Strain identifier

BacDive ID: 5579

Type strain: Yes

Species: Flavobacterium fluvii

Strain Designation: H7

Strain history: CIP <- 2010, DSMZ <- C.O. Jeon, GNU, Jinju, Korea: strain H7

NCBI tax ID(s): 468056 (species)

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General

@ref: 8350

BacDive-ID: 5579

DSM-Number: 19978

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

description: Flavobacterium fluvii H7 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from stream sediment.

NCBI tax id

  • NCBI tax id: 468056
  • Matching level: species

strain history

@refhistory
8350<- C. O. Jeon, Gyeongsang Natl. Univ. (GNU), Jinju, Korea; H7
119416CIP <- 2010, DSMZ <- C.O. Jeon, GNU, Jinju, Korea: strain H7

doi: 10.13145/bacdive5579.20230509.8.1

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 fluvii
  • full scientific name: Flavobacterium fluvii Lee et al. 2010

@ref: 8350

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Flavobacteriaceae

genus: Flavobacterium

species: Flavobacterium fluvii

full scientific name: Flavobacterium fluvii Lee et al. 2010

strain designation: H7

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
29321negative2.5 µm0.8 µmrod-shapedno
69480negative99.999
119416negativerod-shapedno

pigmentation

  • @ref: 29321
  • production: no

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
8350R2A 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
42060MEDIUM 566- Reasoner's 2A agar for Flavobacterium micromatiyesDistilled water make up to (1000.000 ml);R2A agar (18.200 g)
119416CIP Medium 566yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=566

culture temp

@refgrowthtypetemperaturerange
8350positivegrowth28mesophilic
29321positivegrowth15-35
29321positiveoptimum27.5mesophilic
42060positivegrowth25mesophilic

culture pH

@refabilitytypepH
29321positivegrowth06-08
29321positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 29321
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.998

halophily

  • @ref: 29321
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: <1 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2932122599arabinose+carbon source
2932117234glucose+carbon source
2932117306maltose+carbon source
2932137684mannose+carbon source
293214853esculin+hydrolysis
11941617632nitrate-reduction
11941616301nitrite-reduction

metabolite production

  • @ref: 119416
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
29321acid phosphatase+3.1.3.2
29321alkaline phosphatase+3.1.3.1
29321catalase+1.11.1.6
29321cytochrome oxidase+1.9.3.1
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
119416oxidase+
119416catalase+1.11.1.6
119416urease-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
119416-++-------++-+-+----

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitude
8350stream sedimentGazwa stream, Jinju city (35° 11' N 128° 05' E)Republic of KoreaKORAsia35.1833128.083
119416Environment, Stream sediment from the Gazwa streamJinjuRepublic of KoreaKORAsia

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Aquatic
  • Cat3: #Sediment

taxonmaps

  • @ref: 69479
  • File name: preview.99_1384.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_66;96_799;97_933;98_1093;99_1384&stattab=map
  • Last taxonomy: Flavobacterium fluvii
  • 16S sequence: EU109724
  • Sequence Identity:
  • Total samples: 2103
  • soil counts: 187
  • aquatic counts: 1141
  • animal counts: 178
  • plant counts: 597

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
83501Risk group (German classification)
1194161Risk group (French classification)

Sequence information

16S sequences

  • @ref: 8350
  • description: Flavobacterium fluvii strain H7 16S ribosomal RNA gene, partial sequence
  • accession: EU109724
  • length: 1479
  • database: ena
  • NCBI tax ID: 468056

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Flavobacterium fluvii DSM 19978GCA_900129545contigncbi468056
66792Flavobacterium fluvii strain DSM 19978468056.5wgspatric468056
66792Flavobacterium fluvii DSM 199782695420956draftimg468056

GC content

@refGC-contentmethod
835037.2high performance liquid chromatography (HPLC)
2932137.2

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
gram-positiveno98.051yes
anaerobicno99.493no
halophileno97.887no
spore-formingno95.873no
glucose-utilyes89.359yes
aerobicyes85.327no
flagellatedno95.341yes
thermophileno99.108yes
motileno92.061yes
glucose-fermentno87.281no

External links

@ref: 8350

culture collection no.: DSM 19978, KACC 12818, CIP 110184

straininfo link

  • @ref: 75061
  • straininfo: 363754

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19651737Flavobacterium fluvii sp. nov., isolated from stream sediment.Lee SH, Kim JM, Lee JR, Park W, Jeon COInt J Syst Evol Microbiol10.1099/ijs.0.010850-02009Base Composition, Base Sequence, DNA, Bacterial/chemistry, Flavobacterium/chemistry/*classification/physiology, Geologic Sediments/*microbiology, Molecular Sequence Data, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Republic of Korea, Rivers/*microbiology, Sequence Homology, Nucleic Acid, *Water MicrobiologyGenetics
Phylogeny30994432Flavobacterium laiguense sp. nov., a psychrophilic bacterium isolated from Laigu glacier on the Tibetan Plateau.Yang LL, Liu Q, Liu HC, Zhou YG, Xin YHInt J Syst Evol Microbiol10.1099/ijsem.0.0034002019Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Flavobacterium/*classification/isolation & purification, Ice Cover/*microbiology, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Tibet, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
8350Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19978)https://www.dsmz.de/collection/catalogue/details/culture/DSM-19978
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
29321Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2573328776041
42060Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/8016
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)
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
75061Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID363754.1StrainInfo: A central database for resolving microbial strain identifiers
119416Curators of the CIPCollection of Institut Pasteur (CIP 110184)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20110184