Strain identifier

BacDive ID: 3818

Type strain: Yes

Species: Runella defluvii

Strain Designation: EMB13

Strain history: <- CO Jeon, Gyungsang Univ.

NCBI tax ID(s): 1123076 (strain), 370973 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 9.1 (current version):
version 9:
version 8.1:
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 9.1 (current version)

General

@ref: 7308

BacDive-ID: 3818

DSM-Number: 17976

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

description: Runella defluvii EMB13 is an aerobe, Gram-negative, rod-shaped bacterium that was isolated from activated sludge.

NCBI tax id

NCBI tax idMatching level
370973species
1123076strain

strain history

@refhistory
7308<- C. O. Jeon, Gyeongsang Nat. Univ. (GSNU), Jinju, Korea; EMB13
67771<- CO Jeon, Gyungsang Univ.

doi: 10.13145/bacdive3818.20240916.9.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Cytophagia
  • order: Cytophagales
  • family: Spirosomataceae
  • genus: Runella
  • species: Runella defluvii
  • full scientific name: Runella defluvii Lu et al. 2007

@ref: 7308

domain: Bacteria

phylum: Bacteroidetes

class: Cytophagia

order: Cytophagales

family: Spirosomaceae

genus: Runella

species: Runella defluvii

full scientific name: Runella defluvii Lu et al. 2007

strain designation: EMB13

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
32281negative4.1 µm0.7 µmrod-shapedno
67771rod-shapedno
67771negative
69480negative97.319

Culture and growth conditions

culture medium

  • @ref: 7308
  • 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

@refgrowthtypetemperature
7308positivegrowth25
32281positivegrowth15-40
32281positiveoptimum32.5
67771positivegrowth30-35

culture pH

@refabilitytypepHPH range
32281positivegrowth6.0-9.5alkaliphile
32281positiveoptimum7.75

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
32281aerobe
67771aerobe

observation

  • @ref: 67771
  • observation: quinones: MK-7

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
32281581435-dehydro-D-gluconate+carbon source
3228122599arabinose+carbon source
3228133984fucose+carbon source
3228128260galactose+carbon source
3228117754glycerol+carbon source
3228128087glycogen+carbon source
3228117716lactose+carbon source
3228129864mannitol+carbon source
3228137684mannose+carbon source
3228128053melibiose+carbon source
3228137657methyl D-glucoside+carbon source
3228117268myo-inositol+carbon source
3228116634raffinose+carbon source
3228126546rhamnose+carbon source
3228133942ribose+carbon source
3228117151xylitol+carbon source
3228118222xylose+carbon source
322814853esculin+hydrolysis

enzymes

@refvalueactivityec
32281acid phosphatase+3.1.3.2
32281alkaline phosphatase+3.1.3.1
32281alpha-galactosidase+3.2.1.22
32281catalase+1.11.1.6

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
7308activated sludgePohangRepublic of KoreaKORAsia
67771From a wastewater treatment plant in KoreaRepublic of KoreaKORAsia

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_151313.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_516;96_2585;97_3167;98_58392;99_151313&stattab=map
  • Last taxonomy: Runella defluvii subclade
  • 16S sequence: DQ372980
  • Sequence Identity:
  • Total samples: 75
  • aquatic counts: 20
  • animal counts: 55

Safety information

risk assessment

  • @ref: 7308
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 7308
  • description: Runella defluvii strain EMB13 16S ribosomal RNA gene, partial sequence
  • accession: DQ372980
  • length: 1427
  • database: nuccore
  • NCBI tax ID: 370973

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Runella defluvii DSM 17976GCA_014195535scaffoldncbi370973
66792Runella defluvii strain DSM 17976370973.3wgspatric370973
66792Runella defluvii DSM 179762827964551draftimg370973

GC content

  • @ref: 7308
  • GC-content: 40.1

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69480gram-positivegram-positivePositive reaction to Gram-stainingno97.319yes
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no96.02yes
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes88.607yes
69480spore-formingspore-formingAbility to form endo- or exosporesno87.469no
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno97.471yes
69480flagellatedmotile2+Ability to perform flagellated movementno84.5yes

External links

@ref: 7308

culture collection no.: DSM 17976, KCTC 12614

straininfo link

  • @ref: 73329
  • straininfo: 401913

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny17978225Runella defluvii sp. nov., isolated from a domestic wastewater treatment plant.Lu S, Lee JR, Ryu SH, Chung BS, Choe WS, Jeon COInt J Syst Evol Microbiol10.1099/ijs.0.65252-02007Bacterial Typing Techniques, Cytophagaceae/chemistry/*classification/genetics/*isolation & purification, DNA, Ribosomal/analysis, Genes, rRNA, Korea, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Water Microbiology, *Water PurificationEnzymology
Phylogeny27902287Runella palustris sp. nov., isolated from wetland freshwater.Kim H, Kang H, Joung Y, Joh KInt J Syst Evol Microbiol10.1099/ijsem.0.0016922017Bacterial Typing Techniques, Base Composition, Cytophagaceae/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Fresh Water/*microbiology, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry, *WetlandsTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
7308Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17976)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17976
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
32281Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2852128776041
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)
73329Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID401913.1StrainInfo: A central database for resolving microbial strain identifiers