Strain identifier

BacDive ID: 6104

Type strain: Yes

Species: Helicobacter muridarum

Strain Designation: ST1

Strain history: CIP <- 1996, ATCC <- 1991, F.E. Dewhirst, FDC, Boston, USA <- J.G. Fox, Cambridge, USA <- A. Lee, Sydney, Australia: strain ST1

NCBI tax ID(s): 216 (species)

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General

@ref: 16211

BacDive-ID: 6104

DSM-Number: 22221

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

description: Helicobacter muridarum ST1 is a microaerophile, mesophilic, Gram-negative animal pathogen that was isolated from intestinal mucosa of rats and mice.

NCBI tax id

  • NCBI tax id: 216
  • Matching level: species

strain history

@refhistory
16211<- CCUG; CCUG 29262 <- F. E. Dewhirst, Forsyth Dental Center, Boston, USA <- J. G. Fox, Massachusetts Inst. Technology, Cambridge, USA <- A. Lee, School Microbiology and Immunology, Univ. New South Wales, Sydney, Australia
121194CIP <- 1996, ATCC <- 1991, F.E. Dewhirst, FDC, Boston, USA <- J.G. Fox, Cambridge, USA <- A. Lee, Sydney, Australia: strain ST1

doi: 10.13145/bacdive6104.20230509.8.1

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 muridarum
  • full scientific name: Helicobacter muridarum Lee et al. 1992

@ref: 16211

domain: Bacteria

phylum: Proteobacteria

class: Epsilonproteobacteria

order: Campylobacterales

family: Helicobacteraceae

genus: Helicobacter

species: Helicobacter muridarum

full scientific name: Helicobacter muridarum Lee et al. 1992

strain designation: ST1

type strain: yes

Morphology

cell morphology

  • @ref: 121194
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: yes

colony morphology

  • @ref: 49563
  • incubation period: 4-6 days

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
16211COLUMBIA 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
41070MEDIUM 45 - for Columbia agar with sheep bloodyesDistilled water make up to (1000.000 ml);Columbia agar (39.000 g);Sheepblood (100.000 ml)
121194CIP Medium 45yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=45

culture temp

@refgrowthtypetemperaturerange
16211positivegrowth37mesophilic
41070positivegrowth37mesophilic
121194positivegrowth30-37mesophilic
121194nogrowth25mesophilic
121194nogrowth41thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
16211microaerophile
49563microaerophile

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
121194606565hippurate-hydrolysis
12119417632nitrate-reduction
12119416301nitrite-reduction
6837316199urea+hydrolysis
6837317632nitrate-reduction
68373606565hippurate-hydrolysis
6837378019triphenyltetrazolium chloride+reduction
6837317634D-glucose-assimilation
6837330089acetate-assimilation
6837317272propionate-assimilation
6837325115malate-assimilation

antibiotic resistance

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

metabolite production

@refChebi-IDmetaboliteproduction
6837316136hydrogen sulfideno
12119435581indoleno

enzymes

@refvalueactivityec
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
68382alpha-glucosidase+3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase-3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase-
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin-3.4.21.4
68382cystine arylamidase-3.4.11.3
68382valine arylamidase-
68382leucine arylamidase-3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)+
68382esterase (C 4)+
68382alkaline phosphatase-3.1.3.1
68373catalase+1.11.1.6
68373alkaline phosphatase+3.1.3.1
68373L-aspartate arylamidase-3.4.11.21
68373pyrrolidonyl arylamidase-3.4.19.3
68373gamma-glutamyltransferase+2.3.2.2
68373urease+3.5.1.5
121194oxidase+
121194catalase+1.11.1.6
121194urease+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
121194--++------+----+----

API CAM

@refURENITESTHIPGGTTTCPYRAArgAAspAPALH2SGLUSUTNALCFZACEPROPMLTCITEROCAT
16211+---++-+/--+--+-----+/--+
16211+-+/--++-+-+----------+

Isolation, sampling and environmental information

isolation

@refsample type
16211intestinal mucosa of rats and mice
49563Rat ileum
121194Animal, Rat, ileum

isolation source categories

Cat1Cat2Cat3
#Host#Mammals#Muridae (Mouse/Rat)
#Host Body-Site#Gastrointestinal tract

taxonmaps

  • @ref: 69479
  • File name: preview.99_4850.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_36;96_946;97_1292;98_3630;99_4850&stattab=map
  • Last taxonomy: Helicobacter muridarum subclade
  • 16S sequence: M80205
  • Sequence Identity:
  • Total samples: 953
  • soil counts: 10
  • aquatic counts: 20
  • animal counts: 918
  • plant counts: 5

Safety information

risk assessment

@refpathogenicity animalbiosafety levelbiosafety level comment
16211yes2Risk group (German classification)
1211942Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Helicobacter muridarum 16S ribosomal RNA gene, partial sequenceAF3021041440ena216
16211Helicobacter muridarum strain ST1 16S ribosomal RNA gene, complete sequenceM802051478ena216

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Helicobacter muridarum NCTC12714GCA_900450885contigncbi216
66792Helicobacter muridarum ST1GCA_000765805contigncbi216
66792Helicobacter muridarum strain NCTC12714216.15wgspatric216
66792Helicobacter muridarum ST12663763499draftimg216
66792Helicobacter muridarum NCTC 127142808606664draftimg216

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileyes90.211no
gram-positiveno98.953no
anaerobicno65.941no
aerobicno96.264yes
halophileno79.661no
spore-formingno95.996no
glucose-utilno87.625yes
flagellatedyes57.929no
thermophileno76.546yes
glucose-fermentno82.891no

External links

@ref: 16211

culture collection no.: DSM 22221, ATCC 49282, CCUG 29262, CIP 104248, LMG 13646, NCTC 12714

straininfo link

  • @ref: 75592
  • straininfo: 7689

literature

  • topic: Phylogeny
  • Pubmed-ID: 1736969
  • title: Helicobacter muridarum sp. nov., a microaerophilic helical bacterium with a novel ultrastructure isolated from the intestinal mucosa of rodents.
  • authors: Lee A, Phillips MW, O'Rourke JL, Paster BJ, Dewhirst FE, Fraser GJ, Fox JG, Sly LI, Romaniuk PJ, Trust TJ, et al.
  • journal: Int J Syst Bacteriol
  • DOI: 10.1099/00207713-42-1-27
  • year: 1992
  • mesh: Animals, Base Sequence, Helicobacter/genetics/metabolism/*ultrastructure, Intestinal Mucosa/*microbiology, Mice, RNA, Ribosomal, 16S/chemistry, Rats
  • topic2: Metabolism

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
16211Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 22221)https://www.dsmz.de/collection/catalogue/details/culture/DSM-22221
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
41070Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/16136
49563Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 29262)https://www.ccug.se/strain?id=29262
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
68373Automatically annotated from API CAM
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
75592Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID7689.1StrainInfo: A central database for resolving microbial strain identifiers
121194Curators of the CIPCollection of Institut Pasteur (CIP 104248)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104248