Strain identifier

BacDive ID: 5772

Type strain: Yes

Species: Fusobacterium simiae

Strain Designation: 7511 R2-13

Strain history: KCTC 5548 <-- J. K. Kook <-- CCUG 16798 <-- CCM 3660 <-- J. Slots 7511 R2-13.

NCBI tax ID(s): 855 (species)

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General

@ref: 8287

BacDive-ID: 5772

DSM-Number: 19848

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

description: Fusobacterium simiae 7511 R2-13 is an anaerobe, mesophilic bacterium that was isolated from Monkey dental plaque .

NCBI tax id

  • NCBI tax id: 855
  • Matching level: species

strain history

@refhistory
8287<- CCUG; 7511 R2-13 {2007} <- CCM <- J. Slots
67770KCTC 5548 <-- J. K. Kook <-- CCUG 16798 <-- CCM 3660 <-- J. Slots 7511 R2-13.

doi: 10.13145/bacdive5772.20230509.8.1

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 simiae
  • full scientific name: Fusobacterium simiae Slots and Potts 1982

@ref: 8287

domain: Bacteria

phylum: Fusobacteria

class: Fusobacteriia

order: Fusobacteriales

family: Fusobacteriaceae

genus: Fusobacterium

species: Fusobacterium simiae

full scientific name: Fusobacterium simiae Slots and Potts 1982

strain designation: 7511 R2-13

type strain: yes

Morphology

colony morphology

  • @ref: 46531
  • incubation period: 2 days

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
8287CHOPPED 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
8287COLUMBIA 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

culture temp

@refgrowthtypetemperaturerange
8287positivegrowth37mesophilic
67770positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
8287anaerobe
46531anaerobe

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
8287------------+--+-------------

Isolation, sampling and environmental information

isolation

@refsample type
8287Monkey dental plaque (Macaca arctoides)
46531Monkey dental plaque (Macaca arctoides)
67770Monkey dental plaque

isolation source categories

Cat1Cat2Cat3
#Host#Mammals#Primates
#Host Body-Site#Oral cavity and airways#Plaque
#Host Body-Site#Oral cavity and airways#Tooth

taxonmaps

  • @ref: 69479
  • File name: preview.99_5719.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_140;96_436;97_498;98_4257;99_5719&stattab=map
  • Last taxonomy: Fusobacterium
  • 16S sequence: AB616133
  • Sequence Identity:
  • Total samples: 1714
  • soil counts: 5
  • aquatic counts: 30
  • animal counts: 1679

Safety information

risk assessment

  • @ref: 8287
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Fusobacterium simiae strain ATCC 33568 16S ribosomal RNA gene, partial sequenceM586851466ena855
20218Fusobacterium simiae rRNA small subunitX554071332ena855
8287Fusobacterium simiae strain ATCC 33568 16S ribosomal RNA gene, partial sequence; internal transcribed spacer 1, complete sequence; and 23S ribosomal RNA gene, partial sequenceAF342838741ena855
67770Fusobacterium simiae gene for 16S ribosomal RNA, partial sequence, strain: JCM 17465AB6161331466ena855

Genome sequences

  • @ref: 66792
  • description: Fusobacterium simiae DSM 19848
  • accession: GCA_026089295
  • assembly level: contig
  • database: ncbi
  • NCBI tax ID: 855

GC content

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

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno92.33no
flagellatedno95.382no
gram-positiveno91.574no
anaerobicyes99.609yes
aerobicno98.218yes
halophileno76.06no
spore-formingno90.308no
glucose-fermentyes56.925no
thermophileno98.474yes
glucose-utilyes85.204no

External links

@ref: 8287

culture collection no.: DSM 19848, ATCC 33568, CCM 3660, CCUG 16798, JCM 17465, KCTC 5548

straininfo link

  • @ref: 75251
  • straininfo: 44964

literature

  • topic: Metabolism
  • Pubmed-ID: 18793368
  • title: Stimulation of epithelial cell matrix metalloproteinase (MMP-2, -9, -13) and interleukin-8 secretion by fusobacteria.
  • authors: Gursoy UK, Kononen E, Uitto VJ
  • journal: Oral Microbiol Immunol
  • DOI: 10.1111/j.1399-302X.2008.00453.x
  • year: 2008
  • mesh: Blotting, Western, Cell Line, Epithelial Cells, Fusobacterium/classification/*physiology, Fusobacterium necrophorum/physiology, Fusobacterium nucleatum/physiology, Humans, Interleukin-8/analysis/*metabolism, Keratinocytes/*enzymology/microbiology, Matrix Metalloproteinase 1/analysis/metabolism, Matrix Metalloproteinase 13/analysis/metabolism, Matrix Metalloproteinase 9/analysis/metabolism, Matrix Metalloproteinases/analysis/*metabolism, Mouth/microbiology, Time Factors
  • topic2: Pathogenicity

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
8287Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19848)https://www.dsmz.de/collection/catalogue/details/culture/DSM-19848
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
46531Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 16798)https://www.ccug.se/strain?id=16798
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
75251Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID44964.1StrainInfo: A central database for resolving microbial strain identifiers