Strain identifier
BacDive ID: 17148
Type strain: 
Species: Propionispira arboris
Strain Designation: 12B4
Strain history: <- J.G. Zeikus, 12B4
NCBI tax ID(s): 1123002 (strain), 84035 (species)
version 9.1 (current version)
General
@ref: 996
BacDive-ID: 17148
DSM-Number: 2179
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, Gram-negative
description: Propionispira arboris 12B4 is an anaerobe, Gram-negative bacterium that was isolated from wetwood, Cotton Wood tree.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 84035 | species |
| 1123002 | strain |
strain history
- @ref: 996
- history: <- J.G. Zeikus, 12B4
doi: 10.13145/bacdive17148.20240916.9.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacillota
- domain: Bacteria
- phylum: Bacillota
- class: Negativicutes
- order: Selenomonadales
- family: Selenomonadaceae
- genus: Propionispira
- species: Propionispira arboris
- full scientific name: Propionispira arboris Schink et al. 1983
@ref: 996
domain: Bacteria
phylum: Firmicutes
class: Negativicutes
order: Selenomonadales
family: Selenomonadaceae
genus: Propionispira
species: Propionispira arboris
full scientific name: Propionispira arboris Schink et al. 1983
strain designation: 12B4
type strain: yes
Culture and growth conditions
culture medium
- @ref: 996
- name: PROPIONISPIRA MEDIUM (DSMZ Medium 207)
- growth: yes
- link: https://mediadive.dsmz.de/medium/207
- composition: Name: PROPIONISPIRA MEDIUM (DSMZ Medium 207) Composition: Na-lactate 5.0 g/l NaHCO3 4.0 g/l Na2HPO4 x 12 H2O 2.1 g/l Yeast extract 2.0 g/l NH4Cl 1.0 g/l Na2S x 9 H2O 0.5 g/l KH2PO4 0.3 g/l MgCl2 x 6 H2O 0.2 g/l Nitrilotriacetic acid 0.128 g/l NaCl 0.01 g/l FeCl2 x 4 H2O 0.002 g/l CoCl2 x 6 H2O 0.0017 g/l FeSO4 x 7 H2O 0.0015 g/l MnCl2 x 4 H2O 0.001 g/l Resazurin 0.001 g/l ZnCl2 0.001 g/l CaCl2 x 2 H2O 0.001 g/l Na2SeO3 x 5 H2O 0.0003 g/l NiCl2 x 6 H2O 0.0003 g/l CuCl2 0.0002 g/l H3BO3 0.0001 g/l Na2MoO4 x 2 H2O 0.0001 g/l Pyridoxine hydrochloride 5e-05 g/l Calcium D-(+)-pantothenate 2.5e-05 g/l Nicotinic acid 2.5e-05 g/l Riboflavin 2.5e-05 g/l (DL)-alpha-Lipoic acid 2.5e-05 g/l Thiamine HCl 2.5e-05 g/l p-Aminobenzoic acid 2.5e-05 g/l Folic acid 1e-05 g/l Biotin 1e-05 g/l Vitamin B12 5e-07 g/l Distilled water
culture temp
- @ref: 996
- growth: positive
- type: growth
- temperature: 30
Physiology and metabolism
oxygen tolerance
- @ref: 996
- oxygen tolerance: anaerobe
Isolation, sampling and environmental information
isolation
- @ref: 996
- sample type: wetwood, Cotton Wood tree
- country: USA
- origin.country: USA
- continent: North America
isolation source categories
- Cat1: #Host
- Cat2: #Plants
- Cat3: #Tree
taxonmaps
- @ref: 69479
- File name: preview.99_55248.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_138;96_24642;97_30858;98_39481;99_55248&stattab=map
- Last taxonomy: Propionispira arboris
- 16S sequence: Y18190
- Sequence Identity:
- Total samples: 172
- soil counts: 85
- aquatic counts: 55
- animal counts: 32
Safety information
risk assessment
- @ref: 996
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 996
- description: Propionispira arboris 16S rRNA gene, partial, strain DSM 2179
- accession: Y18190
- length: 1470
- database: nuccore
- NCBI tax ID: 84035
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Propionispira arboris DSM 2179 | GCA_900109225 | contig | ncbi | 84035 |
| 66792 | Propionispira arboris strain DSM 2179 | 84035.3 | wgs | patric | 84035 |
| 66792 | Propionispira arboris DSM 2179 | 2602042026 | draft | img | 84035 |
GC content
- @ref: 996
- GC-content: 36.7
Genome-based predictions
predictions
| @ref | trait | model | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 69481 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 66 | no |
| 69480 | gram-positive | gram-positive | Positive reaction to Gram-staining | no | 83.419 | no |
| 69480 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | yes | 79.969 | yes |
| 69480 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | no | 88.62 | no |
| 69480 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 54.376 | no |
| 69480 | thermophilic | thermophile | Ability to grow at temperatures above or equal to 45°C | no | 87.973 | yes |
| 69480 | flagellated | motile2+ | Ability to perform flagellated movement | yes | 72.163 | no |
External links
@ref: 996
culture collection no.: DSM 2179, ATCC 33732
straininfo link
- @ref: 86147
- straininfo: 40656
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 996 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 2179) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-2179 | |||
| 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) | |||
| 66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | 10.1093/nar/gkaa1025 | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | Nucleic Acids Res. 49: D498-D508 2020 | 33211880 | |
| 69479 | João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich. | https://microbeatlas.org/ | MicrobeAtlas 1.0 beta | |||
| 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 | |||
| 86147 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID40656.1 | StrainInfo: A central database for resolving microbial strain identifiers |