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)

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General

@ref: 7308

BacDive-ID: 3818

DSM-Number: 17976

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

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

NCBI tax id

NCBI tax idMatching level
1123076strain
370973species

strain history

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

doi: 10.13145/bacdive3818.20230509.8.1

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 shapemotility
32281negative4.1 µm0.7 µmrod-shapedno
67771rod-shapedno
67771negative

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

@refgrowthtypetemperaturerange
7308positivegrowth25mesophilic
32281positivegrowth15-40
32281positiveoptimum32.5mesophilic
67771positivegrowth30-35mesophilic

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: ena
  • 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

traitpredictionconfidencetraining_data
flagellatedno97.261yes
gram-positiveno97.745yes
anaerobicno99.306yes
aerobicyes88.336no
halophileno96.894no
spore-formingno94.512no
glucose-utilyes84.024no
thermophileno98.25yes
motileno93.307yes
glucose-fermentno88.038no

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
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