Strain identifier
BacDive ID: 2467
Type strain: 
Species: Thiococcus pfennigii
Strain Designation: 9111
Strain history: <- N. Pfennig, 9111
NCBI tax ID(s): 1057 (species)
version 8.1 (current version)
General
@ref: 56
BacDive-ID: 2467
DSM-Number: 228
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic
description: Thiococcus pfennigii 9111 is an anaerobe, mesophilic bacterium that was isolated from Salt marshes.
NCBI tax id
- NCBI tax id: 1057
- Matching level: species
strain history
- @ref: 56
- history: <- N. Pfennig, 9111
doi: 10.13145/bacdive2467.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Gammaproteobacteria
- order: Chromatiales
- family: Chromatiaceae
- genus: Thiococcus
- species: Thiococcus pfennigii
- full scientific name: Thiococcus pfennigii (Eimhjellen 1970) Imhoff et al. 1998
synonyms
- @ref: 20215
- synonym: Thiocapsa pfennigii
@ref: 56
domain: Bacteria
phylum: Proteobacteria
class: Gammaproteobacteria
order: Chromatiales
family: Chromatiaceae
genus: Thiococcus
species: Thiococcus pfennigii
full scientific name: Thiococcus pfennigii (Eimhjellen 1970) Imhoff et al. 1998
strain designation: 9111
type strain: no
Culture and growth conditions
culture medium
- @ref: 56
- name: PFENNIG'S MEDIUM I (modified 1988, for purple sulfur bacteria) (DSMZ Medium 28)
- growth: yes
- link: https://mediadive.dsmz.de/medium/28
- composition: Name: PFENNIG'S MEDIUM I (DSMZ Medium 28) Composition: NaHCO3 1.5 g/l Na2S x 9 H2O 0.592592 g/l MgSO4 x 7 H2O 0.500001 g/l KCl 0.349999 g/l KH2PO4 0.349999 g/l Ammonium chloride 0.349999 g/l Pyruvic acid sodium salt 0.25 g/l Dextrose 0.25 g/l CaCl2 x 2 H2O 0.25 g/l Yeast extract 0.25 g/l Ammonium acetate 0.25 g/l Na2-EDTA 0.003 g/l Resazurin 0.00225 g/l FeSO4 x 7 H2O 0.0011 g/l Vitamin B12 0.001 g/l H3BO3 0.0003 g/l CoCl2 x 6 H2O 0.00019 g/l MnCl2 x 2 H2O 5e-05 g/l ZnCl2 4.2e-05 g/l NiCl2 x 6 H2O 2.4e-05 g/l Na2MoO4 x 2 H2O 1.8e-05 g/l CuCl2 x 2 H2O 2e-06 g/l Distilled water
culture temp
- @ref: 56
- growth: positive
- type: growth
- temperature: 25
- range: mesophilic
Physiology and metabolism
oxygen tolerance
- @ref: 56
- oxygen tolerance: anaerobe
Isolation, sampling and environmental information
isolation
- @ref: 56
- sample type: Salt marshes
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Terrestrial | #Salt marsh |
| #Condition | #Saline |
taxonmaps
- @ref: 69479
- File name: preview.99_18826.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_169;96_2220;97_2687;98_14222;99_18826&stattab=map
- Last taxonomy: Thioflavicoccus
- 16S sequence: FN293055
- Sequence Identity:
- Total samples: 387
- soil counts: 3
- aquatic counts: 377
- animal counts: 7
Safety information
risk assessment
- @ref: 56
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
| @ref | description | accession | length | database | NCBI tax ID |
|---|---|---|---|---|---|
| 20218 | Thiococcus pfennigii strain DSM 228 16S ribosomal RNA gene, partial sequence | EF675611 | 565 | ena | 1057 |
| 56 | Thiococcus pfennigii partial 16S rRNA gene, strain 4252 = DSM 228 | FN293055 | 1459 | ena | 1057 |
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Thiococcus pfennigii DSM 228 | GCA_016583935 | scaffold | ncbi | 1057 |
| 66792 | Thiococcus pfennigii strain DSM 228 | 1057.10 | wgs | patric | 1057 |
GC content
- @ref: 56
- GC-content: 69.4
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| motile | no | 76.358 | no |
| flagellated | no | 90.997 | no |
| gram-positive | no | 98.995 | no |
| anaerobic | yes | 97.542 | yes |
| aerobic | no | 96.303 | yes |
| halophile | no | 83.845 | no |
| spore-forming | no | 93.315 | no |
| thermophile | no | 96.182 | no |
| glucose-util | yes | 67.869 | no |
| glucose-ferment | no | 83.661 | no |
External links
@ref: 56
culture collection no.: DSM 228
straininfo link
- @ref: 72011
- straininfo: 47099
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 56 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 228) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-228 | |||
| 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) | |||
| 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 | |||
| 72011 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID47099.1 | StrainInfo: A central database for resolving microbial strain identifiers |