Strain identifier

BacDive ID: 6102

Type strain: Yes

Species: Campylobacter pylori

Strain Designation: RPH 13487

Strain history: CIP 103995 <-- CCUG 17874 <-- E. Blincow and C. S. Goodwin K0045659.

NCBI tax ID(s): 102618 (strain), 210 (species)

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General

@ref: 15441

BacDive-ID: 6102

DSM-Number: 21031

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

description: Campylobacter pylori RPH 13487 is a microaerophile, mesophilic, Gram-negative bacterium that was isolated from endoscopic biopsy specimen of human gastric mucosa.

NCBI tax id

NCBI tax idMatching level
210species
102618strain

strain history

@refhistory
15441<- NCTC; NCTC 11637 <- C. S. Goodwin and D. I. Annear;
67770CIP 103995 <-- CCUG 17874 <-- E. Blincow and C. S. Goodwin K0045659.

doi: 10.13145/bacdive6102.20230509.8.1

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 pylori
  • full scientific name: Campylobacter pylori corrig. Marshall et al. 1985

  • synonyms

    @refsynonym
    20215Campylobacter pyloridis
    20215Helicobacter pylori
    20215Helicobacter nemestrinae

@ref: 15441

domain: Bacteria

phylum: Proteobacteria

class: Epsilonproteobacteria

order: Campylobacterales

family: Helicobacteraceae

genus: Helicobacter

species: Helicobacter pylori

full scientific name: Helicobacter pylori (Marshall et al. 1985) Goodwin et al. 1989

strain designation: RPH 13487

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapeflagellum arrangementmotilityconfidence
22920negative2.5-5 µm0.5-1 µmrod-shapedpolar
69480yes93.089
69480negative99.999

colony morphology

  • @ref: 15441
  • incubation period: 1-2 days

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
22920Brain heart infusionyes
15441COLUMBIA 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
41863MEDIUM 6 - Columbia agar with 10 % horse bloodyesDistilled water make up to (1000.000 ml);Columbia agar (39.000 g);Horseblood (100.000 ml)

culture temp

@refgrowthtypetemperaturerange
22920positivegrowth37mesophilic
15441positivegrowth37mesophilic
41863positivegrowth37mesophilic
46705positivegrowth37mesophilic
67770positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 46705
  • oxygen tolerance: microaerophile

spore formation

@refspore formationconfidence
69481no100
69480no99.997

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
22920606565hippurate-hydrolysis
2292016199urea+hydrolysis
2292017632nitrate-reduction
6837316199urea+hydrolysis
6837317272propionate-assimilation

antibiotic resistance

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

metabolite production

@refChebi-IDmetaboliteproduction
2292016136hydrogen sulfideno
6837316136hydrogen sulfideno

enzymes

@refvalueactivityec
22920alkaline phosphatase-3.1.3.1
22920catalase+1.11.1.6
22920leucine arylamidase+/-3.4.11.1
22920cytochrome oxidase+1.9.3.1
22920urease+3.5.1.5
15441catalase+1.11.1.6
15441cytochrome-c oxidase+1.9.3.1
68373catalase+1.11.1.6
68373alkaline phosphatase+3.1.3.1
68373L-aspartate arylamidase-3.4.11.21
68373L-arginine arylamidase-
68373gamma-glutamyltransferase+2.3.2.2
68373urease+3.5.1.5

fatty acid profile

  • fatty acids

    @reffatty acidpercentageECL
    46705C12:00.612
    46705C13:00.513
    46705C14:050.914
    46705C15:01.115
    46705C16:0216
    46705C18:04.618
    46705C19:00.519
    46705C13:0 ISO 2OH0.513.814
    46705C13:1 at 12-130.912.931
    46705C16:0 3OH5.517.52
    46705C17:0 3OH0.818.535
    46705C18:0 3OH3.919.551
    46705C18:1 ω7c /12t/9t6.417.824
    46705C18:2 ω6,9c/C18:0 ANTE1.117.724
    46705C19:0 CYCLO ω8c19.718.9
    46705unknown 14.9661.114.966
  • type of FA analysis: whole cell analysis
  • method/protocol: CCUG

API CAM

@refURENITESTHIPGGTTTCPYRAArgAAspAPALH2SGLUSUTNALCFZACEPROPMLTCITEROCAT
15441+---++/----+-+/---------+
15441+--++----+----------+
15441+---+----+----------+
15441+---+----+----------+
15441+---+----+----------+
15441+---+----+--+/--------+
15441+-+-+----+----------+
15441+---+----+----------+
15441+---++---+----------+
15441+---+----+----------+
15441+---++---+----------+
15441+---+----+----------+
15441+---++---+----------+
15441+---++---+----------+
15441+---+----+----------+
15441+-+-+----+----------+
15441+++-+++/---+-++/---+-+/-+-+

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentsampling dategeographic location
15441endoscopic biopsy specimen of human gastric mucosaAustraliaAUSAustralia and Oceania
46705Human gastric biopsyAustraliaAUSAustralia and Oceania1982-05-05Perth
67770Endoscopic biopsy specimen of human gastric mucosaAustraliaAUSAustralia and OceaniaRoyal Perth Hospital

isolation source categories

Cat1Cat2Cat3
#Infection#Patient#Biopsy
#Infection#Patient#Specimen
#Host#Human
#Host Body-Site#Gastrointestinal tract#Stomach

taxonmaps

  • @ref: 69479
  • File name: preview.99_91.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_36;96_72;97_75;98_82;99_91&stattab=map
  • Last taxonomy: Helicobacter pylori subclade
  • 16S sequence: Z25741
  • Sequence Identity:
  • Total samples: 18084
  • soil counts: 670
  • aquatic counts: 829
  • animal counts: 16307
  • plant counts: 278

Safety information

risk assessment

  • @ref: 15441
  • biosafety level: 2
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Helicobacter pylori 16S ribosomal RNA gene, partial sequenceAF3021061445ena210
20218Helicobacter pylori (ATCC 43504) partial 16S ribosomal RNAM881571450ena210
20218Helicobacter pylori isolate ATCC 43504 16S rRNA geneU013301503ena210
20218H.pylori gene for 16S ribosomal RNA (partial)Z257411454ena102618
15441Helicobacter pylori strain ATCC 43504 16S ribosomal RNA, partial sequenceNR_0447611503nuccore210
67770Helicobacter pylori JCM 12093 gene for 16S ribosomal RNA, partial sequenceLC5074471426ena210

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Helicobacter pylori ATCC 43504GCA_004295525completencbi210
66792Helicobacter pylori NCTC 11637 = CCUG 17874 = ATCC 43504 = JCM 12093GCA_900478295completencbi102618
66792Helicobacter pylori JCM 12093GCA_014654435scaffoldncbi210
66792Helicobacter pylori NCTC 11637 = CCUG 17874 = ATCC 43504 = JCM 12093GCA_001312765contigncbi102618
66792Helicobacter pylori JCM 120931300157.3wgspatric1300157
66792Helicobacter pylori NCTC 11637 = CCUG 17874102618.3wgspatric102618
66792Helicobacter pylori NCTC 11637 = CCUG 17874 = ATCC 43504 strain NCTC11637102618.7completepatric102618
66792Helicobacter pylori strain ATCC 43504 strain PMSS1210.5630completepatric210
66792Helicobacter pylori strain JCM 12093210.7428wgspatric210
66792Helicobacter pylori strain PMSS1 strain ATCC 43504210.5631completepatric210
66792Helicobacter pylori NCTC 116372896621630completeimg102618
66792Helicobacter pylori JCM 120932734481914draftimg1300157
66792Helicobacter pylori ATCC 435042879776430completeimg210
66792Helicobacter pylori CCUG 178742537562118draftimg102618
67770Helicobacter pylori NCTC 11637 = CCUG 17874 = ATCC 43504 = JCM 12093GCA_000258845contigncbi102618
67770Helicobacter pylori FDAARGOS_299GCA_002206465contigncbi210

GC content

@refGC-contentmethod
2292037.1
6777037.1thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedno59.198no
gram-positiveno98.878yes
anaerobicno87.648yes
aerobicno97.199yes
halophileno85.466no
spore-formingno96.585no
thermophileno57.146no
glucose-utilno74.193no
motileyes90.039no
glucose-fermentno81.486no

External links

@ref: 15441

culture collection no.: CCUG 15815, LMG 7540, CIP 103995, DSM 21031, ATCC 43504, CCUG 17874, DSM 4867, LMG 7539, NCTC 11637, JCM 12093, JCM 7653, LMG 18041, LMG 18045

straininfo link

  • @ref: 75590
  • straininfo: 10524

literature

topicPubmed-IDtitleauthorsjournalyearmeshDOItopic2
Phylogeny2499346DNA-DNA hybridization incompatibility of Campylobacter pylori with other Campylobacter and Wolinella species.Bukholm G, Nedenskov-Sorensen P, Bovre KAPMIS1989Bacteria/classification/*genetics, Campylobacter/classification/*genetics, DNA, Bacterial/*genetics, Nucleic Acid Hybridization, Sequence Homology, Nucleic Acid
2753837The effect of cooling rate, freeze-drying suspending fluid and culture age on the preservation of Campylobacter pylori.Owen RJ, On SL, Costas MJ Appl Bacteriol1989*Campylobacter, Freeze Drying, *Preservation, Biological, Time Factors10.1111/j.1365-2672.1989.tb02486.x
Phylogeny2757368Strain variation in Campylobacter pylori detected by numerical analysis of one-dimensional electrophoretic protein patterns.Owen RJ, Costas M, Morgan DD, On SL, Hill LR, Pearson AD, Morgan DRAntonie Van Leeuwenhoek1989Bacterial Proteins/*analysis, Campylobacter/analysis/*classification/genetics/isolation & purification, Densitometry, Electrophoresis, Polyacrylamide Gel, *Genetic Variation, Humans, Numerical Analysis, Computer-Assisted, Reproducibility of Results, Species Specificity10.1007/BF00393854Enzymology
Pathogenicity3209524Susceptibility of Campylobacter pylori to macrolides and fluoroquinolones.Hardy DJ, Hanson CW, Hensey DM, Beyer JM, Fernandes PBJ Antimicrob Chemother19884-Quinolones, Anti-Bacterial Agents/*pharmacology, Anti-Infective Agents/*pharmacology, Campylobacter/*drug effects, Microbial Sensitivity Tests10.1093/jac/22.5.631
Pathogenicity3252903GC content of DNA of Campylobacter pylori and other species belonging or related to the genus Campylobacter.Beji A, Megraud F, Vincent P, Gavini F, Izard D, Leclerc HAnn Inst Pasteur Microbiol1988Base Composition, Campylobacter/*genetics, Cytosine/*analysis, DNA, Bacterial/*analysis, Guanine/*analysis, Humans, Nucleic Acid Denaturation, Pyloric Antrum/microbiology, Species Specificity10.1016/0769-2609(88)90152-4Phylogeny

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
15441Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21031)https://www.dsmz.de/collection/catalogue/details/culture/DSM-21031
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
22920C. STEWART GOODWIN, JOHN A. ARMSTRONG, TERRY CHILVERS, MICHELLE PETERS, M. DAVID COLLINS, LINDSAY SLY, WILLIAM McCONNELL, WILLIAM E. S. HARPER10.1099/00207713-39-4-397Transfer of Campylobacter pylori and Campylobacter mustelae to Helicobacter gen. nov. as Helicobacter pylori comb. nov. and Helicobacter mustelae comb. nov., RespectivelyIJSEM 39: 397-405 1989
41863Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/15853
46705Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 17874)https://www.ccug.se/strain?id=17874
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)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68373Automatically annotated from API CAM
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
75590Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID10524.1StrainInfo: A central database for resolving microbial strain identifiers