Strain identifier

BacDive ID: 5513

Type strain: Yes

Species: Flavobacterium flevense

Strain Designation: A-34

Strain history: CIP <- 1996, J.F. Bernardet, INRA, Jouy en Josas, France <- 1983, CCUG <- CCM <- H.J. van der Meulen: strain A-34

NCBI tax ID(s): 983 (species)

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General

@ref: 535

BacDive-ID: 5513

DSM-Number: 1076

keywords: genome sequence, 16S sequence, Bacteria, psychrophilic, Gram-negative, motile, rod-shaped, colony-forming

description: Flavobacterium flevense A-34 is a psychrophilic, Gram-negative, motile bacterium that forms circular colonies and was isolated from freshwater lake.

NCBI tax id

  • NCBI tax id: 983
  • Matching level: species

strain history

@refhistory
535<- H.J. van der Meulen, A-34 (Cytophaga flevensis)
67770IAM 14303 <-- IFO 14960 <-- ATCC 27944 <-- H. J. van der Meulen A-34.
119395CIP <- 1996, J.F. Bernardet, INRA, Jouy en Josas, France <- 1983, CCUG <- CCM <- H.J. van der Meulen: strain A-34

doi: 10.13145/bacdive5513.20230509.8.1

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 flevense
  • full scientific name: Flavobacterium flevense (van der Meulen et al. 1974) Bernardet et al. 1996

  • synonyms

    • @ref: 20215
    • synonym: Cytophaga flevensis

@ref: 535

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Flavobacteriaceae

genus: Flavobacterium

species: Flavobacterium flevense

full scientific name: Flavobacterium flevense (van der Meulen et al. 1974) Bernardet et al. 1996 emend. Chen et al. 2014

strain designation: A-34

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityflagellum arrangementconfidence
43344negative2-5 µm0.5-0.7 µmrod-shapedyesgliding
69480negative99.949
119395negativerod-shapedno

colony morphology

  • @ref: 43344
  • colony color: yellow
  • colony shape: circular

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
535R2A 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
535C/10 MEDIUM (DSMZ Medium 49)yeshttps://mediadive.dsmz.de/medium/49Name: C/10 MEDIUM (DSMZ Medium 49) Composition: Agar 15.0 g/l Casitone 3.0 g/l CaCl2 x 2 H2O 1.36 g/l Distilled water
39764MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
43344Marine agar (MA)yes
43344Nutrient agar (NA)yes
43344Tryptic Soy Agar (TSA)yes
119395CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperaturerange
535positivegrowth20psychrophilic
39764positivegrowth22psychrophilic
43344positiveoptimum15psychrophilic
43344positivegrowth0-24psychrophilic
67770positivegrowth25mesophilic
119395positivegrowth10-30
119395nogrowth37mesophilic
119395nogrowth41thermophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481no100
69480no99.995

compound production

  • @ref: 535
  • compound: agarase

halophily

@refsaltgrowthtested relationconcentration
43344NaClpositivegrowth0-9 %(w/v)
119395NaClpositivegrowth0-4 %
119395NaClnogrowth6 %
119395NaClnogrowth8 %
119395NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
433442509agar+assimilation
433442509agar+degradation
433442511agarose+assimilation
4334458187alginate-degradation
4334428938ammonium+nitrogen source
4334422599arabinose+assimilation
4334485146carboxymethylcellulose-degradation
43344casamino acids+nitrogen source
43344casein-degradation
4334417057cellobiose-assimilation
4334417029chitin-degradation
4334416991dna-degradation
433444853esculin+degradation
4334433984fucose-assimilation
4334428260galactose+assimilation
433445291gelatin-degradation
4334417234glucose+assimilation
4334415443inulin+assimilation
4334417716lactose+assimilation
4334461995lecithin-hydrolysis
4334417306maltose+assimilation
4334437684mannose+assimilation
4334417632nitrate+nitrogen source
4334417309pectin+assimilation
4334417309pectin+degradation
43344peptone+nitrogen source
43344peptone+growth
4334416634raffinose+assimilation
4334426546rhamnose+assimilation
4334433942ribose-assimilation
4334417992sucrose+assimilation
4334427082trehalose-assimilation
4334435020tributyrin+hydrolysis
4334453424tween 20+degradation
4334453423tween 40+degradation
4334453425tween 60+degradation
4334453426tween 80+degradation
4334418186tyrosine-degradation
4334416199urea-degradation
4334418222xylose+assimilation
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
6837124265gluconate-builds acid from
6837118403L-arabitol-builds acid from
6837118333D-arabitol-builds acid from
6837118287L-fucose+builds acid from
6837128847D-fucose-builds acid from
6837116443D-tagatose-builds acid from
6837162318D-lyxose-builds acid from
6837132528turanose+builds acid from
6837128066gentiobiose-builds acid from
6837117151xylitol-builds acid from
6837128087glycogen+builds acid from
6837128017starch+builds acid from
6837116634raffinose+builds acid from
683716731melezitose-builds acid from
6837115443inulin+builds acid from
6837127082trehalose-builds acid from
6837117992sucrose+builds acid from
6837128053melibiose+builds acid from
6837117716lactose+builds acid from
6837117306maltose+builds acid from
6837117814salicin-builds acid from
683714853esculin+builds acid from
6837118305arbutin-builds acid from
68371320061methyl alpha-D-glucopyranoside-builds acid from
6837143943methyl alpha-D-mannoside-builds acid from
6837117924D-sorbitol-builds acid from
6837116899D-mannitol-builds acid from
6837117268myo-inositol-builds acid from
6837116813galactitol-builds acid from
6837117266L-sorbose-builds acid from
6837116024D-mannose+builds acid from
6837115824D-fructose+builds acid from
6837117634D-glucose+builds acid from
6837112936D-galactose+builds acid from
6837174863methyl beta-D-xylopyranoside-builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837165327D-xylose+builds acid from
6837116988D-ribose-builds acid from
6837130849L-arabinose+builds acid from
6837117108D-arabinose+builds acid from
6837117113erythritol-builds acid from
6837117754glycerol-builds acid from
11939516947citrate-carbon source
1193954853esculin+hydrolysis
11939517632nitrate+reduction
11939516301nitrite-reduction
119395132112sodium thiosulfate-builds gas from

antibiotic resistance

@refChEBImetaboliteis antibioticis sensitiveis resistant
4334417698chloramphenicolyesyes
4334428368novobiocinyesyes
4334418208penicillin gyesyes
433448309polymyxin byesyes
4334417076streptomycinyesyes
1193950129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)yesyesno

metabolite production

@refChebi-IDmetaboliteproduction
4334416136hydrogen sulfideno
4334435581indoleno

enzymes

@refvalueactivityec
43344cytochrome oxidase+1.9.3.1
43344beta-galactosidase+3.2.1.23
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
119395oxidase-
119395beta-galactosidase+3.2.1.23
119395alcohol dehydrogenase-1.1.1.1
119395gelatinase-
119395amylase+
119395DNase-
119395caseinase-3.4.21.50
119395catalase+1.11.1.6
119395gamma-glutamyltransferase-2.3.2.2
119395lecithinase-
119395lysine decarboxylase-4.1.1.18
119395ornithine decarboxylase-4.1.1.17
119395phenylalanine ammonia-lyase-4.3.1.24
119395tryptophan deaminase-

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
119395-+++-++-+-++++-+-+--

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
119395--++-+---++++-+/-------+/-+/--+-+/-++++-+-+++--+---+-----

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
119395+++-+-++++++++----+-++-+------------------------------++-------------------------------------------

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentgeographic location
535freshwater lakeNetherlandsNLDEurope
67770Lake waterNetherlandsNLDEuropeIjsselmeer
119395Environment, Freshwater lakeNetherlandsNLDEuropeIJssel lake

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Freshwater
#Environmental#Aquatic#Lake (large)

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
5351Risk group (German classification)
1193951Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Flavobacterium flevense gene for 16S ribosomal RNA, partial sequence, strain: IFO 14960D126621256ena983
20218Flavobacterium flevense gene for 16S rRNA, partial sequence, strain: NBRC 14960AB6807231439ena983
4334416S rRNA gene sequenceM58767nuccore
535Flavobacterium flevense partial 16S rRNA gene, type strain DSM 1076AM2304861501ena983

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Flavobacterium flevense strain DSM 1076983.4wgspatric983
66792Flavobacterium flevense strain NBRC 14960983.10wgspatric983
66792Flavobacterium flevense DSM 10762700988729draftimg983
67770Flavobacterium flevense NBRC 14960GCA_006539745contigncbi983
67770Flavobacterium flevense DSM 1076GCA_900142775scaffoldncbi983

GC content

@refGC-contentmethod
4334433-34.9thermal denaturation, midpoint method (Tm)
53534.9high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno89.151no
flagellatedno94.567yes
gram-positiveno98.372no
anaerobicno99.745no
halophileno97.086no
spore-formingno93.988no
thermophileno99.586yes
glucose-utilyes91.427yes
aerobicyes92.913no
glucose-fermentno91.392no

External links

@ref: 535

culture collection no.: DSM 1076, ATCC 27944, IAM 14303, JCM 21143, ACAM 579, CCM 2740, CCUG 14832, CIP 104740, IFO 14960, LMG 8328, NBRC 14960, NCIMB 12056

straininfo link

  • @ref: 74998
  • straininfo: 92587

literature

  • topic: Phylogeny
  • Pubmed-ID: 25106925
  • title: Flavobacterium oryzae sp. nov., isolated from a flooded rice field, and emended descriptions of Flavobacterium flevense, Flavobacterium yonginense and Flavobacterium myungsuense.
  • authors: Chen WM, Chen JC, Sheu SY
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.065524-0
  • year: 2014
  • mesh: Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Flavobacterium/*classification/genetics/isolation & purification, Molecular Sequence Data, Nucleic Acid Hybridization, Oryza/*microbiology, Phosphatidylethanolamines/chemistry, Phospholipids/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Spermidine/chemistry, Taiwan, Vitamin K 2/analogs & derivatives/chemistry, *Water Microbiology
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
535Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 1076)https://www.dsmz.de/collection/catalogue/details/culture/DSM-1076
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
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
39764Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/16682
4334410.1007/978-0-387-68572-4
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)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68371Automatically annotated from API 50CH acid
68382Automatically annotated from API zym
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
74998Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID92587.1StrainInfo: A central database for resolving microbial strain identifiers
119395Curators of the CIPCollection of Institut Pasteur (CIP 104740)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104740