Strain identifier
BacDive ID: 6104
Type strain:
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)
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
@ref | history |
---|---|
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 |
121194 | CIP <- 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
@ref | name | growth | link | composition |
---|---|---|---|---|
16211 | COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) | yes | https://mediadive.dsmz.de/medium/693 | Name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar base |
41070 | MEDIUM 45 - for Columbia agar with sheep blood | yes | Distilled water make up to (1000.000 ml);Columbia agar (39.000 g);Sheepblood (100.000 ml) | |
121194 | CIP Medium 45 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=45 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
16211 | positive | growth | 37 | mesophilic |
41070 | positive | growth | 37 | mesophilic |
121194 | positive | growth | 30-37 | mesophilic |
121194 | no | growth | 25 | mesophilic |
121194 | no | growth | 41 | thermophilic |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
16211 | microaerophile |
49563 | microaerophile |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
121194 | 606565 | hippurate | - | hydrolysis |
121194 | 17632 | nitrate | - | reduction |
121194 | 16301 | nitrite | - | reduction |
68373 | 16199 | urea | + | hydrolysis |
68373 | 17632 | nitrate | - | reduction |
68373 | 606565 | hippurate | - | hydrolysis |
68373 | 78019 | triphenyltetrazolium chloride | + | reduction |
68373 | 17634 | D-glucose | - | assimilation |
68373 | 30089 | acetate | - | assimilation |
68373 | 17272 | propionate | - | assimilation |
68373 | 25115 | malate | - | assimilation |
antibiotic resistance
@ref | ChEBI | metabolite | is antibiotic | is sensitive | sensitivity conc. |
---|---|---|---|---|---|
68373 | 48923 | erythromycin | yes | yes | 14 µg |
68373 | 474053 | cefazolin | yes | yes | 224 µg |
68373 | 100147 | nalidixic acid | yes | yes | 84 µg |
metabolite production
@ref | Chebi-ID | metabolite | production |
---|---|---|---|
68373 | 16136 | hydrogen sulfide | no |
121194 | 35581 | indole | no |
enzymes
@ref | value | activity | ec |
---|---|---|---|
68382 | alpha-fucosidase | - | 3.2.1.51 |
68382 | alpha-mannosidase | - | 3.2.1.24 |
68382 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
68382 | beta-glucosidase | - | 3.2.1.21 |
68382 | alpha-glucosidase | + | 3.2.1.20 |
68382 | beta-glucuronidase | - | 3.2.1.31 |
68382 | beta-galactosidase | - | 3.2.1.23 |
68382 | alpha-galactosidase | - | 3.2.1.22 |
68382 | naphthol-AS-BI-phosphohydrolase | - | |
68382 | acid phosphatase | + | 3.1.3.2 |
68382 | alpha-chymotrypsin | - | 3.4.21.1 |
68382 | trypsin | - | 3.4.21.4 |
68382 | cystine arylamidase | - | 3.4.11.3 |
68382 | valine arylamidase | - | |
68382 | leucine arylamidase | - | 3.4.11.1 |
68382 | lipase (C 14) | - | |
68382 | esterase lipase (C 8) | + | |
68382 | esterase (C 4) | + | |
68382 | alkaline phosphatase | - | 3.1.3.1 |
68373 | catalase | + | 1.11.1.6 |
68373 | alkaline phosphatase | + | 3.1.3.1 |
68373 | L-aspartate arylamidase | - | 3.4.11.21 |
68373 | pyrrolidonyl arylamidase | - | 3.4.19.3 |
68373 | gamma-glutamyltransferase | + | 2.3.2.2 |
68373 | urease | + | 3.5.1.5 |
121194 | oxidase | + | |
121194 | catalase | + | 1.11.1.6 |
121194 | urease | + | 3.5.1.5 |
API zym
@ref | Control | Alkaline phosphatase | Esterase | Esterase Lipase | Lipase | Leucine arylamidase | Valine arylamidase | Cystine arylamidase | Trypsin | alpha- Chymotrypsin | Acid phosphatase | Naphthol-AS-BI-phosphohydrolase | alpha- Galactosidase | beta- Galactosidase | beta- Glucuronidase | alpha- Glucosidase | beta- Glucosidase | N-acetyl-beta- glucosaminidase | alpha- Mannosidase | alpha- Fucosidase |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
121194 | - | - | + | + | - | - | - | - | - | - | + | - | - | - | - | + | - | - | - | - |
API CAM
@ref | URE | NIT | EST | HIP | GGT | TTC | PYRA | ArgA | AspA | PAL | H2S | GLU | SUT | NAL | CFZ | ACE | PROP | MLT | CIT | ERO | CAT |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
16211 | + | - | - | - | + | + | - | +/- | - | + | - | - | + | - | - | - | - | - | +/- | - | + |
16211 | + | - | +/- | - | + | + | - | + | - | + | - | - | - | - | - | - | - | - | - | - | + |
Isolation, sampling and environmental information
isolation
@ref | sample type |
---|---|
16211 | intestinal mucosa of rats and mice |
49563 | Rat ileum |
121194 | Animal, Rat, ileum |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#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
@ref | pathogenicity animal | biosafety level | biosafety level comment |
---|---|---|---|
16211 | yes | 2 | Risk group (German classification) |
121194 | 2 | Risk group (French classification) |
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Helicobacter muridarum 16S ribosomal RNA gene, partial sequence | AF302104 | 1440 | ena | 216 |
16211 | Helicobacter muridarum strain ST1 16S ribosomal RNA gene, complete sequence | M80205 | 1478 | ena | 216 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Helicobacter muridarum NCTC12714 | GCA_900450885 | contig | ncbi | 216 |
66792 | Helicobacter muridarum ST1 | GCA_000765805 | contig | ncbi | 216 |
66792 | Helicobacter muridarum strain NCTC12714 | 216.15 | wgs | patric | 216 |
66792 | Helicobacter muridarum ST1 | 2663763499 | draft | img | 216 |
66792 | Helicobacter muridarum NCTC 12714 | 2808606664 | draft | img | 216 |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
motile | yes | 90.211 | no |
gram-positive | no | 98.953 | no |
anaerobic | no | 65.941 | no |
aerobic | no | 96.264 | yes |
halophile | no | 79.661 | no |
spore-forming | no | 95.996 | no |
glucose-util | no | 87.625 | yes |
flagellated | yes | 57.929 | no |
thermophile | no | 76.546 | yes |
glucose-ferment | no | 82.891 | no |
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
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
16211 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 22221) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-22221 | |||
20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | |||
20218 | Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P. | 10.1016/j.syapm.2013.11.002 | StrainInfo introduces electronic passports for microorganisms. | Syst Appl Microbiol. 37: 42-50 2014 | 24321274 | |
41070 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/16136 | ||||
49563 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 29262) | https://www.ccug.se/strain?id=29262 | |||
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | 10.1093/nar/gkaa1025 | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | Nucleic Acids Res. 49: D498-D508 2020 | 33211880 | |
68373 | Automatically annotated from API CAM | |||||
68382 | Automatically annotated from API zym | |||||
69479 | João 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 | |||
75592 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID7689.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
121194 | Curators of the CIP | Collection of Institut Pasteur (CIP 104248) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104248 |