Strain identifier

BacDive ID: 5494

Type strain: Yes

Species: Capnocytophaga cynodegmi

Strain Designation: 79120329, E6447

Strain history: CIP <- 1994, CCTM <- 1993, ATCC <- R.E. Weaver, CDC: strain 79120329 <- Virginia State Hlth. Lab., USA <- 1979, F.J. Marsik, Clinical Lab. Univ., Virginia Hosp., USA

NCBI tax ID(s): 926551 (strain), 28189 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 8133

BacDive-ID: 5494

DSM-Number: 19736

keywords: genome sequence, 16S sequence, Bacteria, microaerophile, mesophilic, Gram-negative, rod-shaped, human pathogen

description: Capnocytophaga cynodegmi 79120329 is a microaerophile, mesophilic, Gram-negative human pathogen that was isolated from mouth of a dog.

NCBI tax id

NCBI tax idMatching level
28189species
926551strain

strain history

@refhistory
8133<- CIP <- ATCC <- R. E. Weaver, CDC; strain 79120329, strain E6447 <- Virginia State Hlth. Lab., USA <- F. J. Marsik, Clinical Lab. Univ., Virginia Hosp., USA
118831CIP <- 1994, CCTM <- 1993, ATCC <- R.E. Weaver, CDC: strain 79120329 <- Virginia State Hlth. Lab., USA <- 1979, F.J. Marsik, Clinical Lab. Univ., Virginia Hosp., USA

doi: 10.13145/bacdive5494.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Flavobacteriia
  • order: Flavobacteriales
  • family: Flavobacteriaceae
  • genus: Capnocytophaga
  • species: Capnocytophaga cynodegmi
  • full scientific name: Capnocytophaga cynodegmi Brenner et al. 1990

@ref: 8133

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Flavobacteriaceae

genus: Capnocytophaga

species: Capnocytophaga cynodegmi

full scientific name: Capnocytophaga cynodegmi Brenner et al. 1990

strain designation: 79120329, E6447

type strain: yes

Morphology

cell morphology

  • @ref: 118831
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: no

colony morphology

  • @ref: 8133
  • incubation period: 2-3 days

multimedia

  • @ref: 66793
  • multimedia content: EM_DSM_19736_1.jpg
  • caption: electron microscopic image
  • intellectual property rights: © HZI/Manfred Rohde

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
8133COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)yeshttps://mediadive.dsmz.de/medium/693Name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar base
34432MEDIUM 10 - Chocolate medium for Actinobacillus pleuropneumoniae, Capnocytophaga cynodegmi, Haemophilus and NeisseriayesDistilled water make up to (1000.000 ml);Columbia agar (39.000 g);Horseblood (100.000 ml);PolyVitex mischung (10.000 ml)
118831CIP Medium 10yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=10

culture temp

@refgrowthtypetemperaturerange
8133positivegrowth37mesophilic
34432positivegrowth37mesophilic
118831positivegrowth37mesophilic
118831nogrowth30mesophilic
118831nogrowth41thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
8133microaerophile
118831facultative anaerobe

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
11883115824D-fructose+degradation
11883117634D-glucose-degradation
11883116947citrate-carbon source
1188314853esculin+hydrolysis
118831606565hippurate-hydrolysis
11883117632nitrate-reduction
11883116301nitrite-reduction

metabolite production

  • @ref: 118831
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

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
118831oxidase+
118831beta-galactosidase+3.2.1.23
118831alcohol dehydrogenase+1.1.1.1
118831gelatinase-
118831catalase+1.11.1.6
118831gamma-glutamyltransferase-2.3.2.2
118831lysine decarboxylase-4.1.1.18
118831ornithine decarboxylase-4.1.1.17
118831phenylalanine ammonia-lyase-4.3.1.24
118831urease-3.5.1.5

fatty acid profile

  • @reffatty acidpercentageECL
    48031C14:01.414
    48031C16:04.416
    48031C18:0118
    48031C13:0 iso0.812.612
    48031C13:1 at 12-131.312.931
    48031C15:0 ANTEISO3.114.711
    48031C15:0 ISO59.114.621
    48031C15:0 ISO 3OH316.135
    48031C16:0 3OH3.517.52
    48031C16:0 iso0.515.626
    48031C17:0 iso1.216.629
    48031C17:0 iso 3OH10.918.161
    48031C18:1 ω9c1.417.769
    48031C18:2 ω6,9c/C18:0 ANTE2.717.724
    48031unknown 13.5664.813.566
    48031unknown 16.580116.58
  • type of FA analysis: whole cell analysis
  • method/protocol: CCUG
  • @reffatty acidpercentageECL
    48031C14:01.714
    48031C16:01.916
    48031C18:00.618
    48031C13:0 iso112.612
    48031C13:1 at 12-131.312.931
    48031C15:0 ANTEISO2.614.711
    48031C15:0 ISO68.314.621
    48031C15:0 ISO 3OH3.816.135
    48031C16:1 ω7c0.215.819
    48031C17:0 iso0.516.629
    48031C17:0 iso 3OH10.818.161
    48031C18:1 2OH0.419.088
    48031C18:1 ω9c1.417.769
    48031C18:2 ω6,9c/C18:0 ANTE1.617.724
    48031unknown 13.5663.513.566
    48031unknown 16.5800.416.58
  • type of FA analysis: whole cell analysis
  • method/protocol: CCUG

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
118831-+++-+----++---+-+--

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
118831---------------------------------------------------------------------------------------------------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling dateisolation date
8133mouth of a dogVirginiaUSAUSANorth America
48031Dog mouthVirginiaUSAUSANorth America1979
118831Animal, Dog, mouthVirginiaUnited States of AmericaUSANorth America1979

isolation source categories

Cat1Cat2Cat3
#Host#Mammals#Canidae (Dog)
#Host Body-Site#Oral cavity and airways#Mouth

taxonmaps

  • @ref: 69479
  • File name: preview.99_3018.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15818;96_589;97_689;98_804;99_3018&stattab=map
  • Last taxonomy: Capnocytophaga cynodegmi
  • 16S sequence: X97245
  • Sequence Identity:
  • Total samples: 1913
  • soil counts: 19
  • aquatic counts: 2
  • animal counts: 1891
  • plant counts: 1

Safety information

risk assessment

@refpathogenicity humanpathogenicity animalbiosafety levelbiosafety level comment
8133yesyes2Risk group (German classification)
1188311Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Capnocytophaga cynodegmi strain CIP 103937 16S ribosomal RNA gene, partial sequenceAY6430761438ena926551
20218Capnocytophaga cynodegmi 16S ribosomal RNAL146381463ena28189
20218C.cynodegmi 16S rRNA geneX972451427ena28189
8133Capnocytophaga cynodegmi strain CIP 103937 16S ribosomal RNA gene, partial sequence; 16S-23S ribosomal RNA intergenic spacer, complete sequence; and 23S ribosomal RNA gene, partial sequenceAY6618543547ena926551

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Capnocytophaga cynodegmi DSM 19736 E6447, DSM 19736GCA_000379185scaffoldncbi926551
66792Capnocytophaga cynodegmi Ccyn_ATCC4904428189.4wgspatric28189
66792Capnocytophaga cynodegmi DSM 19736926551.3wgspatric926551
66792Capnocytophaga cynodegmi E6447, DSM 197362513237123draftimg926551

GC content

  • @ref: 8133
  • GC-content: 34

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno87.807no
flagellatedno95.373no
gram-positiveno98.015no
anaerobicno93.846no
aerobicno83.109no
halophileno79.561no
spore-formingno95.585no
thermophileno98.479no
glucose-utilyes84.524no
glucose-fermentno82.866no

External links

@ref: 8133

culture collection no.: MCCM 00247, LMG 11513, MCCM 00265, LMG 11540, DSM 19736, ATCC 49044, CCUG 24742, CIP 103937, NCTC 12243, CCTM La 3495

straininfo link

  • @ref: 74981
  • straininfo: 7608

literature

  • topic: Phylogeny
  • Pubmed-ID: 30118139
  • title: Characterization of three strains of Capnocytophaga canis isolated from patients with sepsis.
  • authors: Suzuki M, Imaoka K, Haga Y, Mohri M, Nogami A, Shimojima Y, Irie Y, Sugimura S, Morikawa S
  • journal: Microbiol Immunol
  • DOI: 10.1111/1348-0421.12642
  • year: 2018
  • mesh: Aged, Aged, 80 and over, Animals, Bacterial Typing Techniques, Base Composition, Benzoquinones/analysis, Bites and Stings/microbiology, Capnocytophaga/*classification/genetics/*isolation & purification/*pathogenicity, Cat Diseases/microbiology, Cats, DNA Gyrase/genetics, DNA, Bacterial/isolation & purification, Dog Diseases/microbiology, Dogs, Female, Genes, Bacterial/genetics, Gram-Negative Bacterial Infections/*microbiology, Humans, Japan, Male, Middle Aged, Multilocus Sequence Typing, Phenotype, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sepsis/*microbiology, Sequence Analysis, DNA, Species Specificity, Whole Genome Sequencing, Zoonoses/microbiology
  • topic2: Enzymology

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
8133Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19736)https://www.dsmz.de/collection/catalogue/details/culture/DSM-19736
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
34432Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/15790
48031Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 24742)https://www.ccug.se/strain?id=24742
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)
66793Mukherjee et al.10.1038/nbt.3886GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life 35: 676-683 201728604660
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
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
74981Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID7608.1StrainInfo: A central database for resolving microbial strain identifiers
118831Curators of the CIPCollection of Institut Pasteur (CIP 103937)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103937