Strain identifier
BacDive ID: 5392
Type strain: 
Species: Porphyrobacter tepidarius
Strain Designation: OT 3
Strain history: <- J. M. González, OT3
NCBI tax ID(s): 60454 (species)
version 8.1 (current version)
General
@ref: 3980
BacDive-ID: 5392
DSM-Number: 10594
keywords: genome sequence, 16S sequence, Bacteria, thermophilic
description: Porphyrobacter tepidarius OT 3 is a thermophilic bacterium that was isolated from Ottotomura hot spring.
NCBI tax id
- NCBI tax id: 60454
- Matching level: species
strain history
- @ref: 3980
- history: <- J. M. González, OT3
doi: 10.13145/bacdive5392.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Alphaproteobacteria
- order: Sphingomonadales
- family: Erythrobacteraceae
- genus: Porphyrobacter
- species: Porphyrobacter tepidarius
- full scientific name: Porphyrobacter tepidarius Hanada et al. 1997
synonyms
- @ref: 20215
- synonym: Erythrobacter tepidarius
@ref: 3980
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Sphingomonadales
family: Erythrobacteraceae
genus: Porphyrobacter
species: Porphyrobacter tepidarius
full scientific name: Porphyrobacter tepidarius Hanada et al. 1997
strain designation: OT 3
type strain: yes
Morphology
cell morphology
| @ref | motility | confidence | gram stain |
|---|---|---|---|
| 69480 | no | 91.109 | |
| 69480 | 99.99 | negative |
Culture and growth conditions
culture medium
- @ref: 3980
- name: PORPHYROBACTER TEPIDARIUS MEDIUM (DSMZ Medium 791)
- growth: yes
- link: https://mediadive.dsmz.de/medium/791
- composition: Name: PORPHYROBACTER TEPIDARIUS MEDIUM (DSMZ Medium 791) Composition: Yeast extract 0.5 g/l Na glutamate 0.5 g/l Sodium succinate 0.5 g/l Sodium acetate 0.5 g/l Casamino acids 0.5 g/l (NH4)2SO4 0.5 g/l Sodium thiosulphate 0.5 g/l K2HPO4 0.39 g/l KH2PO4 0.375 g/l MgSO4 x 7 H2O 0.12325 g/l NaCl 0.117 g/l CaCl2 x 2 H2O 0.0147 g/l FeSO4 x 7 H2O 0.00555 g/l Na3-EDTA 0.002 g/l Thiamine 0.001 g/l Nicotinic acid 0.001 g/l MnSO4 x 4 H2O 0.00056 g/l p-Aminobenzoic acid 0.0005 g/l Calcium pantothenate 0.0005 g/l Pyridoxine hydrochloride 0.0005 g/l Folic acid 0.0005 g/l H3BO3 0.000155 g/l ZnSO4 x 7 H2O 0.000145 g/l Co(NO3)2 x 6 H2O 0.000145 g/l CuSO4 x 5 H2O 0.000125 g/l Na2Mo4 x 2 H2O 0.00012 g/l Biotin 5e-05 g/l Vitamin B12 1e-05 g/l Distilled water
culture temp
- @ref: 3980
- growth: positive
- type: growth
- temperature: 45
- range: thermophilic
Physiology and metabolism
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | no | 100 |
| 69480 | no | 99.996 |
Isolation, sampling and environmental information
isolation
- @ref: 3980
- sample type: Ottotomura hot spring
- geographic location: Shidzuoka Prefecture, Usami
- country: Japan
- origin.country: JPN
- continent: Asia
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Aquatic | #Thermal spring |
| #Condition | #Thermophilic (>45°C) |
Safety information
risk assessment
- @ref: 3980
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
| @ref | description | accession | length | database | NCBI tax ID |
|---|---|---|---|---|---|
| 20218 | Porphyrobacter tepidarius gene for 16S ribosomal RNA, partial sequence | AB033328 | 1478 | ena | 60454 |
| 3980 | Porphyrobacter tepidarius gene for 16S rRNA, partial sequence | D84429 | 1442 | ena | 60454 |
| 3980 | Porphyrobacter tepidarius strain DSM 10594 16S ribosomal RNA gene, partial sequence | AF465839 | 1413 | ena | 60454 |
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Erythrobacter tepidarius DSM 10594 | GCA_002155695 | contig | ncbi | 60454 |
| 66792 | Porphyrobacter tepidarius strain DSM 10594 | 60454.4 | wgs | patric | 60454 |
| 66792 | Erythrobacter tepidarius DSM 10594 | 2839482000 | draft | img | 60454 |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| gram-positive | no | 97.797 | no |
| anaerobic | no | 99.269 | no |
| halophile | no | 82.037 | no |
| spore-forming | no | 94.461 | no |
| glucose-util | yes | 82.703 | no |
| thermophile | no | 86.219 | yes |
| flagellated | no | 83.73 | no |
| motile | yes | 60.024 | no |
| aerobic | yes | 93.597 | no |
| glucose-ferment | no | 92.507 | no |
External links
@ref: 3980
culture collection no.: DSM 10594
straininfo link
- @ref: 74882
- straininfo: 48849
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 3980 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 10594) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-10594 | |||
| 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 | |
| 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) | |||
| 69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
| 69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 | |||
| 74882 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID48849.1 | StrainInfo: A central database for resolving microbial strain identifiers |