Strain identifier
BacDive ID: 5494
Type strain:
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)
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 id | Matching level |
---|---|
28189 | species |
926551 | strain |
strain history
@ref | history |
---|---|
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 |
118831 | 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 |
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
@ref | name | growth | link | composition |
---|---|---|---|---|
8133 | COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) | yes | https://mediadive.dsmz.de/medium/693 | Name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar base |
34432 | MEDIUM 10 - Chocolate medium for Actinobacillus pleuropneumoniae, Capnocytophaga cynodegmi, Haemophilus and Neisseria | yes | Distilled water make up to (1000.000 ml);Columbia agar (39.000 g);Horseblood (100.000 ml);PolyVitex mischung (10.000 ml) | |
118831 | CIP Medium 10 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=10 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
8133 | positive | growth | 37 | mesophilic |
34432 | positive | growth | 37 | mesophilic |
118831 | positive | growth | 37 | mesophilic |
118831 | no | growth | 30 | mesophilic |
118831 | no | growth | 41 | thermophilic |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
8133 | microaerophile |
118831 | facultative anaerobe |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
118831 | 15824 | D-fructose | + | degradation |
118831 | 17634 | D-glucose | - | degradation |
118831 | 16947 | citrate | - | carbon source |
118831 | 4853 | esculin | + | hydrolysis |
118831 | 606565 | hippurate | - | hydrolysis |
118831 | 17632 | nitrate | - | reduction |
118831 | 16301 | nitrite | - | reduction |
metabolite production
- @ref: 118831
- Chebi-ID: 35581
- metabolite: indole
- production: no
enzymes
@ref | value | activity | ec |
---|---|---|---|
68382 | alpha-fucosidase | - | 3.2.1.51 |
68382 | alpha-mannosidase | - | 3.2.1.24 |
68382 | N-acetyl-beta-glucosaminidase | + | 3.2.1.52 |
68382 | beta-glucosidase | - | 3.2.1.21 |
68382 | alpha-glucosidase | + | 3.2.1.20 |
68382 | beta-glucuronidase | - | 3.2.1.31 |
68382 | beta-galactosidase | - | 3.2.1.23 |
68382 | alpha-galactosidase | - | 3.2.1.22 |
68382 | naphthol-AS-BI-phosphohydrolase | + | |
68382 | acid phosphatase | + | 3.1.3.2 |
68382 | alpha-chymotrypsin | - | 3.4.21.1 |
68382 | trypsin | - | 3.4.21.4 |
68382 | cystine arylamidase | - | 3.4.11.3 |
68382 | valine arylamidase | - | |
68382 | leucine arylamidase | + | 3.4.11.1 |
68382 | lipase (C 14) | - | |
68382 | esterase lipase (C 8) | + | |
68382 | esterase (C 4) | + | |
68382 | alkaline phosphatase | + | 3.1.3.1 |
118831 | oxidase | + | |
118831 | beta-galactosidase | + | 3.2.1.23 |
118831 | alcohol dehydrogenase | + | 1.1.1.1 |
118831 | gelatinase | - | |
118831 | catalase | + | 1.11.1.6 |
118831 | gamma-glutamyltransferase | - | 2.3.2.2 |
118831 | lysine decarboxylase | - | 4.1.1.18 |
118831 | ornithine decarboxylase | - | 4.1.1.17 |
118831 | phenylalanine ammonia-lyase | - | 4.3.1.24 |
118831 | urease | - | 3.5.1.5 |
fatty acid profile
@ref fatty acid percentage ECL 48031 C14:0 1.4 14 48031 C16:0 4.4 16 48031 C18:0 1 18 48031 C13:0 iso 0.8 12.612 48031 C13:1 at 12-13 1.3 12.931 48031 C15:0 ANTEISO 3.1 14.711 48031 C15:0 ISO 59.1 14.621 48031 C15:0 ISO 3OH 3 16.135 48031 C16:0 3OH 3.5 17.52 48031 C16:0 iso 0.5 15.626 48031 C17:0 iso 1.2 16.629 48031 C17:0 iso 3OH 10.9 18.161 48031 C18:1 ω9c 1.4 17.769 48031 C18:2 ω6,9c/C18:0 ANTE 2.7 17.724 48031 unknown 13.566 4.8 13.566 48031 unknown 16.580 1 16.58 - type of FA analysis: whole cell analysis
- method/protocol: CCUG
@ref fatty acid percentage ECL 48031 C14:0 1.7 14 48031 C16:0 1.9 16 48031 C18:0 0.6 18 48031 C13:0 iso 1 12.612 48031 C13:1 at 12-13 1.3 12.931 48031 C15:0 ANTEISO 2.6 14.711 48031 C15:0 ISO 68.3 14.621 48031 C15:0 ISO 3OH 3.8 16.135 48031 C16:1 ω7c 0.2 15.819 48031 C17:0 iso 0.5 16.629 48031 C17:0 iso 3OH 10.8 18.161 48031 C18:1 2OH 0.4 19.088 48031 C18:1 ω9c 1.4 17.769 48031 C18:2 ω6,9c/C18:0 ANTE 1.6 17.724 48031 unknown 13.566 3.5 13.566 48031 unknown 16.580 0.4 16.58 - type of FA analysis: whole cell analysis
- method/protocol: CCUG
API zym
@ref | Control | Alkaline phosphatase | Esterase | Esterase Lipase | Lipase | Leucine arylamidase | Valine arylamidase | Cystine arylamidase | Trypsin | alpha- Chymotrypsin | Acid phosphatase | Naphthol-AS-BI-phosphohydrolase | alpha- Galactosidase | beta- Galactosidase | beta- Glucuronidase | alpha- Glucosidase | beta- Glucosidase | N-acetyl-beta- glucosaminidase | alpha- Mannosidase | alpha- Fucosidase |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
118831 | - | + | + | + | - | + | - | - | - | - | + | + | - | - | - | + | - | + | - | - |
API biotype100
@ref | GLU | FRU | GAL | TRE | MNE | SBE | MEL | SAC | RAF | MTE | MAL | LAC | LTE | MbGa | MaGa | CEL | GEN | MbGu | ESC | RIB | ARA | XYL | PLE | RHA | FUC | MLZ | DARL | LARL | XLT | DUL | TAG | GLY | INO | MAN | MTL | TUR | SOR | ADO | HBG | LYX | ERY | MDG | 3MDG | SAT | MUC | LTAT | DTAT | MTAT | DMLT | LMLT | CATE | TATE | TTE | CIT | GRT | GAT | 2KG | 5KG | TRY | NAG | GNT | PAC | PAT | pOBE | QAT | GTE | mOBE | BAT | PPAT | CMT | TGE | BET | PCE | ABT | HIN | LAT | CAP | CYT | HIS | SUC | FUM | GRE | GYT | AVT | ETN | TTN | GLN | ITA | 3OBU | APT | GTT | PRO | DALA | LALA | SER | MNT | PROP | TYR | 2KT |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
118831 | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent | sampling date | isolation date |
---|---|---|---|---|---|---|---|
8133 | mouth of a dog | Virginia | USA | USA | North America | ||
48031 | Dog mouth | Virginia | USA | USA | North America | 1979 | |
118831 | Animal, Dog, mouth | Virginia | United States of America | USA | North America | 1979 |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#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
@ref | pathogenicity human | pathogenicity animal | biosafety level | biosafety level comment |
---|---|---|---|---|
8133 | yes | yes | 2 | Risk group (German classification) |
118831 | 1 | Risk group (French classification) |
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Capnocytophaga cynodegmi strain CIP 103937 16S ribosomal RNA gene, partial sequence | AY643076 | 1438 | ena | 926551 |
20218 | Capnocytophaga cynodegmi 16S ribosomal RNA | L14638 | 1463 | ena | 28189 |
20218 | C.cynodegmi 16S rRNA gene | X97245 | 1427 | ena | 28189 |
8133 | Capnocytophaga cynodegmi strain CIP 103937 16S ribosomal RNA gene, partial sequence; 16S-23S ribosomal RNA intergenic spacer, complete sequence; and 23S ribosomal RNA gene, partial sequence | AY661854 | 3547 | ena | 926551 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Capnocytophaga cynodegmi DSM 19736 E6447, DSM 19736 | GCA_000379185 | scaffold | ncbi | 926551 |
66792 | Capnocytophaga cynodegmi Ccyn_ATCC49044 | 28189.4 | wgs | patric | 28189 |
66792 | Capnocytophaga cynodegmi DSM 19736 | 926551.3 | wgs | patric | 926551 |
66792 | Capnocytophaga cynodegmi E6447, DSM 19736 | 2513237123 | draft | img | 926551 |
GC content
- @ref: 8133
- GC-content: 34
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
motile | no | 87.807 | no |
flagellated | no | 95.373 | no |
gram-positive | no | 98.015 | no |
anaerobic | no | 93.846 | no |
aerobic | no | 83.109 | no |
halophile | no | 79.561 | no |
spore-forming | no | 95.585 | no |
thermophile | no | 98.479 | no |
glucose-util | yes | 84.524 | no |
glucose-ferment | no | 82.866 | no |
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
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
8133 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19736) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-19736 | |||
20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | |||
20218 | Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P. | 10.1016/j.syapm.2013.11.002 | StrainInfo introduces electronic passports for microorganisms. | Syst Appl Microbiol. 37: 42-50 2014 | 24321274 | |
34432 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/15790 | ||||
48031 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 24742) | https://www.ccug.se/strain?id=24742 | |||
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
66793 | Mukherjee et al. | 10.1038/nbt.3886 | GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life | 35: 676-683 2017 | 28604660 | |
66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | 10.1093/nar/gkaa1025 | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | Nucleic Acids Res. 49: D498-D508 2020 | 33211880 | |
68382 | Automatically annotated from API zym | |||||
69479 | João 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 | |||
74981 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID7608.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
118831 | Curators of the CIP | Collection of Institut Pasteur (CIP 103937) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103937 |