Strain identifier
BacDive ID: 140488
Type strain:
Species: Campylobacter pinnipediorum
Strain history: <- CCUG; CCUG 69570 <- W. C. Miller, University of California, Davis; RM17260
NCBI tax ID(s): 1965231 (species)
General
@ref: 67674
BacDive-ID: 140488
DSM-Number: 112337
keywords: genome sequence, Bacteria, microaerotolerant, thermophilic, Gram-negative, rod-shaped, colony-forming
description: Campylobacter pinnipediorum CCUG 69570 is a microaerotolerant, thermophilic, Gram-negative bacterium that forms circular colonies and was isolated from Abscess of California sea lion Juvenile.
NCBI tax id
- NCBI tax id: 1965231
- Matching level: species
strain history
- @ref: 67674
- history: <- CCUG; CCUG 69570 <- W. C. Miller, University of California, Davis; RM17260
doi: 10.13145/bacdive140488.20230509.8.1
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 pinnipediorum
- full scientific name: Campylobacter pinnipediorum Gilbert et al. 2017
@ref: 67674
domain: Bacteria
phylum: Proteobacteria
class: Epsilonproteobacteria
order: Campylobacterales
family: Campylobacteraceae
genus: Campylobacter
species: Campylobacter pinnipediorum
full scientific name: Campylobacter pinnipediorum Gilbert et al. 2017
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell shape | motility | confidence |
---|---|---|---|---|
43235 | negative | rod-shaped | ||
69480 | yes | 90.342 | ||
69480 | negative | 99.992 |
colony morphology
- @ref: 43235
- type of hemolysis: alpha
- hemolysis ability: 1
- colony size: 0.5-1 mm
- colony color: transparent to beige or white
- colony shape: circular
- incubation period: 3 days
- medium used: Columbia agar with 5 % sheep blood (microaerobic)
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
43235 | Columbia agar with 5 % sheep blood (microaerobic) | yes | ||
43235 | Skirrow agar | yes | ||
43235 | charcoal cefoperazone deoxycholate agar | no | ||
43235 | Mueller - Hinton agar | no | ||
67674 | 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 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
43235 | no | growth | 42 | thermophilic |
43235 | no | growth | 22 | psychrophilic |
43235 | positive | growth | 25 | mesophilic |
43235 | positive | growth | 37 | mesophilic |
63624 | positive | growth | 37 | mesophilic |
67674 | positive | growth | 37 | mesophilic |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
43235 | microaerotolerant |
63624 | microaerophile |
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 100 |
69480 | no | 99.996 |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
43235 | 16199 | urea | + | hydrolysis |
43235 | 17632 | nitrate | + | reduction |
43235 | 606565 | hippurate | - | hydrolysis |
43235 | indoxyl acetate | - | hydrolysis |
antibiotic resistance
@ref | ChEBI | metabolite | is antibiotic | is sensitive | sensitivity conc. |
---|---|---|---|---|---|
43235 | 124991 | cefalotin | yes | yes | 30 µg (disc) |
43235 | 100147 | nalidixic acid | yes | yes | 30 µg (disc) |
metabolite production
- @ref: 43235
- Chebi-ID: 16136
- metabolite: hydrogen sulfide
- production: yes
enzymes
@ref | value | activity | ec |
---|---|---|---|
43235 | cytochrome oxidase | + | 1.9.3.1 |
43235 | catalase | +/- | 1.11.1.6 |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent | sampling date | latitude | longitude |
---|---|---|---|---|---|---|---|---|
43235 | Abscess of California sea lion (Z. californianus) Juvenile | San Diego, California | USA | USA | North America | |||
63624 | Abscess,californian sea lion | San Diego,California | USA | USA | North America | 2013-07-02 | ||
67674 | abscess; californian sea lion | San Diego, California | USA | USA | North America | 32.7 | -117.167 |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Host | #Mammals | #Aquatic mammal |
#Host Body-Site | #Other | #Abscess |
Sequence information
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Campylobacter pinnipediorum subsp. pinnipediorum RM17260 | GCA_002021925 | complete | ncbi | 1660067 |
66792 | Campylobacter pinnipediorum subsp. pinnipediorum strain RM17260 | 1660067.5 | complete | patric | 1660067 |
66792 | Campylobacter pinnipediorum pinnipediorum RM17260 | 2791355309 | complete | img | 1660067 |
GC content
- @ref: 43235
- GC-content: 30.4-31
- method: genome sequence analysis
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
flagellated | yes | 69.141 | no |
gram-positive | no | 99.009 | yes |
anaerobic | no | 75.521 | no |
aerobic | no | 97.641 | yes |
halophile | no | 76.743 | no |
spore-forming | no | 94.463 | no |
glucose-util | no | 89.286 | no |
thermophile | no | 91.159 | no |
motile | yes | 90.4 | no |
glucose-ferment | no | 88.225 | no |
External links
@ref: 67674
culture collection no.: CCUG 69570, LMG 29472, RM 17260, DSM 112337
straininfo link
- @ref: 96730
- straininfo: 400007
literature
- topic: Phylogeny
- Pubmed-ID: 28629508
- title: Campylobacter pinnipediorum sp. nov., isolated from pinnipeds, comprising Campylobacter pinnipediorum subsp. pinnipediorum subsp. nov. and Campylobacter pinnipediorum subsp. caledonicus subsp. nov.
- authors: Gilbert MJ, Miller WG, Leger JS, Chapman MH, Timmerman AJ, Duim B, Foster G, Wagenaar JA
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijsem.0.001894
- year: 2017
- mesh: Animals, Bacterial Typing Techniques, Base Composition, California, Campylobacter/*classification/genetics/isolation & purification, Caniformia/*microbiology, DNA, Bacterial/genetics, Genes, Bacterial, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, Scotland, Sequence Analysis, DNA
- topic2: Genetics
Reference
@id | authors | title | doi/url | journal | pubmed | 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 | |||
43235 | Maarten J. Gilbert, William G. Miller, Judy St. Leger, Mary H. Chapman, Arjen J. Timmerman, Birgitta Duim, Geoffrey Foster, Jaap A. Wagenaar | Campylobacter pinnipediorum sp. nov., isolated from pinnipeds, comprising Campylobacter pinnipediorum subsp. Pinnipediorum subsp. nov. and Campylobacter pinnipediorum subsp. caledonicus subsp. nov. | 10.1099/ijsem.0.001894 | IJSEM 67: 1961-1968 2017 | 28629508 | |
63624 | Curators of the CCUG | https://www.ccug.se/strain?id=69570 | Culture Collection University of Gothenburg (CCUG) (CCUG 69570) | |||
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 | |||
67674 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-112337 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 112337) | |||
69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | |||
69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | Predictions based on the model GenomeNet Sporulation v. 1 | 10.21203/rs.3.rs-2527258/v1 | |||
96730 | 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-ID400007.1 |