Strain identifier

BacDive ID: 5569

Type strain: Yes

Species: Flavobacterium filum

Strain Designation: EMB 34, EMB34

Strain history: CIP <- 2007, KCTC <- C.O. Jeon, Korea Univ., Seoul, Korea: strain EMB34

NCBI tax ID(s): 1121889 (strain), 370974 (species)

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General

@ref: 7293

BacDive-ID: 5569

DSM-Number: 17961

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

description: Flavobacterium filum EMB 34 is a facultative anaerobe, mesophilic, Gram-negative bacterium that was isolated from activated sludge.

NCBI tax id

NCBI tax idMatching level
370974species
1121889strain

strain history

@refhistory
7293<- C. O. Jeon, Gyeongsang Nat. Univ. (GSNU), Jinju, Korea; EMB 34
67771<- CO Jeon, Gyungsang Univ.
119349CIP <- 2007, KCTC <- C.O. Jeon, Korea Univ., Seoul, Korea: strain EMB34

doi: 10.13145/bacdive5569.20230509.8.1

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 filum
  • full scientific name: Flavobacterium filum Ryu et al. 2007

@ref: 7293

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Flavobacteriaceae

genus: Flavobacterium

species: Flavobacterium filum

full scientific name: Flavobacterium filum Ryu et al. 2007 emend. Li et al. 2014

strain designation: EMB 34, EMB34

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
32214negative1.55 µm0.55 µmrod-shapedno
67771rod-shapedno
67771negative
69480negative99.999
119349negativerod-shapedno

pigmentation

  • @ref: 32214
  • production: no

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7293R2A 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
37833MEDIUM 566- Reasoner's 2A agar for Flavobacterium micromatiyesDistilled water make up to (1000.000 ml);R2A agar (18.200 g)
119349CIP Medium 566yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=566

culture temp

@refgrowthtypetemperaturerange
7293positivegrowth25mesophilic
32214positivegrowth10-40
32214positiveoptimum30mesophilic
37833positivegrowth30mesophilic
67771positivegrowth25-32mesophilic

culture pH

@refabilitytypepHPH range
32214positivegrowth6.0-9.5alkaliphile
32214positiveoptimum7.75

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
32214facultative anaerobe
67771aerobe
119349obligate aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.994

halophily

  • @ref: 32214
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: <2 %

observation

@refobservation
32214aggregates in clumps
67771quinones: MK-6

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3221417234glucose+carbon source
3221417716lactose+carbon source
3221428053melibiose+carbon source
3221417268myo-inositol+carbon source
3221416634raffinose+carbon source
3221417632nitrate+reduction
11934917632nitrate+reduction
11934916301nitrite-reduction

metabolite production

  • @ref: 119349
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
32214alkaline phosphatase+3.1.3.1
32214catalase+1.11.1.6
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
119349oxidase+
119349catalase+1.11.1.6
119349urease-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
119349-+++-++-+-++---+-+--

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
7293activated sludgePohangRepublic of KoreaKORAsia
67771From activated sludgeRepublic of KoreaKORAsia
119349Environment, Wastewater, treatment plant, that performed enhanced biological phosphorus removalSeoulRepublic of KoreaKORAsia

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_151314.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_66;96_1199;97_1414;98_1721;99_151314&stattab=map
  • Last taxonomy: Flavobacterium filum subclade
  • 16S sequence: DQ372981
  • Sequence Identity:
  • Total samples: 20
  • aquatic counts: 18
  • animal counts: 2

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
72931Risk group (German classification)
1193491Risk group (French classification)

Sequence information

16S sequences

  • @ref: 7293
  • description: Flavobacterium filum strain EMB34 16S ribosomal RNA gene, partial sequence
  • accession: DQ372981
  • length: 1436
  • database: ena
  • NCBI tax ID: 1121889

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Flavobacterium filum DSM 17961GCA_000425465scaffoldncbi1121889
66792Flavobacterium filum DSM 179611121889.3wgspatric1121889
66792Flavobacterium filum DSM 179612523533606draftimg1121889

GC content

@refGC-contentmethod
729334.2high performance liquid chromatography (HPLC)
3221434.2

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno90.551yes
flagellatedno95.408yes
gram-positiveno98.809yes
anaerobicno98.912yes
aerobicyes78.403no
halophileno86.446no
spore-formingno96.209no
thermophileno96.877yes
glucose-utilyes87.313yes
glucose-fermentno89.846no

External links

@ref: 7293

culture collection no.: DSM 17961, KCTC 12610, CIP 109743

straininfo link

  • @ref: 75052
  • straininfo: 309532

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny17766867Flavobacterium filum sp. nov., isolated from a wastewater treatment plant in Korea.Ryu SH, Park M, Jeon Y, Lee JR, Park W, Jeon COInt J Syst Evol Microbiol10.1099/ijs.0.65138-02007Bacterial Typing Techniques, Base Composition, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Flavobacterium/*classification/genetics/*isolation & purification/physiology, Genes, rRNA, Hydrogen-Ion Concentration, Korea, Molecular Sequence Data, Phospholipids/analysis, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Temperature, *Water Microbiology, Water PurificationEnzymology
Phylogeny24425814Flavobacterium lacus sp. nov., isolated from a high-altitude lake, and emended description of Flavobacterium filum.Li A, Liu H, Sun B, Zhou Y, Xin YInt J Syst Evol Microbiol10.1099/ijs.0.056689-02013*Altitude, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Flavobacterium/*classification/genetics/isolation & purification, Lakes/*microbiology, Likelihood Functions, Molecular Sequence Data, Nucleic Acid Hybridization, Phosphatidylethanolamines/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Tibet, Vitamin K 2/analogs & derivatives/chemistryGenetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
7293Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17961)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17961
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
32214Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2845628776041
37833Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7520
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
75052Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID309532.1StrainInfo: A central database for resolving microbial strain identifiers
119349Curators of the CIPCollection of Institut Pasteur (CIP 109743)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109743