Strain identifier

BacDive ID: 5771

Type strain: Yes

Species: Fusobacterium periodonticum

Strain Designation: EK1-15

Strain history: CCUG 14345 <-- J. Slots <-- ATCC 33693 <-- J. Slots EK1-15.

NCBI tax ID(s): 546275 (strain), 860 (species)

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General

@ref: 8164

BacDive-ID: 5771

DSM-Number: 19545

keywords: genome sequence, 16S sequence, Bacteria, anaerobe

description: Fusobacterium periodonticum EK1-15 is an anaerobe bacterium that was isolated from Human periodontitis,17-yr-old male,diabetes.

NCBI tax id

NCBI tax idMatching level
860species
546275strain

strain history

@refhistory
8164<- JCM/RIKEN <- CCUG <- J. Slots <- ATCC <- J. Slots; EK1-15
67770CCUG 14345 <-- J. Slots <-- ATCC 33693 <-- J. Slots EK1-15.

doi: 10.13145/bacdive5771.20240916.9.1

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 periodonticum
  • full scientific name: Fusobacterium periodonticum Slots et al. 1984

@ref: 8164

domain: Bacteria

phylum: Fusobacteria

class: Fusobacteriia

order: Fusobacteriales

family: Fusobacteriaceae

genus: Fusobacterium

species: Fusobacterium periodonticum

full scientific name: Fusobacterium periodonticum Slots et al. 1984

strain designation: EK1-15

type strain: yes

Morphology

colony morphology

  • @ref: 46094
  • incubation period: 1 day

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
8164COLUMBIA 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
8164CHOPPED MEAT MEDIUM WITH CARBOHYDRATES (DSMZ Medium 110)yeshttps://mediadive.dsmz.de/medium/110Name: CHOPPED MEAT MEDIUM WITH CARBOHYDRATES (DSMZ Medium 110) Composition: Ground beef 500.0 g/l Casitone 30.0 g/l Agar 15.0 g/l K2HPO4 5.0 g/l Yeast extract 5.0 g/l D-Glucose 4.0 g/l Starch 1.0 g/l Maltose 1.0 g/l Cellobiose 1.0 g/l L-Cysteine HCl 0.5 g/l Ethanol 0.19 g/l Vitamin K3 0.05 g/l Hemin 0.005 g/l Sodium resazurin 0.0005 g/l Vitamin K1 NaOH Distilled water

culture temp

@refgrowthtypetemperature
8164positivegrowth37
46094positivegrowth37
67770positivegrowth37

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
8164anaerobe
46094anaerobe

metabolite utilization

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

metabolite production

  • @ref: 68380
  • Chebi-ID: 35581
  • metabolite: indole
  • production: yes

metabolite tests

  • @ref: 68380
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: +

enzymes

@refvalueactivityec
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

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
8164---------------+-------------
8164---------------+-------------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
8164Human periodontitis,17-yr-old male,diabetesBuffalo, New YorkUSAUSANorth America
46094Human periodontitis,17-yr-old male,diabetesBuffaloUSAUSANorth America
67770Advanced periodontitis lesions of patient with insulin-dependent diabetes mellitus

isolation source categories

Cat1Cat2Cat3
#Infection#Inflammation
#Host#Human#Male

taxonmaps

  • @ref: 69479
  • File name: preview.99_2721.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_140;96_436;97_498;98_572;99_2721&stattab=map
  • Last taxonomy: Fusobacterium
  • 16S sequence: HM347071
  • Sequence Identity:
  • Total samples: 40002
  • soil counts: 483
  • aquatic counts: 511
  • animal counts: 38777
  • plant counts: 231

Safety information

risk assessment

  • @ref: 8164
  • biosafety level: 2
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Fusobacterium periodonticum strain ATCC 33693 16S ribosomal RNA gene, partial sequenceFJ196709825nuccore860
20218Fusobacterium periodonticum strain ATCC 33693 16S ribosomal RNA gene, partial sequenceGQ3010431428nuccore860
20218Fusobacterium periodonticum strain ATCC 33693 16S ribosomal RNA gene, partial sequenceHM3470711381nuccore860
20218Fusobacterium periodonticum rRNA small subunitX554051331nuccore860
8164Fusobacterium periodonticum gene for 16S ribosomal RNA, partial sequenceAB9107491467nuccore860
124043Fusobacterium periodonticum ATCC 33693 gene for 16S rRNA, partial sequence.LC752442562nuccore860

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Fusobacterium periodonticum ATCC 33693546275.3wgspatric546275
66792Fusobacterium periodonticum ATCC 33693645951848draftimg546275
67770Fusobacterium periodonticum ATCC 33693GCA_000160475scaffoldncbi546275

GC content

  • @ref: 67770
  • GC-content: 28
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69480gram-positivegram-positivePositive reaction to Gram-stainingno87.677no
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)yes88.637no
69480spore-formingspore-formingAbility to form endo- or exosporesno84.247no
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno94.182yes
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)no97.262yes
69480flagellatedmotile2+Ability to perform flagellated movementno83no

External links

@ref: 8164

culture collection no.: DSM 19545, ATCC 33693, CCUG 14345, JCM 12991, KCTC 15383

straininfo link

  • @ref: 75250
  • straininfo: 44968

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny6575999Fusobacterium periodonticum, a new species from the human oral cavity.Slots J, Potts TV, Mashimo PAJ Dent Res10.1177/002203458306200909011983Adolescent, Fusobacterium/classification/cytology/*isolation & purification/physiology, Humans, Male, Periodontitis/*microbiologyPathogenicity
Genetics8596666Molecular characterization of a 40-kDa outer membrane protein, FomA, of Fusobacterium periodonticum and comparison with Fusobacterium nucleatum.Bolstad AI, Hogh BT, Jensen HBOral Microbiol Immunol10.1111/j.1399-302x.1995.tb00151.x1995Amino Acid Sequence, Bacterial Outer Membrane Proteins/*chemistry/*genetics, Base Sequence, Codon, Codon, Terminator, Fusobacterium/*chemistry/*genetics, Fusobacterium nucleatum/chemistry/genetics, Genes, Bacterial/*genetics, Genes, Regulator/genetics, Molecular Sequence Data, Molecular Weight, Open Reading Frames, Porins/chemistry/genetics, Protein Conformation, Protein Sorting Signals, Protein Structure, Secondary, Sequence Analysis, DNA, Sequence Homology, Amino Acid, Sequence Homology, Nucleic Acid, Species SpecificityTranscriptome
Pathogenicity9573823Helicobacter pylori adheres selectively to Fusobacterium spp.Andersen RN, Ganeshkumar N, Kolenbrander PEOral Microbiol Immunol10.1111/j.1399-302x.1998.tb00751.x1998*Bacterial Adhesion/drug effects, Culture Media, Depression, Chemical, Fusobacterium/drug effects/*physiology, Helicobacter pylori/drug effects/*physiology, Hot Temperature, Humans, Lactose/pharmacology, Mouth/microbiology, Species SpecificityCultivation
Phylogeny21223363Development of species-specific polymerase chain reaction primers for detection of Fusobacterium periodonticum.Park SN, Park JY, Kook JKMicrobiol Immunol10.1111/j.1348-0421.2010.00279.x2010DNA Primers/*genetics, Fusobacterium/genetics/*isolation & purification, Polymerase Chain Reaction/*methods, Species SpecificityEnzymology

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
8164Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19545)https://www.dsmz.de/collection/catalogue/details/culture/DSM-19545
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
46094Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 14345)https://www.ccug.se/strain?id=14345
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/
68380Automatically annotated from API rID32A
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)
75250Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID44968.1StrainInfo: A central database for resolving microbial strain identifiers
124043Dr. Isabel Schober, Dr. Julia KoblitzData extracted from sequence databases, automatically matched based on designation and taxonomy