Strain identifier
BacDive ID: 5220
Type strain:
Species: Yersinia rohdei
Strain Designation: H 271-36/78, H271-36/78, 3022-85
Strain history: CIP <- 1988, ATCC <- D.J. Brenner, CDC, Atlanta, Georgia, USA: strain 3022-85 <- S. Aleksic: strain H271-36/78
NCBI tax ID(s): 527004 (strain), 29485 (species)
General
@ref: 7468
BacDive-ID: 5220
DSM-Number: 18270
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, motile, rod-shaped, human pathogen
description: Yersinia rohdei H 271-36/78 is an aerobe, mesophilic, Gram-negative human pathogen that was isolated from dog faeces.
NCBI tax id
NCBI tax id | Matching level |
---|---|
29485 | species |
527004 | strain |
strain history
@ref | history |
---|---|
7468 | <- CCUG <- S. Aleksic, Inst. of Hygiene, Hamburg; H 271-36/78 |
67770 | CDC 3022-85. |
122247 | CIP <- 1988, ATCC <- D.J. Brenner, CDC, Atlanta, Georgia, USA: strain 3022-85 <- S. Aleksic: strain H271-36/78 |
doi: 10.13145/bacdive5220.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Gammaproteobacteria
- order: Enterobacterales
- family: Yersiniaceae
- genus: Yersinia
- species: Yersinia rohdei
- full scientific name: Yersinia rohdei Aleksic et al. 1987
@ref: 7468
domain: Bacteria
phylum: Proteobacteria
class: Gammaproteobacteria
order: Enterobacteriales, not validated
family: Yersiniaceae
genus: Yersinia
species: Yersinia rohdei
full scientific name: Yersinia rohdei Aleksic et al. 1987
strain designation: H 271-36/78, H271-36/78, 3022-85
type strain: yes
Morphology
cell morphology
- @ref: 122247
- gram stain: negative
- cell shape: rod-shaped
- motility: yes
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
7468 | TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) | yes | https://mediadive.dsmz.de/medium/535 | Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water |
36553 | MEDIUM 72- for trypto casein soja agar | yes | Distilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g) | |
122247 | CIP Medium 3 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3 | |
122247 | CIP Medium 72 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
7468 | positive | growth | 30 | mesophilic |
36553 | positive | growth | 30 | mesophilic |
54500 | positive | growth | 26-30 | mesophilic |
67770 | positive | growth | 36 | mesophilic |
Physiology and metabolism
oxygen tolerance
- @ref: 54500
- oxygen tolerance: aerobe
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent | sampling date | isolation date |
---|---|---|---|---|---|---|---|
7468 | dog faeces | Hamburg | Germany | DEU | Europe | ||
54500 | Dog feces | Germany | DEU | Europe | 1978 | ||
67770 | Dog feces | ||||||
122247 | Animal, Dog, feces | Germany | DEU | Europe | 1978 |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Host | #Mammals | #Canidae (Dog) |
#Host Body Product | #Gastrointestinal tract | #Feces (Stool) |
Safety information
risk assessment
@ref | pathogenicity human | biosafety level | biosafety level comment |
---|---|---|---|
7468 | yes, in single cases | 1 | Risk group (German classification) |
122247 | 2 | Risk group (French classification) |
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Yersinia rohdei strain ATCC 43380 16S ribosomal RNA gene, partial sequence | AY332843 | 501 | ena | 29485 |
7468 | Yersinia rohdei 16S ribosomal RNA gene, partial sequence | AF366384 | 1461 | ena | 29485 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Yersinia rohdei ATCC 43380 | 527004.3 | wgs | patric | 527004 |
66792 | Yersinia rohdei ATCC 43380 | 645058789 | draft | img | 527004 |
67770 | Yersinia rohdei ATCC 43380 | GCA_000173775 | contig | ncbi | 527004 |
GC content
- @ref: 67770
- GC-content: 49.1
- method: thermal denaturation, midpoint method (Tm)
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
gram-positive | no | 98.922 | no |
anaerobic | no | 94.65 | no |
halophile | no | 94.502 | no |
spore-forming | no | 94.365 | no |
glucose-util | yes | 93.626 | no |
thermophile | no | 98.899 | no |
motile | yes | 90.497 | no |
aerobic | yes | 88.56 | yes |
flagellated | yes | 56.985 | no |
glucose-ferment | yes | 92.915 | no |
External links
@ref: 7468
culture collection no.: DSM 18270, ATCC 43380, CCUG 38833, CDC 3022-85, CIP 103163, LMG 8454, JCM 7376, NBRC 105715
straininfo link
- @ref: 74712
- straininfo: 6457
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
7468 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18270) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-18270 | |||
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 | |
36553 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/14930 | ||||
54500 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 38833) | https://www.ccug.se/strain?id=38833 | |||
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) | |||
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
74712 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID6457.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
122247 | Curators of the CIP | Collection of Institut Pasteur (CIP 103163) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103163 |