Strain identifier
BacDive ID: 1919
Type strain:
Species: Burkholderia glumae
Strain Designation: MD1, P1-22-1
Strain history: CIP <- 2000, CFBP <- NCPPB
NCBI tax ID(s): 1176492 (strain), 337 (species)
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 id | Matching level |
---|---|
1176492 | strain |
337 | species |
strain history
@ref | history |
---|---|
3624 | <- NCPPB <- PDDCC <- D.W. Dye; MD1 <- T. Tominaga; P1-22-1 |
119695 | CIP <- 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
@ref | gram stain | confidence | cell shape | motility |
---|---|---|---|---|
69480 | negative | 99.982 | ||
119695 | negative | rod-shaped | yes |
colony morphology
- @ref: 3624
- incubation period: 1-2 days
pigmentation
- @ref: 119695
- production: no
- name: Pyocyanin
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
3624 | NUTRIENT AGAR (DSMZ Medium 1) | yes | https://mediadive.dsmz.de/medium/1 | Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water |
39516 | MEDIUM 3 - Columbia agar | yes | Columbia agar (39.000 g);distilled water (1000.000 ml) | |
119695 | CIP Medium 3 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3 | |
119695 | CIP Medium 72 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
3624 | positive | growth | 28 | mesophilic |
39516 | positive | growth | 30 | mesophilic |
119695 | positive | growth | 25-41 | |
119695 | no | growth | 5 | psychrophilic |
119695 | no | growth | 10 | psychrophilic |
Physiology and metabolism
oxygen tolerance
- @ref: 119695
- oxygen tolerance: obligate aerobe
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 95 |
69480 | no | 99.992 |
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
119695 | NaCl | positive | growth | 0-4 % |
119695 | NaCl | no | growth | 6 % |
119695 | NaCl | no | growth | 8 % |
119695 | NaCl | no | growth | 10 % |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
68369 | 25115 | malate | + | assimilation |
68369 | 17306 | maltose | - | assimilation |
68369 | 16899 | D-mannitol | + | assimilation |
68369 | 16024 | D-mannose | + | assimilation |
68369 | 30849 | L-arabinose | + | assimilation |
68369 | 17634 | D-glucose | + | assimilation |
68369 | 4853 | esculin | - | hydrolysis |
68369 | 16199 | urea | - | hydrolysis |
68369 | 29016 | arginine | - | hydrolysis |
68369 | 17634 | D-glucose | - | fermentation |
68369 | 27897 | tryptophan | - | energy source |
119695 | 16947 | citrate | + | carbon source |
119695 | 4853 | esculin | + | hydrolysis |
119695 | 17632 | nitrate | + | reduction |
119695 | 16301 | nitrite | - | reduction |
119695 | 17632 | nitrate | - | 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
@ref | Chebi-ID | metabolite | production |
---|---|---|---|
68369 | 35581 | indole | no |
119695 | 35581 | indole | no |
metabolite tests
- @ref: 68369
- Chebi-ID: 35581
- metabolite: indole
- indole test: -
enzymes
@ref | value | activity | ec |
---|---|---|---|
3624 | catalase | + | 1.11.1.6 |
3624 | cytochrome-c oxidase | + | 1.9.3.1 |
68382 | alpha-fucosidase | - | 3.2.1.51 |
68382 | alpha-mannosidase | - | 3.2.1.24 |
68382 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
68382 | beta-glucosidase | - | 3.2.1.21 |
68382 | alpha-glucosidase | - | 3.2.1.20 |
68382 | beta-glucuronidase | - | 3.2.1.31 |
68382 | beta-galactosidase | + | 3.2.1.23 |
68382 | alpha-galactosidase | - | 3.2.1.22 |
68382 | naphthol-AS-BI-phosphohydrolase | + | |
68382 | acid phosphatase | + | 3.1.3.2 |
68382 | alpha-chymotrypsin | - | 3.4.21.1 |
68382 | trypsin | - | 3.4.21.4 |
68382 | cystine arylamidase | - | 3.4.11.3 |
68382 | valine arylamidase | - | |
68382 | leucine arylamidase | + | 3.4.11.1 |
68382 | lipase (C 14) | + | |
68382 | esterase lipase (C 8) | + | |
68382 | esterase (C 4) | - | |
68382 | alkaline phosphatase | + | 3.1.3.1 |
68369 | beta-glucosidase | - | 3.2.1.21 |
68369 | urease | - | 3.5.1.5 |
68369 | arginine dihydrolase | - | 3.5.3.6 |
119695 | oxidase | + | |
119695 | beta-galactosidase | + | 3.2.1.23 |
119695 | alcohol dehydrogenase | - | 1.1.1.1 |
119695 | gelatinase | - | |
119695 | amylase | - | |
119695 | DNase | - | |
119695 | caseinase | - | 3.4.21.50 |
119695 | catalase | + | 1.11.1.6 |
119695 | tween esterase | + | |
119695 | lecithinase | + | |
119695 | lipase | + | |
119695 | lysine decarboxylase | - | 4.1.1.18 |
119695 | ornithine decarboxylase | - | 4.1.1.17 |
119695 | protease | + | |
119695 | tryptophan deaminase | - | |
119695 | urease | - | 3.5.1.5 |
API zym
@ref | Control | Alkaline phosphatase | Esterase | Esterase Lipase | Lipase | Leucine arylamidase | Valine arylamidase | Cystine arylamidase | Trypsin | alpha- Chymotrypsin | Acid phosphatase | Naphthol-AS-BI-phosphohydrolase | alpha- Galactosidase | beta- Galactosidase | beta- Glucuronidase | alpha- Glucosidase | beta- Glucosidase | N-acetyl-beta- glucosaminidase | alpha- Mannosidase | alpha- Fucosidase |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
119695 | - | + | - | + | + | + | - | - | - | - | + | + | - | + | - | - | - | - | - | - |
API 20NE
@ref | NO3 | TRP | GLU_ Ferm | ADH Arg | URE | ESC | GEL | PNPG | GLU_ Assim | ARA | MNE | MAN | NAG | MAL | GNT | CAP | ADI | MLT | CIT | PAC | OX |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
3624 | - | - | - | - | - | - | - | + | + | + | + | + | - | - | - | - | - | + | - | - | - |
3624 | + | - | - | - | - | - | + | + | + | + | + | + | + | - | + | + | +/- | + | + | - | + |
API biotype100
@ref | GLU | FRU | GAL | TRE | MNE | SBE | MEL | SAC | RAF | MTE | MAL | LAC | LTE | MbGa | MaGa | CEL | GEN | MbGu | ESC | RIB | ARA | XYL | PLE | RHA | FUC | MLZ | DARL | LARL | XLT | DUL | TAG | GLY | INO | MAN | MTL | TUR | SOR | ADO | HBG | LYX | ERY | MDG | 3MDG | SAT | MUC | LTAT | DTAT | MTAT | DMLT | LMLT | CATE | TATE | TTE | CIT | GRT | GAT | 2KG | 5KG | TRY | NAG | GNT | PAC | PAT | pOBE | QAT | GTE | mOBE | BAT | PPAT | CMT | TGE | BET | PCE | ABT | HIN | LAT | CAP | CYT | HIS | SUC | FUM | GRE | GYT | AVT | ETN | TTN | GLN | ITA | 3OBU | APT | GTT | PRO | DALA | LALA | SER | MNT | PROP | TYR | 2KT |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
119695 | + | + | + | + | + | - | + | - | + | - | - | - | + | + | + | - | - | - | - | + | + | + | - | - | + | - | + | - | - | + | + | + | + | + | - | - | + | + | - | + | - | - | - | + | + | - | + | + | + | + | + | + | - | + | + | + | + | - | + | + | + | - | + | + | + | - | - | - | - | - | - | + | - | + | - | + | + | + | + | + | + | - | - | - | + | + | + | - | + | + | + | + | + | + | + | + | + | + | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | host species | country | origin.country | continent | sampling date | geographic location |
---|---|---|---|---|---|---|---|
3624 | Oryza sativa | Oryza sativa | Japan | JPN | Asia | ||
47210 | Oryza sativa,grain | Japan | JPN | Asia | 1967 | Ehime | |
119695 | Oryza sativa, grain |
isolation source categories
- Cat1: #Host
- Cat2: #Plants
- Cat3: #Herbaceous plants (Grass,Crops)
Safety information
risk assessment
@ref | pathogenicity plant | biosafety level | biosafety level comment |
---|---|---|---|
3624 | yes | 1 | Risk group (German classification) |
119695 | 1 | Risk 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
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Burkholderia glumae LMG 2196 = ATCC 33617 | GCA_000960995 | complete | ncbi | 1176492 |
66792 | Burkholderia glumae LMG 2196 = ATCC 33617 | GCA_902832765 | scaffold | ncbi | 1176492 |
66792 | Burkholderia glumae LMG 2196 = ATCC 33617 | GCA_000300755 | contig | ncbi | 1176492 |
66792 | Burkholderia glumae LMG 2196 | 1176492.3 | wgs | patric | 1176492 |
66792 | Burkholderia glumae LMG 2196 = ATCC 33617 | 1176492.12 | wgs | patric | 1176492 |
66792 | Burkholderia glumae LMG 2196 = ATCC 33617 | 1176492.7 | plasmid | patric | 1176492 |
66792 | Burkholderia glumae LMG 2196 = ATCC 33617 | 1176492.8 | plasmid | patric | 1176492 |
66792 | Burkholderia glumae LMG 2196 = ATCC 33617 | 1176492.5 | complete | patric | 1176492 |
66792 | Burkholderia glumae LMG 2196 | 2519103049 | draft | img | 1176492 |
66792 | Burkholderia glumae ATCC 33617 | 2648501169 | complete | img | 1176492 |
GC content
- @ref: 3624
- GC-content: 68.2
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 95 | no |
motile | yes | 89.159 | no |
flagellated | no | 82.9 | no |
gram-positive | no | 98.236 | no |
anaerobic | no | 98.107 | no |
aerobic | yes | 92.28 | no |
halophile | no | 93.888 | no |
spore-forming | no | 93.398 | no |
glucose-util | yes | 92.675 | no |
thermophile | no | 98.927 | yes |
glucose-ferment | no | 89.679 | no |
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
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Metabolism | 17557855 | Involvement 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 V | Appl Environ Microbiol | 10.1128/AEM.00105-07 | 2007 | Bacterial 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/metabolism | Enzymology |
Genetics | 26454852 | Understanding the direction of evolution in Burkholderia glumae through comparative genomics. | Lee HH, Park J, Kim J, Park I, Seo YS | Curr Genet | 10.1007/s00294-015-0523-9 | 2015 | *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/genetics | Metabolism |
32032827 | Metabolic 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 YH | Phytochemistry | 10.1016/j.phytochem.2020.112272 | 2020 | Flavonoids, Fruit, *Musa, *Passiflora, Quorum Sensing | ||
Phylogeny | 32147231 | [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 J | Rev Argent Microbiol | 10.1016/j.ram.2019.12.002 | 2020 | *Anti-Infective Agents, Bacillus, *Burkholderia/genetics, *Oryza, RNA, Ribosomal, 16S/genetics, Virulence | |
Genetics | 33498266 | Genome 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 B | Pathogens | 10.3390/pathogens10020087 | 2021 | ||
Phylogeny | 34287810 | Burkholderia 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 P | Braz J Microbiol | 10.1007/s42770-021-00560-w | 2021 | Agaricales/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/pharmacology | Pathogenicity |
Reference
@id | authors | catalogue | doi/url | title |
---|---|---|---|---|
3624 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 9512) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-9512 | |
20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | |
39516 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/18547 | ||
47210 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 20835) | https://www.ccug.se/strain?id=20835 | |
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |
68369 | Automatically annotated from API 20NE | |||
68382 | Automatically annotated from API zym | |||
69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |
69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 | |
71563 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID4106.1 | StrainInfo: A central database for resolving microbial strain identifiers | |
119695 | Curators of the CIP | Collection of Institut Pasteur (CIP 106418) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106418 |