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, Gram-negative, rod-shaped

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

NCBI tax id

NCBI tax idMatching level
998species
927664strain

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/bacdive3790.20250331.9.3

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

@refgram staincell shapemotilityconfidence
119396negativerod-shapedno
125438no91
125438negative94.96
125439negative99.8

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

@refgrowthtypetemperature
2821positivegrowth30
34601positivegrowth25
119396positivegrowth15-30
119396nogrowth37
119396nogrowth41

Physiology and metabolism

oxygen tolerance

  • @ref: 125439
  • oxygen tolerance: obligate aerobe
  • confidence: 99

spore formation

  • @ref: 125439
  • spore formation: no
  • confidence: 99.2

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
119396606565hippurate-hydrolysis
11939617632nitrate-reduction
11939616301nitrite-reduction
68371Potassium 5-ketogluconate-builds acid from
68371320061methyl alpha-D-glucopyranoside-builds acid from
6837117754glycerol-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
6837117057cellobiose-builds acid from
6837117814salicin-builds acid from
683714853esculin-builds acid from
6837118305arbutin-builds acid from
6837127613amygdalin-builds acid from
6837159640N-acetylglucosamine-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
6837162345L-rhamnose-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

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
68382beta-glucosidase-3.2.1.21
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
68382trypsin-3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382cystine arylamidase+3.4.11.3
68382valine arylamidase+
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
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
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-glucosidase-3.2.1.20
68382esterase lipase (C 8)+

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 sequenceM627941460nuccore927664
20218Flexibacter flexilis gene for 16S rRNA, strain:IFO 15060AB0780501466nuccore927664
20218Flexibacter flexilis gene for 16S rRNA, partial sequence, strain: NBRC 15060AB6807631436nuccore998
2821Flexibacter flexilis DSM 6793 16S ribosomal RNA gene, partial sequenceM62794.21460nuccore927664

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

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingno94.96no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no94.696no
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes82.165no
125438spore-formingspore-formingAbility to form endo- or exosporesno88.327no
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno92.953yes
125438motile2+flagellatedAbility to perform flagellated movementno91no
125439BacteriaNetspore_formationAbility to form endo- or exosporesno99.2
125439BacteriaNetmotilityAbility to perform movementyes51
125439BacteriaNetgram_stainReaction to gram-stainingnegative99.8
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate aerobe99

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
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
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann10.1101/2024.08.12.607695Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardyhttps://github.com/GenomeNet/deepGdeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1