Strain identifier
BacDive ID: 164881
Type strain: 
Species: Yokenella regensburgei
Strain history: Y. Kosako 85574 <-- R. Sakazaki 85036 <-- CDC 1443-77 <-- New Jersey State Health Dept., USA.
NCBI tax ID(s): 1002368 (strain), 158877 (species)
version 9.1 (current version)
General
@ref: 67770
BacDive-ID: 164881
keywords: genome sequence, 16S sequence, Bacteria, Gram-negative
description: Yokenella regensburgei JCM 3961 is a Gram-negative bacterium that was isolated from Human stool.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 1002368 | strain |
| 158877 | species |
strain history
- @ref: 67770
- history: Y. Kosako 85574 <-- R. Sakazaki 85036 <-- CDC 1443-77 <-- New Jersey State Health Dept., USA.
doi: 10.13145/bacdive164881.20240916.9.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Gammaproteobacteria
- order: Enterobacterales
- family: Enterobacteriaceae
- genus: Yokenella
- species: Yokenella regensburgei
- full scientific name: Yokenella regensburgei Kosako et al. 1985
synonyms
- @ref: 20215
- synonym: Koserella trabulsii
@ref: 67770
domain: Bacteria
phylum: Proteobacteria
class: Gammaproteobacteria
order: Enterobacterales
family: Enterobacteriaceae
genus: Yokenella
species: Yokenella regensburgei
full scientific name: Yokenella regensburgei Kosako et al. 1985
type strain: no
Morphology
cell morphology
- @ref: 69480
- gram stain: negative
- confidence: 98.982
Culture and growth conditions
culture temp
- @ref: 67770
- growth: positive
- type: growth
- temperature: 37
Physiology and metabolism
spore formation
- @ref: 69481
- spore formation: no
- confidence: 100
Isolation, sampling and environmental information
isolation
- @ref: 67770
- sample type: Human stool
- geographic location: NJ
- country: USA
- origin.country: USA
- continent: North America
Sequence information
16S sequences
- @ref: 67770
- description: Yokenella regensburgei JCM 3961 gene for 16S ribosomal RNA, partial sequence
- accession: LC420110
- length: 1462
- database: nuccore
- NCBI tax ID: 158877
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Yokenella regensburgei ATCC 43003 | 1002368.3 | wgs | patric | 1002368 |
| 66792 | Yokenella regensburgei ATCC 43003 | 2534682241 | draft | img | 1002368 |
| 67770 | Yokenella regensburgei ATCC 43003 | GCA_000239335 | scaffold | ncbi | 1002368 |
Genome-based predictions
predictions
| @ref | trait | model | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 69481 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 100 | no |
| 69480 | gram-positive | gram-positive | Positive reaction to Gram-staining | no | 98.982 | no |
| 69480 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 95.099 | no |
| 69480 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 87.109 | no |
| 69480 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | no | 69.731 | no |
| 69480 | thermophilic | thermophile | Ability to grow at temperatures above or equal to 45°C | no | 98 | yes |
| 69480 | flagellated | motile2+ | Ability to perform flagellated movement | yes | 77.203 | no |
External links
@ref: 67770
culture collection no.: JCM 3961, ATCC 43003, CDC 1443-77
straininfo link
- @ref: 114298
- straininfo: 41588
Reference
| @id | authors | title | doi/url |
|---|---|---|---|
| 20215 | Parte, 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 DSMZ | 10.1099/ijsem.0.004332 |
| 66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes |
| 67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | |
| 69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Predictions 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 |
| 69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | Predictions based on the model GenomeNet Sporulation v. 1 | 10.21203/rs.3.rs-2527258/v1 |
| 114298 | Reimer, 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 identifiers | 10.60712/SI-ID41588.1 |