Strain identifier

BacDive ID: 1911

Type strain: Yes

Species: Burkholderia gladioli

Strain Designation: PM 107

Strain history: CIP <- 1998, DSM <- NCPPB <- ICPB: strain PM 107 <- NRRL: strain B-793, "Pseudomonas marginata"

NCBI tax ID(s): 1218079 (strain), 28095 (species)

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General

@ref: 1642

BacDive-ID: 1911

DSM-Number: 4285

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, motile, plant pathogen

description: Burkholderia gladioli PM 107 is an aerobe, mesophilic, motile plant pathogen that was isolated from Gladiolus sp..

NCBI tax id

NCBI tax idMatching level
28095species
1218079strain

strain history

@refhistory
1642<- NCPPB <- ICPB <- NRRL
119637CIP <- 1998, DSM <- NCPPB <- ICPB: strain PM 107 <- NRRL: strain B-793, "Pseudomonas marginata"

doi: 10.13145/bacdive1911.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Betaproteobacteria
  • order: Burkholderiales
  • family: Burkholderiaceae
  • genus: Burkholderia
  • species: Burkholderia gladioli
  • full scientific name: Burkholderia gladioli (Severini 1913) Yabuuchi et al. 1993

  • synonyms

    @refsynonym
    20215Pseudomonas gladioli
    20215Pseudomonas cocovenenans
    20215Pseudomonas antimicrobica
    20215Burkholderia cocovenenans

@ref: 1642

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Burkholderiaceae

genus: Burkholderia

species: Burkholderia gladioli

full scientific name: Burkholderia gladioli (Severini 1913) Yabuuchi et al. 1993

strain designation: PM 107

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480yes92.46
6948099.936negative
119637yesnegativerod-shaped

colony morphology

  • @ref: 1642
  • incubation period: 1-2 days

pigmentation

  • @ref: 119637
  • production: yes
  • name: Pyocyanin

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
1642R2A MEDIUM (DSMZ Medium 830)yeshttps://mediadive.dsmz.de/medium/830Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 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
1642NUTRIENT AGAR (DSMZ Medium 1)yeshttps://mediadive.dsmz.de/medium/1Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
32729MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
119637CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72
119637CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperaturerange
1642positivegrowth30mesophilic
32729positivegrowth30mesophilic
44421positivegrowth28-37mesophilic
119637positivegrowth10-41
119637nogrowth5psychrophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
44421aerobe
119637obligate aerobe

spore formation

@refspore formationconfidence
69481no94
69480no99.913

halophily

@refsaltgrowthtested relationconcentration
119637NaClpositivegrowth0-2 %
119637NaClnogrowth4 %
119637NaClnogrowth6 %
119637NaClnogrowth8 %
119637NaClnogrowth10 %

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
11963716947citrate+carbon source
1196374853esculin-hydrolysis
11963717632nitrate-reduction
11963716301nitrite-reduction
11963717632nitrate-respiration

antibiotic resistance

  • @ref: 119637
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

@refChebi-IDmetaboliteproduction
6836935581indoleno
11963735581indoleno

metabolite tests

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

enzymes

@refvalueactivityec
1642catalase+1.11.1.6
1642cytochrome-c oxidase+1.9.3.1
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucosidase+3.2.1.21
68382alpha-glucosidase-3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase-3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin-3.4.21.4
68382cystine arylamidase-3.4.11.3
68382valine arylamidase-
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)+
68382esterase lipase (C 8)+
68382esterase (C 4)+
68382alkaline phosphatase+3.1.3.1
68369cytochrome oxidase+1.9.3.1
68369gelatinase+
68369beta-glucosidase-3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6
119637oxidase+
119637beta-galactosidase+3.2.1.23
119637alcohol dehydrogenase-1.1.1.1
119637gelatinase+
119637amylase-
119637DNase-
119637caseinase+3.4.21.50
119637catalase+1.11.1.6
119637tween esterase-
119637lecithinase+
119637lipase+
119637lysine decarboxylase-4.1.1.18
119637ornithine decarboxylase-4.1.1.17
119637tryptophan deaminase-
119637urease-3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
119637-+++++----++----+---

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
1642------+++++++-+++++++

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
119637+++++--------+-----+++--+-+--+++++--++-+---+++++++++-++-++++++++++++---+-+-++++++-+-+-+-+++++++++++

Isolation, sampling and environmental information

isolation

  • @ref: 44421
  • sample type: Gladiolus sp.
  • country: USA
  • origin.country: USA
  • continent: North America

isolation source categories

  • Cat1: #Host
  • Cat2: #Plants
  • Cat3: #Herbaceous plants (Grass,Crops)

Safety information

risk assessment

@refpathogenicity plantbiosafety levelbiosafety level comment
1642yes2Risk group (German classification)
1196371Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Burkholderia gladioli gene for 16S rRNA, partial sequence, strain: NBRC 13700AB6804841458ena28095
20218Burkholderia gladioli pv. gladioli strain NCPPB1891 16S ribosomal RNA gene, partial sequence; tRNA-Ile and tRNA-Ala genes, complete sequence; and 23S ribosomal RNA gene, partial sequenceEF552070715ena32009
20218Pseudomonas gladioli 16S ribosomal RNA (16S rRNA) gene, transfer RNA-Ile (tRNA-Ile) gene, transfer RNA-Ala (tRNA-Ala) gene, 23S ribosomal RNA (23S rRNA) geneL28156770ena28095
20218Pseudomonas gladioli 16S ribosomal RNA (16S rRNA) gene, transfer RNA-Ile (tRNA-Ile) gene, transfer RNA-Ala (tRNA-Ala) gene, 23S ribosomal RNA (23S rRNA) geneL28157737ena28095
20218P.gladioli 16S ribosomal RNAX670381467ena28095
1642Burkholderia gladioli strain CIP 105410 16S ribosomal RNA gene, partial sequenceEU0241681313ena28095

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Burkholderia gladioli ATCC 10248GCA_000959725completencbi28095
66792Burkholderia gladioli NBRC 13700GCA_000739755contigncbi1218079
66792Burkholderia gladioli NBRC 137001218079.3wgspatric1218079
66792Burkholderia gladioli strain ATCC 1024828095.23plasmidpatric28095
66792Burkholderia gladioli strain ATCC 1024828095.24plasmidpatric28095
66792Burkholderia gladioli strain ATCC 1024828095.22plasmidpatric28095
66792Burkholderia gladioli strain ATCC 1024828095.12completepatric28095
66792Burkholderia gladioli ATCC 102482639762983completeimg28095
66792Burkholderia gladioli NBRC 137002600255057draftimg1218079

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno94no
motileyes88.637no
flagellatedno83.095no
gram-positiveno97.863no
anaerobicno98.698yes
aerobicyes92.961yes
halophileno92.521no
spore-formingno92.786no
glucose-utilyes92.883no
thermophileno99.469no
glucose-fermentno89.648yes

External links

@ref: 1642

culture collection no.: DSM 4285, ATCC 10248, CIP 105410, ICPB PM 107, IFO 13700, NBRC 13700, NCPPB 1891, NRRL B-793, PDDCC 3950, CCUG 1782, LMG 2216, ICMP 3950

straininfo link

  • @ref: 71556
  • straininfo: 4102

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Genetics9352638Structural studies of the O-specific side-chain of lipopolysaccharide from Burkholderia gladioli pv. gladioli strain NCPPB 1891.Galbraith L, Wilkinson SGCarbohydr Res10.1016/s0008-6215(97)00158-41997Burkholderia/*chemistry, Carbohydrate Sequence, Magnetic Resonance Spectroscopy, Molecular Sequence Data, O Antigens/*chemistry
Metabolism11472796A novel esterase from Burkholderia gladioli which shows high deacetylation activity on cephalosporins is related to beta-lactamases and DD-peptidases.Petersen EI, Valinger G, Solkner B, Stubenrauch G, Schwab HJ Biotechnol10.1016/s0168-1656(01)00284-x2001Acetylation, Amino Acid Sequence, Base Sequence, Burkholderia/*enzymology, Carboxypeptidases/*metabolism, Cephalosporins/*metabolism, Cloning, Molecular, DNA Primers, Escherichia coli/genetics, Hydrolysis, Molecular Sequence Data, Mutagenesis, Site-Directed, Open Reading Frames, Promoter Regions, Genetic, Sequence Homology, Amino Acid, Serine/metabolism, Serine Endopeptidases/chemistry/genetics/isolation & purification/*metabolism, Serine-Type D-Ala-D-Ala Carboxypeptidase, beta-Lactamases/*metabolismEnzymology
Phylogeny32147231[Genetic characterization of rice endophytic bacteria (Oryza sativa L.) with antimicrobial activity against Burkholderia glumae].Valdez-Nunez RA, Rios-Ruiz WF, Ormeno-Orrillo E, Torres-Chavez EE, Torres-Delgado JRev Argent Microbiol10.1016/j.ram.2019.12.0022020*Anti-Infective Agents, Bacillus, *Burkholderia/genetics, *Oryza, RNA, Ribosomal, 16S/genetics, Virulence
Genetics33572733Genomics-Driven Activation of Silent Biosynthetic Gene Clusters in Burkholderia gladioli by Screening Recombineering System.Chen H, Sun T, Bai X, Yang J, Yan F, Yu L, Tu Q, Li A, Tang Y, Zhang Y, Bian X, Zhou HMolecules10.3390/molecules260307002021Biosynthetic Pathways/*genetics, Burkholderia gladioli/genetics, Genome, Bacterial/*genetics, Genomics, Lipopeptides/genetics, Multigene Family/*genetics, Peptide Synthases/*genetics, Promoter Regions, Genetic, Recombinases/genetics
Phylogeny34287810Burkholderia perseverans sp. nov., a bacterium isolated from the Restinga ecosystem, is a producer of volatile and diffusible compounds that inhibit plant pathogens.Andrade JP, de Souza HG, Ferreira LC, Cnockaert M, De Canck E, Wieme AD, Peeters C, Gross E, De Souza JT, Marbach PAS, Goes-Neto A, Vandamme PBraz J Microbiol10.1007/s42770-021-00560-w2021Agaricales/drug effects/physiology, *Antibiosis/physiology, Aspergillus/drug effects/physiology, Bacterial Typing Techniques, Brazil, *Burkholderia/chemistry/classification/genetics, DNA, Bacterial/genetics, *Ecosystem, Phospholipids/analysis, Phylogeny, Phytophthora/drug effects/physiology, Plant Leaves/microbiology, RNA, Ribosomal, 16S/genetics, Species Specificity, Volatile Organic Compounds/metabolism/pharmacologyPathogenicity

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
1642Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 4285)https://www.dsmz.de/collection/catalogue/details/culture/DSM-4285
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
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
32729Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/17427
44421Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 1782)https://www.ccug.se/strain?id=1782
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)
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
71556Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID4102.1StrainInfo: A central database for resolving microbial strain identifiers
119637Curators of the CIPCollection of Institut Pasteur (CIP 105410)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105410