Strain identifier

BacDive ID: 5516

Type strain: Yes

Species: Flavobacterium saccharophilum

Strain Designation: 024

Strain history: CIP <- 1996, J.F. Bernardet, INRA, Jouy en Josas, France <- NCIMB <- M.O. Moss

NCBI tax ID(s): 29534 (species)

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General

@ref: 663

BacDive-ID: 5516

DSM-Number: 1811

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

description: Flavobacterium saccharophilum 024 is an aerobe, mesophilic, Gram-negative bacterium that forms circular colonies and was isolated from silt-water interface.

NCBI tax id

  • NCBI tax id: 29534
  • Matching level: species

strain history

@refhistory
663<- M.O. Moss, 024
67770NCIMB 2072 <-- M. O. Moss 024.
122339CIP <- 1996, J.F. Bernardet, INRA, Jouy en Josas, France <- NCIMB <- M.O. Moss

doi: 10.13145/bacdive5516.20230509.8.1

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 saccharophilum
  • full scientific name: Flavobacterium saccharophilum (Reichenbach 1989 ex Agbo and Moss 1979) Bernardet et al. 1996

  • synonyms

    • @ref: 20215
    • synonym: Cytophaga saccharophila

@ref: 663

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Flavobacteriaceae

genus: Flavobacterium

species: Flavobacterium saccharophilum

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

strain designation: 024

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityflagellum arrangementconfidence
43349negative2.5-6 µm0.5-0.7 µmrod-shapedyesgliding
69480negative99.989
122339negativerod-shapedno

colony morphology

  • @ref: 43349
  • colony color: yellow
  • colony shape: circular

pigmentation

  • @ref: 43349
  • production: yes
  • name: Flexirubin

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
663CY-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
39085MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
43349Marine agar (MA)no
43349Nutrient agar (NA)yes
43349Tryptic Soy Agar (TSA)yes
663R2A 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
122339CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3
122339CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
663positivegrowth25mesophilic
39085positivegrowth22psychrophilic
43349positiveoptimum25mesophilic
43349positivegrowth4-30
663positivegrowth28mesophilic
67770positivegrowth25mesophilic
122339positivegrowth10-30
122339nogrowth37mesophilic
122339nogrowth41thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 43349
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.995

halophily

@refsaltgrowthtested relationconcentration
43349NaClpositivegrowth0-2 %(w/v)
122339NaClpositivegrowth0-2 %
122339NaClnogrowth4 %
122339NaClnogrowth6 %
122339NaClnogrowth8 %
122339NaClnogrowth10 %

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
433492509agar+carbon source
433492509agar+energy source
433492509agar+degradation
433492511agarose+carbon source
433492511agarose+energy source
4334927569arabinogalactan+carbon source
4334927569arabinogalactan+energy source
4334922599arabinose+carbon source
4334922599arabinose+energy source
4334985146carboxymethylcellulose+degradation
433493435carrageenan+carbon source
433493435carrageenan+energy source
43349casein+degradation
4334917057cellobiose+carbon source
4334917057cellobiose+energy source
4334917029chitin-degradation
4334916991dna-degradation
433494853esculin+degradation
4334928757fructose+carbon source
4334928757fructose+energy source
4334928260galactose+carbon source
4334928260galactose+energy source
433495291gelatin+degradation
4334917234glucose+carbon source
4334917234glucose+energy source
4334917234glucose+assimilation
4334917716lactose+carbon source
4334917716lactose+energy source
4334917306maltose+carbon source
4334917306maltose+energy source
4334937684mannose+carbon source
4334937684mannose+energy source
4334928053melibiose+carbon source
4334928053melibiose+energy source
4334917632nitrate+reduction
4334917309pectin+carbon source
4334917309pectin+energy source
4334917309pectin+degradation
4334916634raffinose+carbon source
4334916634raffinose+energy source
4334926546rhamnose+carbon source
4334926546rhamnose+energy source
4334928017starch+carbon source
4334928017starch+energy source
4334928017starch+degradation
4334917992sucrose+carbon source
4334917992sucrose+energy source
4334927082trehalose+carbon source
4334927082trehalose+energy source
4334953424tween 20+degradation
4334953423tween 40+degradation
4334953425tween 60+degradation
4334953426tween 80+degradation
4334918186tyrosine+degradation
4334916199urea-degradation
4334918222xylose+carbon source
4334918222xylose+energy source
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
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
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
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
1223394853esculin+hydrolysis
12233917632nitrate+reduction
12233916301nitrite-reduction
122339132112sodium thiosulfate+builds gas from

antibiotic resistance

  • @ref: 122339
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

@refChebi-IDmetaboliteproduction
4334916136hydrogen sulfideyes
4334935581indoleno
12233935581indoleno

enzymes

@refvalueactivityec
43349catalase+1.11.1.6
43349cytochrome oxidase+/-1.9.3.1
43349beta-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
122339oxidase-
122339beta-galactosidase+3.2.1.23
122339alcohol dehydrogenase-1.1.1.1
122339gelatinase-
122339DNase+
122339caseinase-3.4.21.50
122339catalase+1.11.1.6
122339tween esterase-
122339gamma-glutamyltransferase+2.3.2.2
122339lecithinase-
122339lysine decarboxylase-4.1.1.18
122339ornithine decarboxylase-4.1.1.17
122339urease-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
122339-++++++++-++++-+++--

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
122339---+-+---++++--------++-+-+++-+-+-+++-+----------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
122339+++-+--++++----++-+-++-------------------------------------+--------------------------+--++--------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
663silt-water interfaceSurrey, Guildford, River WeyUnited KingdomGBREurope
67770The River WeySurreyUnited KingdomGBREurope
122339Environment, Wey River waterGuildford, SurreyUnited KingdomGBREurope1976

isolation source categories

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

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
6631Risk group (German classification)
1223391Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessiondatabaselengthNCBI tax ID
4334916S rRNA gene sequenceD12671nuccore
663Flavobacterium saccharophilum partial 16S rRNA gene, type strain DSM 1811AM230491ena149529534

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Flavobacterium saccharophilum strain DSM 181129534.3wgspatric29534
66792Flavobacterium saccharophilum DSM 18112698536752draftimg29534
67770Flavobacterium saccharophilum DSM 1811GCA_900142735contigncbi29534

GC content

@refGC-contentmethod
66336.2
4334935.7thermal denaturation, midpoint method (Tm)
6777032Buoyant density centrifugation (BD)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
gram-positiveno98.061no
anaerobicno99.594yes
halophileno96.77no
spore-formingno94.087no
glucose-utilyes92.331yes
motileno81.678no
flagellatedno94.313no
thermophileno99.832yes
aerobicyes91.744no
glucose-fermentno89.108no

External links

@ref: 663

culture collection no.: DSM 1811, IAM 14309, NCMB 2072, JCM 8520, ACAM 581, ATCC 49530, CIP 104743, IFO 15944, LMG 8384, NBRC 15944, NCIMB 2072

straininfo link

  • @ref: 75000
  • straininfo: 14015

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny17267958Flavobacterium aquidurense sp. nov. and Flavobacterium hercynium sp. nov., from a hard-water creek.Cousin S, Pauker O, Stackebrandt EInt J Syst Evol Microbiol10.1099/ijs.0.64556-02007Bacterial Typing Techniques, Base Composition, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis/chemistry, Flavobacterium/*classification/cytology/*isolation & purification/physiology, Fresh Water/*microbiology, Genes, rRNA, Germany, Molecular Sequence Data, Nucleic Acid Hybridization, Organic Chemicals/metabolism, Phylogeny, Pigments, Biological/biosynthesis, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Water MicrobiologyGenetics
Phylogeny30095387Flavobacterium chryseum sp. nov. and Flavobacterium psychroterrae sp. nov., novel environmental bacteria isolated from Antarctica.Kralova S, Svec P, Busse HJ, Stankova E, Vaczi P, Sedlacek IInt J Syst Evol Microbiol10.1099/ijsem.0.0029522018Antarctic Regions, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Flavobacterium/*classification/genetics/isolation & purification, Nucleic Acid Hybridization, Phosphatidylethanolamines/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Spermidine/analogs & derivatives/chemistry, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitle
663Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 1811)https://www.dsmz.de/collection/catalogue/details/culture/DSM-1811
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
39085Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/16685
4334910.1007/978-0-387-68572-4
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
75000Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID14015.1StrainInfo: A central database for resolving microbial strain identifiers
122339Curators of the CIPCollection of Institut Pasteur (CIP 104743)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104743