Strain identifier

BacDive ID: 24100

Type strain: Yes

Species: Helicobacter pametensis

Strain Designation: B9, B9A

Strain history: CIP <- 1996, ATCC <- 1991, F.E. Dewhirst, FDC, Boston, USA <- C. Seymour, Boston, USA: strain B9A

NCBI tax ID(s): 1408442 (strain), 95149 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 8.1 (current version)

General

@ref: 20607

BacDive-ID: 24100

DSM-Number: 29139

keywords: genome sequence, 16S sequence, Bacteria, microaerophile, mesophilic, motile

description: Helicobacter pametensis B9 is a microaerophile, mesophilic, motile bacterium that was isolated from Tern faeces.

NCBI tax id

NCBI tax idMatching level
95149species
1408442strain

strain history

@refhistory
20607<- CIP <- ATCC <- F. E. Dewhirst, Forsyth Dental Center, Boston, USA <- C. Seymor; B9
121522CIP <- 1996, ATCC <- 1991, F.E. Dewhirst, FDC, Boston, USA <- C. Seymour, Boston, USA: strain B9A

doi: 10.13145/bacdive24100.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Epsilonproteobacteria
  • order: Campylobacterales
  • family: Helicobacteraceae
  • genus: Helicobacter
  • species: Helicobacter pametensis
  • full scientific name: Helicobacter pametensis Dewhirst et al. 1994

@ref: 20607

domain: Bacteria

phylum: Proteobacteria

class: Epsilonproteobacteria

order: Campylobacterales

family: Helicobacteraceae

genus: Helicobacter

species: Helicobacter pametensis

full scientific name: Helicobacter pametensis Dewhirst et al. 1994

strain designation: B9, B9A

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480yes92.816
6948099.998negative
121522yesnegativerod-shaped

colony morphology

@refincubation periodhemolysis ability
206072-3 days
1215221

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
20607COLUMBIA 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
37167MEDIUM 6 - Columbia agar with 10 % horse bloodyesDistilled water make up to (1000.000 ml);Columbia agar (39.000 g);Horseblood (100.000 ml)
121522Brucella brothyes
121522CIP Medium 6yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=6
121522CIP Medium 45yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=45

culture temp

@refgrowthtypetemperaturerange
20607positivegrowth37mesophilic
37167positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 20607
  • oxygen tolerance: microaerophile

spore formation

@refspore formationconfidence
69481no100
69480no99.997

halophily

  • @ref: 121522
  • salt: NaCl
  • growth: no
  • tested relation: growth
  • concentration: 3.5 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
12152217632nitrate+reduction
12152216301nitrite-reduction

antibiotic resistance

  • @ref: 121522
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

  • @ref: 121522
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
121522oxidase+
121522gelatinase-
121522catalase+1.11.1.6
121522gamma-glutamyltransferase+2.3.2.2
121522urease-3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase-
68382cystine arylamidase-3.4.11.3
68382trypsin-3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase-3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase+3.2.1.20
68382beta-glucosidase-3.2.1.21
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

fatty acid profile

  • fatty acids

    @reffatty acidpercentageECL
    65611C12:02.712
    65611C13:00.213
    65611C14:026.814
    65611C15:00.515
    65611C16:030.216
    65611C17:00.217
    65611C18:00.818
    65611C13:0 ISO 2OH0.213.814
    65611C14:0 3OH/C16:1 ISO I3.415.485
    65611C16:0 3OH4.117.52
    65611C16:1 ω7c1.215.819
    65611C18:1 ω7c /12t/9t23.917.824
    65611C18:1 ω9c0.917.769
    65611C18:2 ω6,9c/C18:0 ANTE4.117.724
    65611C20:2 ω6,9c0.119.735
    65611Unidentified0.313.936
    65611Unidentified0.315.943
    65611unknown 14.5030.214.503
  • type of FA analysis: whole cell analysis
  • method/protocol: CCUG

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
121522-+++-+----++---+----

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
20607Tern faecesUSAUSANorth America
121522Tern, feces

isolation source categories

Cat1Cat2Cat3
#Host#Birds
#Host Body Product#Gastrointestinal tract#Feces (Stool)

taxonmaps

  • @ref: 69479
  • File name: preview.99_3472.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_36;96_378;97_2171;98_2665;99_3472&stattab=map
  • Last taxonomy: Helicobacter pametensis subclade
  • 16S sequence: NR_114586
  • Sequence Identity:
  • Total samples: 906
  • soil counts: 44
  • aquatic counts: 68
  • animal counts: 790
  • plant counts: 4

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
206071Risk group (German classification)
1215222Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20607Helicobacter pametensis strain B9A Seymour 16S small subunit ribosomal RNA gene, partial sequenceM881471481ena95149
20607Helicobacter pametensis strain ATCC 51478 16S ribosomal RNA, partial sequenceNR_1145861439nuccore95149

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Helicobacter pametensis ATCC 51478GCA_000518225scaffoldncbi1408442
66792Helicobacter pametensis ATCC 514781408442.3wgspatric1408442
66792Helicobacter pametensis ATCC 514782546825547draftimg1408442

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes88.632no
flagellatedno50no
gram-positiveno99.247no
anaerobicno76.638yes
halophileno79.653no
spore-formingno96.528no
thermophileno65.608yes
glucose-utilno76.776no
aerobicno97.795yes
glucose-fermentno80.579no

External links

@ref: 20607

culture collection no.: DSM 29139, ATCC 51478, CCUG 29255, CIP 104249, LMG 12678

straininfo link

  • @ref: 88062
  • straininfo: 13918

Reference

@idauthorstitledoi/urlcatalogue
20215Parte, 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 DSMZ10.1099/ijsem.0.004332
20607Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-29139Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 29139)
37167Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/16137
65611Curators of the CCUGhttps://www.ccug.se/strain?id=29255Culture Collection University of Gothenburg (CCUG) (CCUG 29255)
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions 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
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1
88062Reimer, 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 identifiers10.60712/SI-ID13918.1
121522Curators of the CIPhttps://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104249Collection of Institut Pasteur (CIP 104249)