Strain identifier

BacDive ID: 5515

Type strain: Yes

Species: Flavobacterium johnsoniae

Strain Designation: UW 101

Strain history: CIP <- 1984, DSMZ, Cytophaga johnsonae <- H. Reichenbach: strain Cy j3 <- NCIB <- ATCC <- C.B. van Niel: strain MYX 1.1.1. <- R.Y. Stanier

NCBI tax ID(s): 986 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 8.1 (current version)

General

@ref: 700

BacDive-ID: 5515

DSM-Number: 2064

keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, mesophilic, Gram-negative, motile, rod-shaped, colony-forming, animal pathogen

description: Flavobacterium johnsoniae UW 101 is an obligate aerobe, mesophilic, Gram-negative animal pathogen that forms circular colonies and was isolated from Soil or mud.

NCBI tax id

  • NCBI tax id: 986
  • Matching level: species

strain history

@refhistory
700<- H. Reichenbach, Cy j3 <- NCIB <- ATCC <- C.B. van Niel, MYX 1.1.1 <- R.Y. Stanier (Cytophaga johnsonae)
67770NCIMB 11054 <-- ATCC 17061 <-- C. B. van Niel MYX.1.1.1..
120355CIP <- 1984, DSMZ, Cytophaga johnsonae <- H. Reichenbach: strain Cy j3 <- NCIB <- ATCC <- C.B. van Niel: strain MYX 1.1.1. <- R.Y. Stanier

doi: 10.13145/bacdive5515.20230509.8.1

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 johnsoniae
  • full scientific name: Flavobacterium johnsoniae corrig. (Stanier 1947) Bernardet et al. 1996

  • synonyms

    @refsynonym
    20215Flavobacterium johnsonae
    20215Cytophaga johnsonae

@ref: 700

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Flavobacteriaceae

genus: Flavobacterium

species: Flavobacterium johnsoniae subsp. johnsoniae

full scientific name: Flavobacterium johnsoniae subsp. johnsoniae (Stanier 1947) García-López et al. 2020

strain designation: UW 101

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityflagellum arrangementconfidence
43346negative1.5-15 µm0.3-0.4 µmrod-shapedyesgliding
69480negative99.998
120355negativerod-shapedno

colony morphology

@refcolony colorcolony shape
43346deep orange, pale yellowcircular
120355

pigmentation

  • @ref: 120355
  • production: no
  • name: Flexirubin

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
700R2A MEDIUM (DSMZ Medium 830)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium830.pdf
700CY-AGAR (DSMZ Medium 67)yeshttps://mediadive.dsmz.de/medium/67Name: CY-AGAR (DSMZ Medium 67) Composition: Agar 15.0 g/l Casitone 3.0 g/l CaCl2 x 2 H2O 1.36 g/l Yeast extract 1.0 g/l Distilled water
39783MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
43346Marine agar (MA)no
43346Nutrient agar (NA)yes
43346Tryptic Soy Agar (TSA)yes
120355CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3
120355CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
700positivegrowth28mesophilic
39783positivegrowth25mesophilic
43346positiveoptimum25-30mesophilic
43346positivegrowth10-30
52589positivegrowth30mesophilic
67770positivegrowth25mesophilic
120355positivegrowth10-30
120355nogrowth5psychrophilic
120355nogrowth37mesophilic
120355nogrowth41thermophilic
120355nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
43346obligate aerobe
52589aerobe
120355obligate aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.995

halophily

@refsaltgrowthtested relationconcentration
43346NaClpositivegrowth0-1 %(w/v)
120355NaClpositivegrowth0-2 %
120355NaClnogrowth4 %
120355NaClnogrowth6 %
120355NaClnogrowth8 %
120355NaClnogrowth10 %

observation

  • @ref: 67770
  • observation: quinones: MK-6

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
433462509agar-degradation
4334658187alginate+degradation
4334628938ammonium+nitrogen source
4334622599arabinose+growth
4334685146carboxymethylcellulose+degradation
43346casamino acids+nitrogen source
43346casein+degradation
4334617057cellobiose+growth
4334617029chitin+growth
4334617029chitin+degradation
4334616991dna+degradation
433464853esculin+degradation
4334628260galactose+growth
433465291gelatin+degradation
4334617234glucose+growth
4334617234glucose+assimilation
4334615443inulin+growth
4334629985L-glutamate+nitrogen source
4334617716lactose+growth
4334661995lecithin-degradation
4334617306maltose+growth
4334637684mannose+growth
4334617632nitrate+nitrogen source
4334617309pectin+degradation
43346peptone+nitrogen source
4334616634raffinose+growth
4334628017starch+growth
4334628017starch+degradation
4334617992sucrose+growth
4334635020tributyrin+degradation
4334653424tween 20+degradation
4334653423tween 40+degradation
4334653425tween 60+degradation
4334653426tween 80+degradation
4334618186tyrosine+degradation
4334616199urea+degradation
4334618222xylose+growth
6836925115malate-assimilation
6836917128adipate-assimilation
6836927689decanoate-assimilation
6836924265gluconate-assimilation
6836917306maltose+assimilation
6836959640N-acetylglucosamine+assimilation
6836916899D-mannitol-assimilation
6836916024D-mannose+assimilation
6836930849L-arabinose+assimilation
6836917634D-glucose+assimilation
683695291gelatin+hydrolysis
683694853esculin+hydrolysis
6836916199urea-hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate-reduction
12035516947citrate-carbon source
1203554853esculin+hydrolysis
120355606565hippurate-hydrolysis
12035517632nitrate-builds gas from
12035517632nitrate+reduction
12035516301nitrite-builds gas from
12035516301nitrite+reduction
12035515792malonate-assimilation

antibiotic resistance

  • @ref: 120355
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

@refChebi-IDmetaboliteproduction
4334616136hydrogen sulfideno
4334635581indoleno
6836935581indoleno
12035535581indoleno

metabolite tests

@refChebi-IDmetaboliteindole testvoges-proskauer-testmethylred-test
6836935581indole-
12035515688acetoin-
12035517234glucose-

enzymes

@refvalueactivityec
43346catalase+1.11.1.6
43346cytochrome oxidase+1.9.3.1
43346beta-galactosidase+3.2.1.23
68382alpha-fucosidase-3.2.1.51
68382N-acetyl-beta-glucosaminidase+3.2.1.52
68382beta-glucosidase+3.2.1.21
68382alpha-glucosidase+3.2.1.20
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase+3.1.3.2
68382valine arylamidase+
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)+
68382alkaline phosphatase+3.1.3.1
68369cytochrome oxidase+1.9.3.1
68369gelatinase+
68369beta-glucosidase+3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6
120355oxidase+
120355beta-galactosidase-3.2.1.23
120355alcohol dehydrogenase-1.1.1.1
120355gelatinase+/-
120355amylase-
120355DNase-
120355caseinase+3.4.21.50
120355catalase+1.11.1.6
120355tween esterase-
120355gamma-glutamyltransferase+2.3.2.2
120355lecithinase-
120355lipase-
120355lysine decarboxylase-4.1.1.18
120355ornithine decarboxylase-4.1.1.17
120355phenylalanine ammonia-lyase-4.3.1.24
120355protease-
120355tryptophan deaminase-
120355urease-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
52589-+-+-++---++---+++--
120355-+++-+++++++-++++++-

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
52589-----++++++-++------+

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
120355+++++----++----++++-++--------------------------------++---+--------------------------+--+++-------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
52589Soil or mudRothamsted or CambridgeUnited KingdomGBREurope
67770Soil or mudRothamsted or CambridgeUnited KingdomGBREurope

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Mud (Sludge)
#Environmental#Terrestrial#Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_4117.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_66;96_207;97_2514;98_3111;99_4117&stattab=map
  • Last taxonomy: Flavobacterium johnsoniae subclade
  • 16S sequence: AM230489
  • Sequence Identity:
  • Total samples: 1079
  • soil counts: 358
  • aquatic counts: 268
  • animal counts: 368
  • plant counts: 85

Safety information

risk assessment

@refpathogenicity animalbiosafety levelbiosafety level comment
700yes1Risk group (German classification)
1203551Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Flavobacterium johnsoniae strain ATCC 17061 16S-23S ribosomal RNA intergenic spacer, partial sequenceAY753067629ena376686
20218Flavobacterium johnsoniae gene for 16S ribosomal RNA, partial sequence, strain: IFO 14942D126641256ena376686
20218Flavobacterium johnsoniae strain DSM 2064 16S ribosomal RNA gene, partial sequenceJX6570501264ena986
20218Flavobacterium johnsoniae 16S ribosomal RNA gene, partial sequenceM590511463ena986
700Flavobacterium johnsoniae partial 16S rRNA gene, type strain DSM 2064AM2304891501ena376686

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Flavobacterium johnsoniae UW101376686.10completepatric376686
66792Flavobacterium johnsoniae UW101376686.29wgspatric376686
66792Flavobacterium johnsoniae strain DSM 2064986.10wgspatric986
66792Flavobacterium johnsoniae DSM 20642698536700draftimg986
66792Flavobacterium johnsoniae UW101, ATCC 17061644736369completeimg376686
67770Flavobacterium johnsoniae UW101 UW101; ATCC 17061GCA_000016645completencbi376686
67770Flavobacterium johnsoniae DSM 2064GCA_900142355scaffoldncbi986
67770Flavobacterium johnsoniae UW101 ATCC 17061GCA_002221975scaffoldncbi376686

GC content

@refGC-contentmethod
70033.0
4334633-35.2thermal denaturation, midpoint method (Tm)
6777033Buoyant density centrifugation (BD)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
gram-positiveno98.479no
anaerobicno99.623yes
halophileno95.779yes
spore-formingno92.889no
glucose-utilyes90.375yes
aerobicyes88.503yes
motileno84.17no
flagellatedno93.895yes
thermophileno99.68yes
glucose-fermentno88.066no

External links

@ref: 700

culture collection no.: CCUG 35202, NCIMB 11054, LMG 1341, CFBP 3036, CIP 100931, JCM 8514, DSM 2064, ATCC 17061, IAM 14304, IFO 14942, NBRC 14942, NCIB 11054, Cy j3, MYX 1.1.1, BCRC 14874, GIFU 2500, LMG 1340, NCCB 96103, MYX 1.1.1.

straininfo link

  • @ref: 74999
  • straininfo: 2148

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Biotechnology3789718Properties of Cytophaga johnsonae strains causing spoilage of fresh produce at food markets.Liao CH, Wells JMAppl Environ Microbiol10.1128/aem.52.6.1261-1265.19861986Bacterial Proteins/analysis, Cytophaga/analysis/*isolation & purification/physiology, *Food Microbiology, *Fruit, Polysaccharide-Lyases/metabolism, *VegetablesEnzymology
Enzymology12562690Molecular and biochemical characterization of a carbapenem-hydrolysing beta-lactamase from Flavobacterium johnsoniae.Naas T, Bellais S, Nordmann PJ Antimicrob Chemother10.1093/jac/dkg0692003Amino Acid Sequence, Carbapenems/*metabolism, DNA, Bacterial/genetics, Escherichia coli/enzymology/metabolism, Flavobacterium/*enzymology, Isoenzymes/chemistry/metabolism, Kinetics, Microbial Sensitivity Tests, Molecular Sequence Data, Molecular Weight, beta-Lactamases/*genetics/*metabolismMetabolism
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
Phylogeny23291764Identification and characterization of cellobiose 2-epimerases from various aerobes.Ojima T, Saburi W, Yamamoto T, Mori H, Matsui HBiosci Biotechnol Biochem10.1271/bbb.1207422013Aerobiosis, Bacteria, Aerobic/chemistry/*enzymology, Bacterial Proteins/classification/*isolation & purification/*metabolism, Carbohydrate Epimerases/classification/*isolation & purification/*metabolism, Cellobiose/*metabolism, Enzyme Assays, Enzyme Stability, Escherichia coli/genetics, Glucose/metabolism, Hydrogen-Ion Concentration, Isoenzymes/classification/isolation & purification/metabolism, Kinetics, Lactose/metabolism, Mannose/metabolism, Phylogeny, Recombinant Proteins/classification/isolation & purification/metabolism, Species Specificity, Stereoisomerism, Substrate Specificity, TemperatureEnzymology
Metabolism27170214A glycoside hydrolase family 31 dextranase with high transglucosylation activity from Flavobacterium johnsoniae.Gozu Y, Ishizaki Y, Hosoyama Y, Miyazaki T, Nishikawa A, Tonozuka TBiosci Biotechnol Biochem10.1080/09168451.2016.11828522016Bacterial Proteins/genetics/*metabolism, Dextranase/genetics/*metabolism, Dextrans/chemistry/*metabolism, Escherichia coli/*enzymology/genetics, Flavobacterium/*enzymology/genetics, Glucans/chemistry/metabolism, Glucosyltransferases/genetics/*metabolism, Hydrogen-Ion Concentration, Hydrolysis, Isomaltose/chemistry/metabolism, Oligosaccharides/chemistry/metabolism, Protein Engineering, Recombinant Proteins/genetics/metabolism, Substrate Specificity, TemperatureEnzymology

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
700Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 2064)https://www.dsmz.de/collection/catalogue/details/culture/DSM-2064
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
39783Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/12450
4334610.1007/978-0-387-68572-4
52589Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 35202)https://www.ccug.se/strain?id=35202
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/
68369Automatically annotated from API 20NE
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
74999Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID2148.1StrainInfo: A central database for resolving microbial strain identifiers
120355Curators of the CIPCollection of Institut Pasteur (CIP 100931)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20100931