Strain identifier

BacDive ID: 11374

Type strain: Yes

Species: Undibacterium parvum

Strain Designation: CMB NF2a

Strain history: CIP <- 2006, CCUG, Undibacterium pigrum <- 2004, F. Persson, Göteborg Univ., Göteborg, Sweden: strain CMB NF2a

NCBI tax ID(s): 401471 (species)

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General

@ref: 16684

BacDive-ID: 11374

DSM-Number: 23061

keywords: genome sequence, 16S sequence, Bacteria, aerobe, psychrophilic, motile

description: Undibacterium parvum CMB NF2a is an aerobe, psychrophilic, motile bacterium that was isolated from drinking water.

NCBI tax id

  • NCBI tax id: 401471
  • Matching level: species

strain history

@refhistory
16684<- CCUG <- F. Persson, Univ. Göteborg, Sweden
67772The type strain CCUG 49012 (= DSM 23061) was previouly described by Kämpfer et al. 2007 as a second genomovar of Undibacterium pigrum because of the lack of differentiating characters.
121604CIP <- 2006, CCUG, Undibacterium pigrum <- 2004, F. Persson, Göteborg Univ., Göteborg, Sweden: strain CMB NF2a

doi: 10.13145/bacdive11374.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Betaproteobacteria
  • order: Burkholderiales
  • family: Oxalobacteraceae
  • genus: Undibacterium
  • species: Undibacterium parvum
  • full scientific name: Undibacterium parvum Eder et al. 2011

@ref: 16684

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Oxalobacteraceae

genus: Undibacterium

species: Undibacterium parvum

full scientific name: Undibacterium parvum Eder et al. 2011

strain designation: CMB NF2a

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480yes94.092
6948099.998negative
121604yesnegativerod-shaped

colony morphology

  • @ref: 58437
  • incubation period: 5 days

multimedia

  • @ref: 16684
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_23061.jpg
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
16684REACTIVATION WITH LIQUID MEDIUM 830 (DSMZ Medium 830c)yeshttps://mediadive.dsmz.de/medium/830cName: REACTIVATION WITH LIQUID MEDIUM 830 (DSMZ Medium 830c) Composition: Agar 15.0 g/l Yeast extract 0.5 g/l Proteose peptone 0.5 g/l Casamino acids 0.5 g/l Glucose 0.5 g/l Starch 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water
32695MEDIUM 566- Reasoner's 2A agar for Flavobacterium micromatiyesDistilled water make up to (1000.000 ml);R2A agar (18.200 g)
121604CIP Medium 566yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=566

culture temp

@refgrowthtypetemperaturerange
16684positivegrowth22psychrophilic
32695positivegrowth22psychrophilic
58437positivegrowth22psychrophilic
67772positiveminimum5psychrophilic
67772positiveoptimum22psychrophilic
67772positivemaximum30mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 58437
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.999

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6836925115malate-assimilation
6836917128adipate-assimilation
6836927689decanoate-assimilation
6836924265gluconate-assimilation
6836917306maltose-assimilation
6836959640N-acetylglucosamine-assimilation
6836916899D-mannitol-assimilation
6836916024D-mannose-assimilation
6836930849L-arabinose-assimilation
6836917634D-glucose-assimilation
683695291gelatin-hydrolysis
683694853esculin-hydrolysis
6836916199urea-hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate+reduction
12160417632nitrate+reduction
12160416301nitrite-reduction

metabolite production

@refChebi-IDmetaboliteproduction
6836935581indoleno
12160435581indoleno

metabolite tests

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
68369cytochrome oxidase+1.9.3.1
68369gelatinase-
68369beta-glucosidase-3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6
121604oxidase+
121604catalase-1.11.1.6
121604urease-3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)-
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase-
68382cystine arylamidase-3.4.11.3
68382trypsin-3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase-3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase-3.2.1.20
68382beta-glucosidase-3.2.1.21
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
58437-+---+-----+--------
121604-+-+-+----++--------

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
58437+-------------------+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling datelatitudelongitudeisolation date
16684drinking waterGöteborgSwedenSWEEurope
58437Water,biofilm,drinking waterGöteborgSwedenSWEEurope2004-03-10
67772Water, biofilm, drinking waterVästergötland and Bohuslän, GothenburgSwedenSWEEurope200457.711.9667
121604Environment, Water, biofilm, drinking waterGöteborgSwedenSWEEurope2004

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Aquatic
  • Cat3: #Freshwater

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
166841Risk group (German classification)
677721
1216041Risk group (French classification)

Sequence information

16S sequences

  • @ref: 16684
  • description: Undibacterium parvum partial 16S rRNA gene, type strain CCUG 49012T
  • accession: AM397629
  • length: 1442
  • database: ena
  • NCBI tax ID: 401471

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Undibacterium parvum DSM 23061GCA_003955735completencbi401471
66792Undibacterium parvum strain DSM 23061401471.8completepatric401471
66792Undibacterium parvum DSM 230612836680013completeimg401471

GC content

  • @ref: 16684
  • GC-content: 50.6
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes85.425no
flagellatedyes86.111no
gram-positiveno98.5no
anaerobicno97.975no
aerobicyes86.092yes
halophileno94.938no
spore-formingno93.372no
glucose-utilno50.787yes
thermophileno99.391yes
glucose-fermentno88.795yes

External links

@ref: 16684

culture collection no.: DSM 23061, CCUG 49012, CIP 109317, UCCCB17

straininfo link

  • @ref: 80604
  • straininfo: 215184

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny20305060Description of Undibacterium oligocarboniphilum sp. nov., isolated from purified water, and Undibacterium pigrum strain CCUG 49012 as the type strain of Undibacterium parvum sp. nov., and emended descriptions of the genus Undibacterium and the species Undibacterium pigrum.Eder W, Wanner G, Ludwig W, Busse HJ, Ziemke-Kageler F, Lang EInt J Syst Evol Microbiol10.1099/ijs.0.018648-02010Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Genotype, Glycerophospholipids/analysis, Molecular Sequence Data, Oxalobacteraceae/*classification/genetics/isolation & purification/ultrastructure, Phenotype, *Phylogeny, Polyamines/analysis, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Water Microbiology, Water PurificationGenetics
Phylogeny31385778Undibacterium piscinae sp. nov., isolated from Korean shiner intestine.Lee SY, Kang W, Kim PS, Kim HS, Sung H, Shin NR, Whon TW, Yun JH, Lee JY, Lee JY, Jung MJ, Jeong YS, Tak EJ, Han JE, Hyun DW, Kang MS, Lee KE, Lee BH, Bae JWInt J Syst Evol Microbiol10.1099/ijsem.0.0036042019Animals, Bacterial Typing Techniques, Base Composition, Cyprinidae/*microbiology, DNA, Bacterial/genetics, Fatty Acids/chemistry, Intestines/*microbiology, Oxalobacteraceae/*classification/isolation & purification, Phospholipids/chemistry, *Phylogeny, Polyamines/chemistry, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Ubiquinone/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitle
16684Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23061)https://www.dsmz.de/collection/catalogue/details/culture/DSM-23061
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
32695Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7045
58437Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 49012)https://www.ccug.se/strain?id=49012
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)
67772Curators of the UCCCBhttps://ucccb.uc.pt/
68369Automatically annotated from API 20NE
68382Automatically annotated from API zym
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
80604Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID215184.1StrainInfo: A central database for resolving microbial strain identifiers
121604Curators of the CIPCollection of Institut Pasteur (CIP 109317)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109317