Strain identifier

BacDive ID: 3128

Type strain: Yes

Species: Corynebacterium vitaeruminis

Strain history: CIP <- 1982, ATCC <- M.A. Farrell, Flavobacterium vitarumen

NCBI tax ID(s): 1224164 (strain), 38305 (species)

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General

@ref: 8697

BacDive-ID: 3128

DSM-Number: 20294

keywords: genome sequence, 16S sequence, Bacteria, microaerophile, mesophilic

description: Corynebacterium vitaeruminis CCUG 28792 is a microaerophile, mesophilic bacterium that was isolated from Rumen.

NCBI tax id

NCBI tax idMatching level
1224164strain
38305species

strain history

@refhistory
8697<- H.G. Schlegel <- K. Komagata <- ATCC <- M.A. Rarrell (Flavobacterium vitarum)
67770K. Suzuki CNF 008 <-- AJ 1525 <-- ATCC 10234 <-- M. A. Farrell.
123877CIP <- 1982, ATCC <- M.A. Farrell, Flavobacterium vitarumen

doi: 10.13145/bacdive3128.20230509.8.1

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 vitaeruminis
  • full scientific name: Corynebacterium vitaeruminis corrig. (Bechdel et al. 1928) Lanéelle et al. 1980

  • synonyms

    @refsynonym
    20215Brevibacterium vitaeruminis
    20215Flavobacterium vitarumen
    20215Corynebacterium vitarumen
    20215Brevibacterium vitarumen

@ref: 8697

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Corynebacteriaceae

genus: Corynebacterium

species: Corynebacterium vitaeruminis

full scientific name: Corynebacterium vitaeruminis (Bechdel et al. 1928) Lanéelle et al. 1980

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram stain
69480no95.941
69480100positive

colony morphology

@refcolony colorincubation periodmedium used
18636Ochre yellow (1024)10-14 daysISP 2
18636Ivory (1014)10-14 daysISP 3
18636Colorless10-14 daysISP 4
18636Colorless10-14 daysISP 5
18636Ivory (1014)10-14 daysISP 6

multicellular morphology

@refforms multicellular complexmedium name
18636noISP 2
18636noISP 3
18636noISP 4
18636noISP 5
18636noISP 6

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
18636ISP 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
18636ISP 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:
18636ISP 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
18636ISP 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
18636ISP 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
8697CORYNEBACTERIUM 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
39821MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
123877CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperaturerange
18636positiveoptimum28mesophilic
8697positivegrowth30mesophilic
39821positivegrowth30mesophilic
67770positivegrowth30mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 49382
  • oxygen tolerance: microaerophile

spore formation

@refspore formationconfidence
69481no100
69480no99.938

halophily

  • @ref: 18636
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0 %

murein

  • @ref: 8697
  • murein short key: A31
  • type: A1gamma m-Dpm-direct

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1863662968cellulose-
1863616634raffinose-
1863626546rhamnose+
1863628757fructose-
1863629864mannitol-
1863617268myo-inositol+
1863618222xylose+
1863617992sucrose+
1863622599arabinose-
1863617234glucose+
683685291gelatin-hydrolysis
6836827897tryptophan-energy source
6836816199urea+hydrolysis
6836816947citrate-assimilation
6836818257ornithine-degradation
6836825094lysine-degradation
6836829016arginine-hydrolysis
6837917632nitrate-reduction
6837916199urea+hydrolysis
683795291gelatin+hydrolysis
6837917634D-glucose-fermentation
6837916988D-ribose+fermentation
6837965327D-xylose-fermentation
6837916899D-mannitol+fermentation
6837917306maltose+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
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

fatty acid profile

  • fatty acids

    @reffatty acidpercentageECL
    49382C16:037.916
    49382C17:03.617
    49382C18:01.918
    49382C16:1 ω7c25.815.819
    49382C17:1 ω8c3.816.792
    49382C18:1 ω9c22.917.769
    49382C18:2 ω6,9c/C18:0 ANTE417.724
  • type of FA analysis: whole cell analysis
  • method/protocol: CCUG

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
18636-++-+++++/-++-+-+++/-+-

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
18636+++-+++++++-+-+++--

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
18636------+--+-

Isolation, sampling and environmental information

isolation

@refsample type
67770Rumen
123877Unknown source

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
186361Risk group (German classification)
86971Risk group (German classification)
1238772Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
67770Corynebacterium vitaeruminis strain LMG 19075 16S ribosomal RNA gene, partial sequenceJX9869711472ena38305
67770Corynebacterium vitarumen 16S rRNA gene, strain NCTC 20294X846801434ena1224164

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Corynebacterium vitaeruminis DSM 20294GCA_000550805completencbi1224164
66792Corynebacterium vitaeruminis DSM 202941224164.3completepatric1224164
66792Corynebacterium vitaeruminis DSM 20294 Genome sequencing2558860221completeimg1224164

GC content

@refGC-contentmethod
869764.4
6777064.8thermal denaturation, midpoint method (Tm)
6777064.4thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno94.665no
flagellatedno97.474no
gram-positiveyes93.158no
anaerobicno98.524yes
halophileno62.258yes
spore-formingno89.491no
thermophileno93.984yes
glucose-utilyes90.536no
aerobicno71.421yes
glucose-fermentyes52.52no

External links

@ref: 8697

culture collection no.: CCUG 28792, DSM 20294, ATCC 10234, NCIB 9291, JCM 1323, CECT 537, CGMCC 1.1889, CIP 82.7, IAM 12429, IFO 12143, IMSNU 21210, KCCM 12165, KCTC 9648, LMG 19075, NBRC 12143, NCCB 52028, NCIMB 9291, VKM B-1211, VTT E-97777

straininfo link

  • @ref: 72645
  • straininfo: 14091

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Genetics25193714Complete genome sequence of Corynebacterium vitaeruminis DSM 20294T, isolated from the cow rumen as a vitamin B producer.Al-Dilaimi A, Albersmeier A, Kalinowski J, Ruckert CJ Biotechnol10.1016/j.jbiotec.2014.08.0362014Animals, Base Composition/genetics, Cattle, Corynebacterium/genetics/*metabolism, Molecular Sequence Data, Rumen/*microbiology, Vitamins/*metabolismMetabolism
Metabolism34878813The Pathway of Sulfide Oxidation to Octasulfur Globules in the Cytoplasm of Aerobic Bacteria.Wang T, Ran M, Li X, Liu Y, Xin Y, Liu H, Liu H, Xia Y, Xun LAppl Environ Microbiol10.1128/AEM.01941-212021Bacteria, Aerobic/metabolism, Cytoplasm/metabolism, *Hydrogen Sulfide/metabolism, Oxidation-Reduction, *Quinone Reductases/metabolism, Sulfides/metabolismEnzymology

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
8697Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 20294)https://www.dsmz.de/collection/catalogue/details/culture/DSM-20294
18636Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM20294.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
39821Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/11274
49382Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 28792)https://www.ccug.se/strain?id=28792
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
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
72645Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID14091.1StrainInfo: A central database for resolving microbial strain identifiers
123877Curators of the CIPCollection of Institut Pasteur (CIP 82.7)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%2082.7