Strain identifier

BacDive ID: 5526

Type strain: Yes

Species: Flavobacterium succinicans

Strain Designation: 8

Strain history: CIP <- 1996, J.F. Bernardet, INRA, Jouy en Josas, France <- NCIMB <- H. Reichenbach: strain Cy su 3 <- J.T. Staley <- R.L. Anderson and E.J. Ordal: strain 8, Washington Univ., USA

NCBI tax ID(s): 1450525 (strain), 29536 (species)

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General

@ref: 1569

BacDive-ID: 5526

DSM-Number: 4002

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

description: Flavobacterium succinicans 8 is a facultative anaerobe, mesophilic, Gram-negative bacterium that was isolated from eroded caudal fin of a fingerling chinook salmon.

NCBI tax id

NCBI tax idMatching level
1450525strain
29536species

strain history

@refhistory
1569<- H. Reichenbach, Cy su3 <- J.T. Staley <- R.L. Anderson, E.J. Ordal, 8 (Cytophaga succinicans)
67770IAM 14311 <-- IFO 14905 <-- DSM 4002 ("Flexibacter succinicans") <-- H. Reichenbach Cy su3 <-- J. T. Staley <-- R. L. Anderson and E. J. Ordal 8.
123365CIP <- 1996, J.F. Bernardet, INRA, Jouy en Josas, France <- NCIMB <- H. Reichenbach: strain Cy su 3 <- J.T. Staley <- R.L. Anderson and E.J. Ordal: strain 8, Washington Univ., USA

doi: 10.13145/bacdive5526.20250331.9.3

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 succinicans
  • full scientific name: Flavobacterium succinicans (Reichenbach 1989 ex Anderson and Ordal 1961) Bernardet et al. 1996

  • synonyms

    • @ref: 20215
    • synonym: Cytophaga succinicans

@ref: 1569

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Flavobacteriaceae

genus: Flavobacterium

species: Flavobacterium succinicans

full scientific name: Flavobacterium succinicans (Reichenbach 1989) Bernardet et al. 1996

strain designation: 8

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
123365negativerod-shapedno
125438no93.75
125438negative98
125439negative99.9

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
1569CY-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
39086MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
1569R2A MEDIUM (DSMZ Medium 830)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium830.pdf
123365CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72
123365CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperature
1569positivegrowth28
39086positivegrowth22
67770positivegrowth25
123365positivegrowth10-22
123365nogrowth30
123365nogrowth41

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
1569facultative anaerobe
123365facultative anaerobe
125439aerobe95.8

spore formation

@refspore formationconfidence
125438no94.458
125439no99.7

halophily

@refsaltgrowthtested relationconcentration
123365NaClpositivegrowth0 %
123365NaClnogrowth2 %
123365NaClnogrowth4 %
123365NaClnogrowth6 %
123365NaClnogrowth8 %
123365NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
12336516947citrate-carbon source
12336517234glucose-fermentation
12336517716lactose-fermentation
12336517632nitrate+reduction
12336516301nitrite-reduction
123365132112sodium thiosulfate-builds gas from
68371320061methyl alpha-D-glucopyranoside-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
6837117754glycerol-builds acid from

metabolite production

  • @ref: 123365
  • 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
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase-3.2.1.23
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
68382leucine arylamidase+3.4.11.1
68382valine arylamidase+
68382lipase (C 14)-
68382esterase lipase (C 8)+
68382esterase (C 4)+
123365oxidase-
123365beta-galactosidase+3.2.1.23
123365alcohol dehydrogenase-1.1.1.1
123365gelatinase-
123365DNase+
123365caseinase-3.4.21.50
123365catalase-1.11.1.6
123365gamma-glutamyltransferase+2.3.2.2
123365lecithinase-
123365lysine decarboxylase-4.1.1.18
123365ornithine decarboxylase-4.1.1.17
123365phenylalanine ammonia-lyase-4.3.1.24
123365tryptophan deaminase-
123365urease-3.5.1.5
68382alkaline phosphatase+3.1.3.1

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
123365-+++-+++--++---+++--

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
123365---------++++---------+-+--++------++-+---------+/-

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
123365+-+------++--+--+-+----------------------------------------+--------------------------+------------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
1569eroded caudal fin of a fingerling chinook salmonWashingtonUSAUSANorth America
67770Eroded caudal fin of a fingerling chinook salmon inflicted with furunculosis diseaseUniversity of Washington, HatcheryUSAUSANorth America
123365Animal, Eroded caudal fin of a farmed chinook salmonWashingtonUnited States of AmericaUSANorth America1954

isolation source categories

Cat1Cat2Cat3
#Host#Fishes#Salmonidae
#Host Body-Site#Limb

taxonmaps

  • @ref: 69479
  • File name: preview.99_1141.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_66;96_352;97_772;98_895;99_1141&stattab=map
  • Last taxonomy: Flavobacterium
  • 16S sequence: AM230492
  • Sequence Identity:
  • Total samples: 4251
  • soil counts: 465
  • aquatic counts: 2713
  • animal counts: 986
  • plant counts: 87

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
15691Risk group (German classification)
1233651Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Flavobacterium succinicans strain DSM 4002 16S ribosomal RNA gene, partial sequenceJX6570461256nuccore29536
20218Flavobacterium succinicans gene for 16S ribosomal RNA, partial sequence, strain: IFO 14905D126731256nuccore29536
1569Flavobacterium succinicans partial 16S rRNA gene, type strain DSM 4002AM2304921501nuccore29536
1569Flavobacterium succinicans gene for 16S rRNA, partial sequence, strain: NBRC 14905AB6806951439nuccore29536

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Flavobacterium succinicans LMG 104021450525.5wgspatric1450525
66792Flavobacterium succinicans strain DSM 400229536.15wgspatric29536
66792Flavobacterium succinicans DSM 40022693429891draftimg29536
66792Flavobacterium succinicans LMG 104022585427837draftimg1450525
67770Flavobacterium succinicans DSM 4002GCA_900114945scaffoldncbi29536
67770Flavobacterium succinicans LMG 10402GCA_000611675contigncbi1450525

GC content

@refGC-content
156938.0
156935.0

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingno98no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no96.337no
125438spore-formingspore-formingAbility to form endo- or exosporesno94.458no
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes80.624no
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno97.968no
125438motile2+flagellatedAbility to perform flagellated movementno93.75no
125439BacteriaNetspore_formationAbility to form endo- or exosporesno99.7
125439BacteriaNetmotilityAbility to perform movementno59.2
125439BacteriaNetgram_stainReaction to gram-stainingnegative99.9
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthaerobe95.8

External links

@ref: 1569

culture collection no.: DSM 4002, IAM 14311, IFO 14905, NBRC 14905, Cy su3, JCM 21151, BCRC 81041, CIP 104744, LMG 10402, NCIMB 2277, Cy su 3

straininfo link

  • @ref: 75009
  • straininfo: 10490

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny25563922Flavobacterium palustre sp. nov., isolated from wetland soil.Feng H, Zeng Y, Huang YInt J Syst Evol Microbiol10.1099/ijs.0.0000542015Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Flavobacterium/*classification/genetics/isolation & purification, Molecular Sequence Data, Phosphatidylethanolamines/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistry, *WetlandsGenetics
Phylogeny28671526Flavobacterium keumense sp. nov., isolated from freshwater.Ekwe AP, Ahn JH, Kim SBInt J Syst Evol Microbiol10.1099/ijsem.0.0019202017Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Flavobacterium/*classification/genetics/isolation & purification, Fresh Water/*microbiology, Phospholipids/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Spermidine/chemistry, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny30320544Flavobacterium riviphilum sp. nov., isolated from a freshwater creek.Sheu SY, Su CL, Chen WMInt J Syst Evol Microbiol10.1099/ijsem.0.0030702018Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Flavobacterium/*classification/genetics/isolation & purification, Phospholipids/chemistry, *Phylogeny, Polyamines/chemistry, RNA, Ribosomal, 16S/genetics, Rivers/*microbiology, Sequence Analysis, DNA, Taiwan, Vitamin K 2/analogs & derivatives/chemistry, Water MicrobiologyTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
1569Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 4002)https://www.dsmz.de/collection/catalogue/details/culture/DSM-4002
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
39086Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/16686
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
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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
75009Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID10490.1StrainInfo: A central database for resolving microbial strain identifiers
123365Curators of the CIPCollection of Institut Pasteur (CIP 104744)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104744
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