Strain identifier

BacDive ID: 2102

Type strain: Yes

Species: Campylobacter ureolyticus

Strain Designation: EDMH-1

Strain history: <- NCTC (Bacteroides corrodens) <- F.L. Jackson, EDMH-1

NCBI tax ID(s): 1121102 (strain), 827 (species)

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General

@ref: 8781

BacDive-ID: 2102

DSM-Number: 20703

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, Gram-negative, human pathogen

description: Campylobacter ureolyticus EDMH-1 is an anaerobe, mesophilic, Gram-negative human pathogen that was isolated from amniotic fluid.

NCBI tax id

NCBI tax idMatching level
827species
1121102strain

strain history

  • @ref: 8781
  • history: <- NCTC (Bacteroides corrodens) <- F.L. Jackson, EDMH-1

doi: 10.13145/bacdive2102.20230509.8.1

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 ureolyticus
  • full scientific name: Campylobacter ureolyticus (Jackson and Goodman 1978) Vandamme et al. 2010

  • synonyms

    • @ref: 20215
    • synonym: Bacteroides ureolyticus

@ref: 8781

domain: Bacteria

phylum: Proteobacteria

class: Epsilonproteobacteria

order: Campylobacterales

family: Campylobacteraceae

genus: Campylobacter

species: Campylobacter ureolyticus

full scientific name: Campylobacter ureolyticus (Jackson and Goodman 1978) Vandamme et al. 2010

strain designation: EDMH-1

type strain: yes

Morphology

cell morphology

  • @ref: 69480
  • gram stain: negative
  • confidence: 99.985

colony morphology

@refincubation period
87811-2 days
449712-3 days

Culture and growth conditions

culture medium

  • @ref: 8781
  • name: BTU MEDIUM (DSMZ Medium 413)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/413
  • composition: Name: BTU MEDIUM (DSMZ Medium 413) Composition: Ground beef 500.0 g/l Casitone 30.0 g/l Agar 15.0 g/l K2HPO4 5.0 g/l Yeast extract 5.0 g/l Na-formiate 1.8 g/l Na-fumarate 1.8 g/l L-Cysteine HCl 0.5 g/l Ethanol 0.19 g/l Vitamin K3 0.05 g/l Hemin 0.005 g/l Resazurin 0.001 g/l Vitamin K1 NaOH Distilled water

culture temp

@refgrowthtypetemperaturerange
8781positivegrowth37mesophilic
44971positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
8781anaerobe
44971anaerobe

spore formation

@refspore formationconfidence
69481no99
69480no99.997

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6836727082trehalose-builds acid from
6836762345L-rhamnose-builds acid from
6836730911sorbitol-builds acid from
6836716634raffinose-builds acid from
683676731melezitose-builds acid from
6836716024D-mannose-builds acid from
6836717057cellobiose-builds acid from
6836717754glycerol-builds acid from
683674853esculin-hydrolysis
683675291gelatin-hydrolysis
6836730849L-arabinose-builds acid from
6836765327D-xylose-builds acid from
6836717814salicin-builds acid from
6836717306maltose-builds acid from
6836717992sucrose-builds acid from
6836717716lactose-builds acid from
6836716899D-mannitol-builds acid from
6836717634D-glucose-builds acid from
6836716199urea+hydrolysis
6836727897tryptophan-energy source
6837316199urea+hydrolysis
6837317634D-glucose-assimilation
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 sulfideyes
6836735581indoleno
6838035581indoleno

metabolite tests

@refChebi-IDmetaboliteindole test
6838035581indole-
6836735581indole-

enzymes

@refvalueactivityec
8781catalase-1.11.1.6
8781cytochrome-c oxidase-1.9.3.1
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
68373catalase-1.11.1.6
68373pyrrolidonyl arylamidase-3.4.19.3
68373gamma-glutamyltransferase-2.3.2.2
68373urease+3.5.1.5
68367catalase-1.11.1.6
68367beta-glucosidase-3.2.1.21
68367gelatinase-
68367urease+3.5.1.5

fatty acid profile

  • @reffatty acidpercentageECL
    44971C12:04.212
    44971C14:05.514
    44971C16:07.816
    44971C18:0618
    44971C14:0 3OH/C16:1 ISO I6.215.485
    44971C16:0 3OH6.617.52
    44971C18:1 ω7c /12t/9t60.617.824
    44971C18:2 ω6,9c/C18:0 ANTE0.717.724
    44971unknown 14.5032.514.503
  • type of FA analysis: whole cell analysis
  • method/protocol: CCUG
  • @reffatty acidpercentageECL
    44971C12:06.112
    44971C14:05.114
    44971C16:0516
    44971C18:02.218
    44971C12:0 ALDE ?1.210.915
    44971C13:1 at 12-131.612.931
    44971C14:0 3OH/C16:1 ISO I7.915.485
    44971C16:0 3OH4.417.52
    44971C18:1 ω7c /12t/9t65.217.824
    44971C18:2 ω6,9c/C18:0 ANTE1.117.724
  • type of FA analysis: whole cell analysis
  • method/protocol: CCUG
  • @reffatty acidpercentageECL
    44971C12:06.812
    44971C14:08.214
    44971C16:08.616
    44971C18:02.518
    44971C14:0 3OH/C16:1 ISO I10.515.485
    44971C16:1 ω7c1.815.819
    44971C18:1 ω5c0.317.919
    44971C18:1 ω7c /12t/9t57.717.824
    44971C18:1 ω9c0.617.769
    44971C18:2 ω6,9c/C18:0 ANTE1.417.724
    44971Unidentified0.313.737
    44971Unidentified0.513.94
    44971unknown 14.5030.914.503
  • type of FA analysis: whole cell analysis
  • method/protocol: CCUG

API 20A

@refINDUREGLUMANLACSACMALSALXYLARAGELESCGLYCELMNEMLZRAFSORRHATRECAT
8781-+-------------------

API CAM

@refURENITESTHIPGGTTTCPYRAArgAAspAPALH2SGLUSUTNALCFZACEPROPMLTCITEROCAT
8781++++-+-+/-+++----------
8781+-------+/--+----------

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
8781+----------------------------
8781+----------------------------

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
8781amniotic fluidCanadaCANNorth America
44971Amniotic fluid

isolation source categories

  • Cat1: #Host Body Product
  • Cat2: #Fluids

taxonmaps

  • @ref: 69479
  • File name: preview.99_2816.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15775;96_1498;97_1787;98_2184;99_2816&stattab=map
  • Last taxonomy: Campylobacter ureolyticus subclade
  • 16S sequence: HM007586
  • Sequence Identity:
  • Total samples: 52866
  • soil counts: 1363
  • aquatic counts: 1261
  • animal counts: 50004
  • plant counts: 238

Safety information

risk assessment

  • @ref: 8781
  • pathogenicity human: yes
  • pathogenicity animal: yes
  • biosafety level: 2
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Bacteroides ureolyticus strain CCUG 7319 clone 1 16S ribosomal RNA gene, partial sequence; 16S-23S ribosomal RNA intergenic spacer, complete sequence; and 23S ribosomal RNA gene, partial sequenceGQ4964841214ena827
20218Bacteroides ureolyticus strain DSM 20703 16S ribosomal RNA gene, partial sequenceHM0075861312ena1121102
8781Campylobacter ureolyticus strain ATCC 33387 16S ribosomal RNA gene, partial sequenceL043211453ena827

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Campylobacter ureolyticus DSM 20703GCA_000374605scaffoldncbi1121102
66792Campylobacter ureolyticus LMG 6451GCA_013372225completencbi827
66792Campylobacter ureolyticus NCTC10941GCA_900460885contigncbi827
66792Bacteroides ureolyticus DSM 207031121102.3wgspatric1121102
66792Campylobacter ureolyticus strain FDAARGOS_1102827.100completepatric827
66792Campylobacter ureolyticus strain LMG 6451827.97completepatric827
66792Campylobacter ureolyticus strain NCTC10941827.23wgspatric827
66792Campylobacter ureolyticus DSM 207032517572240draftimg1121102
66792Campylobacter ureolyticus NCTC 109412823244376draftimg827

GC content

  • @ref: 8781
  • GC-content: 28
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno99no
motileno87.742no
flagellatedno90.38no
gram-positiveno97.876no
anaerobicyes85.369yes
aerobicno97.885no
halophileno86.932no
spore-formingno96.116no
thermophileno88.094yes
glucose-utilno84.224no
glucose-fermentno84.593no

External links

@ref: 8781

culture collection no.: DSM 20703, ATCC 33387, CCUG 7319, LMG 6451, NCTC 10941

straininfo link

  • @ref: 71749
  • straininfo: 1216

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Enzymology3571475Numerical analysis of electrophoretic protein patterns of Bacteroides ureolyticus clinical isolates.Taylor AJ, Costas M, Owen RJJ Clin Microbiol10.1128/jcm.25.4.660-666.19871987Animals, Bacterial Proteins/*analysis, Bacteroides/*analysis/classification, Electrophoresis, Polyacrylamide Gel, Humans, SoftwarePathogenicity
Phylogeny6490858Comparison of strains of gram-negative, anaerobic, agar-corroding rods isolated from soft tissue infections in cats and dogs with type strains of Bacteroides gracilis, Wolinella recta, Wolinella succinogenes, and Campylobacter concisus.Love DN, Jones RF, Bailey M, Calverley AJ Clin Microbiol10.1128/jcm.20.4.747-750.19841984Agar, Animals, Bacteria/classification/*isolation & purification, Bacterial Infections/microbiology/*veterinary, Bacteroides/*isolation & purification, Campylobacter/*isolation & purification, Cat Diseases/*microbiology, Cats, Dog Diseases/*microbiology, DogsEnzymology
Phylogeny19801389Reclassification of Bacteroides ureolyticus as Campylobacter ureolyticus comb. nov., and emended description of the genus Campylobacter.Vandamme P, Debruyne L, De Brandt E, Falsen EInt J Syst Evol Microbiol10.1099/ijs.0.017152-02009Bacteroides/*classification/genetics/isolation & purification/metabolism, Campylobacter/*classification/genetics/isolation & purification/metabolism, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/metabolism, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/geneticsMetabolism

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
8781Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 20703)https://www.dsmz.de/collection/catalogue/details/culture/DSM-20703
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
44971Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 7319)https://www.ccug.se/strain?id=7319
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)
68367Automatically annotated from API 20A
68373Automatically annotated from API CAM
68380Automatically annotated from API rID32A
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
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
71749Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID1216.1StrainInfo: A central database for resolving microbial strain identifiers