Strain identifier

BacDive ID: 2297

Type strain: No

Species: Brevundimonas diminuta

Strain history: CIP <- 1987, NCIB, Pseudomonas diminuta <- C.R.S. Byrne <- ATCC <- FDA: strain PCI 818, Pseudomonas sp. <- F. Bowman

NCBI tax ID(s): 293 (species)

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General

@ref: 839

BacDive-ID: 2297

DSM-Number: 1635

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

description: Brevundimonas diminuta DSM 1635 is an obligate aerobe, mesophilic, Gram-negative bacterium that has multiple antibiotic resistances and was isolated from Contaminant.

NCBI tax id

  • NCBI tax id: 293
  • Matching level: species

strain history

@refhistory
839<- ATCC <- FDA; PCI 818 <- F. Bowman
67770ATCC 19146 <-- FDA strain PCI 818 <-- F. Bowman.
118937CIP <- 1987, NCIB, Pseudomonas diminuta <- C.R.S. Byrne <- ATCC <- FDA: strain PCI 818, Pseudomonas sp. <- F. Bowman

doi: 10.13145/bacdive2297.20250331.9.3

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: 839

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

type strain: no

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
118937negativerod-shapedno
125439negative94
125438negative97

pigmentation

  • @ref: 118937
  • production: no
  • name: Pyocyanin

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
839NUTRIENT AGAR (DSMZ Medium 1)yeshttps://mediadive.dsmz.de/medium/1Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
42085MEDIUM 29- Brain heart agaryesDistilled water make up to (1000.000 ml);Brain heart infusion agar (52.000 g)
118937CIP Medium 29yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=29

culture temp

@refgrowthtypetemperature
839positivegrowth28
42085positivegrowth30
67770positivegrowth37
118937positivegrowth10-37
118937nogrowth5
118937nogrowth41
118937nogrowth45

Physiology and metabolism

oxygen tolerance

  • @ref: 118937
  • oxygen tolerance: obligate aerobe

antibiogram

  • @ref: 839
  • medium: Mueller-Hinton Agar
  • Penicillin G: 0
  • oxacillin: 0
  • ampicillin: 0
  • ticarcillin: 30
  • mezlocillin: 30
  • cefalotin: 14
  • cefazolin: 0
  • cefotaxime: 30
  • aztreonam: 0
  • imipenem: 32
  • tetracycline: 40
  • chloramphenicol: 38-40
  • gentamycin: 20
  • amikacin: 22
  • vancomycin: 12
  • erythromycin: 18
  • lincomycin: 0
  • ofloxacin: 12
  • norfloxacin: 0
  • colistin: 0
  • pipemidic acid: 0
  • nitrofurantoin: 0
  • bacitracin: 18
  • polymyxin b: 10
  • kanamycin: 40-42
  • neomycin: 22
  • doxycycline: 46
  • ceftriaxone: 26-28
  • clindamycin: 10
  • fosfomycin: 30
  • moxifloxacin: 16-18
  • linezolid: 26-28
  • nystatin: 0
  • quinupristin/dalfopristin: 0
  • teicoplanin: 0
  • piperacillin/tazobactam: 34

spore formation

  • @ref: 125439
  • spore formation: no
  • confidence: 90.1

halophily

@refsaltgrowthtested relationconcentration
118937NaClpositivegrowth0-2 %
118937NaClnogrowth4 %
118937NaClnogrowth6 %
118937NaClnogrowth8 %
118937NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
11893717632nitrate-reduction
11893716301nitrite-reduction
11893717632nitrate-respiration
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

metabolite production

@refChebi-IDmetaboliteproduction
6836935581indoleno
11893735581indoleno

metabolite tests

@refChebi-IDmetaboliteindole testvoges-proskauer-test
6836935581indole-
11893715688acetoin-

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382beta-glucosidase-3.2.1.21
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase-3.2.1.20
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase-3.2.1.23
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 (C 4)+
68382esterase lipase (C 8)+
68382alkaline phosphatase+3.1.3.1
118937oxidase+
118937beta-galactosidase-3.2.1.23
118937alcohol dehydrogenase-1.1.1.1
118937gelatinase-
118937amylase-
118937DNase-
118937caseinase-3.4.21.50
118937catalase+1.11.1.6
118937tween esterase-
118937lecithinase-
118937lysine decarboxylase-4.1.1.18
118937ornithine decarboxylase-4.1.1.17
118937phenylalanine ammonia-lyase-4.3.1.24
118937tryptophan deaminase-
118937urease-3.5.1.5
68382acid phosphatase+3.1.3.2
68369cytochrome oxidase+1.9.3.1
68369gelatinase-
68369beta-glucosidase-3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6

fatty acid profile

  • fatty acids

    @reffatty acidpercentageECL
    48015C14:01.414
    48015C15:01.415
    48015C16:027.216
    48015C17:0117
    48015C12:0 3OH2.513.455
    48015C13:0 ISO 2OH2.213.814
    48015C16:1 ω7c1.915.819
    48015C17:1 ω8c1.216.792
    48015C18:1 ω7c /12t/9t56.817.824
    48015C19:0 CYCLO ω8c3.618.9
    48015Unidentified0.9
  • 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
48015-+++-+--++++--------
118937-+++-+--++++-----+--

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
48015--------------------+

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
118937----------------------------------------------------------------------------------------+----++----

Isolation, sampling and environmental information

isolation

@refsample typehost species
48015Contaminant
67770Found as a contaminant in a culture of Bacillus cereusBacillus cereus
118937Other, Contaminant of Bacillus cereus culture

isolation source categories

Cat1Cat2Cat3
#Engineered#Contamination
#Engineered#Laboratory#Contaminant

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: LC383926
  • 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
839yes, in single cases1Risk group (German classification)
1189371Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Brevundimonas diminuta strain ATCC 19146 16S ribosomal RNA gene, partial sequenceDQ650706434nuccore293
20218Brevundimonas diminuta strain ATCC 19146 16S ribosomal RNA gene, partial sequenceEU4970531339nuccore293
20218B.diminuta 16S rRNA geneX872741456nuccore293
67770Brevundimonas diminuta JCM 2428 gene for 16S ribosomal RNA, partial sequenceLC3839261385nuccore293
124043Brevundimonas diminuta gene for 16S rRNA, partial sequence, strain: NBRC 14213.AB6805921388nuccore293

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Brevundimonas diminuta strain ATCC(B) 19146 strain ATCC(B) 19146 strain ATCC(B) 19146293.22completepatric293
66792Brevundimonas diminuta strain NBRC 14213293.23wgspatric293
67770Brevundimonas diminuta NBRC 14213GCA_006539485contigncbi293
67770Brevundimonas diminuta strain ATCC(B) 19146 chromosome, complete genomeCP035093ncbi293

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingno97no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no85.906no
125438spore-formingspore-formingAbility to form endo- or exosporesno89.321no
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes85.058yes
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno97.5yes
125438motile2+flagellatedAbility to perform flagellated movementyes59.428no
125439BacteriaNetspore_formationAbility to form endo- or exosporesno90.1
125439BacteriaNetmotilityAbility to perform movementyes72.2
125439BacteriaNetgram_stainReaction to gram-stainingnegative94
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthaerobe88.6

External links

@ref: 839

culture collection no.: DSM 1635, ATCC 19146, CCUG 24715, LMG 10743, CCM 4623, PCI 818, JCM 2428, CECT 313, CGMCC 1.8867, CIP 103020, IFO 14213, NBRC 14213, NCIMB 11091

straininfo link

  • @ref: 71855
  • straininfo: 265207

literature

topicPubmed-IDtitleauthorsjournalyearmeshtopic2DOI
Enzymology1457036[RoTrac capillary pore membranes for laboratory filtration. II. Bacteria-free filtration].Gemende B, Heinrich B, Selassie GG, Knaack D, Witzleb WZentralbl Hyg Umweltmed1992Colony Count, Microbial, Filtration/*instrumentation, *Membranes, Artificial, Mycoplasma/growth & development/*isolation & purification, Pseudomonas/growth & development/*isolation & purificationPhylogeny
7780747Microbial retention characteristics of 0.2-microns-rated nylon membrane filters during filtration of high viscosity fluids at high differential pressure and varied temperatures.Aranha H, Meeker JPDA J Pharm Sci Technol1995Membranes, Artificial, Nylons, Pressure, Pseudomonas, Sterilization/*instrumentation, Temperature, Ultrafiltration/*instrumentation, Viscosity
Enzymology8696777Evaluation of recovery filters for use in bacterial retention testing of sterilizing-grade filters.Carter JPDA J Pharm Sci Technol1996*Filtration, Pseudomonas/*isolation & purification, SterilizationPhylogeny
Cultivation11766824Method for qualifying microbial removal performance of 0.1 micron rated filters. Part III: bacterial challenge tests on 0.2/0.22 and 0.1 micron rated filter cartridges with Hydrogenophaga (formerly Pseudomonas) pseudoflava.Sundaram S, Eisenhuth J, Lewis M, Howard G Jr, Brandwein HPDA J Pharm Sci Technol2001Acholeplasma/physiology, Bacteriological Techniques/methods/standards, Betaproteobacteria/growth & development/*isolation & purification/physiology, Caulobacter/physiology, Cellulose/*analogs & derivatives, Culture Media, *Drug Contamination/prevention & control, Micropore Filters, Nylons, Polyvinyls, Sterilization/*methods/*standards, Ultrafiltration/*methodsEnzymology
Cultivation11977409Changes in the cell size of Brevundimonas diminuta using different growth agitation rates.Lee SH, Lee SS, Kim CWPDA J Pharm Sci Technol2002Bacteriological Techniques, Caulobacter/*cytology/growth & development, Culture Media, Micropore Filters/standards, Microscopy, Electron, Scanning, Particle Size, Ultrafiltration, Vibration
Enzymology20495940Quantitative real-time PCR and fluorescence in situ hybridization approaches for enumerating Brevundimonas diminuta in drinking water.Donofrio RS, Bestervelt LL, Saha R, Bagley STJ Ind Microbiol Biotechnol2010Bacterial Load/*methods, Bacterial Proteins/genetics, Caulobacteraceae/*isolation & purification, DNA Gyrase/genetics, In Situ Hybridization, Fluorescence/*methods, Polymerase Chain Reaction/*methods, Sensitivity and Specificity, Sigma Factor/genetics, *Water Microbiology, *Water SupplyPhylogeny10.1007/s10295-010-0738-1
21502070The importance of accurate microorganism identification in microbial challenge tests of membrane filters--part I.Kaesler I, Haake G, Hennig H, Rosenhagen A, Meltzer TH, Jornitz MWPDA J Pharm Sci Technol2011Bacteria, Filtration, Microbial Sensitivity Tests, Micropore Filters, *Sterilization, *Ultrafiltration65/2/92
22767883The Importance of Accurate Microorganism Identification in Microbial Challenge Tests of Membrane Filters. Part II. The Comparison of Hydrogenophaga pseudoflava ATTC 33668 and Curvibacter sp. ATCC 700892 by Microbial Challenge Tests with Membrane Filters.Haake G, Kaesler-Neumann I, Hennig H, Meltzer TH, Jornitz MWPDA J Pharm Sci Technol2012Colony Count, Microbial, Comamonadaceae, *Filtration, Microbial Sensitivity Tests, Micropore Filters, Sterilization, *Ultrafiltration10.5731/pdajpst.2012.00876
Enzymology28073586Experimental comparison of point-of-use filters for drinking water ultrafiltration.Totaro M, Valentini P, Casini B, Miccoli M, Costa AL, Baggiani AJ Hosp Infect2016Caulobacteraceae/isolation & purification, Drinking Water/*microbiology, *Point-of-Care Systems, Pseudomonas aeruginosa/isolation & purification, Ultrafiltration/*methods, Water Purification/*methodsPhylogeny10.1016/j.jhin.2016.11.017

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
839Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 1635)https://www.dsmz.de/collection/catalogue/details/culture/DSM-1635
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
42085Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/14771
48015Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 24715)https://www.ccug.se/strain?id=24715
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
71855Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID265207.1StrainInfo: A central database for resolving microbial strain identifiers
118937Curators of the CIPCollection of Institut Pasteur (CIP 103020)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103020
124043Isabel Schober, Julia KoblitzData extracted from sequence databases, automatically matched based on designation and taxonomy
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