Strain identifier

BacDive ID: 13897

Type strain: Yes

Species: Propionivibrio dicarboxylicus

Strain Designation: CreMal1

Strain history: DSM 5885 <-- K. Tanaka strain CreMal1.

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General

@ref: 2343

BacDive-ID: 13897

DSM-Number: 5885

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, motile

description: Propionivibrio dicarboxylicus CreMal1 is an anaerobe, mesophilic, motile bacterium that was isolated from anaerobic mud.

NCBI tax id

NCBI tax idMatching level
83767species
1123005strain

strain history

@refhistory
2343<- K. Tanaka, CreMal1
67770DSM 5885 <-- K. Tanaka strain CreMal1.

doi: 10.13145/bacdive13897.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Betaproteobacteria
  • order: Rhodocyclales
  • family: Rhodocyclaceae
  • genus: Propionivibrio
  • species: Propionivibrio dicarboxylicus
  • full scientific name: Propionivibrio dicarboxylicus Tanaka et al. 1991

@ref: 2343

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Rhizobiales

family: Rhodocyclaceae

genus: Propionivibrio

species: Propionivibrio dicarboxylicus

full scientific name: Propionivibrio dicarboxylicus Tanaka et al. 1991

strain designation: CreMal1

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram stain
69480yes97.65
69480100negative

Culture and growth conditions

culture medium

  • @ref: 2343
  • name: ANAEROBIC FRESHWATER (FWM) MEDIUM (DSMZ Medium 503)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/503
  • composition: Name: ANAEROBIC FRESHWATER (FWM) MEDIUM (DSMZ Medium 503; with strain-specific modifications) Composition: Sodium maleate 1.59521 g/l Na2CO3 1.49551 g/l NaCl 0.997008 g/l KCl 0.498505 g/l MgCl2 x 6 H2O 0.398803 g/l Na2S x 9 H2O 0.299103 g/l NH4Cl 0.249252 g/l KH2PO4 0.199402 g/l CaCl2 x 2 H2O 0.149552 g/l HCl 0.00249252 g/l FeCl2 x 4 H2O 0.00149551 g/l Sodium resazurin 0.000498505 g/l NaOH 0.000498504 g/l Pyridoxine hydrochloride 0.000299103 g/l Nicotinic acid 0.000199402 g/l Thiamine-HCl x 2 H2O 0.000199402 g/l CoCl2 x 6 H2O 0.000189432 g/l Calcium pantothenate 9.97009e-05 g/l MnCl2 x 4 H2O 9.97009e-05 g/l Vitamin B12 9.97009e-05 g/l p-Aminobenzoic acid 7.97607e-05 g/l ZnCl2 6.97906e-05 g/l Na2MoO4 x 2 H2O 3.58923e-05 g/l NiCl2 x 6 H2O 2.39282e-05 g/l D-(+)-biotin 1.99402e-05 g/l H3BO3 5.98205e-06 g/l Na2WO4 x 2 H2O 3.98804e-06 g/l Na2SeO3 x 5 H2O 2.99103e-06 g/l CuCl2 x 2 H2O 1.99402e-06 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
2343positivegrowth30mesophilic
67770positivegrowth30mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 2343
  • oxygen tolerance: anaerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.998

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
2343anaerobic mudcreek near Lake KasumigauraJapanJPNAsia
67770Anaerobic mud sample from a creek near Lake KasumigauraIbaraki Pref.JapanJPNAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Mud (Sludge)
#Condition#Anoxic (anaerobic)

taxonmaps

  • @ref: 69479
  • File name: preview.99_55709.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_129;96_24828;97_31085;98_39783;99_55709&stattab=map
  • Last taxonomy: Propionivibrio dicarboxylicus subclade
  • 16S sequence: Y17601
  • Sequence Identity:
  • Total samples: 69
  • soil counts: 3
  • aquatic counts: 61
  • animal counts: 1
  • plant counts: 4

Safety information

risk assessment

  • @ref: 2343
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 2343
  • description: Propionivibrio dicarboxylicus 16S rRNA gene, partial
  • accession: Y17601
  • length: 1496
  • database: ena
  • NCBI tax ID: 83767

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Propionivibrio dicarboxylicus strain DSM 588583767.3wgspatric83767
66792Propionivibrio dicarboxylicus DSM 58852599185173draftimg83767
67770Propionivibrio dicarboxylicus DSM 5885GCA_900099695scaffoldncbi83767

GC content

@refGC-contentmethod
234361.0
6777061high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes90.717no
flagellatedyes60.005no
gram-positiveno99.316no
anaerobicyes84.32yes
halophileno93.914no
spore-formingno95.834no
thermophileno97.848no
glucose-utilyes69.119no
aerobicno91.561no
glucose-fermentno73.613no

External links

@ref: 2343

culture collection no.: DSM 5885, JCM 12339, JCM 7784

straininfo link

  • @ref: 83072
  • straininfo: 48020

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
2343Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 5885)https://www.dsmz.de/collection/catalogue/details/culture/DSM-5885
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
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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
83072Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID48020.1StrainInfo: A central database for resolving microbial strain identifiers