Strain identifier

BacDive ID: 2478

Type strain: Yes

Species: Thiocapsa rosea

Strain Designation: 6611

Strain history: <- N. Pfennig, 6611

NCBI tax ID(s): 69360 (species)

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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

@refoxygen toleranceconfidence
60anaerobe
69480anaerobe97.899

spore formation

@refspore formationconfidence
69481no97
69480no99.89

Isolation, sampling and environmental information

isolation

  • @ref: 60
  • sample type: sewage lagoon

isolation source categories

Cat1Cat2Cat3
#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

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Thiocapsa rosea partial 16S rRNA gene, type strain DSM 235TAJ0027981463ena69360
20218Thiocapsa rosea partial 16S rRNA gene, type strain DSM 235TFM1782691463ena69360
60Amoebobacter roseus 16S ribosomal RNA, strain DSM 235AJ0060621391ena69360

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Thiocapsa rosea DSM 235GCA_003634315contigncbi69360
66792Thiocapsa rosea strain DSM 23569360.3wgspatric69360
66792Thiocapsa rosea DSM 2352778260931draftimg69360

GC content

  • @ref: 60
  • GC-content: 64.3

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno97no
gram-positiveno98.963no
anaerobicyes91.515no
halophileno78.628no
spore-formingno93.264no
glucose-utilyes81.727no
thermophileno99.359no
flagellatedno86.941no
motileno80.989no
aerobicno88.51no
glucose-fermentno81.54no

External links

@ref: 60

culture collection no.: DSM 235

straininfo link

  • @ref: 72020
  • straininfo: 47103

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
60Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 235)https://www.dsmz.de/collection/catalogue/details/culture/DSM-235
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69479João 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
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
72020Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID47103.1StrainInfo: A central database for resolving microbial strain identifiers