Strain identifier

BacDive ID: 5775

Type strain: Yes

Species: Fusobacterium vincentii

Strain Designation: EM48

Strain history: CIP <- 1996, ATCC <- J.L. Dzink: strain EM48

NCBI tax ID(s): 209882 (strain), 155615 (subspecies)

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General

@ref: 8137

BacDive-ID: 5775

DSM-Number: 19507

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

description: Fusobacterium vincentii EM48 is an anaerobe, mesophilic, Gram-negative bacterium that was isolated from human, periodontal pocket.

NCBI tax id

NCBI tax idMatching level
209882strain
155615subspecies

strain history

@refhistory
8137<- JCM; JCM 11023 <- CIP; CIP 104988 <- ATCC; ATCC 49256 <- J. L. Dzink; EM48
67770CIP 104988 <-- ATCC 49256 <-- J. L. Dzink EM48.
121370CIP <- 1996, ATCC <- J.L. Dzink: strain EM48

doi: 10.13145/bacdive5775.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/fusobacteriota
  • domain: Bacteria
  • phylum: Fusobacteriota
  • class: Fusobacteriia
  • order: Fusobacteriales
  • family: Fusobacteriaceae
  • genus: Fusobacterium
  • species: Fusobacterium vincentii
  • full scientific name: Fusobacterium vincentii (Dzink et al. 1990 ex Knorr 1922) Kook et al. 2022

  • synonyms

    @refsynonym
    20215Fusobacterium nucleatum subsp. fusiforme
    20215Fusobacterium nucleatum subsp. vincentii

@ref: 8137

domain: Bacteria

phylum: Fusobacteria

class: Fusobacteriia

order: Fusobacteriales

family: Fusobacteriaceae

genus: Fusobacterium

species: Fusobacterium nucleatum subsp. vincentii

full scientific name: Fusobacterium nucleatum subsp. vincentii (ex Knorr 1922) Dzink et al. 1990

strain designation: EM48

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480negative99.854
121370negativerod-shapedno

colony morphology

@refincubation period
81371-2 days
539082-3 days

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
8137CHOPPED MEAT MEDIUM (DSMZ Medium 78)yeshttps://mediadive.dsmz.de/medium/78Name: CHOPPED MEAT MEDIUM (DSMZ Medium 78; with strain-specific modifications) Composition: Ground beef 500.0 g/l Casitone 30.0 g/l Agar 15.0 g/l Ethanol 9.5 g/l (optional) Yeast extract 5.0 g/l K2HPO4 5.0 g/l L-Cysteine HCl 0.5 g/l Haemin 0.005 g/l Resazurin 0.001 g/l Vitamin K3 0.0005 g/l (optional) Vitamin K1 (optional) NaOH (optional) Distilled water
8137COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)yeshttps://mediadive.dsmz.de/medium/693Name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar base
41412MEDIUM 20 - for Anaerobic bacteriayesAgar (15.000 g);Glucose (5.000 g);Yeast extract (20.000 g);Tryptone (30.000 g);Cysteine hydrochloride (0.500 g);distilled water (1000.000 ml);Hemin solution -M00149 (25.000 ml)
121370CIP Medium 20yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=20

culture temp

@refgrowthtypetemperaturerange
8137positivegrowth37mesophilic
41412positivegrowth37mesophilic
53908positivegrowth37mesophilic
67770positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
8137anaerobe
53908anaerobe
69480anaerobe99.315
121370anaerobe

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 99.99

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6836727082trehalose-builds acid from
6836762345L-rhamnose-builds acid from
6836730911sorbitol-builds acid from
6836716634raffinose-builds acid from
683676731melezitose-builds acid from
6836716024D-mannose-builds acid from
6836717057cellobiose-builds acid from
6836717754glycerol-builds acid from
683674853esculin+hydrolysis
683675291gelatin-hydrolysis
6836730849L-arabinose-builds acid from
6836765327D-xylose-builds acid from
6836717814salicin-builds acid from
6836717306maltose-builds acid from
6836717992sucrose-builds acid from
6836717716lactose-builds acid from
6836716899D-mannitol-builds acid from
6836717634D-glucose-builds acid from
6836716199urea-hydrolysis
6836727897tryptophan+energy source
12137017632nitrate+reduction
12137016301nitrite+reduction
6838016199urea-hydrolysis
6838029016arginine-hydrolysis
6838016024D-mannose-fermentation
6838016634raffinose-fermentation
6838029985L-glutamate-degradation
6838017632nitrate-reduction
6838027897tryptophan+energy source

metabolite production

@refChebi-IDmetaboliteproduction
6836735581indoleyes
12137035581indoleyes
6838035581indoleyes

metabolite tests

@refChebi-IDmetaboliteindole test
6838035581indole+
6836735581indole+

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
68380serine arylamidase-
68380glutamyl-glutamate arylamidase-
68380histidine arylamidase-
68380glycin arylamidase-
68380alanine arylamidase-3.4.11.2
68380tyrosine arylamidase-
68380pyrrolidonyl arylamidase-3.4.19.3
68380leucine arylamidase-3.4.11.1
68380phenylalanine arylamidase-
68380leucyl glycin arylamidase-3.4.11.1
68380proline-arylamidase-3.4.11.5
68380L-arginine arylamidase-
68380alkaline phosphatase-3.1.3.1
68380tryptophan deaminase+4.1.99.1
68380alpha-fucosidase-3.2.1.51
68380glutamate decarboxylase-4.1.1.15
68380N-acetyl-beta-glucosaminidase-3.2.1.52
68380beta-glucuronidase-3.2.1.31
68380alpha-arabinosidase-3.2.1.55
68380beta-glucosidase-3.2.1.21
68380alpha-glucosidase-3.2.1.20
68380beta-Galactosidase 6-phosphate-
68380beta-galactosidase-3.2.1.23
68380alpha-galactosidase-3.2.1.22
68380arginine dihydrolase-3.5.3.6
68380urease-3.5.1.5
68367beta-glucosidase+3.2.1.21
68367gelatinase-
68367urease-3.5.1.5
121370oxidase-
121370catalase-1.11.1.6
121370urease-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
121370----------++--------

API 20A

@refINDUREGLUMANLACSACMALSALXYLARAGELESCGLYCELMNEMLZRAFSORRHATRE
8137+----------+--------

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
8137---------------+-------------
8137---------------+-------------

Isolation, sampling and environmental information

isolation

@refsample type
8137human, periodontal pocket
53908Human periodontal pocket
67770Human oral cavity
121370Human, Periodontal pocket

isolation source categories

Cat1Cat2Cat3
#Host#Human
#Host Body-Site#Oral cavity and airways#Periodontal pocket

taxonmaps

  • @ref: 69479
  • File name: preview.99_1686.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_140;96_436;97_498;98_572;99_1686&stattab=map
  • Last taxonomy: Fusobacterium
  • 16S sequence: AM887529
  • Sequence Identity:
  • Total samples: 4004
  • soil counts: 16
  • aquatic counts: 32
  • animal counts: 3941
  • plant counts: 15

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
81372Risk group (German classification)
1213701Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Fusobacterium nucleatum subsp. vincentii ATCC 49256 16S ribosomal RNA, partialAJ0069641406ena209882
20218Fusobacterium nucleatum subsp. vincentii partial 16S rRNA gene, type strain DSM 19507TAM8875291431ena155615
20218Fusobacterium nucleatum subsp. vincentii strain ATCC 49256 16S ribosomal RNA gene, partial sequenceGQ3010401415ena209882
20218Fusobacterium nucleatum subsp. vincentii ATCC 49256 16S ribosomal RNA gene, partial sequenceHM3470721399ena209882
8137Fusobacterium nucleatum subsp. vincentii gene for 16S ribosomal RNA, partial sequence, strain: JCM 11023AB9718191480ena155615
8137Fusobacterium nucleatum subsp. vincentii strain ATCC 49256 16S ribosomal RNA gene, partial sequence; internal transcribed spacer 1, complete sequence; and 23S ribosomal RNA gene, partial sequenceAF342834729ena209882

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Fusobacterium nucleatum subsp. vincentii ATCC 49256209882.4wgspatric209882
66792Fusobacterium nucleatum vincentii ATCC 49256638341097draftimg209882
67770Fusobacterium vincentii ATCC 49256GCA_000182945contigncbi209882

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes66no
motileno92.404no
gram-positiveno93.096no
anaerobicyes99.999yes
aerobicno98.836yes
halophileno76.225no
spore-formingno89.789no
glucose-utilyes79.431no
flagellatedno95.006no
thermophileno94.686no
glucose-fermentyes60.669no

External links

@ref: 8137

culture collection no.: DSM 19507, ATCC 49256, CIP 104988, JCM 11023, CCUG 37843

straininfo link

  • @ref: 75254
  • straininfo: 42385

literature

  • topic: Phylogeny
  • Pubmed-ID: 2223601
  • title: Proposal of three subspecies of Fusobacterium nucleatum Knorr 1922: Fusobacterium nucleatum subsp. nucleatum subsp. nov., comb. nov.; Fusobacterium nucleatum subsp. polymorphum subsp. nov., nom. rev., comb. nov.; and Fusobacterium nucleatum subsp. vincentii subsp. nov., nom. rev., comb. nov.
  • authors: Dzink JL, Sheenan MT, Socransky SS
  • journal: Int J Syst Bacteriol
  • DOI: 10.1099/00207713-40-1-74
  • year: 1990
  • mesh: Bacterial Proteins/analysis, DNA, Bacterial/genetics, Electrophoresis, Polyacrylamide Gel, Fusobacterium/analysis/*classification/genetics, Nucleic Acid Hybridization, Sequence Homology, Nucleic Acid, Species Specificity
  • topic2: Enzymology

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
8137Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19507)https://www.dsmz.de/collection/catalogue/details/culture/DSM-19507
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
41412Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/16957
53908Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 37843)https://www.ccug.se/strain?id=37843
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/
68367Automatically annotated from API 20A
68380Automatically annotated from API rID32A
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)
75254Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID42385.1StrainInfo: A central database for resolving microbial strain identifiers
121370Curators of the CIPCollection of Institut Pasteur (CIP 104988)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104988