Strain identifier
BacDive ID: 131048
Type strain: 
Species: Prosthecomicrobium pneumaticum
Strain Designation: 3a
Variant: Isotype of BacDive ID 139829
Strain history: <- J. T. Staley, Univ. of Washington, Seattle, USA
NCBI tax ID(s): 81895 (species)
version 8.1 (current version)
General
@ref: 22340
BacDive-ID: 131048
DSM-Number: 16268
keywords: genome sequence, Bacteria, mesophilic, Gram-negative
description: Prosthecomicrobium pneumaticum 3a is a mesophilic, Gram-negative bacterium that was isolated from Putah Creek overflow.
NCBI tax id
- NCBI tax id: 81895
- Matching level: species
strain history
- @ref: 22340
- history: <- J. T. Staley, Univ. of Washington, Seattle, USA
doi: 10.13145/bacdive131048.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Alphaproteobacteria
- order: Hyphomicrobiales
- family: Hyphomicrobiaceae
- genus: Prosthecomicrobium
- species: Prosthecomicrobium pneumaticum
- full scientific name: Prosthecomicrobium pneumaticum Staley 1968 (Approved Lists 1980)
@ref: 22340
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Rhizobiales
family: Hyphomicrobiaceae
genus: Prosthecomicrobium
species: Prosthecomicrobium pneumaticum
full scientific name: Prosthecomicrobium pneumaticum Staley 1968
strain designation: 3a
variant: Isotype of BacDive ID 139829
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: negative
- confidence: 99.977
Culture and growth conditions
culture medium
- @ref: 22340
- name: MMB MEDIUM (DSMZ Medium 1417)
- growth: yes
- link: https://mediadive.dsmz.de/medium/1417
- composition: Name: MMB MEDIUM (DSMZ Medium 1417) Composition: Agar 15.0 g/l Glucose 1.0 g/l MgSO4 x 7 H2O 0.565714 g/l Ammonium Sulfate 0.25 g/l Nitrilotriacetic acid 0.190476 g/l Peptone 0.15 g/l Yeast extract 0.15 g/l CaCl2 x 2 H2O 0.063619 g/l ZnSO4 x 7 H2O 0.00104762 g/l FeSO4 x 7 H2O 0.00047619 g/l EDTA 0.000238095 g/l Ammonium Molybdate 0.00017619 g/l MnSO4 x 7 H2O 0.000146667 g/l Thiamine HCl 5e-05 g/l Riboflavin 5e-05 g/l D-Calcium pantothenate 5e-05 g/l CuSO4 x 5 H2O 3.80952e-05 g/l Co(NO3)2 x 6 H2O 2.38095e-05 g/l Folic acid 2e-05 g/l Biotin 2e-05 g/l Na2B4O7 x 10 H2O 1.71429e-05 g/l Vitamin B12 1e-06 g/l Distilled water
culture temp
- @ref: 22340
- growth: positive
- type: growth
- temperature: 28
- range: mesophilic
Physiology and metabolism
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | no | 100 |
| 69480 | no | 99.993 |
Isolation, sampling and environmental information
isolation
- @ref: 22340
- sample type: Putah Creek overflow
- geographic location: Davis, California
- country: USA
- origin.country: USA
- continent: North America
isolation source categories
- Cat1: #Environmental
- Cat2: #Aquatic
- Cat3: #River (Creek)
Safety information
risk assessment
- @ref: 22340
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Prosthecomicrobium pneumaticum DSM 16268 | GCA_014199915 | scaffold | ncbi | 81895 |
| 66792 | Prosthecomicrobium pneumaticum strain DSM 16268 | 81895.3 | wgs | patric | 81895 |
| 66792 | Prosthecomicrobium pneumaticum DSM 16268 | 2829732774 | draft | img | 81895 |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| flagellated | no | 83.536 | no |
| gram-positive | no | 97.508 | no |
| anaerobic | no | 98.129 | no |
| aerobic | yes | 86.71 | no |
| halophile | no | 92.088 | no |
| spore-forming | no | 95.779 | no |
| glucose-util | yes | 91.231 | no |
| thermophile | no | 90.906 | yes |
| motile | yes | 68.941 | no |
| glucose-ferment | no | 92.63 | no |
External links
@ref: 22340
culture collection no.: DSM 16268, ATCC 23633
Reference
| @id | authors | title | doi/url | catalogue |
|---|---|---|---|---|
| 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 | |
| 22340 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-16268 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16268) | |
| 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 | |
| 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 |