Strain identifier

BacDive ID: 2298

Type strain: Yes

Species: Brevundimonas diminuta

Strain Designation: Pickett K-248

Strain history: CIP <- 1963, O. Lysenko, Inst. Biol., Prague, Czechoslovakia: strain CCEB 513, Pseudomonas diminuta

NCBI tax ID(s): 751586 (strain), 293 (species)

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General

@ref: 3069

BacDive-ID: 2298

DSM-Number: 7234

keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, mesophilic, motile, human pathogen

description: Brevundimonas diminuta Pickett K-248 is an obligate aerobe, mesophilic, motile human pathogen that was isolated from water.

NCBI tax id

NCBI tax idMatching level
751586strain
293species

strain history

@refhistory
3069<- LMG <- CCEB 513 <- NCTC <- E. Leifson
419971963, O. Lysenko, Inst. Biol., Prague, Czechoslovakia: strain CCEB 513, Pseudomonas diminuta
67770K. Komagata KS 0016 <-- AJ 2067 <-- ATCC 11568 <-- E. Leifson.
118936CIP <- 1963, O. Lysenko, Inst. Biol., Prague, Czechoslovakia: strain CCEB 513, Pseudomonas diminuta

doi: 10.13145/bacdive2298.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Caulobacterales
  • family: Caulobacteraceae
  • genus: Brevundimonas
  • species: Brevundimonas diminuta
  • full scientific name: Brevundimonas diminuta (Leifson and Hugh 1954) Segers et al. 1994

  • synonyms

    • @ref: 20215
    • synonym: Pseudomonas diminuta

@ref: 3069

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhizobiales

family: Caulobacteraceae

genus: Brevundimonas

species: Brevundimonas diminuta

full scientific name: Brevundimonas diminuta (Leifson and Hugh 1954) Segers et al. 1994

strain designation: Pickett K-248

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram stain
69480yes90.562
6948099.987negative
118936yesnegative

pigmentation

  • @ref: 118936
  • production: no
  • name: Pyocyanin

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
3069NUTRIENT AGAR (OXOID CM3) WITH PHOSPHATE (DSMZ Medium 605a)yeshttps://mediadive.dsmz.de/medium/605aName: NUTRIENT AGAR (OXOID CM3) WITH PHOSPHATE (DSMZ Medium 605a) Composition: Agar 15.0 g/l Peptone 5.0 g/l NaCl 5.0 g/l Na2HPO4 x 12 H2O 2.39 g/l Yeast extract 2.0 g/l Lab-Lemco beef extract 1.0 g/l KH2PO4 0.45 g/l Distilled water
41997MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
118936CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
3069positivegrowth26mesophilic
41997positivegrowth30mesophilic
67770positivegrowth30mesophilic
118936positivegrowth10-37
118936nogrowth5psychrophilic
118936nogrowth41thermophilic
118936nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 118936
  • oxygen tolerance: obligate aerobe

spore formation

@refspore formationconfidence
69481no93
69480no100

compound production

  • @ref: 3069
  • compound: Q10 coenzyme

halophily

  • @ref: 118936
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-8 %

observation

  • @ref: 67770
  • observation: quinones: Q-10

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6836925115malate+assimilation
6836917128adipate-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
11893616947citrate-carbon source
1189364853esculin-hydrolysis
11893617632nitrate-reduction
11893616301nitrite-reduction
11893615882phenol-degradation
11893617632nitrate-respiration

antibiotic resistance

  • @ref: 118936
  • 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
11893635581indoleno

metabolite tests

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

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
68382valine arylamidase-
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)+
68382esterase (C 4)+
68382alkaline phosphatase+3.1.3.1
68369cytochrome oxidase+1.9.3.1
68369gelatinase+
68369beta-glucosidase-3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6
118936oxidase+
118936beta-galactosidase-3.2.1.23
118936alcohol dehydrogenase-1.1.1.1
118936gelatinase+/-
118936amylase-
118936caseinase+3.4.21.50
118936catalase+1.11.1.6
118936tween esterase+
118936lecithinase-
118936lipase-
118936lysine decarboxylase-4.1.1.18
118936ornithine decarboxylase-4.1.1.17
118936phenylalanine ammonia-lyase-4.3.1.24
118936protease-
118936tryptophan deaminase-
118936urease-3.5.1.5

fatty acid profile

  • fatty acids

    @reffatty acidpercentageECL
    65600C14:01.414
    65600C15:00.915
    65600C16:029.916
    65600C17:00.817
    65600C18:00.418
    65600C12:0 3OH2.213.455
    65600C13:0 ISO 2OH1.613.814
    65600C15:1 ω8c0.214.792
    65600C16:1 ω7c1.915.819
    65600C17:1 ω6c0.316.862
    65600C17:1 ω8c0.616.792
    65600C18:1 2OH119.088
    65600C18:1 ω6c55.117.858
    65600C19:0 CYCLO ω8c4.418.9
    65600C20:2 ω6,9c0.319.735
  • type of FA analysis: whole cell analysis
  • method/protocol: CCUG

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
65600-+++-+--++++--------
118936-+++-+-+++++--------

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
65600------+----------+--+

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
118936---------------------------------------------------------------------------+--+---------++++++-----

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
3069water
118936Environment, WaterChicago, IllinoisUnited States of AmericaUSANorth America1953

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Aquatic

taxonmaps

  • @ref: 69479
  • File name: preview.99_3595.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_73;96_180;97_196;98_2755;99_3595&stattab=map
  • Last taxonomy: Brevundimonas diminuta
  • 16S sequence: AJ227778
  • Sequence Identity:
  • Total samples: 4000
  • soil counts: 454
  • aquatic counts: 792
  • animal counts: 2639
  • plant counts: 115

Safety information

risk assessment

@refpathogenicity humanbiosafety levelbiosafety level comment
3069yes, in single cases1Risk group (German classification)
1189361Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Brevundimonas diminuta partial 16S rRNA gene, type strain ATCC 11568TFR7754511334ena293
20218Pseudomonas diminuta 16S ribosomal RNAM590641445ena293
20218Brevundimonas diminuta gene for 16S rRNA, strain: IAM 12691AB0214151452ena293
20218Brevundimonas diminuta gene for 16S rRNA, partial sequence, strain: JCM 2788AB5947661385ena293
20218Brevundimonas diminuta DNA for 16S ribosomal RNA, strain LMG 2089 (T)AJ2277781418ena751586
20218Brevundimonas diminuta gene for 16S rRNA, partial sequence, strain: NBRC 12697AB6803251388ena293

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Brevundimonas diminuta ATCC 11568751586.3wgspatric751586
66792Brevundimonas diminuta strain NCTC8545293.17wgspatric293
66792Brevundimonas diminuta strain TVB1293.26wgspatric293
66792Brevundimonas diminuta ATCC 11568651285001draftimg751586
66792Brevundimonas diminuta NCTC 85452814123189draftimg293
67770Brevundimonas diminuta ATCC 11568GCA_000204035scaffoldncbi751586
67770Brevundimonas diminuta NCTC8545GCA_900445995contigncbi293

GC content

  • @ref: 67770
  • GC-content: 67.3
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno93no
motileyes89.149no
flagellatedno87.975no
gram-positiveno98.212no
anaerobicno95no
aerobicyes81.787no
halophileno94.964no
spore-formingno94.93no
glucose-utilyes55.221yes
thermophileno99.265yes
glucose-fermentno90.939yes

External links

@ref: 3069

culture collection no.: DSM 7234, ATCC 11568, CCEB 513, CCEB 516, CCM 2657, CCTM 1850, CCUG 1187, CCUG 1256, CCUG 1427, CECT 317, CIP 63.27, CNCTC Ps170/79, HNCMB 173005, IAM 1513, IMET 10409, JCM 2788, LMG 2088, LMG 2089, NCIB 9393, NCTC 8545, NRRL B-1496, USCC 1337, VKM B-893, AJ 2067, Hugh 342, Komagata KS 0016, BCRC 11894, CGMCC 1.1798, IAM 12691, IFO 12697, KCTC 12488, LMG 1793, NBRC 12697, NCIMB 9393, VKM B-1297

straininfo link

  • @ref: 71856
  • straininfo: 3530

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Metabolism405393Glucuronosyl diacylglycerol of Pseudomonas diminuta ATCC 11568. In vitro biosynthesis from UDP-glucuronate and diacylglycerol.Shaw JM, Pieringer RAJ Biol ChemS0021-9258(17)40277-81977Diglycerides/*biosynthesis, Glucuronosyltransferase/metabolism, Glycerides/*biosynthesis, Glycolipids/*biosynthesis, Pseudomonas/*metabolism, Structure-Activity Relationship, Temperature, Time Factors, Uridine Diphosphate Glucuronic Acid/*metabolism, Uridine Diphosphate Sugars/*metabolism
Cultivation2116781[Transfer of various markers in Lactobacilli during transformation of plasmid DNA and joint cultivation].Tiurin MV, Shenderov BA, Grigor'ev AE, Zhukov VG, Navashin SMAntibiot Khimioter1990Anti-Bacterial Agents/pharmacology, Culture Media, DNA, DNA, Bacterial/*genetics, DNA, Recombinant, Genetic Markers, Lactobacillus/drug effects/*genetics/growth & development, Lactobacillus casei/drug effects/genetics/growth & development, Nucleic Acid Hybridization, Plasmids/*genetics, *Transformation, GeneticPathogenicity
Pathogenicity2228245Cytokine induction by lipopolysaccharide (LPS) corresponds to lethal toxicity and is inhibited by nontoxic Rhodobacter capsulatus LPS.Loppnow H, Libby P, Freudenberg M, Krauss JH, Weckesser J, Mayer HInfect Immun10.1128/iai.58.11.3743-3750.19901990Animals, Cytokines/*biosynthesis, Leukocytes, Mononuclear/drug effects/metabolism, Lipopolysaccharides/chemistry/*toxicity, Mice, Mice, Inbred C57BL, Mortality, *Rhodobacter capsulatus/analysis, Structure-Activity RelationshipMetabolism
Phylogeny2777066Isolation of 9-hydroxy-delta-tetradecalactone from lipid A of Pseudomonas diminuta and Pseudomonas vesicularis.Arata S, Hirayama T, Kasai N, Itoh T, Ohsawa AFEMS Microbiol Lett10.1016/0378-1097(89)90512-01989Lactones/*isolation & purification, Lipid A/*analysis, Magnetic Resonance Spectroscopy, Mass Spectrometry, Molecular Structure, Pseudomonas/*analysisEnzymology
Enzymology3057331Structural heterogeneity regarding local Shwartzman activity of lipid A.Mashimo J, Tanaka C, Arata S, Akiyama Y, Hata S, Hirayama T, Egawa K, Kasai NMicrobiol Immunol10.1111/j.1348-0421.1988.tb01427.x1988Animals, Chromobacterium/analysis, Escherichia coli/analysis, Female, Lipid A/isolation & purification/*pharmacology, Molecular Structure, Pseudomonas/analysis, Rabbits, Salmonella/analysis, Shwartzman Phenomenon/*etiology, Structure-Activity RelationshipPhylogeny
Enzymology7054141Peptidoglycan of Rhodopseudomonas viridis: partial lack of N-acetyl substitution of glucosamine.Schmelzer E, Weckesser J, Warth R, Mayer HJ Bacteriol10.1128/jb.149.1.151-155.19821982Acetylation, Disaccharides/analysis, Glucosamine/analysis, Hydrolysis, Muramidase/pharmacology, Peptidoglycan/*analysis/isolation & purification, Rhodopseudomonas/*analysisPhylogeny
Pathogenicity15883180Brevundimonas diminuta infections and its resistance to fluoroquinolones.Han XY, Andrade RAJ Antimicrob Chemother10.1093/jac/dki1392005Adult, Aged, Base Sequence, DNA Gyrase/genetics, DNA Topoisomerase IV/genetics, Dipeptides/pharmacology, Drug Resistance, Bacterial, Female, Fluoroquinolones/*pharmacology, Humans, Male, Microbial Sensitivity Tests, Middle Aged, Molecular Sequence Data, Pseudomonas/*drug effects, Pseudomonas Infections/*drug therapyGenetics
Enzymology16914053Chemical resistance of the gram-negative bacteria to different sanitizers in a water purification system.Mazzola PG, Martins AM, Penna TCBMC Infect Dis10.1186/1471-2334-6-1312006*Disinfectants, Drug Industry, Gram-Negative Bacteria/*growth & development/metabolism, Water Purification/instrumentation/*methodsMetabolism
Phylogeny19643873Brevundimonas naejangsanensis sp. nov., a proteolytic bacterium isolated from soil, and reclassification of Mycoplana bullata into the genus Brevundimonas as Brevundimonas bullata comb. nov.Kang SJ, Choi NS, Choi JH, Lee JS, Yoon JH, Song JJInt J Syst Evol Microbiol10.1099/ijs.0.011700-02009Brucellaceae/*classification/genetics/isolation & purification/metabolism, Caulobacteraceae/*classification/genetics/*isolation & purification/metabolism, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/chemistry/metabolism, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Soil MicrobiologyMetabolism
Phylogeny19880635Brevundimonas vancanneytii sp. nov., isolated from blood of a patient with endocarditis.Estrela AB, Abraham WRInt J Syst Evol Microbiol10.1099/ijs.0.015651-02009Blood/*microbiology, Caulobacteraceae/*classification/genetics/*isolation & purification/metabolism, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Endocarditis/*microbiology, Fatty Acids/metabolism, Gram-Negative Bacterial Infections/*microbiology, Humans, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/geneticsMetabolism

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
3069Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 7234)https://www.dsmz.de/collection/catalogue/details/culture/DSM-7234
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
41997Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/10034
65600Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 1427)https://www.ccug.se/strain?id=1427
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
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
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
71856Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID3530.1StrainInfo: A central database for resolving microbial strain identifiers
118936Curators of the CIPCollection of Institut Pasteur (CIP 63.27)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%2063.27