Strain identifier

BacDive ID: 5567

Type strain: Yes

Species: Flavobacterium defluvii

Strain Designation: EMB 117

Strain history: CIP <- 2008, DSMZ <- C.O. Jeon, GSNU, Jinju, Korea: strain EMB 117

NCBI tax ID(s): 370979 (species)

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General

@ref: 7295

BacDive-ID: 5567

DSM-Number: 17963

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

description: Flavobacterium defluvii EMB 117 is a facultative anaerobe, mesophilic, Gram-negative bacterium that was isolated from activated sludge.

NCBI tax id

  • NCBI tax id: 370979
  • Matching level: species

strain history

@refhistory
7295<- C. O. Jeon, Gyeongsang Nat. Univ. (GSNU), Jinju, Korea; EMB 117
67771<- CO Jeon, Gyungsang Univ.
118867CIP <- 2008, DSMZ <- C.O. Jeon, GSNU, Jinju, Korea: strain EMB 117

doi: 10.13145/bacdive5567.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Flavobacteriia
  • order: Flavobacteriales
  • family: Flavobacteriaceae
  • genus: Flavobacterium
  • species: Flavobacterium defluvii
  • full scientific name: Flavobacterium defluvii Park et al. 2007

@ref: 7295

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Flavobacteriaceae

genus: Flavobacterium

species: Flavobacterium defluvii

full scientific name: Flavobacterium defluvii Park et al. 2007 emend. Chen et al. 2013

strain designation: EMB 117

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityflagellum arrangementconfidence
31931negative2.3-6.5 µm0.4-0.5 µmrod-shapedyesgliding
67771rod-shapedgliding
67771negative
69480negative99.994
118867negativerod-shapedno

pigmentation

  • @ref: 31931
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7295R2A MEDIUM (DSMZ Medium 830)yeshttps://mediadive.dsmz.de/medium/830Name: 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
33691MEDIUM 566- Reasoner's 2A agar for Flavobacterium micromatiyesDistilled water make up to (1000.000 ml);R2A agar (18.200 g)
118867CIP Medium 566yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=566

culture temp

@refgrowthtypetemperaturerange
7295positivegrowth25mesophilic
31931positivegrowth10-40
31931positiveoptimum27.5mesophilic
33691positivegrowth25mesophilic
62143positivegrowth30mesophilic
67771positivegrowth25-30mesophilic

culture pH

@refabilitytypepHPH range
31931positivegrowth5.0-10.0alkaliphile
31931positiveoptimum7.5

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31931facultative anaerobe
62143aerobe
67771aerobe
118867obligate aerobe

spore formation

@refspore formationconfidence
31931no
67771no
69481no100
69480no99.993

halophily

@refsaltgrowthtested relationconcentration
31931NaClpositivegrowth1 %
31931NaClpositiveoptimum0.5 %

observation

  • @ref: 67771
  • observation: quinones: MK-6

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3193122599arabinose+carbon source
3193128757fructose+carbon source
3193128260galactose+carbon source
3193117234glucose+carbon source
3193117716lactose+carbon source
3193129864mannitol+carbon source
3193137684mannose+carbon source
3193128053melibiose+carbon source
3193117268myo-inositol+carbon source
3193116634raffinose+carbon source
319314853esculin+hydrolysis
11886717632nitrate-reduction
11886716301nitrite-reduction

metabolite production

  • @ref: 118867
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
31931alkaline phosphatase+3.1.3.1
31931catalase+1.11.1.6
31931gelatinase+
68382alpha-fucosidase+3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase+3.2.1.52
68382beta-glucosidase+3.2.1.21
68382alpha-glucosidase+3.2.1.20
68382beta-glucuronidase+3.2.1.31
68382beta-galactosidase+3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin-3.4.21.4
68382cystine arylamidase+3.4.11.3
68382valine arylamidase+
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)+
68382esterase (C 4)+
68382alkaline phosphatase+3.1.3.1
118867oxidase+
118867catalase+1.11.1.6
118867urease-3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
118867-+++-+++--++-+++++-+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
7295activated sludgePohangRepublic of KoreaKORAsia
62143Activated sludgePohangRepublic of KoreaKORAsia
67771From activated sludgeRepublic of KoreaKORAsia
118867Environment, Activated sludge, domestic wastewater treatment plantPohangRepublic of KoreaKORAsia

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_2688.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_66;96_352;97_1709;98_2085;99_2688&stattab=map
  • Last taxonomy: Flavobacterium defluvii
  • 16S sequence: DQ372986
  • Sequence Identity:
  • Total samples: 147
  • soil counts: 26
  • aquatic counts: 89
  • animal counts: 23
  • plant counts: 9

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
72951Risk group (German classification)
1188671Risk group (French classification)

Sequence information

16S sequences

  • @ref: 7295
  • description: Flavobacterium defluvii strain EMB117 16S ribosomal RNA gene, partial sequence
  • accession: DQ372986
  • length: 1436
  • database: ena
  • NCBI tax ID: 370979

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Flavobacterium defluvii DSM 17963GCA_900129555scaffoldncbi370979
66792Flavobacterium defluvii strain DSM 17963370979.5wgspatric370979
66792Flavobacterium defluvii DSM 179632695420958draftimg370979

GC content

@refGC-contentmethod
729533.5high performance liquid chromatography (HPLC)
3193133.5

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno81.633no
flagellatedno93.934yes
gram-positiveno98.537yes
anaerobicno99.677yes
aerobicyes89.672no
halophileno96.177no
spore-formingno92.639yes
thermophileno99.58no
glucose-utilyes92.121no
glucose-fermentno89.213no

External links

@ref: 7295

culture collection no.: CCUG 59869, DSM 17963, CIP 109898, KCTC 12612

straininfo link

  • @ref: 75050
  • straininfo: 297198

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny17267956Flavobacterium defluvii sp. nov., isolated from activated sludge.Park M, Ryu SH, Vu TT, Ro HS, Yun PY, Jeon COInt J Syst Evol Microbiol10.1099/ijs.0.64669-02007Bacterial Typing Techniques, Base Composition, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis/chemistry, Flavobacterium/*classification/cytology/*isolation & purification/physiology, Genes, rRNA/genetics, Hydrogen-Ion Concentration, Korea, Molecular Sequence Data, Movement, Nucleic Acid Hybridization, Phosphatidylethanolamines/analysis/isolation & purification, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sewage/*microbiology, Temperature, Water MicrobiologyEnzymology
Phylogeny22611198Flavobacterium tilapiae sp. nov., isolated from a freshwater pond, and emended descriptions of Flavobacterium defluvii and Flavobacterium johnsoniae.Chen WM, Huang WC, Young CC, Sheu SYInt J Syst Evol Microbiol10.1099/ijs.0.041178-02012Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Flavobacterium/*classification/genetics/isolation & purification, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, Polyamines/analysis, Ponds/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Taiwan, Vitamin K 2/analogs & derivatives/analysis, *Water MicrobiologyGenetics
Phylogeny28920840Flavobacterium dispersum sp. nov., isolated from a freshwater spring.Chen WM, Su CL, Sheu SYInt J Syst Evol Microbiol10.1099/ijsem.0.0023052017Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Flavobacterium/*classification/genetics/isolation & purification, Fresh Water/*microbiology, Natural Springs/*microbiology, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Spermidine/chemistry, Taiwan, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny28984563Flavobacterium limi sp. nov., isolated from forest mud.Moya G, Yan ZF, Won KH, Yang JE, Kook MC, Yi THInt J Syst Evol Microbiol10.1099/ijsem.0.0023542017Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Flavobacterium/*classification/genetics/isolation & purification, *Forests, Glycolipids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny29498618Flavobacterium fluviatile sp. nov., isolated from a freshwater creek.Chen WM, Su CL, Young CC, Sheu SYInt J Syst Evol Microbiol10.1099/ijsem.0.0026592018Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Flavobacterium/*classification/genetics/isolation & purification, Fresh Water/*microbiology, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, Pigmentation, Polyamines/chemistry, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Taiwan, Vitamin K 2/analogs & derivatives/chemistry, *Water MicrobiologyTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
7295Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17963)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17963
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
31931Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2818828776041
33691Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7694
62143Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 59869)https://www.ccug.se/strain?id=59869
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
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
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
75050Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID297198.1StrainInfo: A central database for resolving microbial strain identifiers
118867Curators of the CIPCollection of Institut Pasteur (CIP 109898)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109898