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BacDive ID 5775
Type strain
Strain Designation EM48
Culture col. no. DSM 19507 ATCC 49256 CIP 104988 JCM 11023 CCUG 37843 EM48 1 more
NCBI tax ID(s) 851
Links
For citation purpose refer to the digital object identifier (doi) of the current version.

Archive

version 9.3 (current version):
version 9.3 (current version)

General

@ref: 8137

BacDive-ID: 5775

DSM-Number: 19507

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

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

NCBI tax id

  • NCBI tax id: 851
  • Matching level: species

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/bacdive5775.20250331.9.3

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. vincentii
    20215Fusobacterium nucleatum subsp. fusiforme

@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

  • @ref: 121370
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: no

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

@refgrowthtypetemperature
8137positivegrowth37
41412positivegrowth37
53908positivegrowth37
67770positivegrowth37

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
8137anaerobe
53908anaerobe
121370anaerobe
125438anaerobe94.896

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6838027897tryptophan+energy source
6838029985L-glutamate-degradation
6838017632nitrate-reduction
6838029016arginine-hydrolysis
6838016199urea-hydrolysis
12137017632nitrate+reduction
12137016301nitrite+reduction
6838016634raffinose-fermentation
6838016024D-mannose-fermentation
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

metabolite production

@refChebi-IDmetaboliteproduction
6838035581indoleyes
12137035581indoleyes
6836735581indoleyes

metabolite tests

@refChebi-IDmetaboliteindole test
6838035581indole+
6836735581indole+

enzymes

@refvalueactivityec
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-glucosidase-3.2.1.20
68382beta-glucosidase-3.2.1.21
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
68382leucine arylamidase-3.4.11.1
68382valine arylamidase-
68382lipase (C 14)-
68382esterase lipase (C 8)-
68382esterase (C 4)-
68382alkaline phosphatase-3.1.3.1
121370oxidase-
121370catalase-1.11.1.6
121370urease-3.5.1.5
68380tyrosine arylamidase-
68380pyrrolidonyl arylamidase-3.4.19.3
68380leucine arylamidase-3.4.11.1
68380alpha-fucosidase-3.2.1.51
68380glutamate decarboxylase-4.1.1.15
68380beta-galactosidase-3.2.1.23
68380alpha-galactosidase-3.2.1.22
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382beta-glucuronidase-3.2.1.31
68380serine arylamidase-
68380glutamyl-glutamate arylamidase-
68380histidine arylamidase-
68380glycin arylamidase-
68380alanine arylamidase-3.4.11.2
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
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-
68380arginine dihydrolase-3.5.3.6
68380urease-3.5.1.5
68367beta-glucosidase+3.2.1.21
68367gelatinase-
68367urease-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, partialAJ0069641406nuccore209882
20218Fusobacterium nucleatum subsp. vincentii partial 16S rRNA gene, type strain DSM 19507TAM8875291431nuccore155615
20218Fusobacterium nucleatum subsp. vincentii strain ATCC 49256 16S ribosomal RNA gene, partial sequenceGQ3010401415nuccore209882
20218Fusobacterium nucleatum subsp. vincentii ATCC 49256 16S ribosomal RNA gene, partial sequenceHM3470721399nuccore209882
8137Fusobacterium nucleatum subsp. vincentii gene for 16S ribosomal RNA, partial sequence, strain: JCM 11023AB9718191480nuccore155615
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 sequenceAF342834729nuccore209882
124043Fusobacterium nucleatum subsp. vincentii strain DSM 19507 clone C2_short_clone19 16S ribosomal RNA gene, partial sequence; 16S-23S ribosomal RNA intergenic spacer, complete sequence; and 23S ribosomal RNA gene, partial sequence.JQ7246891018nuccore155615
124043Fusobacterium nucleatum subsp. vincentii strain DSM 19507 clone C2_short_clone19 16S ribosomal RNA gene, partial sequence; 16S-23S ribosomal RNA intergenic spacer, complete sequence; and 23S ribosomal RNA gene, partial sequence.JQ7246901192nuccore155615
124043Fusobacterium nucleatum subsp. vincentii strain DSM 19507 clone C2_short_clone19 16S ribosomal RNA gene, partial sequence; 16S-23S ribosomal RNA intergenic spacer, complete sequence; and 23S ribosomal RNA gene, partial sequence.JQ7246911016nuccore155615
124043Fusobacterium nucleatum subsp. vincentii strain DSM 19507 clone C2_short_clone19 16S ribosomal RNA gene, partial sequence; 16S-23S ribosomal RNA intergenic spacer, complete sequence; and 23S ribosomal RNA gene, partial sequence.JQ7246921193nuccore155615
124043Fusobacterium nucleatum subsp. vincentii strain DSM 19507 clone C2_short_clone19 16S ribosomal RNA gene, partial sequence; 16S-23S ribosomal RNA intergenic spacer, complete sequence; and 23S ribosomal RNA gene, partial sequence.JQ7246931015nuccore155615
124043Fusobacterium nucleatum subsp. vincentii strain DSM 19507 clone C2_short_clone19 16S ribosomal RNA gene, partial sequence; 16S-23S ribosomal RNA intergenic spacer, complete sequence; and 23S ribosomal RNA gene, partial sequence.JQ7246941017nuccore155615

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

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingno86.03no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)yes94.896yes
125438spore-formingspore-formingAbility to form endo- or exosporesno84.929no
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)no98.838yes
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno93.73no
125438motile2+flagellatedAbility to perform flagellated movementno84.875no
125439BacteriaNetspore_formationAbility to form endo- or exosporesno68.3
125439BacteriaNetmotilityAbility to perform movementyes59.1
125439BacteriaNetgram_stainReaction to gram-stainingpositive65.7
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthanaerobe88

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
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
124043Isabel Schober, Julia KoblitzData extracted from sequence databases, automatically matched based on designation and taxonomy
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

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