Strain identifier
BacDive ID: 130888
Type strain: 
Species: Campylobacter coli
Strain Designation: 4039, CNET056
Strain history: <- F. van der Wal, Animal Sciences Group, Wageningen UR, Lelystad, Netherlands; CNET056 <- S. L. W. On, Danish Institute for Food and Veterinary Research, Copenhagen, Denmark; 4039
NCBI tax ID(s): 195 (species)
version 9.3 (current version)
General
@ref: 22808
BacDive-ID: 130888
DSM-Number: 24266
keywords: genome sequence, Bacteria, microaerophile, mesophilic, Gram-negative
description: Campylobacter coli 4039 is a microaerophile, mesophilic, Gram-negative bacterium that was isolated from cattle.
NCBI tax id
- NCBI tax id: 195
- Matching level: species
strain history
- @ref: 22808
- history: <- F. van der Wal, Animal Sciences Group, Wageningen UR, Lelystad, Netherlands; CNET056 <- S. L. W. On, Danish Institute for Food and Veterinary Research, Copenhagen, Denmark; 4039
doi: 10.13145/bacdive130888.20250331.9.3
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Epsilonproteobacteria
- order: Campylobacterales
- family: Campylobacteraceae
- genus: Campylobacter
- species: Campylobacter coli
- full scientific name: Campylobacter coli (Doyle 1948) Véron and Chatelain 1973 (Approved Lists 1980)
synonyms
@ref synonym 20215 Campylobacter hyoilei 20215 Vibrio coli
@ref: 22808
domain: Bacteria
phylum: Proteobacteria
class: Epsilonproteobacteria
order: Campylobacterales
family: Campylobacteraceae
genus: Campylobacter
species: Campylobacter coli
full scientific name: Campylobacter coli (Doyle 1948) Véron and Chatelain 1973
strain designation: 4039, CNET056
type strain: no
Morphology
cell morphology
| @ref | gram stain | confidence |
|---|---|---|
| 125438 | negative | 97.955 |
| 125439 | negative | 98.4 |
colony morphology
- @ref: 22808
- incubation period: 1-2 days
Culture and growth conditions
culture medium
- @ref: 22808
- name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)
- growth: yes
- link: https://mediadive.dsmz.de/medium/693
- composition: Name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar base
culture temp
- @ref: 22808
- growth: positive
- type: growth
- temperature: 37
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance | confidence |
|---|---|---|
| 22808 | microaerophile | |
| 125439 | obligate aerobe | 90.6 |
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 125438 | no | 96.341 |
| 125439 | no | 97.3 |
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 68373 | 16947 | citrate | - | assimilation |
| 68373 | 25115 | malate | + | assimilation |
| 68373 | 17272 | propionate | - | assimilation |
| 68373 | 30089 | acetate | - | assimilation |
| 68373 | 606565 | hippurate | + | hydrolysis |
| 68373 | 78019 | triphenyltetrazolium chloride | + | reduction |
| 68373 | 17632 | nitrate | + | reduction |
| 68373 | 16199 | urea | - | hydrolysis |
| 68373 | 30031 | succinate | + | assimilation |
| 68373 | 17634 | D-glucose | - | assimilation |
antibiotic resistance
| @ref | ChEBI | metabolite | is antibiotic | is resistant | resistance conc. | is sensitive | sensitivity conc. |
|---|---|---|---|---|---|---|---|
| 68373 | 474053 | cefazolin | yes | yes | 224 µg | ||
| 68373 | 48923 | erythromycin | yes | yes | 14 µg | ||
| 68373 | 100147 | nalidixic acid | yes | yes | 84 µg |
metabolite production
- @ref: 68373
- Chebi-ID: 16136
- metabolite: hydrogen sulfide
- production: no
enzymes
| @ref | value | activity | ec |
|---|---|---|---|
| 68373 | catalase | + | 1.11.1.6 |
| 68373 | alkaline phosphatase | + | 3.1.3.1 |
| 68373 | L-aspartate arylamidase | - | 3.4.11.21 |
| 68373 | L-arginine arylamidase | - | |
| 68373 | esterase | + | |
| 68373 | urease | - | 3.5.1.5 |
API CAM
| @ref | URE | NIT | EST | HIP | GGT | TTC | PYRA | ArgA | AspA | PAL | H2S | GLU | SUT | NAL | CFZ | ACE | PROP | MLT | CIT | ERO | CAT |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 22808 | - | + | + | + | +/- | + | +/- | - | - | + | - | - | + | - | + | - | - | + | - | - | + |
Isolation, sampling and environmental information
isolation
- @ref: 22808
- sample type: cattle
- country: Denmark
- origin.country: DNK
- continent: Europe
isolation source categories
- Cat1: #Host
- Cat2: #Mammals
- Cat3: #Bovinae (Cow, Cattle)
Safety information
risk assessment
- @ref: 22808
- biosafety level: 2
- biosafety level comment: Risk group (German classification)
Sequence information
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Campylobacter coli strain FDAARGOS_1464 | 195.3706 | complete | patric | 195 |
| 66792 | Campylobacter coli strain FDAARGOS_1464 | 195.3614 | complete | patric | 195 |
Genome-based predictions
predictions
| @ref | model | trait | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 125438 | gram-positive | gram-positive | Positive reaction to Gram-staining | no | 97.955 | no |
| 125438 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 83.85 | yes |
| 125438 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 96.341 | no |
| 125438 | thermophile | thermophilic | Ability to grow at temperatures above or equal to 45°C | no | 89.567 | yes |
| 125438 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | no | 83.257 | yes |
| 125438 | motile2+ | flagellated | Ability to perform flagellated movement | yes | 63.064 | no |
| 125439 | BacteriaNet | spore_formation | Ability to form endo- or exospores | no | 97.3 | |
| 125439 | BacteriaNet | motility | Ability to perform movement | no | 61.9 | |
| 125439 | BacteriaNet | gram_stain | Reaction to gram-staining | negative | 98.4 | |
| 125439 | BacteriaNet | oxygen_tolerance | Oxygenic conditions needed for growth | obligate aerobe | 90.6 |
External links
@ref: 22808
culture collection no.: DSM 24266
straininfo link
- @ref: 89370
- straininfo: 398702
Reference
| @id | authors | title | doi/url | catalogue |
|---|---|---|---|---|
| 20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | 10.1099/ijsem.0.004332 | |
| 22808 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-24266 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 24266) | |
| 66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | |
| 68373 | Automatically annotated from API CAM | |||
| 89370 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | StrainInfo: A central database for resolving microbial strain identifiers | 10.60712/SI-ID398702.1 | |
| 125438 | Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann | Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets | 10.1101/2024.08.12.607695 | |
| 125439 | Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy | deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 | https://github.com/GenomeNet/deepG |