Strain identifier

BacDive ID: 3790

Type strain: Yes

Species: Flexibacter flexilis

Strain Designation: CR-63, Fx f1

Strain history: CIP <- 1994, NCIMB <- R.A. Lewin, San Jose Univ., Costa Rica: strain CR-63

NCBI tax ID(s): 927664 (strain), 998 (species)

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General

@ref: 2821

BacDive-ID: 3790

DSM-Number: 6793

keywords: genome sequence, 16S sequence, Bacteria, mesophilic

description: Flexibacter flexilis CR-63 is a mesophilic bacterium that was isolated from water, pond.

NCBI tax id

NCBI tax idMatching level
927664strain
998species

strain history

@refhistory
2821<- H. Reichenbach, Fx f1 <- ATCC <- R.A. Lewin, CR-63
119396CIP <- 1994, NCIMB <- R.A. Lewin, San Jose Univ., Costa Rica: strain CR-63

doi: 10.13145/bacdive3790.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Cytophagia
  • order: Cytophagales
  • family: Flexibacteraceae
  • genus: Flexibacter
  • species: Flexibacter flexilis
  • full scientific name: Flexibacter flexilis Soriano 1945 (Approved Lists 1980)

@ref: 2821

domain: Bacteria

phylum: Bacteroidetes

class: Cytophagia

order: Cytophagales

family: Flexibacteraceae

genus: Flexibacter

species: Flexibacter flexilis

full scientific name: Flexibacter flexilis Soriano 1945

strain designation: CR-63, Fx f1

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480no92.503
6948099.999negative
119396nonegativerod-shaped

pigmentation

  • @ref: 119396
  • production: no
  • name: Flexirubin

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
2821CY-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
34601MEDIUM 103 - for Flexibacter flexilisyesDistilled water make up to (990.000 ml);Magnesium sulphate heptahydrate (0.100 g);Calcium chloride dihydrate (0.100 g);Agar (15.000 g);Glucose (1.000 g);Potassium nitrate (0.100 g);Casamino acids (1.000 g);Sodium glycerophosphate hexahydrate (0.100 g);Tri
119396CIP Medium 33yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=33

culture temp

@refgrowthtypetemperaturerange
2821positivegrowth30mesophilic
34601positivegrowth25mesophilic
119396positivegrowth15-30
119396nogrowth37mesophilic
119396nogrowth41thermophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481no100
69480no99.994

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
68371gluconate-builds acid from24265
68371L-arabitol-builds acid from18403
68371D-arabitol-builds acid from18333
68371L-fucose-builds acid from18287
68371D-fucose-builds acid from28847
68371D-tagatose-builds acid from16443
68371D-lyxose-builds acid from62318
68371turanose-builds acid from32528
68371gentiobiose-builds acid from28066
68371xylitol-builds acid from17151
68371glycogen-builds acid from28087
68371starch-builds acid from28017
68371raffinose-builds acid from16634
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371trehalose-builds acid from27082
68371sucrose-builds acid from17992
68371melibiose-builds acid from28053
68371lactose-builds acid from17716
68371maltose-builds acid from17306
68371cellobiose-builds acid from17057
68371salicin-builds acid from17814
68371esculin-builds acid from4853
68371arbutin-builds acid from18305
68371amygdalin-builds acid from27613
68371N-acetylglucosamine-builds acid from59640
68371methyl alpha-D-glucopyranoside-builds acid from320061
68371methyl alpha-D-mannoside-builds acid from43943
68371D-sorbitol-builds acid from17924
68371D-mannitol-builds acid from16899
68371myo-inositol-builds acid from17268
68371galactitol-builds acid from16813
68371L-rhamnose-builds acid from62345
68371L-sorbose-builds acid from17266
68371D-mannose-builds acid from16024
68371D-fructose-builds acid from15824
68371D-glucose-builds acid from17634
68371D-galactose-builds acid from12936
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-xylose-builds acid from65327
68371D-ribose-builds acid from16988
68371L-arabinose-builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
68371glycerol-builds acid from17754
119396hippurate-hydrolysis606565
119396nitrate-reduction17632
119396nitrite-reduction16301

metabolite production

  • @ref: 119396
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
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
119396oxidase+
119396beta-galactosidase-3.2.1.23
119396alcohol dehydrogenase-1.1.1.1
119396gelatinase-
119396catalase+1.11.1.6
119396gamma-glutamyltransferase-2.3.2.2
119396lysine decarboxylase-4.1.1.18
119396ornithine decarboxylase-4.1.1.17
119396tryptophan deaminase-
119396urease-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
119396-+++-+++---+--------

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
119396-------------------------------------------------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
2821water, pondSan JoseCosta RicaCRIMiddle and South America
119396Lily pondCosta RicaCRINorth America

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Aquatic
  • Cat3: #Pond (small)

taxonmaps

  • @ref: 69479
  • File name: preview.99_19303.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_16353;96_9532;97_11476;98_14105;99_19303&stattab=map
  • Last taxonomy: Flexibacter flexilis subclade
  • 16S sequence: AB680763
  • Sequence Identity:
  • Total samples: 1417
  • soil counts: 46
  • aquatic counts: 1177
  • animal counts: 156
  • plant counts: 38

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
28211Risk group (German classification)
1193961Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Flexibacter flexilis DSM 6793 16S ribosomal RNA gene, partial sequenceM627941460ena927664
20218Flexibacter flexilis gene for 16S rRNA, strain:IFO 15060AB0780501466ena927664
20218Flexibacter flexilis gene for 16S rRNA, partial sequence, strain: NBRC 15060AB6807631436ena998
2821Flexibacter flexilis DSM 6793 16S ribosomal RNA gene, partial sequenceM62794.21460ena927664

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Flexibacter flexilis DSM 6793GCA_900112255scaffoldncbi927664
66792Flexibacter flexilis DSM 6793927664.3wgspatric927664
66792Flexibacter flexilis DSM 67932675903165draftimg927664

GC content

  • @ref: 2821
  • GC-content: 40.8

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno92.554no
flagellatedno96.723no
gram-positiveno98.61no
anaerobicno97.894no
aerobicyes79.796no
halophileno95.91no
spore-formingno93.824no
glucose-fermentno87.181no
thermophileno94.672no
glucose-utilyes79.332no

External links

@ref: 2821

culture collection no.: DSM 6793, ATCC 23079, CIP 103988, CCUG 5119, IFO 15060, LMG 3990, NCIMB 12853, NCMB 1377

straininfo link

  • @ref: 73302
  • straininfo: 9859

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
2821Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 6793)https://www.dsmz.de/collection/catalogue/details/culture/DSM-6793
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
34601Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/15846
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
68371Automatically annotated from API 50CH acid
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
73302Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID9859.1StrainInfo: A central database for resolving microbial strain identifiers
119396Curators of the CIPCollection of Institut Pasteur (CIP 103988)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103988