Strain identifier
BacDive ID: 2478
Type strain:
Species: Thiocapsa rosea
Strain Designation: 6611
Strain history: <- N. Pfennig, 6611
NCBI tax ID(s): 69360 (species)
General
@ref: 60
BacDive-ID: 2478
DSM-Number: 235
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, Gram-negative
description: Thiocapsa rosea 6611 is an anaerobe, mesophilic, Gram-negative bacterium that was isolated from sewage lagoon.
NCBI tax id
- NCBI tax id: 69360
- Matching level: species
strain history
- @ref: 60
- history: <- N. Pfennig, 6611
doi: 10.13145/bacdive2478.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Gammaproteobacteria
- order: Chromatiales
- family: Chromatiaceae
- genus: Thiocapsa
- species: Thiocapsa rosea
- full scientific name: Thiocapsa rosea (Winogradsky 1888) Guyoneaud et al. 1998
synonyms
- @ref: 20215
- synonym: Amoebobacter roseus
@ref: 60
domain: Bacteria
phylum: Proteobacteria
class: Gammaproteobacteria
order: Chromatiales
family: Chromatiaceae
genus: Thiocapsa
species: Thiocapsa rosea
full scientific name: Thiocapsa rosea (Winogradsky 1888) Guyoneaud et al. 1998
strain designation: 6611
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: negative
- confidence: 99.999
Culture and growth conditions
culture medium
- @ref: 60
- 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: 60
- growth: positive
- type: growth
- temperature: 25
- range: mesophilic
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance | confidence |
---|---|---|
60 | anaerobe | |
69480 | anaerobe | 97.899 |
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 97 |
69480 | no | 99.89 |
Isolation, sampling and environmental information
isolation
- @ref: 60
- sample type: sewage lagoon
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Engineered | #Waste | #Wastewater |
#Environmental | #Aquatic |
taxonmaps
- @ref: 69479
- File name: preview.99_94288.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_169;96_3627;97_4456;98_5717;99_94288&stattab=map
- Last taxonomy: Thiocapsa
- 16S sequence: FM178269
- Sequence Identity:
- Total samples: 11
- soil counts: 2
- aquatic counts: 7
- animal counts: 2
Safety information
risk assessment
- @ref: 60
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Thiocapsa rosea partial 16S rRNA gene, type strain DSM 235T | AJ002798 | 1463 | ena | 69360 |
20218 | Thiocapsa rosea partial 16S rRNA gene, type strain DSM 235T | FM178269 | 1463 | ena | 69360 |
60 | Amoebobacter roseus 16S ribosomal RNA, strain DSM 235 | AJ006062 | 1391 | ena | 69360 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Thiocapsa rosea DSM 235 | GCA_003634315 | contig | ncbi | 69360 |
66792 | Thiocapsa rosea strain DSM 235 | 69360.3 | wgs | patric | 69360 |
66792 | Thiocapsa rosea DSM 235 | 2778260931 | draft | img | 69360 |
GC content
- @ref: 60
- GC-content: 64.3
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 97 | no |
gram-positive | no | 98.963 | no |
anaerobic | yes | 91.515 | no |
halophile | no | 78.628 | no |
spore-forming | no | 93.264 | no |
glucose-util | yes | 81.727 | no |
thermophile | no | 99.359 | no |
flagellated | no | 86.941 | no |
motile | no | 80.989 | no |
aerobic | no | 88.51 | no |
glucose-ferment | no | 81.54 | no |
External links
@ref: 60
culture collection no.: DSM 235
straininfo link
- @ref: 72020
- straininfo: 47103
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
60 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 235) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-235 | |||
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 | |||
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 | |||
72020 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID47103.1 | StrainInfo: A central database for resolving microbial strain identifiers |