Strain identifier

BacDive ID: 11373

Type strain: Yes

Species: Undibacterium pigrum

Strain Designation: CMB NF1b

Strain history: CIP <- 2006, CCUG <- 2004, F. Persson, Göteborg Univ., Göteborg, Sweden: strain CMB NF1b

NCBI tax ID(s): 401470 (species)

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General

@ref: 8321

BacDive-ID: 11373

DSM-Number: 19792

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, rod-shaped

description: Undibacterium pigrum CMB NF1b is an aerobe, mesophilic, Gram-negative bacterium that was isolated from drinking water.

NCBI tax id

  • NCBI tax id: 401470
  • Matching level: species

strain history

@refhistory
8321<- P. Kämpfer, Univ. Giessen <- E. Falsen, CCUG Göteborg
67772Kampfer P. Justus-Liebig-Universitat Giessen < Falsen E., Culture Collection University Of Gothenburg
121831CIP <- 2006, CCUG <- 2004, F. Persson, Göteborg Univ., Göteborg, Sweden: strain CMB NF1b

doi: 10.13145/bacdive11373.20230509.8.1

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 pigrum
  • full scientific name: Undibacterium pigrum Kämpfer et al. 2007

@ref: 8321

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Oxalobacteraceae

genus: Undibacterium

species: Undibacterium pigrum

full scientific name: Undibacterium pigrum Kämpfer et al. 2007 emend. Eder et al. 2011

strain designation: CMB NF1b

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
32000negativerod-shapedno
69480yes98.213
69480negative99.998
121831negativerod-shapedyes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
8321REACTIVATION 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
37510MEDIUM 566- Reasoner's 2A agar for Flavobacterium micromatiyesDistilled water make up to (1000.000 ml);R2A agar (18.200 g)
121831CIP Medium 566yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=566

culture temp

@refgrowthtypetemperaturerange
8321positivegrowth25mesophilic
37510positivegrowth25mesophilic
58435positivegrowth22psychrophilic
67772positiveminimum4psychrophilic
67772positiveoptimum22psychrophilic
67772positivemaximum30mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
32000aerobe
58435aerobe
121831obligate aerobe

spore formation

@refspore formationconfidence
32000no
69481no100
69480no99.995

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
12183117632nitrate+reduction
12183116301nitrite-reduction

metabolite production

@refChebi-IDmetaboliteproduction
6836935581indoleno
12183135581indoleno

metabolite tests

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

enzymes

@refvalueactivityec
32000cytochrome oxidase+1.9.3.1
68369cytochrome oxidase+1.9.3.1
68369gelatinase+
68369beta-glucosidase+3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6
121831oxidase+
121831catalase+1.11.1.6
121831urease+3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
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
68382acid phosphatase+3.1.3.2
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
121831-+++-++-+-++---+----

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
8321+----++-+-+--++-----+

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentsampling dategeographic locationlatitudelongitudeisolation date
8321drinking waterSwedenSWEEurope
58435Water,biofilm,drinking waterSwedenSWEEurope2004-03-10Göteborg,Lackarebäcks vattenverk
67772Water, biofilm, drinking waterSwedenSWEEurope2004Västergötland and Bohuslän, Gothenburg57.711.9667
121831Environment, Water, biofilm, drinking waterSwedenSWEEuropeGöteborg2004

isolation source categories

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

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
83211Risk group (German classification)
677721
1218311Risk group (French classification)

Sequence information

16S sequences

  • @ref: 8321
  • description: Undibacterium pigrum partial 16S rRNA gene, type strain CCUG 49009T
  • accession: AM397630
  • length: 1434
  • database: ena
  • NCBI tax ID: 401470

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Undibacterium pigrum DSM 19792GCA_003201815scaffoldncbi401470
66792Undibacterium pigrum strain DSM 19792401470.3wgspatric401470
66792Undibacterium pigrum DSM 197922770939554draftimg401470

GC content

  • @ref: 32000
  • GC-content: 50.6

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedyes74.032no
gram-positiveno98.076yes
anaerobicno99.164no
halophileno96.96no
spore-formingno91.958yes
glucose-utilyes83.636no
aerobicyes93.266yes
thermophileno99.133no
motileyes81.667yes
glucose-fermentno90.465no

External links

@ref: 8321

culture collection no.: DSM 19792, CCUG 49009, CIP 109318, UCCCB16

straininfo link

  • @ref: 80603
  • straininfo: 215181

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny17625185Undibacterium pigrum gen. nov., sp. nov., isolated from drinking water.Kampfer P, Rossello-Mora R, Hermansson M, Persson F, Huber B, Falsen E, Busse HJInt J Syst Evol Microbiol10.1099/ijs.0.64785-02007Betaproteobacteria, Chromatography, Thin Layer, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Fresh Water/*microbiology, Genes, rRNA, Germany, Molecular Sequence Data, Nucleic Acid Hybridization, Oxalobacteraceae/chemistry/*classification/genetics/*isolation & purification, Phospholipids/analysis, Phylogeny, Polyamines/analysis, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Ubiquinone/analysisGenetics
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

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
8321Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19792)https://www.dsmz.de/collection/catalogue/details/culture/DSM-19792
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
32000Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2825428776041
37510Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7046
58435Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 49009)https://www.ccug.se/strain?id=49009
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 updates33211880Nucleic Acids Res. 49: D498-D508 2020
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
80603Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID215181.1StrainInfo: A central database for resolving microbial strain identifiers
121831Curators of the CIPCollection of Institut Pasteur (CIP 109318)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109318