Strain identifier

BacDive ID: 3017

Type strain: Yes

Species: Variovorax boronicumulans

Strain Designation: BAM-48

Strain history: <- H Miwa, Tokyo Univ.

NCBI tax ID(s): 1321609 (strain), 436515 (species)

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General

@ref: 15896

BacDive-ID: 3017

DSM-Number: 21722

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

description: Variovorax boronicumulans BAM-48 is an aerobe, mesophilic, Gram-negative bacterium that forms circular colonies and was isolated from soil.

NCBI tax id

NCBI tax idMatching level
436515species
1321609strain

strain history

@refhistory
15896<- NBRC <- H. Miwa, Biotechnol. Research Center, Univ. of Tokyo; BAM-48
67770I. Ahmed BAM-48.
67771<- H Miwa, Tokyo Univ.

doi: 10.13145/bacdive3017.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Betaproteobacteria
  • order: Burkholderiales
  • family: Comamonadaceae
  • genus: Variovorax
  • species: Variovorax boronicumulans
  • full scientific name: Variovorax boronicumulans Miwa et al. 2008

@ref: 15896

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Comamonadaceae

genus: Variovorax

species: Variovorax boronicumulans

full scientific name: Variovorax boronicumulans Miwa et al. 2008

strain designation: BAM-48

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
23100negative1.0-2.0 µm0.5-0.7 µmrod-shapedyes
67771negative

colony morphology

  • @ref: 23100
  • colony color: yellow
  • colony shape: circular
  • incubation period: 2 days
  • medium used: TSA plates

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
15896TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)yeshttps://mediadive.dsmz.de/medium/535Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water
23100nutrient agar (Difco)yes
23100TSA agaryes
23100TSA platesyes

culture temp

@refgrowthtypetemperaturerange
15896positivegrowth28mesophilic
23100positivegrowth4.0-37.0
23100nogrowth>45.0thermophilic
23100positiveoptimum30.0mesophilic
67770positivegrowth30mesophilic
67771positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
23100positivegrowth5.0-9.0alkaliphile
23100positiveoptimum7.0
23100nogrowth4.0
23100nogrowth10.0

Physiology and metabolism

oxygen tolerance

  • @ref: 67771
  • oxygen tolerance: aerobe

spore formation

  • @ref: 23100
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
23100NaClpositivegrowth0.0-1.0 %
23100NaClnogrowth>1.0 %(w/v)

observation

  • @ref: 67771
  • observation: quinones: Q-8

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2310017128adipate-assimilation
2310027613amygdalin-assimilation
2310017634D-glucose-assimilation
2310016024D-mannose-assimilation
2310017268myo-inositol-assimilation
2310017306maltose-assimilation
2310028053melibiose-assimilation
23100506227N-acetylglucosamine-assimilation
2310018401phenylacetate-assimilation
2310032032potassium gluconate-assimilation
2310026546rhamnose-assimilation
2310030911sorbitol-assimilation
2310017992sucrose-assimilation
2310027897tryptophan-assimilation
231005291gelatin-hydrolysis
2310017632nitrate-reduction
2310027689decanoate+assimilation
2310030849L-arabinose+assimilation
2310025115malate+assimilation
2310029864mannitol+assimilation
2310016947citrate+carbon source
2310028938ammonium+nitrogen source
6836925115malate-assimilation
6836917128adipate-assimilation
6836927689decanoate+assimilation
6836924265gluconate+assimilation
6836917306maltose-assimilation
6836959640N-acetylglucosamine-assimilation
6836916899D-mannitol+assimilation
6836930849L-arabinose+assimilation
6836917634D-glucose+assimilation
683695291gelatin-hydrolysis
683694853esculin-hydrolysis
6836916199urea+hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate-reduction

metabolite production

@refChebi-IDmetaboliteproduction
2310016136hydrogen sulfideno
2310015688acetoinyes
6836935581indoleno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testcitrate testindole test
2310015688acetoin+
2310016947citrate+
6836935581indole-

enzymes

@refvalueactivityec
23100acid phosphatase+3.1.3.2
23100alkaline phosphatase+3.1.3.1
23100alpha-chymotrypsin-3.4.21.1
23100alpha-fucosidase-3.2.1.51
23100alpha-galactosidase-3.2.1.22
23100alpha-glucosidase-3.2.1.20
23100alpha-mannosidase-3.2.1.24
23100arginine dihydrolase-3.5.3.6
23100beta-galactosidase-3.2.1.23
23100beta-glucosidase-3.2.1.21
23100beta-glucuronidase-3.2.1.31
23100catalase+1.11.1.6
23100cystine arylamidase-3.4.11.3
23100cytochrome oxidase+1.9.3.1
23100esterase (C 4)-
23100esterase lipase (C 8)+
23100leucine arylamidase+3.4.11.1
23100lipase (C 14)-
23100lysine decarboxylase-4.1.1.18
23100N-acetyl-beta-glucosaminidase-3.2.1.52
23100naphthol-AS-BI-phosphohydrolase-
23100ornithine decarboxylase-4.1.1.17
23100trypsin-3.4.21.4
23100tryptophan deaminase-4.1.99.1
23100urease-3.5.1.5
23100valine arylamidase-
68369cytochrome oxidase+1.9.3.1
68369gelatinase-
68369beta-glucosidase-3.2.1.21
68369urease+3.5.1.5
68369arginine dihydrolase-3.5.3.6

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
15896----+---+++/-+--++---++

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentenrichment cultureenrichment culture temperature
15896soilUniv. of Tokyo (Yayoi campus)JapanJPNAsia
23100soil collected in the experimental area of the University of Tokyotryptic soya agar (TSA;Difco)25.0
67770Soil in the University of TokyoTokyoJapanJPNAsia
67771From soilTokyoJapanJPNAsia

isolation source categories

Cat1Cat2Cat3
#Engineered#Built environment
#Environmental#Terrestrial#Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_2305.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_1;96_308;97_342;98_387;99_2305&stattab=map
  • Last taxonomy: Variovorax
  • 16S sequence: AB300597
  • Sequence Identity:
  • Total samples: 9717
  • soil counts: 3106
  • aquatic counts: 2157
  • animal counts: 2122
  • plant counts: 2332

Safety information

risk assessment

  • @ref: 15896
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Variovorax boronicumulans gene for 16S rRNA, partial sequence, strain: NBRC 103145AB6819541460ena1321609
15896Variovorax boronicumulans gene for 16S ribosomal RNA, partial sequenceAB3005971475ena1321609

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Variovorax boronicumulans NBRC 1031451321609.3wgspatric1321609
66792Variovorax boronicumulans NBRC 1031452731957647draftimg1321609
67770Variovorax boronicumulans NBRC 103145GCA_001591345contigncbi1321609

GC content

@refGC-contentmethod
2310071.2high performance liquid chromatography (HPLC)
6777171.0

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileyes87.997no
gram-positiveno98.48no
anaerobicno98.991yes
halophileno94.024yes
spore-formingno94.548no
glucose-utilyes52.391yes
aerobicyes96.315yes
flagellatedyes62.486no
thermophileno99.504no
glucose-fermentno89.874no

External links

@ref: 15896

culture collection no.: DSM 21722, KCTC 22010, NBRC 103145, JCM 18805, NCIMB 14573, BAM 48

straininfo link

  • @ref: 72539
  • straininfo: 397257

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny18175723Variovorax boronicumulans sp. nov., a boron-accumulating bacterium isolated from soil.Miwa H, Ahmed I, Yoon J, Yokota A, Fujiwara TInt J Syst Evol Microbiol10.1099/ijs.0.65315-02008Bacterial Typing Techniques, Base Composition, Boron/*metabolism, Comamonadaceae/*classification/genetics/*isolation & purification/physiology, DNA, Bacterial/analysis, Genes, rRNA, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Species SpecificityGenetics
Phylogeny21948092Variovorax defluvii sp. nov., isolated from sewage.Jin L, Kim KK, Ahn CY, Oh HMInt J Syst Evol Microbiol10.1099/ijs.0.035295-02011Bacterial Typing Techniques, Base Composition, Comamonadaceae/*classification/genetics/*isolation & purification, DNA, Bacterial/genetics, Fatty Acids/analysis, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Rivers/microbiology, Sequence Analysis, DNA, Sewage/*microbiologyGenetics
Phylogeny25504533Variovorax guangxiensis sp. nov., an aerobic, 1-aminocyclopropane-1-carboxylate deaminase producing bacterium isolated from banana rhizosphere.Gao JL, Yuan M, Wang XM, Qiu TL, Li JW, Liu HC, Li XA, Chen J, Sun JGAntonie Van Leeuwenhoek10.1007/s10482-014-0304-32014Bacterial Typing Techniques, Base Composition, Carbon-Carbon Lyases/*metabolism, China, Cluster Analysis, Comamonadaceae/*classification/enzymology/genetics/*isolation & purification, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Molecular Sequence Data, Musa, Nucleic Acid Hybridization, Phospholipids/analysis, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Rhizosphere, Sequence Analysis, DNA, *Soil MicrobiologyEnzymology

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
15896Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21722)https://www.dsmz.de/collection/catalogue/details/culture/DSM-21722
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
23100Hiroki Miwa,Iftikhar Ahmed,Jaewoo Yoon,Akira Yokota,Toru Fujiwara10.1099/ijs.0.65315-0Variovorax boronicumulans sp. nov., a boron-accumulating bacterium isolated from soilIJSEM 58: 286-289 200818175723
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/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
68369Automatically annotated from API 20NE
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
72539Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID397257.1StrainInfo: A central database for resolving microbial strain identifiers