Strain identifier

BacDive ID: 11311

Type strain: Yes

Species: Collimonas pratensis

Strain history: Vandamme P., Gent University < de Boer W, Centre for Terrestrial Ecology

NCBI tax ID(s): 279113 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 8.1 (current version)

General

@ref: 15677

BacDive-ID: 11311

DSM-Number: 21399

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

description: Collimonas pratensis DSM 21399 is a mesophilic bacterium that was isolated from Acidic dune grassland soil.

NCBI tax id

  • NCBI tax id: 279113
  • Matching level: species

strain history

@refhistory
15677<- W. de Boer, Centre for Terrestrial Ecology, Heteren
67772Vandamme P., Gent University < de Boer W, Centre for Terrestrial Ecology

doi: 10.13145/bacdive11311.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Betaproteobacteria
  • order: Burkholderiales
  • family: Oxalobacteraceae
  • genus: Collimonas
  • species: Collimonas pratensis
  • full scientific name: Collimonas pratensis Höppener-Ogawa et al. 2008

@ref: 15677

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Oxalobacteraceae

genus: Collimonas

species: Collimonas pratensis

full scientific name: Collimonas pratensis Höppener-Ogawa et al. 2008

type strain: yes

Culture and growth conditions

culture medium

  • @ref: 15677
  • name: NUTRIENT AGAR (DSMZ Medium 1)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/1
  • composition: Name: NUTRIENT AGAR (DSMZ Medium 1; with strain-specific modifications) Composition: Agar 15.0 g/l NaCl 5.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
15677positivegrowth28mesophilic
32359positivegrowth20psychrophilic
67772positiveoptimum28mesophilic

Physiology and metabolism

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3235922599arabinose+carbon source
3235918403L-arabitol+carbon source
3235935391aspartate+carbon source
3235915740formate+carbon source
3235933984fucose+carbon source
3235924265gluconate+carbon source
3235917754glycerol+carbon source
3235917596inosine+carbon source
3235937684mannose+carbon source
3235917268myo-inositol+carbon source
3235926271proline+carbon source
3235917272propionate+carbon source
3235930031succinate+carbon source
3235927082trehalose+carbon source
3235953258sodium citrate+carbon source
3235916704uridine+carbon source
3235927248urocanic acid+carbon source
3235917151xylitol+carbon source

enzymes

@refvalueactivityec
32359alpha-galactosidase+3.2.1.22
32359cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling date
15677Acidic dune grassland soilTerschellingNetherlandsNLDEurope
60296(Semi-)natural grasslandsNetherlandsNLDEurope
67772(Semi-)Natural grasslandNetherlandsNLDEurope1994

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Grassland
#Environmental#Terrestrial#Soil
#Condition#Acidic

taxonmaps

  • @ref: 69479
  • File name: preview.99_1512.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_12;96_128;97_1012;98_1195;99_1512&stattab=map
  • Last taxonomy: Collimonas
  • 16S sequence: AY281137
  • Sequence Identity:
  • Total samples: 1345
  • soil counts: 741
  • aquatic counts: 386
  • animal counts: 129
  • plant counts: 89

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
156771Risk group (German classification)
677721

Sequence information

16S sequences

  • @ref: 15677
  • description: Collimonas pratensis strain CTO 91 16S ribosomal RNA gene, partial sequence
  • accession: AY281137
  • length: 1453
  • database: ena
  • NCBI tax ID: 279113

Genome sequences

  • @ref: 67772
  • description: Collimonas pratensis Ter91
  • accession: GCA_001584185
  • assembly level: complete
  • database: ncbi
  • NCBI tax ID: 279113

GC content

  • @ref: 32359
  • GC-content: 59

External links

@ref: 15677

culture collection no.: DSM 21399, CCUG 54728, LMG 23965, TER Ter91, TER 91, UCCCB20, CTO 91

straininfo link

  • @ref: 80544
  • straininfo: 136977

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny18218941Collimonas arenae sp. nov. and Collimonas pratensis sp. nov., isolated from (semi-)natural grassland soils.Hoppener-Ogawa S, de Boer W, Leveau JH, van Veen JA, de Brandt E, Vanlaere E, Sutton H, Dare DJ, Vandamme PInt J Syst Evol Microbiol10.1099/ijs.0.65375-02008Bacterial Typing Techniques, DNA Fingerprinting/methods, DNA, Bacterial/analysis, Genes, rRNA, Molecular Sequence Data, Nucleic Acid Hybridization, Oxalobacteraceae/*classification/genetics/isolation & purification/physiology, Poaceae/*growth & development, Polymerase Chain Reaction/methods, Polymorphism, Restriction Fragment Length, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Species Specificity, Spectrometry, Mass, Matrix-Assisted Laser Desorption-IonizationGenetics
Phylogeny20935085Glaciimonas immobilis gen. nov., sp. nov., a member of the family Oxalobacteraceae isolated from alpine glacier cryoconite.Zhang DC, Redzic M, Schinner F, Margesin RInt J Syst Evol Microbiol10.1099/ijs.0.028001-02010Bacterial Typing Techniques, Base Composition, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Ice Cover/*microbiology, Molecular Sequence Data, Oxalobacteraceae/*classification/genetics/*isolation & purification/physiology, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, TemperatureGenetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
15677Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21399)https://www.dsmz.de/collection/catalogue/details/culture/DSM-21399
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
32359Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2858828776041
60296Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 54728)https://www.ccug.se/strain?id=54728
67772Curators of the UCCCBhttps://ucccb.uc.pt/
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
80544Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID136977.1StrainInfo: A central database for resolving microbial strain identifiers