Strain identifier

BacDive ID: 130227

Type strain: Yes

Species: Trinickia symbiotica

Strain Designation: NKMU-JPY-345, JPY-345

Strain history: <- LMG <- W.-M. Chen, National Kaohsiung Marine University; JPY-345

NCBI tax ID(s): 863227 (species)

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General

@ref: 21538

BacDive-ID: 130227

DSM-Number: 29917

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

description: Trinickia symbiotica NKMU-JPY-345 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from Mimosa cordistipula, roots, nitrogen fixing nodules.

NCBI tax id

  • NCBI tax id: 863227
  • Matching level: species

strain history

  • @ref: 21538
  • history: <- LMG <- W.-M. Chen, National Kaohsiung Marine University; JPY-345

doi: 10.13145/bacdive130227.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Betaproteobacteria
  • order: Burkholderiales
  • family: Burkholderiaceae
  • genus: Trinickia
  • species: Trinickia symbiotica
  • full scientific name: Trinickia symbiotica (Sheu et al. 2012) Estrada-de Los Santos et al. 2018

  • synonyms

    @refsynonym
    20215Burkholderia symbiotica
    20215Paraburkholderia symbiotica

@ref: 21538

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Burkholderiaceae

genus: Trinickia

species: Trinickia symbiotica

full scientific name: Trinickia symbiotica (Sheu et al. 2012) Estrada-de Los Santos et al. 2018

strain designation: NKMU-JPY-345, JPY-345

type strain: yes

Morphology

cell morphology

  • @ref: 30496
  • gram stain: negative
  • cell length: 1.25 µm
  • cell width: 0.9 µm
  • cell shape: rod-shaped
  • motility: no

colony morphology

  • @ref: 21538
  • incubation period: 2-3 days

pigmentation

  • @ref: 30496
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 21538
  • name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/535
  • composition: Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
21538positivegrowth30mesophilic
30496positivegrowth15-43
30496positiveoptimum35mesophilic

culture pH

@refabilitytypepHPH range
30496positivegrowth04-07acidophile
30496positiveoptimum5

Physiology and metabolism

oxygen tolerance

  • @ref: 30496
  • oxygen tolerance: aerobe

spore formation

  • @ref: 30496
  • spore formation: no

halophily

  • @ref: 30496
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-2 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3049616449alanine+carbon source
3049622599arabinose+carbon source
3049618403L-arabitol+carbon source
3049622653asparagine+carbon source
3049635391aspartate+carbon source
3049616947citrate+carbon source
3049623652dextrin+carbon source
3049615740formate+carbon source
3049628757fructose+carbon source
3049633984fucose+carbon source
3049628260galactose+carbon source
3049624265gluconate+carbon source
3049617234glucose+carbon source
3049629987glutamate+carbon source
3049617754glycerol+carbon source
3049624996lactate+carbon source
3049629864mannitol+carbon source
3049637684mannose+carbon source
3049617268myo-inositol+carbon source
30496506227N-acetylglucosamine+carbon source
3049628044phenylalanine+carbon source
3049626271proline+carbon source
3049651850methyl pyruvate+carbon source
3049626490quinate+carbon source
3049626546rhamnose+carbon source
3049630911sorbitol+carbon source
3049630031succinate+carbon source
3049653423tween 40+carbon source
3049653426tween 80+carbon source
3049617632nitrate+reduction
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

metabolite production

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

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

enzymes

@refvalueactivityec
21538catalase+1.11.1.6
21538cytochrome-c oxidase+1.9.3.1
30496acid phosphatase+3.1.3.2
30496alkaline phosphatase+3.1.3.1
30496urease+3.5.1.5
68369gelatinase-
68369beta-glucosidase-3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPAC
21538+------++++++-+--+/---

Isolation, sampling and environmental information

isolation

  • @ref: 21538
  • sample type: Mimosa cordistipula, roots, nitrogen fixing nodules
  • host species: Mimosa cordistipula
  • geographic location: Chapada Diamantina highlands, Bahia
  • country: Brazil
  • origin.country: BRA
  • continent: Middle and South America

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Shrub (Scrub)
#Host Body-Site#Plant#Root nodule

Safety information

risk assessment

  • @ref: 21538
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 21538
  • description: Burkholderia symbiotica strain JPY345 16S ribosomal RNA gene, partial sequence
  • accession: HM357233
  • length: 1405
  • database: ena
  • NCBI tax ID: 863227

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Trinickia symbiotica JPY-345GCA_002934455scaffoldncbi863227
66792Trinickia symbiotica JPY-3452708743149draftimg863227

GC content

  • @ref: 30496
  • GC-content: 64.2

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
flagellatedno90.858yes
gram-positiveno97.563yes
anaerobicno99.014yes
aerobicyes86.762yes
halophileno95.736no
spore-formingno93.794yes
glucose-utilyes91.094no
thermophileno98.991no
motileyes87.651no
glucose-fermentno90.051yes

External links

@ref: 21538

culture collection no.: DSM 29917, BCRC 80258, KCTC 23309, LMG 26032

straininfo link

  • @ref: 88769
  • straininfo: 371135

literature

  • topic: Phylogeny
  • Pubmed-ID: 22081715
  • title: Burkholderia symbiotica sp. nov., isolated from root nodules of Mimosa spp. native to north-east Brazil.
  • authors: Sheu SY, Chou JH, Bontemps C, Elliott GN, Gross E, James EK, Sprent JI, Young JPW, Chen WM
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.037408-0
  • year: 2011
  • mesh: Bacterial Typing Techniques, Base Composition, Brazil, Burkholderia/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/analysis, Mimosa/*microbiology, Molecular Sequence Data, Phospholipids/analysis, *Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Root Nodules, Plant/*microbiology, Sequence Analysis, DNA
  • topic2: Genetics

Reference

@idauthorstitledoi/urlcatalogueID_cross_referencepubmedjournal
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
21538Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-29917Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 29917)
30496Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172682928776041
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar SchomburgBRENDA, the ELIXIR core data resource in 2021: new developments and updates10.1093/nar/gkaa102533211880Nucleic Acids Res. 49: D498-D508 2020
68369Automatically annotated from API 20NE
88769Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID371135.1