Strain identifier
BacDive ID: 11914
Type strain: 
Species: Thiomicrospira pelophila
Strain Designation: 4B
Strain history: <- J.G. Kuenen <- ATCC <- J.G. Kuenen, strain 4B
NCBI tax ID(s): 1123517 (strain), 934 (species)
version 9.1 (current version)
General
@ref: 594
BacDive-ID: 11914
DSM-Number: 1534
keywords: genome sequence, 16S sequence, Bacteria, Gram-negative
description: Thiomicrospira pelophila 4B is a Gram-negative bacterium that was isolated from estuarine mud.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 1123517 | strain |
| 934 | species |
strain history
- @ref: 594
- history: <- J.G. Kuenen <- ATCC <- J.G. Kuenen, strain 4B
doi: 10.13145/bacdive11914.20240916.9.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Gammaproteobacteria
- order: Beggiatoales
- family: Piscirickettsiaceae
- genus: Thiomicrospira
- species: Thiomicrospira pelophila
- full scientific name: Thiomicrospira pelophila Kuenen and Veldkamp 1972 (Approved Lists 1980)
@ref: 594
domain: Bacteria
phylum: Proteobacteria
class: Gammaproteobacteria
order: Thiotrichales
family: Piscirickettsiaceae
genus: Thiomicrospira
species: Thiomicrospira pelophila
full scientific name: Thiomicrospira pelophila Kuenen and Veldkamp 1972
strain designation: 4B
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: negative
- confidence: 99.333
Culture and growth conditions
culture medium
- @ref: 594
- name: THIOMICROSPIRA PELOPHILA MEDIUM (DSMZ Medium 142)
- growth: yes
- link: https://mediadive.dsmz.de/medium/142
- composition: Name: THIOMICROSPIRA PELOPHILA MEDIUM (DSMZ Medium 142) Composition: NaCl 24.8756 g/l Na2S2O3 x 5 H2O 4.97512 g/l MgSO4 x 7 H2O 1.49254 g/l (NH4)2SO4 0.995025 g/l K2HPO4 0.497512 g/l Na2-EDTA 0.00995025 g/l ZnSO4 x 7 H2O 0.00437811 g/l Bromothymol blue 0.0039801 g/l CaCl2 x 2 H2O 0.00110249 g/l MnCl2 x 4 H2O 0.00100697 g/l FeSO4 x 7 H2O 0.000995025 g/l CoCl2 x 6 H2O 0.000320398 g/l CuSO4 x 5 H2O 0.000312438 g/l Pyridoxine hydrochloride 0.000298507 g/l (NH4)6Mo7O24 x 4 H2O 0.000218905 g/l Nicotinic acid 0.000199005 g/l Thiamine-HCl x 2 H2O 0.000199005 g/l Vitamin B12 9.95025e-05 g/l Calcium pantothenate 9.95025e-05 g/l p-Aminobenzoic acid 7.9602e-05 g/l D-(+)-biotin 1.99005e-05 g/l Distilled water
culture temp
- @ref: 594
- growth: positive
- type: growth
- temperature: 25
Physiology and metabolism
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69480 | no | 93.037 |
| 69481 | no | 100 |
Isolation, sampling and environmental information
isolation
- @ref: 594
- sample type: estuarine mud
- geographic location: Waddenzee
- country: Netherlands
- origin.country: NLD
- continent: Europe
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Aquatic | #Brackish |
| #Environmental | #Terrestrial | #Mud (Sludge) |
Safety information
risk assessment
- @ref: 594
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 594
- description: Thiomicrospira pelophila 16S ribosomal RNA (16S rRNA) gene, partial sequence
- accession: L40809
- length: 1468
- database: nuccore
- NCBI tax ID: 934
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Thiomicrospira pelophila DSM 1534 | GCA_000711195 | contig | ncbi | 1123517 |
| 66792 | Thiomicrospira pelophila DSM 1534 | 1123517.3 | wgs | patric | 1123517 |
| 66792 | Thiomicrospira pelophila DSM 1534 | 2565957139 | draft | img | 1123517 |
GC content
- @ref: 594
- GC-content: 48.0
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 | 99.333 | no |
| 69480 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 84.66 | no |
| 69480 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 93.037 | no |
| 69480 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | no | 51.837 | no |
| 69480 | thermophilic | thermophile | Ability to grow at temperatures above or equal to 45°C | no | 91.282 | yes |
| 69480 | flagellated | motile2+ | Ability to perform flagellated movement | yes | 80.348 | no |
External links
@ref: 594
culture collection no.: DSM 1534, ATCC 27801
straininfo link
- @ref: 81128
- straininfo: 39183
Reference
| @id | authors | catalogue | doi/url | title |
|---|---|---|---|---|
| 594 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 1534) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-1534 | |
| 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 | |
| 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 | |
| 81128 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID39183.1 | StrainInfo: A central database for resolving microbial strain identifiers |