Strain identifier

BacDive ID: 1956

Type strain: Yes

Species: Paraburkholderia graminis

Strain history: CIP <- 2000, CCUG <- 1999, P. Vandamme and T. Coenye, Ghent, Belgium <- ATCC <- V. Viallard <- I. Poirier

NCBI tax ID(s): 60548 (species)

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General

@ref: 6792

BacDive-ID: 1956

DSM-Number: 17151

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

description: Paraburkholderia graminis DSM 17151 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from maize senescent root system.

NCBI tax id

  • NCBI tax id: 60548
  • Matching level: species

strain history

@refhistory
6792<- CCUG <- T. Coenye and P. Vandamme, LMG <- ATCC <- V. Viallard <- I. Poirier
67770CIP 106649 <-- CCUG 42231 <-- P. Vandamme and T. Coenye <-- ATCC 700544 <-- V. Viallard C4D1M <-- I. Poirier.
119725CIP <- 2000, CCUG <- 1999, P. Vandamme and T. Coenye, Ghent, Belgium <- ATCC <- V. Viallard <- I. Poirier

doi: 10.13145/bacdive1956.20250331.9.3

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Betaproteobacteria
  • order: Burkholderiales
  • family: Burkholderiaceae
  • genus: Paraburkholderia
  • species: Paraburkholderia graminis
  • full scientific name: Paraburkholderia graminis (Viallard et al. 1998) Sawana et al. 2015

  • synonyms

    • @ref: 20215
    • synonym: Burkholderia graminis

@ref: 6792

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Burkholderiaceae

genus: Paraburkholderia

species: Paraburkholderia graminis

full scientific name: Paraburkholderia graminis (Viallard et al. 1998) Sawana et al. 2015

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
119725negativerod-shapedyes
125439negative94.7
125438negative98

colony morphology

@reftype of hemolysisincubation period
6792gamma1-2 days
119725

pigmentation

  • @ref: 119725
  • production: no
  • name: Pyocyanin

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
41966MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
6792TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)yesName: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled waterhttps://mediadive.dsmz.de/medium/535
119725CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperature
6792positivegrowth28
41966positivegrowth30
55370positivegrowth28
67770positivegrowth30
119725positivegrowth25-37
119725nogrowth5
119725nogrowth10
119725nogrowth41

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
55370aerobe
119725obligate aerobe
125438aerobe90.012
125439obligate aerobe99.8

spore formation

  • @ref: 125439
  • spore formation: no
  • confidence: 93

halophily

@refsaltgrowthtested relationconcentration
119725NaClpositivegrowth0 %
119725NaClnogrowth4 %
119725NaClnogrowth6 %
119725NaClnogrowth8 %
119725NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
11972516947citrate+carbon source
1197254853esculin-hydrolysis
11972517632nitrate+reduction
11972516301nitrite-reduction
11972517632nitrate-respiration
68371Potassium 5-ketogluconate-builds acid from
68371320061methyl alpha-D-glucopyranoside-builds acid from
6837162345L-rhamnose+builds acid from
6837117266L-sorbose-builds acid from
6837116024D-mannose+builds acid from
6837115824D-fructose+builds acid from
6837117634D-glucose+builds acid from
6837112936D-galactose+builds acid from
68371Potassium 2-ketogluconate+builds acid from
6837124265gluconate+builds acid from
6837118333D-arabitol+builds acid from
6837118287L-fucose+builds acid from
6837128847D-fucose-builds acid from
6837116443D-tagatose-builds acid from
6837162318D-lyxose-builds acid from
6837132528turanose-builds acid from
6837128066gentiobiose-builds acid from
6837128087glycogen-builds acid from
6837128017starch-builds acid from
6837116634raffinose-builds acid from
683716731melezitose-builds acid from
6837115443inulin-builds acid from
6837127082trehalose-builds acid from
6837117992sucrose+builds acid from
6837128053melibiose-builds acid from
6837117716lactose-builds acid from
6837117306maltose-builds acid from
6837117057cellobiose-builds acid from
6837117814salicin-builds acid from
683714853esculin-builds acid from
6837118305arbutin-builds acid from
6837127613amygdalin-builds acid from
6837159640N-acetylglucosamine+builds acid from
6837143943methyl alpha-D-mannoside-builds acid from
6837117924D-sorbitol+builds acid from
6837116899D-mannitol+builds acid from
6837117268myo-inositol+builds acid from
6837116813galactitol-builds acid from
6837174863methyl beta-D-xylopyranoside-builds acid from
6837165327D-xylose+builds acid from
6837130849L-arabinose+builds acid from
6837117113erythritol-builds acid from
6836925115malate+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

antibiotic resistance

  • @ref: 119725
  • 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
11972535581indoleno

metabolite tests

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

enzymes

@refvalueactivityec
6792catalase+1.11.1.6
6792cytochrome-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
68382alpha-glucosidase+3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase-3.2.1.23
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-chymotrypsin-3.4.21.1
68382trypsin-3.4.21.4
68382valine arylamidase-
68382cystine arylamidase-3.4.11.3
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)+
68382esterase (C 4)+
68382alkaline phosphatase+3.1.3.1
119725oxidase+
119725beta-galactosidase+3.2.1.23
119725alcohol dehydrogenase-1.1.1.1
119725gelatinase-
119725amylase-
119725DNase-
119725caseinase-3.4.21.50
119725catalase+1.11.1.6
119725tween esterase-
119725lecithinase-
119725lipase-
119725lysine decarboxylase-4.1.1.18
119725ornithine decarboxylase-4.1.1.17
119725protease-
119725tryptophan deaminase-
119725urease-3.5.1.5
68369urease-3.5.1.5
68382beta-glucosidase-3.2.1.21
68369gelatinase-
68369beta-glucosidase-3.2.1.21
68369arginine dihydrolase-3.5.3.6

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
119725-+++-+----++---+----

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
6792+------++++++-+++++-+/-
6792+------++++++-++-++++
6792+------++++++-+++++++

API 50CHac

@refQGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
6792-+--++++/-+-++++-+-+++--+--------+------+-----+++++-
6792-+/--+++/-+-+/--++++-+-+++--+--------+------+/------++-++-

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
119725+++++--++--+-+-++--+++-++-+++--+++--++-+---+++++++++-+++++-++++++--+---+-+-+++-++++-+-+-++++-++++++

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling dateisolation date
6792maize senescent root systemCote saint AndréFranceFRAEurope
55370Maize senescent root systemCôte Saint AndréFranceFRAEurope1994
67770Maize Senescent root system in Côte Saint AndréFranceFRAEurope
119725Plant, Maize senescent root systemCôte Saint AndréFranceFRAEurope1994

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Herbaceous plants (Grass,Crops)
#Host Body-Site#Plant#Root (Rhizome)

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
67921Risk group (German classification)
1197251Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Burkholderia graminis strain CIP 106649 16S ribosomal RNA gene, partial sequenceEU0241541315nuccore60548
20218Burkholderia graminis C4D1M strain LMG 18924 16S ribosomal RNA gene, partial sequenceHQ8490861126nuccore396598
6792Burkholderia graminis 16S ribosomal RNA gene, partial sequenceU969391600nuccore396598

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Burkholderia graminis C4D1M396598.3wgspatric396598
66792Paraburkholderia graminis C4D1M strain LMG 18924396598.11wgspatric396598
67770Paraburkholderia graminis C4D1MGCA_000172415contigncbi396598
67770Paraburkholderia graminis C4D1M LMG 18924GCA_902859785contigncbi396598

GC content

@refGC-contentmethod
679263
6777063high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingno98no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no97.858yes
125438spore-formingspore-formingAbility to form endo- or exosporesno84.605no
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes90.012yes
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno97.486yes
125438motile2+flagellatedAbility to perform flagellated movementyes84.199no
125439BacteriaNetspore_formationAbility to form endo- or exosporesno93
125439BacteriaNetmotilityAbility to perform movementyes58.5
125439BacteriaNetgram_stainReaction to gram-stainingnegative94.7
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate aerobe99.8

External links

@ref: 6792

culture collection no.: DSM 17151, ATCC 700544, CCUG 42231, CIP 106649, LMG 18924, JCM 13456, CFBP 6734, NCIMB 13744

straininfo link

  • @ref: 71601
  • straininfo: 12778

literature

topicPubmed-IDtitleauthorsjournalDOIyearmesh
Metabolism36050605Screening and characterization of a nitrilase with significant nitrile hydratase activity.Zhang K, Pan T, Wang L, Wang H, Ren Y, Wei DBiotechnol Lett10.1007/s10529-022-03291-62022Amides, *Aminohydrolases/metabolism, Hydro-Lyases, Molecular Probes, *Nitriles, Substrate Specificity
Metabolism36354305C-Diazeniumdiolate Graminine in the Siderophore Gramibactin Is Photoreactive and Originates from Arginine.Makris C, Carmichael JR, Zhou H, Butler AACS Chem Biol10.1021/acschembio.2c005932022*Siderophores/metabolism, *Arginine, Ferric Compounds, Nitric Oxide, Ligands, Oximes

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
6792Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17151)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17151
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
41966Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/18803
55370Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 42231)https://www.ccug.se/strain?id=42231
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)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68369Automatically annotated from API 20NE
68371Automatically annotated from API 50CH acid
68382Automatically annotated from API zym
71601Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID12778.1StrainInfo: A central database for resolving microbial strain identifiers
119725Curators of the CIPCollection of Institut Pasteur (CIP 106649)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106649
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann10.1101/2024.08.12.607695Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardyhttps://github.com/GenomeNet/deepGdeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1