Strain identifier

BacDive ID: 132626

Type strain: Yes

Species: Undibacterium danionis

Strain Designation: E3/4

Culture col. no.: DSM 102221, CCM 8677, CIP 111017

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 24415

BacDive-ID: 132626

DSM-Number: 102221

keywords: gram-negative, mesophilic, aerobe, Bacteria, 16S sequence, rod-shaped, colony-forming

description: Undibacterium danionis E3/4 is an aerobe, mesophilic, gram-negative bacterium that forms circular colonies and was isolated from zebrafish Danio rerio maintained in the laboratory.

strain history

doi: 10.13145/bacdive132626.20201210.5

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/proteobacteria
  • domain: Bacteria
  • phylum: Proteobacteria
  • class: Betaproteobacteria
  • order: Burkholderiales
  • family: Oxalobacteraceae
  • genus: Undibacterium
  • species: Undibacterium danionis
  • full scientific name: Undibacterium danionis Kämpfer et al. 2016

@ref: 24415

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Oxalobacteraceae

genus: Undibacterium

species: Undibacterium danionis

full scientific name: Undibacterium danionis Kämpfer et al. 2016

strain designation: E3/4

type strain: yes

Morphology

cell morphology

  • @ref: 43163
  • gram stain: negative
  • cell length: 1.6-2.2 µm
  • cell width: 0.9-1.1 µm
  • cell shape: rod-shaped
  • motility: no

colony morphology

  • @ref: 43163
  • colony color: beige
  • colony shape: circular
  • incubation period: 3 days
  • medium used: R2A

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
42164MEDIUM 566- Reasoner's 2A agar for Flavobacterium micromatiyesDistilled water make up to (1000.000 ml);R2A agar (18.200 g)
43163Reasoner's 2A agar (R2A)yes
43163PYE agaryes
43163Malt agarno
43163LB (Luria-Bertani) MEDIUMno
43163CASOno
43163Trypticase Soy Agar (TSA)no
43163Columbia agar with sheep bloodno
43163glycine arginineno
43163DEVno
43163Nutrient agar (NA)no
43163marine agarsno
43163MacConkey agarno
24415R2A MEDIUM (DSMZ Medium 830)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium830.pdf

culture temp

@refgrowthtypetemperaturerange
42164positivegrowth25mesophilic
43163positiveoptimum28mesophilic
43163inconsistentgrowth4psychrophilic
43163inconsistentgrowth15psychrophilic
43163nogrowth30mesophilic
43163positivegrowth20-28
24415positivegrowth25mesophilic

culture pH

@refabilitytypepH
43163positivegrowth5.5-6.5
43163inconsistentgrowth7
43163inconsistentgrowth7.5
43163nogrowth5
43163nogrowth8.5

Physiology and metabolism

oxygen tolerance

  • @ref: 43163
  • oxygen tolerance: aerobe

spore formation

  • @ref: 43163
  • type of spore: spore
  • spore formation: no

halophily

  • @ref: 43163
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-1.0 %(w/v)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
4316330849L-arabinose-builds acid from
4316332032potassium gluconate-builds acid from
4316325115malate-builds acid from
4316327689decanoate-assimilation
4316317128adipate-assimilation
4316353258sodium citrate-assimilation
4316318401phenylacetate-assimilation
4316317634D-glucose+builds acid from
4316316024D-mannose+builds acid from
4316317306maltose+builds acid from
431634853esculin+hydrolysis
4316317632nitrate+reduction
4316317108D-arabinose-builds acid from
4316316988D-ribose-builds acid from
4316365327D-xylose-builds acid from
4316365328L-xylose-builds acid from
4316315963ribitol-builds acid from
43163methyl alpha-D-xylopyranoside-builds acid from
4316312936D-galactose-builds acid from
4316362345L-rhamnose-builds acid from
43163esculin ferric citrate-builds acid from
4316328053melibiose-builds acid from
4316315824D-fructose-builds acid from
4316318287L-fucose-builds acid from
4316343943methyl alpha-D-mannoside-builds acid from
43163320061methyl alpha-D-glucopyranoside-builds acid from
43163506227N-acetylglucosamine-builds acid from
4316327613amygdalin-builds acid from
4316318305arbutin-builds acid from
4316317814salicin-builds acid from
4316317057cellobiose-builds acid from
4316317716lactose-builds acid from
4316315443inulin-builds acid from
431636731melezitose-builds acid from
4316316634raffinose-builds acid from
4316328017starch-builds acid from
4316328087glycogen-builds acid from
4316317151xylitol-builds acid from
4316328066gentiobiose-builds acid from
4316318333D-arabitol-builds acid from
4316318403L-arabitol-builds acid from
43163potassium 2-dehydro-D-gluconate-builds acid from
43163potassium 5-dehydro-D-gluconate-builds acid from
4316317113erythritol-builds acid from
4316317266L-sorbose-builds acid from
4316316813galactitol-builds acid from
4316317268myo-inositol-builds acid from
4316316899D-mannitol-builds acid from
4316317924D-sorbitol-builds acid from
4316317992sucrose-builds acid from
4316327082trehalose-builds acid from
4316332528turanose-builds acid from
4316362318D-lyxose-builds acid from
4316316443D-tagatose-builds acid from
4316317814salicin-assimilation
4316328053melibiose-assimilation
4316330911sorbitol-assimilation
4316316947citrate-assimilation
4316322599arabinose-assimilation
43163506227N-acetylglucosamine-assimilation
4316329864mannitol-assimilation
4316317234glucose+assimilation
4316316988D-ribose-assimilation
4316317268myo-inositol-assimilation
4316317992sucrose-assimilation
4316317306maltose+assimilation
4316333984fucose-assimilation
4316330089acetate-assimilation

metabolite production

  • @ref: 43163
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
43163catalase-1.11.1.6
43163cytochrome oxidase+1.9.3.1
43163arginine dihydrolase-3.5.3.6
43163urease+3.5.1.5
43163alkaline phosphatase+3.1.3.1
43163leucine arylamidase+3.4.11.1
43163acid phosphatase+3.1.3.2
43163naphthol-AS-BI-phosphohydrolase+
43163valine arylamidase+
43163alpha-chymotrypsin+3.4.21.1
43163N-acetyl-beta-glucosaminidase+3.2.1.52
43163cystine arylamidase+/-3.4.11.3
43163trypsin+/-3.4.21.4
43163esterase Lipase (C 8)+/-
43163alpha-glucosidase-3.2.1.20
43163esterase (C 4)-
43163beta-glucuronidase-3.2.1.31
43163lipase (C 14)-
43163alpha-galactosidase-3.2.1.22
43163beta-galactosidase-3.2.1.23
43163beta-glucosidase-3.2.1.21
43163alpha-mannosidase-3.2.1.24
43163alpha-fucosidase-3.2.1.51

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    43163C10:0 3OH9.6
    43163C12:04.9
    43163C16:027.4
    43163C16:1ω7c / C16:1ω6c52.3
    43163C18:1ω6c / C18:1ω7c5.8
  • type of FA analysis: whole cell analysis
  • incubation medium: R2A
  • agar/liquid: agar
  • incubation temperature: 28
  • incubation time: 2
  • system: MIS MIDI
  • method/protocol: Kämpfer & Kroppenstedt 1996
  • cutoff value:

Isolation, sampling and environmental information

isolation

@refsample typehost speciescountryorigin.countrycontinent
24415zebrafish Danio rerio maintained in the laboratoryDanio rerioChileCHLMiddle and South America
43163a zebrafish maintained in E3 medium

isolation source categories

Cat1Cat2Cat3
#Engineered#Laboratory
#Host#Fishes#Zebrafish

Safety information

risk assessment

  • @ref: 24415
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 24415
  • description: Undibacterium danionis strain E3/4 16S ribosomal RNA gene, partial sequence
  • accession: KU695571
  • length: 1478
  • database: ena
  • NCBI tax ID: 1812100

External links

@ref: 24415

culture collection no.: DSM 102221, CCM 8677, CIP 111017

Reference

@idauthorstitledoi/urlcataloguejournal
20215D.Gleim, M.Kracht, N.Weiss et. al.Prokaryotic Nomenclature Up-to-date - compilation of all names of Bacteria and Archaea, validly published according to the Bacteriological Code since 1. Jan. 1980, and validly published nomenclatural changes sincehttp://www.dsmz.de/bacterial-diversity/prokaryotic-nomenclature-up-to-date.html
24415Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-102221Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 102221)
42164Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/34629
43163Peter Kämpfer, Rute Irgang, Hans-Jürgen Busse, Matías Poblete-Morales, Tanita Kleinhagauer, Stefanie P. Glaeser and Ruben Avendaño-HerreraUndibacterium danionis sp. nov. isolated from a zebrafish (Danio rerio)10.1099/ijsem.0.001244IJSEM 66: 3625-3631 2016