Strain identifier

BacDive ID: 1574

Type strain: Yes

Species: Bacteriovorax stolpii

Strain Designation: UKi2

Strain history: <- ATCC <- M. P. Starr, ICPB <- S. F. Conti; UKi2

NCBI tax ID(s): 960 (species)

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General

@ref: 4813

BacDive-ID: 1574

DSM-Number: 12778

keywords: genome sequence, 16S sequence, Bacteria, Gram-negative

description: Bacteriovorax stolpii UKi2 is a Gram-negative bacterium of the family Bacteriovoracaceae.

NCBI tax id

  • NCBI tax id: 960
  • Matching level: species

strain history

  • @ref: 4813
  • history: <- ATCC <- M. P. Starr, ICPB <- S. F. Conti; UKi2

doi: 10.13145/bacdive1574.20250331.9.3

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Oligoflexia
  • order: Bacteriovoracales
  • family: Bacteriovoracaceae
  • genus: Bacteriovorax
  • species: Bacteriovorax stolpii
  • full scientific name: Bacteriovorax stolpii (Seidler et al. 1972) Baer et al. 2000

  • synonyms

    @refsynonym
    20215Bacteriolyticum stolpii
    20215Bdellovibrio stolpii

@ref: 4813

domain: Bacteria

phylum: Proteobacteria

class: Oligoflexia

order: Bdellovibrionales

family: Bacteriovoracaceae

genus: Bacteriovorax

species: Bacteriovorax stolpii

full scientific name: Bacteriovorax stolpii (Seidler et al. 1972) Baer et al. 2000

strain designation: UKi2

type strain: yes

Morphology

cell morphology

@refgram stainconfidence
23067negative
125439negative99
125438negative99.158

Culture and growth conditions

culture medium

  • @ref: 4813
  • name: BDELLOVIBRIO BACTERIOVORUS MEDIUM (DSMZ Medium 844)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/844
  • composition: Name: BDELLOVIBRIO BACTERIOVORUS MEDIUM (DSMZ Medium 844) Composition: Agar 12.0 g/l Proteose peptone no. 3 1.0 g/l MgCl2 x 6 H2O 0.6 g/l CaCl2 x 2 H2O 0.3 g/l Yeast extract 0.3 g/l Distilled water

culture temp

@refgrowthtypetemperature
23067positiveoptimum15.0-35.0
4813positivegrowth30

Physiology and metabolism

oxygen tolerance

  • @ref: 125439
  • oxygen tolerance: obligate aerobe
  • confidence: 91.1

spore formation

  • @ref: 125439
  • spore formation: no
  • confidence: 98.4

antibiotic resistance

@refChEBImetaboliteis antibioticis sensitive
2306717833gentamicinyesyes
230676104kanamycinyesyes
230676827methicillinyesyes
23067100147nalidixic acidyesyes
230677507neomycinyesyes
2306717334penicillinyesyes
2306717076streptomycinyesyes
2306728001vancomycinyesyes

enzymes

@refvalueactivityec
23067catalase+1.11.1.6
23067cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

taxonmaps

  • @ref: 69479
  • File name: preview.99_98257.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15795;96_40015;97_51031;98_67254;99_98257&stattab=map
  • Last taxonomy: Bacteriovorax stolpii subclade
  • 16S sequence: AJ288899
  • Sequence Identity:
  • Total samples: 219
  • soil counts: 7
  • aquatic counts: 39
  • animal counts: 168
  • plant counts: 5

Safety information

risk assessment

  • @ref: 4813
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Bdellovibrio bacteriovorus 16S rRNA gene, partial cdsM61239752nuccore960
4813Bdellovibrio stolpii 16S rRNA gene, strain DSM 12778AJ2888991371nuccore960

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Bacteriovorax stolpii DSM 12778GCA_002872415completencbi960
66792Bacteriovorax stolpii DSM 12778GCA_004362635scaffoldncbi960
66792Bacteriovorax stolpii strain DSM 12778960.3patric960
66792Bacteriovorax stolpii strain DSM 12778960.4wgspatric960
66792Bacteriovorax stolpii DSM 127782756170350draftimg960
66792Bacteriovorax stolpii UKi22802429278completeimg960

GC content

  • @ref: 23067
  • GC-content: 41.8

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingno99.158yes
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no79.319no
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes70.585no
125438spore-formingspore-formingAbility to form endo- or exosporesno85.706no
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno91.613yes
125438motile2+flagellatedAbility to perform flagellated movementyes53.34no
125439BacteriaNetspore_formationAbility to form endo- or exosporesno98.4
125439BacteriaNetmotilityAbility to perform movementno61.9
125439BacteriaNetgram_stainReaction to gram-stainingnegative99
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate aerobe91.1

External links

@ref: 4813

culture collection no.: DSM 12778, ATCC 27052, DSM 50722, ICPB 3291

straininfo link

  • @ref: 71219
  • straininfo: 45782

literature

Pubmed-IDtitleauthorsjournalDOIyearmeshtopictopic2
20094810Chemical structure of Bacteriovorax stolpii lipid A.Beck S, Muller FD, Strauch E, Brecker L, Linscheid MWLipids10.1007/s11745-010-3383-62010Deltaproteobacteria/*chemistry, Fatty Acids/analysis, Lipid A/*chemistry, Nuclear Magnetic Resonance, Biomolecular, Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
21984111Bacterial predators possess unique membrane lipid structures.Muller FD, Beck S, Strauch E, Linscheid MWLipids10.1007/s11745-011-3614-52011Antibiosis/physiology, Bdellovibrio/*chemistry, Cell Wall/*chemistry, Chromatography, High Pressure Liquid, Chromatography, Thin Layer, Deltaproteobacteria/*chemistry, Glutamates/metabolism, Glycerophospholipids/analysis, Membrane Lipids/*analysis, Phosphatidylethanolamines/analysis, Sphingolipids/analysis, Tandem Mass Spectrometry, Threonine/analogs & derivatives/analysisProteomeMetabolism

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
4813Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 12778)https://www.dsmz.de/collection/catalogue/details/culture/DSM-12778
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
23067M. L. Baer,J. Ravel,J. Chun,R. T. Hill,H. N. Williams10.1099/00207713-50-1-219A proposal for the reclassification of Bdellovibrio stolpii and Bdellovibrio starrii into a new genus, Bacteriovorax gen. nov. as Bacteriovorax stolpii comb. nov. and Bacteriovorax starrii comb. nov., respectively.IJSEM 50: 219-224 200010826807
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
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
71219Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID45782.1StrainInfo: A central database for resolving microbial strain identifiers
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