Strain identifier

BacDive ID: 2126

Type strain: Yes

Species: Campylobacter upsaliensis

Strain Designation: Ursing C231, C231

Strain history: CIP <- 1993, DSM <- 1983, CCUG <- J. Ursing Malmo, Sweden <- K. Sandstedt: strain C231

NCBI tax ID(s): 1121269 (strain), 28080 (species)

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General

@ref: 2005

BacDive-ID: 2126

DSM-Number: 5365

keywords: genome sequence, 16S sequence, Bacteria, microaerophile, mesophilic, rod-shaped

description: Campylobacter upsaliensis Ursing C231 is a microaerophile, mesophilic, rod-shaped bacterium that was isolated from faeces.

NCBI tax id

NCBI tax idMatching level
28080species
1121269strain

strain history

@refhistory
2005<- BCCM; LMG 8850 <- NCTC; NCTC 11541 <- J. Ursing;
67771<- CCUG <- J Ursing, PHL, MAS, Malmo, Sweden 14 Dec 1983 <- K Sandstedt, SVA, Uppsala, Sweden
123733CIP <- 1993, DSM <- 1983, CCUG <- J. Ursing Malmo, Sweden <- K. Sandstedt: strain C231

doi: 10.13145/bacdive2126.20230509.8.1

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 upsaliensis
  • full scientific name: Campylobacter upsaliensis Sandstedt and Ursing 1991

@ref: 2005

domain: Bacteria

phylum: Proteobacteria

class: Epsilonproteobacteria

order: Campylobacterales

family: Campylobacteraceae

genus: Campylobacter

species: Campylobacter upsaliensis

full scientific name: Campylobacter upsaliensis Sandstedt and Ursing 1991

strain designation: Ursing C231, C231

type strain: yes

Morphology

cell morphology

@refcell shapegram stainmotility
67771rod-shaped
67771negative
123733rod-shapednegativeyes

colony morphology

  • @ref: 2005
  • incubation period: 1-2 days

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
2005COLUMBIA 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
38135MEDIUM 6 - Columbia agar with 10 % horse bloodyesDistilled water make up to (1000.000 ml);Columbia agar (39.000 g);Horseblood (100.000 ml)
123733CIP Medium 6yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=6

culture temp

@refgrowthtypetemperaturerange
2005positivegrowth37mesophilic
38135positivegrowth37mesophilic
46171positivegrowth37mesophilic
67771positivegrowth37mesophilic
123733positivegrowth37-41
123733nogrowth5psychrophilic
123733nogrowth15psychrophilic
123733nogrowth25mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
2005microaerophile
46171microaerophile
67771microaerophile
123733microaerophile

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
123733606565hippurate-hydrolysis
12373317632nitrate+reduction
12373316301nitrite-reduction
6837316199urea-hydrolysis
6837330031succinate-assimilation
6837330089acetate-assimilation
6837317272propionate-assimilation
6837325115malate-assimilation
6837316947citrate-assimilation
6838016199urea-hydrolysis
6838029016arginine-hydrolysis
6838016024D-mannose-fermentation
6838016634raffinose-fermentation
6838029985L-glutamate-degradation
6838017632nitrate+reduction
6838027897tryptophan-energy source

antibiotic resistance

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

metabolite production

@refChebi-IDmetaboliteproduction
6837316136hydrogen sulfideno
12373335581indoleno
6838035581indoleno

metabolite tests

  • @ref: 68380
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
2005catalase+1.11.1.6
2005cytochrome-c oxidase+1.9.3.1
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
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase-3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase-
68382alpha-chymotrypsin-3.4.21.1
68382trypsin-3.4.21.4
68382cystine arylamidase-3.4.11.3
68382valine arylamidase-
68382lipase (C 14)-
68380serine arylamidase-
68380glutamyl-glutamate arylamidase-
68380histidine arylamidase-
68380glycin arylamidase-
68380alanine arylamidase-3.4.11.2
68380tyrosine arylamidase-
68380pyrrolidonyl arylamidase-3.4.19.3
68380leucine arylamidase-3.4.11.1
68380phenylalanine arylamidase-
68380leucyl glycin arylamidase-3.4.11.1
68380proline-arylamidase-3.4.11.5
68380L-arginine arylamidase-
68380alkaline phosphatase+3.1.3.1
68380tryptophan deaminase-4.1.99.1
68380alpha-fucosidase-3.2.1.51
68380glutamate decarboxylase-4.1.1.15
68380N-acetyl-beta-glucosaminidase-3.2.1.52
68380beta-glucuronidase-3.2.1.31
68380alpha-arabinosidase-3.2.1.55
68380beta-glucosidase-3.2.1.21
68380alpha-glucosidase-3.2.1.20
68380beta-Galactosidase 6-phosphate-
68380beta-galactosidase-3.2.1.23
68380alpha-galactosidase-3.2.1.22
68380arginine dihydrolase-3.5.3.6
68380urease-3.5.1.5
68373alkaline phosphatase+3.1.3.1
68373pyrrolidonyl arylamidase-3.4.19.3
68373gamma-glutamyltransferase-2.3.2.2
68373urease-3.5.1.5
123733oxidase+
123733catalase-1.11.1.6
123733urease-3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
46171-+--------+---------
123733--++-+---------+----

API CAM

@refURENITESTHIPGGTTTCPYRAArgAAspAPALH2SGLUSUTNALCFZACEPROPMLTCITEROCAT
2005-+-------+----------+
2005-++--+--+/-+-----------
2005-++--+--+/-+----------+
2005-++-----++--
2005---------+----------
2005-+-------+----------
2005-+-------+----------+
2005-++--+-+++-----------
2005-+---+-+++-+--------+
2005-+---+/----+----------+
2005-++------+----------+
2005-++/-+/-----++----------
2005-++-----++----------

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
46171--------------+-+------------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitudesampling date
2005faecesUppsalaSwedenSWEEurope59.858817.6389
46171Canine fecesUppsalaSwedenSWEEurope1980
67771From canine fecesUppsalaSwedenSWEEurope
123733Animal, Dog fecesUppsalaSwedenSWEEurope

isolation source categories

  • Cat1: #Host Body Product
  • Cat2: #Gastrointestinal tract
  • Cat3: #Feces (Stool)

taxonmaps

  • @ref: 69479
  • File name: preview.99_7490.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15775;96_1993;97_2396;98_2960;99_7490&stattab=map
  • Last taxonomy: Campylobacter
  • 16S sequence: NR_043602
  • Sequence Identity:
  • Total samples: 6124
  • soil counts: 107
  • aquatic counts: 226
  • animal counts: 5780
  • plant counts: 11

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
20052Risk group (German classification)
1237332Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Campylobacter upsaliensis strain LMG 8850 16S ribosomal RNA gene, partial sequenceAF4978051428ena28080
20218Campylobacter upsaliensis strain ATCC 43954 16S ribosomal RNA gene, partial sequenceAY6211131442ena28080
20218Campylobacter upsaliensis strain CCUG 14913 16S ribosomal RNA (rrs) gene, partial sequenceDQ1741571341ena28080
20218Campylobacter upsaliensis strain NCTC 11541 16S ribosomal RNA gene, partial sequenceJX9125271435ena28080
2005Campylobacter upsaliensis 16S ribosomal RNAL146281460ena28080
67771Campylobacter upsaliensis strain CCUG 14913 16S ribosomal RNA, partial sequenceNR_0436021341nuccore28080
67771NR_11852nuccore

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Campylobacter upsaliensis NCTC11541GCA_900637395completencbi28080
66792Campylobacter upsaliensis Campylobacter upsaliensis CCUG 14913GCA_916098255completencbi28080
66792Campylobacter upsaliensis DSM 53651121269.3wgspatric1121269
66792Campylobacter upsaliensis strain Campylobacter upsaliensis 17-M19705928080.104completepatric28080
66792Campylobacter upsaliensis strain Campylobacter upsaliensis CCUG 1491328080.103completepatric28080
66792Campylobacter upsaliensis strain NCTC1154128080.79completepatric28080
66792Campylobacter upsaliensis DSM 53652556921624draftimg1121269
67771Campylobacter upsaliensis DSM 5365GCA_000620965scaffoldncbi1121269
66792Campylobacter upsaliensis strain Campylobacter upsaliensis CCUG 1491328080.106completepatric28080
66792Campylobacter upsaliensis strain Campylobacter upsaliensis CCUG 1491328080.112completepatric28080
66792Campylobacter upsaliensis strain Campylobacter upsaliensis CCUG 1491328080.109completepatric28080
66792Campylobacter upsaliensis strain Campylobacter upsaliensis 17-M19705928080.107completepatric28080
66792Campylobacter upsaliensis strain Campylobacter upsaliensis 17-M19705928080.113completepatric28080
66792Campylobacter upsaliensis strain Campylobacter upsaliensis 17-M19705928080.110completepatric28080

GC content

  • @ref: 2005
  • GC-content: 33.5
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
flagellatedyes53.657no
gram-positiveno98.764no
anaerobicno88.409yes
aerobicno97.044no
halophileno86.56no
spore-formingno96.728no
thermophileno57.848yes
glucose-utilno87.655no
motileyes88.311no
glucose-fermentno83.562no

External links

@ref: 2005

culture collection no.: LMG 7796, KCTC 15213, DSM 5365, ATCC 43954, CCUG 14913, LMG 8850, NCTC 11541, CIP 103681

straininfo link

  • @ref: 71754
  • straininfo: 1572

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Enzymology7582001Physical and genetic map of the genome of Campylobacter upsaliensis.Bourke B, Sherman P, Louie H, Hani E, Islur P, Chan VLMicrobiology (Reading)10.1099/13500872-141-10-24171995Blotting, Southern, Campylobacter/*genetics, DNA Fingerprinting, Deoxyribonucleases, Type II Site-Specific/metabolism, Electrophoresis, Gel, Pulsed-Field, Genetic Markers, *Genome, Bacterial, *Restriction Mapping, Species SpecificityGenetics
Enzymology8996110Characterization of Campylobacter upsaliensis fur and its localization in a highly conserved region of the Campylobacter genome.Bourke B, al Rashid ST, Bingham HL, Chan VLGene10.1016/s0378-1119(96)00562-81996Amino Acid Sequence, Bacterial Proteins/*genetics, Base Sequence, Binding Sites, Campylobacter/*genetics, Cloning, Molecular, Conserved Sequence/genetics, Genes, Bacterial/*genetics, Lysine-tRNA Ligase/genetics, Molecular Sequence Data, Repressor Proteins/*genetics, *Restriction Mapping, Sequence Alignment, Sequence Analysis, DNA, Sequence Homology, Amino AcidGenetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
2005Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 5365)https://www.dsmz.de/collection/catalogue/details/culture/DSM-5365
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
38135Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/15505
46171Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 14913)https://www.ccug.se/strain?id=14913
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)
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
68373Automatically annotated from API CAM
68380Automatically annotated from API rID32A
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
71754Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID1572.1StrainInfo: A central database for resolving microbial strain identifiers
123733Curators of the CIPCollection of Institut Pasteur (CIP 103681)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103681