Strain identifier

BacDive ID: 2318

Type strain: Yes

Species: Brevundimonas aveniformis

Strain Designation: EMB102

Strain history: <- CO Jeon, Gyungsang Univ.

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 7309

BacDive-ID: 2318

DSM-Number: 17977

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

description: Brevundimonas aveniformis EMB102 is a facultative aerobe, mesophilic, Gram-negative bacterium that was isolated from activated sludge.

NCBI tax id

NCBI tax idMatching level
370977species
1121123strain

strain history

@refhistory
7309<- C. O. Jeon, Gyeongsang Nat. Univ. (GSNU), Jinju, Korea; EMB102
67771<- CO Jeon, Gyungsang Univ.

doi: 10.13145/bacdive2318.20230509.8.1

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 aveniformis
  • full scientific name: Brevundimonas aveniformis Ryu et al. 2007

@ref: 7309

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhizobiales

family: Caulobacteraceae

genus: Brevundimonas

species: Brevundimonas aveniformis

full scientific name: Brevundimonas aveniformis Ryu et al. 2007

strain designation: EMB102

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
31972negative1.5 µm0.35 µmrod-shapedyes
67771negative
69480negative99.974

Culture and growth conditions

culture medium

  • @ref: 7309
  • name: R2A MEDIUM (DSMZ Medium 830)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/830
  • composition: Name: 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

culture temp

@refgrowthtypetemperaturerange
7309positivegrowth25mesophilic
31972positivegrowth15-35
31972positiveoptimum30mesophilic
67771positivegrowth25mesophilic

culture pH

@refabilitytypepHPH range
31972positivegrowth6.0-9.0alkaliphile
31972positiveoptimum8

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31972facultative aerobe
67771aerobe

spore formation

@refspore formationconfidence
69481no96
69480no99.993

halophily

@refsaltgrowthtested relationconcentration
31972NaClpositivegrowth0.0-1.0 %
31972NaClpositiveoptimum0.5 %

observation

  • @ref: 67771
  • observation: quinones: Q-10

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3197221217L-alaninamide+carbon source
3197216449alanine+carbon source
3197222653asparagine+carbon source
3197235391aspartate+carbon source
3197229987glutamate+carbon source
3197228087glycogen+carbon source
3197229864mannitol+carbon source
3197237684mannose+carbon source
3197217268myo-inositol+carbon source
3197226271proline+carbon source
3197215361pyruvate+carbon source
3197216634raffinose+carbon source
3197217822serine+carbon source
3197230031succinate+carbon source
3197226986threonine+carbon source
3197217632nitrate+reduction

enzymes

@refvalueactivityec
31972acid phosphatase+3.1.3.2
31972alkaline phosphatase+3.1.3.1
31972catalase+1.11.1.6
31972gelatinase+
31972cytochrome oxidase+1.9.3.1
31972urease+3.5.1.5

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
7309activated sludgePohangRepublic of KoreaKORAsia
67771From activated sludgeRepublic of KoreaKORAsia

isolation source categories

  • Cat1: #Engineered
  • Cat2: #Waste
  • Cat3: #Activated sludge

taxonmaps

  • @ref: 69479
  • File name: preview.99_6366.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_73;96_3023;97_3713;98_4705;99_6366&stattab=map
  • Last taxonomy: Brevundimonas aveniformis subclade
  • 16S sequence: DQ372984
  • Sequence Identity:
  • Total samples: 2796
  • soil counts: 628
  • aquatic counts: 1194
  • animal counts: 830
  • plant counts: 144

Safety information

risk assessment

  • @ref: 7309
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 7309
  • description: Brevundimonas aveniformis strain EMB102 16S ribosomal RNA gene, partial sequence
  • accession: DQ372984
  • length: 1403
  • database: ena
  • NCBI tax ID: 370977

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Brevundimonas aveniformis DSM 17977GCA_000428765scaffoldncbi1121123
66792Brevundimonas aveniformis DSM 179771121123.3wgspatric1121123
66792Brevundimonas aveniformis DSM 179772524614798draftimg1121123

GC content

  • @ref: 7309
  • GC-content: 64.1

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno96no
motileyes88.601yes
flagellatedno85.595no
gram-positiveno98.564no
anaerobicno98.13yes
aerobicyes79.247no
halophileno94.59yes
spore-formingno96.936no
glucose-utilyes54.563no
thermophileno94.025yes
glucose-fermentno90.562no

External links

@ref: 7309

culture collection no.: DSM 17977, KCTC 12609

straininfo link

  • @ref: 71875
  • straininfo: 401919

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny17625194Brevundimonas aveniformis sp. nov., a stalked species isolated from activated sludge.Ryu SH, Park M, Lee JR, Yun PY, Jeon COInt J Syst Evol Microbiol10.1099/ijs.0.64737-02007Bacterial Typing Techniques, Base Composition, Caulobacteraceae/chemistry/*classification/genetics/*isolation & purification, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Flagella, Genes, rRNA, Hydrogen-Ion Concentration, Locomotion, Microscopy, Electron, Transmission, Molecular Sequence Data, Names, Nucleic Acid Hybridization, Phospholipids/analysis, Phosphorus/metabolism, Phylogeny, Quinones/analysis, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Sewage/*microbiology, TemperatureGenetics
Phylogeny31596194Brevundimonas fluminis sp. nov., isolated from a river.Lee YW, Lee KH, Lee SY, Im WTInt J Syst Evol Microbiol10.1099/ijsem.0.0037362020Bacterial Typing Techniques, Base Composition, Caulobacteraceae/*classification/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Rivers/*microbiology, Sequence Analysis, DNA, Ubiquinone/analogs & derivatives/chemistry, *Water MicrobiologyTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
7309Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17977)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17977
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
31972Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2822728776041
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)
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
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
71875Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID401919.1StrainInfo: A central database for resolving microbial strain identifiers