Strain identifier

BacDive ID: 5774

Type strain: Yes

Species: Fusobacterium varium

Strain history: Y. Benno <-- T. Mitsuoka <-- ATCC 8501 <-- A. H. Eggerth.

NCBI tax ID(s): 856 (species)

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General

@ref: 8363

BacDive-ID: 5774

DSM-Number: 19868

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

description: Fusobacterium varium DSM 19868 is an anaerobe, mesophilic, Gram-negative human pathogen that was isolated from human faeces.

NCBI tax id

  • NCBI tax id: 856
  • Matching level: species

strain history

@refhistory
8363<- CCUG <- NCTC <- ATCC <- A. H. Eggerth
67770Y. Benno <-- T. Mitsuoka <-- ATCC 8501 <-- A. H. Eggerth.

doi: 10.13145/bacdive5774.20230509.8.1

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 varium
  • full scientific name: Fusobacterium varium (Eggerth and Gagnon 1933) Moore and Holdeman 1969 (Approved Lists 1980)

  • synonyms

    @refsynonym
    20215Fusobacterium pseudonecrophorum
    20215Bacteroides varius

@ref: 8363

domain: Bacteria

phylum: Fusobacteria

class: Fusobacteriia

order: Fusobacteriales

family: Fusobacteriaceae

genus: Fusobacterium

species: Fusobacterium varium

full scientific name: Fusobacterium varium (Eggerth and Gagnon 1933) Moore and Holdeman 1969

type strain: yes

Morphology

cell morphology

  • @ref: 69480
  • gram stain: negative
  • confidence: 99.495

colony morphology

@refincubation period
83632-3 days
44797<1 day

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
8363CHOPPED 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
8363COLUMBIA 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
8363positivegrowth37mesophilic
67770positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
8363anaerobe
44797anaerobe
69480anaerobe98.639

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 98.806

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6838016199urea-hydrolysis
6838029016arginine-hydrolysis
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
8363----------+/-----+------+------
44797---------------+------+------
8363---------------+------+------

Isolation, sampling and environmental information

isolation

@refsample type
8363human faeces
44797Human feces

isolation source categories

Cat1Cat2Cat3
#Host#Human
#Host Body Product#Gastrointestinal tract#Feces (Stool)

taxonmaps

  • @ref: 69479
  • File name: preview.99_1233.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_140;96_717;97_839;98_975;99_1233&stattab=map
  • Last taxonomy: Fusobacterium
  • 16S sequence: AB640694
  • Sequence Identity:
  • Total samples: 54826
  • soil counts: 1169
  • aquatic counts: 2796
  • animal counts: 50429
  • plant counts: 432

Safety information

risk assessment

  • @ref: 8363
  • pathogenicity human: yes
  • pathogenicity animal: yes
  • biosafety level: 2
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Fusobacterium varium strain ATCC 8501 16S ribosomal RNA gene, partial sequence; internal transcribed spacer 1, complete sequence; and 23S ribosomal RNA gene, partial sequenceAF342853778ena856
20218Fusobacterium varium 16S rRNA gene, strain ATCC 8501AJ8670361493ena856
20218Fusobacterium varium strain CCUG 4858 clone 2 16S-23S ribosomal RNA intergenic spacer, partial sequenceGQ496444170ena856
20218Fusobacterium varium strain CCUG 4858 clone 9 16S-23S ribosomal RNA intergenic spacer, partial sequenceGQ496445170ena856
20218Fusobacterium varium small subunit rRNA sequenceM586861454ena856
20218Fusobacterium varium rRNA small subunitX554131333ena856
8363Fusobacterium varium strain ATCC 8501 16S ribosomal RNA gene, partial sequence; internal transcribed spacer 1, complete sequence; and 23S ribosomal RNA gene, partial sequenceAF342854778ena856
67770Fusobacterium varium gene for 16S ribosomal RNA, partial sequence, strain: JCM 6320AB6406941469ena856

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Fusobacterium varium NCTC10560GCA_900637705completencbi856
66792Fusobacterium varium strain NCTC10560856.21completepatric856
66792Fusobacterium varium NCTC105602847458331completeimg856

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes62no
flagellatedno93.685no
gram-positiveno89.19no
anaerobicyes99.387no
aerobicno97.765yes
halophileno89.205no
spore-formingno83.379no
thermophileno94.849yes
glucose-utilyes88.242no
motileno90.213no
glucose-fermentyes60.379no

External links

@ref: 8363

culture collection no.: DSM 19868, ATCC 8501, CCUG 4858, NCTC 10560, JCM 6320, BCRC 17682

straininfo link

  • @ref: 75253
  • straininfo: 34971

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny11999453Comparison of the 16S-23S rRNA intergenic spacer regions between Fusobacterium varium and "Fusobacterium pseudonecrophorum" strains.Jin J, Narongwanichgarn W, Xu D, Goto Y, Haga T, Shinjo TJ Vet Med Sci10.1292/jvms.64.2852002Base Sequence, Blotting, Southern, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal Spacer/chemistry/*genetics, Fusobacterium/chemistry/*classification/genetics, Molecular Sequence Data, Polymerase Chain Reaction, RNA, Ribosomal, 16S/chemistry/*genetics, RNA, Ribosomal, 23S/chemistry/*genetics, Sequence AlignmentGenetics
Pathogenicity19484811Seroprevalence of Fusobacterium varium in ulcerative colitis patients in Japan.Minami M, Ando T, Okamoto A, Sasaki N, Ohkura T, Torii K, Hasegawa T, Ohta M, Goto HFEMS Immunol Med Microbiol10.1111/j.1574-695X.2009.00550.x2009Adolescent, Adult, Aged, Animals, Antibodies, Bacterial/blood, Colitis, Ulcerative/blood/*complications/immunology, Female, Fusobacterium/*immunology, Fusobacterium Infections/*complications/*epidemiology/immunology, Humans, Japan/epidemiology, Male, Mice, Mice, Inbred BALB C, Middle Aged, Seroepidemiologic Studies, Severity of Illness Index
Metabolism22046091Corticotropin-releasing factor secretion from dendritic cells stimulated by commensal bacteria.Hojo M, Ohkusa T, Tomeoku H, Koido S, Asaoka D, Nagahara A, Watanabe SWorld J Gastroenterol10.3748/wjg.v17.i35.40172011Animals, Bacteroides/*metabolism, Cell Line, Clostridium/*metabolism, Corticotropin-Releasing Hormone/genetics/*metabolism, Dendritic Cells/cytology/*metabolism/*microbiology, Escherichia coli/*metabolism, Fusobacterium/*metabolism, Mice, RNA, Messenger/metabolism

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
8363Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19868)https://www.dsmz.de/collection/catalogue/details/culture/DSM-19868
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
44797Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 4858)https://www.ccug.se/strain?id=4858
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)
75253Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID34971.1StrainInfo: A central database for resolving microbial strain identifiers