Strain identifier

BacDive ID: 1940

Type strain: Yes

Species: Paraburkholderia caribensis

Strain Designation: MWAP64

Strain history: CIP <- 2000, CCUG <- 1999, LMG <- ? <- T. Heulin, strain: MWAP64

NCBI tax ID(s): 75105 (species)

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General

@ref: 4976

BacDive-ID: 1940

DSM-Number: 13236

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

description: Paraburkholderia caribensis MWAP64 is an obligate aerobe, mesophilic, Gram-negative bacterium that was isolated from soil, vertisol.

NCBI tax id

  • NCBI tax id: 75105
  • Matching level: species

strain history

@refhistory
4976<- LMG <- W. Achouak; MWAP64
117182CIP <- 2000, CCUG <- 1999, LMG <- ? <- T. Heulin, strain: MWAP64

doi: 10.13145/bacdive1940.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Betaproteobacteria
  • order: Burkholderiales
  • family: Burkholderiaceae
  • genus: Paraburkholderia
  • species: Paraburkholderia caribensis
  • full scientific name: Paraburkholderia caribensis (Achouak et al. 1999) Sawana et al. 2015

  • synonyms

    • @ref: 20215
    • synonym: Burkholderia caribensis

@ref: 4976

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Burkholderiaceae

genus: Paraburkholderia

species: Paraburkholderia caribensis

full scientific name: Paraburkholderia caribensis (Achouak et al. 1999) Sawana et al. 2015

strain designation: MWAP64

type strain: yes

Morphology

cell morphology

  • @ref: 117182
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: yes

pigmentation

  • @ref: 117182
  • production: no
  • name: Pyocyanin

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
4976R2A 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
41958MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
117182CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
4976positivegrowth28mesophilic
41958positivegrowth30mesophilic
117182positivegrowth25-30mesophilic
117182nogrowth5psychrophilic
117182nogrowth10psychrophilic
117182nogrowth37mesophilic
117182nogrowth41thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 117182
  • oxygen tolerance: obligate aerobe

halophily

@refsaltgrowthtested relationconcentration
117182NaClpositivegrowth0-4 %
117182NaClnogrowth6 %
117182NaClnogrowth8 %
117182NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
11718216947citrate+carbon source
1171824853esculin-hydrolysis
11718217632nitrate-reduction
11718216301nitrite-reduction
11718217632nitrate-respiration

antibiotic resistance

  • @ref: 117182
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

  • @ref: 117182
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
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
117182oxidase+
117182beta-galactosidase+3.2.1.23
117182alcohol dehydrogenase-1.1.1.1
117182gelatinase-
117182amylase-
117182DNase-
117182caseinase-3.4.21.50
117182catalase+1.11.1.6
117182tween esterase-
117182lecithinase-
117182lipase-
117182lysine decarboxylase-4.1.1.18
117182ornithine decarboxylase-4.1.1.17
117182protease-
117182tryptophan deaminase-
117182urease+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
117182-+++-+----++-+------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
117182+++++--------+-----+++-++-+++--+++--++-+---+++++++++-++++--++++++-++--++-+-+++-+++++++++++++-++++++

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
4976soil, vertisolFrench West IndiesMartiniqueFRAMiddle and South America
55581VertisolMartiniqueFRAMiddle and South America
117182Environment, Soil, vertisolMartiniqueFranceFRAEurope

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_3026.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_12;96_173;97_511;98_587;99_3026&stattab=map
  • Last taxonomy: Paraburkholderia caribensis
  • 16S sequence: HQ849077
  • Sequence Identity:
  • Total samples: 6895
  • soil counts: 4848
  • aquatic counts: 414
  • animal counts: 645
  • plant counts: 988

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
49761Risk group (German classification)
1171821Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Burkholderia caribensis strain LMG 18531 16S ribosomal RNA gene, partial sequenceHQ8490771124ena75105
4976Burkholderia caribiensis 16S rRNA gene, strain MWAP64Y170091432ena75105

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Paraburkholderia caribensis DSM 13236GCA_002902945completencbi75105
66792Paraburkholderia caribensis MWAP64GCA_001449005completencbi75105
66792Paraburkholderia caribensis LMG 18531GCA_902833515scaffoldncbi75105
66792Paraburkholderia caribensis strain DSM 1323675105.13completepatric75105
66792Paraburkholderia caribensis strain LMG 1853175105.16wgspatric75105
66792Paraburkholderia caribensis LMG 185312643221416completeimg75105
66792Paraburkholderia caribensis DSM 132362811995132completeimg75105

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
flagellatedno83.678no
gram-positiveno98.329no
anaerobicno98.415no
aerobicyes89.199no
halophileno93.102no
spore-formingno94.046no
thermophileno99.551yes
glucose-utilyes91.591no
motileyes87.88no
glucose-fermentno89.418no

External links

@ref: 4976

culture collection no.: DSM 13236, CCUG 42847, CIP 106784, LMG 18531

straininfo link

  • @ref: 71585
  • straininfo: 12633

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny10319504Burkholderia caribensis sp. nov., an exopolysaccharide-producing bacterium isolated from vertisol microaggregates in Martinique.Achouak W, Christen R, Barakat M, Martel MH, Heulin TInt J Syst Bacteriol10.1099/00207713-49-2-7871999Burkholderia/*classification/isolation & purification/*physiology, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Genes, rRNA, Martinique, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, Polymerase Chain Reaction/methods, Polysaccharides, Bacterial/*biosynthesis, RNA, Ribosomal, 16S/genetics, Restriction Mapping, Sequence Analysis, DNA, *Soil MicrobiologyGenetics
Phylogeny16449457Burkholderia terrae sp. nov., isolated from a forest soil.Yang HC, Im WT, Kim KK, An DS, Lee STInt J Syst Evol Microbiol10.1099/ijs.0.63968-02006Bacterial Typing Techniques, Burkholderia/chemistry/*classification/genetics/isolation & purification, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Genes, rRNA, Genotype, Korea, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Trees/*microbiologyGenetics
Metabolism23568428Enhanced degradation of haloacid by heterologous expression in related Burkholderia species.Su X, Deng L, Kong KF, Tsang JSBiotechnol Bioeng10.1002/bit.249172013Acetates/metabolism, Bacterial Proteins/genetics/*metabolism, Biodegradation, Environmental, *Burkholderia/enzymology/genetics/metabolism, Hydrolases/genetics/*metabolism, Metabolic Engineering/*methods, RNA, Messenger/analysis/genetics/metabolism, Substrate SpecificityEnzymology
Genetics26823586Complete Genome Sequence of the Exopolysaccharide-Producing Burkholderia caribensis Type Strain MWAP64.Pan Y, Kong KF, Tsang JSGenome Announc10.1128/genomeA.01636-152016
Phylogeny29185955Paraburkholderia azotifigens sp. nov., a nitrogen-fixing bacterium isolated from paddy soil.Choi GM, Im WTInt J Syst Evol Microbiol10.1099/ijsem.0.0025052017Bacterial Typing Techniques, Base Composition, Burkholderiaceae/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nitrogen Fixation, Nucleic Acid Hybridization, Oryza, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Ubiquinone/chemistryTranscriptome
Phylogeny32068849Delineation of a Subgroup of the Genus Paraburkholderia, Including P. terrae DSM 17804T, P. hospita DSM 17164T, and Four Soil-Isolated Fungiphiles, Reveals Remarkable Genomic and Ecological Features-Proposal for the Definition of a P. hospita Species Cluster.Pratama AA, Jimenez DJ, Chen Q, Bunk B, Sproer C, Overmann J, van Elsas JDGenome Biol Evol10.1093/gbe/evaa0312020Burkholderiaceae/*genetics/growth & development/metabolism, Ecology, Fungi/*genetics/growth & development/metabolism, *Genome, Bacterial, *Genome, Fungal, Genomics/*methods, Phylogeny, Soil Microbiology, Species SpecificityGenetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
4976Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 13236)https://www.dsmz.de/collection/catalogue/details/culture/DSM-13236
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
41958Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/18952
55581Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 42847)https://www.ccug.se/strain?id=42847
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)
68382Automatically annotated from API zym
69479João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich.https://microbeatlas.org/MicrobeAtlas 1.0 beta
71585Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID12633.1StrainInfo: A central database for resolving microbial strain identifiers
117182Curators of the CIPCollection of Institut Pasteur (CIP 106784)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106784