Strain identifier

BacDive ID: 2141

Type strain: Yes

Species: Campylobacter volucris

Strain history: <- CCUG; CCUG 57498 <- P. Vandamme and L. Debruyne, LMG; LMG 24380 <- T. Broman, CBRN, Umea, Sweden;

NCBI tax ID(s): 1031542 (species)

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General

@ref: 18009

BacDive-ID: 2141

DSM-Number: 25354

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

description: Campylobacter volucris DSM 25354 is a microaerophile, mesophilic, Gram-negative human pathogen that was isolated from rectal swab from black-headed gulls .

NCBI tax id

  • NCBI tax id: 1031542
  • Matching level: species

strain history

  • @ref: 18009
  • history: <- CCUG; CCUG 57498 <- P. Vandamme and L. Debruyne, LMG; LMG 24380 <- T. Broman, CBRN, Umea, Sweden;

doi: 10.13145/bacdive2141.20230509.8.1

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 volucris
  • full scientific name: Campylobacter volucris Debruyne et al. 2010

@ref: 18009

domain: Bacteria

phylum: Proteobacteria

class: Epsilonproteobacteria

order: Campylobacterales

family: Campylobacteraceae

genus: Campylobacter

species: Campylobacter volucris

full scientific name: Campylobacter volucris Debruyne et al. 2010

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
29469negativerod-shapedyes
69480yes94.409
69480negative99.988

colony morphology

@refincubation period
180091-2 days
613492 days

Culture and growth conditions

culture medium

  • @ref: 18009
  • name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)
  • growth: yes
  • link: https://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium693.pdf

culture temp

@refgrowthtypetemperaturerange
18009positivegrowth37mesophilic
29469positivegrowth37-42
61349positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
18009microaerophile
29469microaerophile
61349microaerophile

spore formation

@refspore formationconfidence
29469no
69481no100
69480no99.998

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2946917632nitrate+reduction
6837316199urea-hydrolysis
6837317632nitrate+reduction
6837330031succinate-assimilation
6837330089acetate-assimilation
6837317272propionate-assimilation
6837325115malate-assimilation
6837316947citrate-assimilation

antibiotic resistance

@refChEBImetaboliteis antibioticis sensitivesensitivity conc.
6837348923erythromycinyesyes14 µg
68373474053cefazolinyesyes224 µg
68373100147nalidixic acidyesyes84 µg

metabolite production

  • @ref: 68373
  • Chebi-ID: 16136
  • metabolite: hydrogen sulfide
  • production: no

enzymes

@refvalueactivityec
18009catalase+1.11.1.6
18009cytochrome-c oxidase+1.9.3.1
29469catalase+1.11.1.6
29469cytochrome oxidase+1.9.3.1
68373catalase+1.11.1.6
68373L-aspartate arylamidase-3.4.11.21
68373pyrrolidonyl arylamidase-3.4.19.3
68373gamma-glutamyltransferase-2.3.2.2
68373esterase-
68373urease-3.5.1.5

API CAM

@refURENITESTHIPGGTTTCPYRAArgAAspAPALH2SGLUSUTNALCFZACEPROPMLTCITEROCAT
18009-+-+-+-----+--------+
18009-+-----+/--+----------+

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinentsampling date
18009rectal swab from black-headed gulls ( Larus ridibundus )Larus ridibundusSouthSwedenSWEEurope
61349Black-headed gull (Larus ridibundus)SouthSwedenSWEEurope1999-03-01

isolation source categories

Cat1Cat2Cat3
#Infection#Patient#Swab
#Host#Birds
#Host Body-Site#Gastrointestinal tract#Rectum

Safety information

risk assessment

  • @ref: 18009
  • pathogenicity human: yes, in single cases
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
29469Campylobacter volucris LMG 24379 partial 16S rRNA gene, strain LMG 24379FM8836931504nuccore580033
18009Campylobacter volucris partial 16S rRNA gene, type strain LMG 24380TFM8836941482ena1031542

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Campylobacter volucris LMG 24380GCA_008245045completencbi1031542
66792Campylobacter volucris CCUG 57498GCA_008801985contigncbi1031542
66792Campylobacter volucris strain CCUG 574981031542.12wgspatric1031542
66792Campylobacter volucris strain LMG 243801031542.11completepatric1031542

GC content

  • @ref: 29469
  • GC-content: 29

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes88.262no
flagellatedyes64.247no
gram-positiveno98.834yes
anaerobicno83.663yes
aerobicno98.45yes
halophileno84.854no
spore-formingno95.786yes
glucose-utilno87.632no
thermophileno78.243yes
glucose-fermentno85.546no

External links

@ref: 18009

culture collection no.: DSM 25354, CCUG 57498, LMG 24380

straininfo link

  • @ref: 71769
  • straininfo: 28765

literature

  • topic: Phylogeny
  • Pubmed-ID: 19767353
  • title: Campylobacter volucris sp. nov., isolated from black-headed gulls (Larus ridibundus).
  • authors: Debruyne L, Broman T, Bergstrom S, Olsen B, On SLW, Vandamme P
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.013748-0
  • year: 2009
  • mesh: Animals, Campylobacter/*classification/genetics/*isolation & purification, Charadriiformes/*microbiology, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
18009Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 25354)https://www.dsmz.de/collection/catalogue/details/culture/DSM-25354
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
29469Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2587228776041
61349Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 57498)https://www.ccug.se/strain?id=57498
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)
68373Automatically annotated from API CAM
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
71769Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID28765.1StrainInfo: A central database for resolving microbial strain identifiers