Strain identifier
BacDive ID: 13694
Type strain: 
Species: Paracoccus pantotrophus
Strain Designation: 1628, Vogt 11
Strain history: <- IMG, 1628 <- M. Vogt, 11 (Micrococcus denitrificans)
NCBI tax ID(s): 82367 (species)
version 8.1 (current version)
General
@ref: 187
BacDive-ID: 13694
DSM-Number: 415
keywords: genome sequence, 16S sequence, Bacteria, mesophilic
description: Paracoccus pantotrophus 1628 is a mesophilic bacterium of the family Paracoccaceae.
NCBI tax id
- NCBI tax id: 82367
- Matching level: species
strain history
- @ref: 187
- history: <- IMG, 1628 <- M. Vogt, 11 (Micrococcus denitrificans)
doi: 10.13145/bacdive13694.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Alphaproteobacteria
- order: Rhodobacterales
- family: Paracoccaceae
- genus: Paracoccus
- species: Paracoccus pantotrophus
- full scientific name: Paracoccus pantotrophus (Robertson and Kuenen 1984) Rainey et al. 1999
synonyms
- @ref: 20215
- synonym: Thiosphaera pantotropha
@ref: 187
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Rhodobacterales
family: Rhodobacteraceae
genus: Paracoccus
species: Paracoccus pantotrophus
full scientific name: Paracoccus pantotrophus (Robertson and Kuenen 1984) Rainey et al. 1999
strain designation: 1628, Vogt 11
type strain: no
Culture and growth conditions
culture medium
| @ref | name | growth | link | composition |
|---|---|---|---|---|
| 187 | MINERAL MEDIUM FOR CHEMOLITHOTROPHIC GROWTH (H-3) (DSMZ Medium 81) | yes | https://mediadive.dsmz.de/medium/81 | Name: MINERAL MEDIUM FOR CHEMOLITHOTROPHIC GROWTH (H-3) (DSMZ Medium 81) Composition: Agar 20.1005 g/l Na2HPO4 x 2 H2O 2.91457 g/l KH2PO4 2.31156 g/l NH4Cl 1.00503 g/l MgSO4 x 7 H2O 0.502512 g/l Ferric ammonium citrate 0.0502513 g/l CaCl2 x 2 H2O 0.0100503 g/l NaVO3 x H2O 0.00502512 g/l Calcium pantothenate 0.00251256 g/l Pyridoxine hydrochloride 0.00251256 g/l Nicotinic acid 0.00251256 g/l Thiamine-HCl x 2 H2O 0.00251256 g/l H3BO3 0.00150754 g/l CoCl2 x 6 H2O 0.00100503 g/l Riboflavin 0.000502513 g/l ZnSO4 x 7 H2O 0.000502513 g/l MnCl2 x 4 H2O 0.000150754 g/l Na2MoO4 x 2 H2O 0.000150754 g/l NiCl2 x 6 H2O 0.000100503 g/l CuCl2 x 2 H2O 5.02513e-05 g/l Vitamin B12 5.02513e-05 g/l Folic acid 1.00503e-05 g/l Biotin 5.02513e-06 g/l Distilled water |
| 187 | NUTRIENT AGAR (DSMZ Medium 1) | yes | https://mediadive.dsmz.de/medium/1 | Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water |
culture temp
- @ref: 187
- growth: positive
- type: growth
- temperature: 30
- range: mesophilic
Safety information
risk assessment
- @ref: 187
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 20218
- description: Paracoccus denitrificans partial 16S rRNA gene, strain DSM 415
- accession: HG917908
- length: 1376
- database: ena
- NCBI tax ID: 266
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Paracoccus denitrificans strain DSM 415 | 266.36 | wgs | patric | 266 |
| 66792 | Paracoccus denitrificans DSM 415 | 2597490358 | draft | img | 266 |
| 66792 | Paracoccus denitrificans DSM 415 | GCA_900115985 | scaffold | ncbi | 266 |
GC content
- @ref: 187
- GC-content: 66.3
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| motile | no | 56.951 | no |
| flagellated | no | 87.456 | no |
| gram-positive | no | 98.544 | no |
| anaerobic | no | 97.242 | no |
| aerobic | yes | 84.384 | no |
| halophile | no | 84.557 | no |
| spore-forming | no | 95.693 | no |
| glucose-ferment | no | 86.898 | no |
| thermophile | no | 98.153 | yes |
| glucose-util | yes | 88.338 | no |
External links
@ref: 187
culture collection no.: DSM 415, CCM 1396, NCIB 9722, IMG 1628
straininfo link
- @ref: 82879
- straininfo: 92760
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 187 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 415) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-415 | |||
| 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) | |||
| 82879 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID92760.1 | StrainInfo: A central database for resolving microbial strain identifiers |