825contigncbi1727
67770Corynebacterium variabile NRRL B-4201GCA_000720035contigncbi1727

GC content

  • @ref: 8557
  • GC-content: 70.0

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno71no
motileno95.565no
gram-positiveyes92.959no
anaerobicno99.589no
aerobicyes76.137no
halophileyes64.371no
spore-formingno93.317no
glucose-utilyes90.994yes
flagellatedno97.696no
thermophileno97.801yes
glucose-fermentno76.381yes

External links

@ref: 8557

culture collection no.: DSM 20132, ATCC 15753, CCM 1565, NCIB 9455, JCM 2154, BCRC 12115, CCUG 23608, CCUG 45246, CECT 4178, CGMCC 1.1922, CIP 102112, HAMBI 1872, IAM 12346, IFO 15286, IMET 10433, LMG 22560, NBRC 15286, NCIMB 9455, NRRL B-4201, VKM Ac-1122, IFM 3030

straininfo link

  • @ref: 72641
  • straininfo: 92622

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny9721308Intraspecific variation of unusual phospholipids from Corynebacterium spp. containing a novel fatty acid.Niepel T, Meyer H, Wray V, Abraham WRJ Bacteriol10.1128/JB.180.17.4650-4657.19981998Corynebacterium/genetics/*metabolism, Fatty Acids/chemistry/*metabolism, Magnetic Resonance Spectroscopy, Phospholipids/chemistry/*metabolism, Phylogeny, Species Specificity, Spectrometry, Mass, Fast Atom BombardmentMetabolism
Phylogeny21075904Corynebacterium nuruki sp. nov., isolated from an alcohol fermentation starter.Shin NR, Jung MJ, Kim MS, Roh SW, Nam YD, Bae JWInt J Syst Evol Microbiol10.1099/ijs.0.027763-02010Alcohols/*metabolism, Amino Acids/analysis, Bacterial Typing Techniques, Base Composition, Carbohydrates/analysis, Catalase/metabolism, Cell Wall/chemistry, Cluster Analysis, Corynebacterium/*classification/genetics/*isolation & purification/physiology, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Fermentation, *Food Microbiology, Hydrogen-Ion Concentration, Molecular Sequence Data, Nucleic Acid Hybridization, Oxidoreductases/metabolism, Peptidoglycan/chemistry, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sodium Chloride/metabolism, TemperatureMetabolism

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
8557Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 20132)https://www.dsmz.de/collection/catalogue/details/culture/DSM-20132
18626Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM20132.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
38093Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/13763
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
68371Automatically annotated from API 50CH acid
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)
72641Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID92622.1StrainInfo: A central database for resolving microbial strain identifiers
123795Curators of the CIPCollection of Institut Pasteur (CIP 102112)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20102112