Strain identifier

BacDive ID: 1919

Type strain: Yes

Species: Burkholderia glumae

Strain Designation: MD1, P1-22-1

Strain history: CIP <- 2000, CFBP <- NCPPB

NCBI tax ID(s): 1176492 (strain), 337 (species)

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

@ref: 3624

BacDive-ID: 1919

DSM-Number: 9512

keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, mesophilic, Gram-negative, plant pathogen

description: Burkholderia glumae MD1 is an obligate aerobe, mesophilic, Gram-negative plant pathogen that was isolated from Oryza sativa.

NCBI tax id

NCBI tax idMatching level
1176492strain
337species

strain history

@refhistory
3624<- NCPPB <- PDDCC <- D.W. Dye; MD1 <- T. Tominaga; P1-22-1
119695CIP <- 2000, CFBP <- NCPPB

doi: 10.13145/bacdive1919.20230509.8.1

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 glumae
  • full scientific name: Burkholderia glumae (Kurita and Tabei 1967) Urakami et al. 1994
  • synonyms

    • @ref: 20215
    • synonym: Pseudomonas glumae

@ref: 3624

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Burkholderiaceae

genus: Burkholderia

species: Burkholderia glumae

full scientific name: Burkholderia glumae (Kurita and Tabei 1967) Urakami et al. 1994

strain designation: MD1, P1-22-1

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480negative99.982
119695negativerod-shapedyes

colony morphology

  • @ref: 3624
  • incubation period: 1-2 days

pigmentation

  • @ref: 119695
  • production: no
  • name: Pyocyanin

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
3624NUTRIENT 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
39516MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
119695CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3
119695CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
3624positivegrowth28mesophilic
39516positivegrowth30mesophilic
119695positivegrowth25-41
119695nogrowth5psychrophilic
119695nogrowth10psychrophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 119695
  • oxygen tolerance: obligate aerobe

spore formation

@refspore formationconfidence
69481no95
69480no99.992

halophily

@refsaltgrowthtested relationconcentration
119695NaClpositivegrowth0-4 %
119695NaClnogrowth6 %
119695NaClnogrowth8 %
119695NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6836925115malate+assimilation
6836917306maltose-assimilation
6836916899D-mannitol+assimilation
6836916024D-mannose+assimilation
6836930849L-arabinose+assimilation
6836917634D-glucose+assimilation
683694853esculin-hydrolysis
6836916199urea-hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
11969516947citrate+carbon source
1196954853esculin+hydrolysis
11969517632nitrate+reduction
11969516301nitrite-reduction
11969517632nitrate-respiration

antibiotic resistance

  • @ref: 119695
  • 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
11969535581indoleno

metabolite tests

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

enzymes

@refvalueactivityec
3624catalase+1.11.1.6
3624cytochrome-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
68369beta-glucosidase-3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6
119695oxidase+
119695beta-galactosidase+3.2.1.23
119695alcohol dehydrogenase-1.1.1.1
119695gelatinase-
119695amylase-
119695DNase-
119695caseinase-3.4.21.50
119695catalase+1.11.1.6
119695tween esterase+
119695lecithinase+
119695lipase+
119695lysine decarboxylase-4.1.1.18
119695ornithine decarboxylase-4.1.1.17
119695protease+
119695tryptophan deaminase-
119695urease-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
119695-+-+++----++-+------

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
3624-------+++++-----+---
3624+-----+++++++-+++/-++-+

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
119695+++++-+-+---+++----+++--+-+--+++++--++-+---++-++++++-++++-+++-+++------+-+-++++++---+++-++++++++++-

Isolation, sampling and environmental information

isolation

@refsample typehost speciescountryorigin.countrycontinentsampling dategeographic location
3624Oryza sativaOryza sativaJapanJPNAsia
47210Oryza sativa,grainJapanJPNAsia1967Ehime
119695Oryza sativa, grain

isolation source categories

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

Safety information

risk assessment

@refpathogenicity plantbiosafety levelbiosafety level comment
3624yes1Risk group (German classification)
1196951Risk group (French classification)

Sequence information

16S sequences

  • @ref: 3624
  • description: Burkholderia glumae 16S ribosomal RNA gene, partial sequence
  • accession: U96931
  • length: 1510
  • database: ena
  • NCBI tax ID: 1176492

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Burkholderia glumae LMG 2196 = ATCC 33617GCA_000960995completencbi1176492
66792Burkholderia glumae LMG 2196 = ATCC 33617GCA_902832765scaffoldncbi1176492
66792Burkholderia glumae LMG 2196 = ATCC 33617GCA_000300755contigncbi1176492
66792Burkholderia glumae LMG 21961176492.3wgspatric1176492
66792Burkholderia glumae LMG 2196 = ATCC 336171176492.12wgspatric1176492
66792Burkholderia glumae LMG 2196 = ATCC 336171176492.7plasmidpatric1176492
66792Burkholderia glumae LMG 2196 = ATCC 336171176492.8plasmidpatric1176492
66792Burkholderia glumae LMG 2196 = ATCC 336171176492.5completepatric1176492
66792Burkholderia glumae LMG 21962519103049draftimg1176492
66792Burkholderia glumae ATCC 336172648501169completeimg1176492

GC content

  • @ref: 3624
  • GC-content: 68.2

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno95no
motileyes89.159no
flagellatedno82.9no
gram-positiveno98.236no
anaerobicno98.107no
aerobicyes92.28no
halophileno93.888no
spore-formingno93.398no
glucose-utilyes92.675no
thermophileno98.927yes
glucose-fermentno89.679no

External links

@ref: 3624

culture collection no.: DSM 9512, ATCC 33617, DSM 7169, NCPPB 2981, PDDCC 3655, CCUG 20835, LMG 2196, CIP 106418, CFBP 4900

straininfo link

  • @ref: 71563
  • straininfo: 4106

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Metabolism17557855Involvement of a quorum-sensing-regulated lipase secreted by a clinical isolate of Burkholderia glumae in severe disease symptoms in rice.Devescovi G, Bigirimana J, Degrassi G, Cabrio L, LiPuma JJ, Kim J, Hwang I, Venturi VAppl Environ Microbiol10.1128/AEM.00105-072007Bacterial Proteins/genetics/metabolism, Burkholderia/enzymology/genetics/isolation & purification/pathogenicity, Burkholderia Infections/microbiology, *Gene Expression Regulation, Bacterial, Humans, Lipase/genetics/*metabolism, Molecular Sequence Data, Oryza/*microbiology, Plant Diseases/*microbiology, Pyrimidinones/metabolism, *Quorum Sensing, Sequence Analysis, DNA, Triazines/metabolismEnzymology
Genetics26454852Understanding the direction of evolution in Burkholderia glumae through comparative genomics.Lee HH, Park J, Kim J, Park I, Seo YSCurr Genet10.1007/s00294-015-0523-92015*Biological Evolution, Burkholderia/classification/*genetics/metabolism, Gene Rearrangement, *Genome, Bacterial, Genome-Wide Association Study, *Genomics/methods, Metabolic Networks and Pathways, Plant Diseases/microbiology, Plant Proteins/genetics/metabolism, Virulence/geneticsMetabolism
32032827Metabolic fingerprinting of banana passion fruits and its correlation with quorum quenching activity.Castellanos L, Naranjo-Gaybor SJ, Forero AM, Morales G, Wilson EG, Ramos FA, Choi YHPhytochemistry10.1016/j.phytochem.2020.1122722020Flavonoids, Fruit, *Musa, *Passiflora, Quorum Sensing
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
Genetics33498266Genome Sequence and Adaptation Analysis of the Human and Rice Pathogenic Strain Burkholderia glumae AU6208.Cui Z, Wang S, Kakar KU, Xie G, Li B, Chen G, Zhu BPathogens10.3390/pathogens100200872021
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/urltitle
3624Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 9512)https://www.dsmz.de/collection/catalogue/details/culture/DSM-9512
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
39516Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/18547
47210Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 20835)https://www.ccug.se/strain?id=20835
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
71563Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID4106.1StrainInfo: A central database for resolving microbial strain identifiers
119695Curators of the CIPCollection of Institut Pasteur (CIP 106418)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106418