Name: Fusobacterium varium DSM 19868
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 5774

Type strain:

Species: Fusobacterium varium

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

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

NCBI tax ID(s): 856 (species)

SI-ID 34971

ATCC 8501, NCTC 10560, CCUG 4858, BCRC 17682, CCRC 17682, DSM 19868, JCM 6320

Special Collections

Other strains from Fusobacterium varium

Section

Fusobacterium varium DSM 19868 is an anaerobe human pathogen that was isolated from human faeces.

anaerobe
human pathogen
16S sequence
Bacteria
genome sequence

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Fusobacteriota*
	Class	*Fusobacteriia*
	Order	*Fusobacteriales*
	Family	*Fusobacteriaceae*
	Genus	*Fusobacterium*
	Species	**Fusobacterium varium**
	Full Scientific Name (LPSN)	Fusobacterium varium (Eggerth and Gagnon 1933) Moore and Holdeman 1969 (Approved Lists 1980)

	Synonym	Fusobacterium pseudonecrophorum
	Synonym	"Bacteroides* varius"*

Information on morphological and physiological properties Morphology

[Ref.: #8363]	Incubation period	2-3 days

[Ref.: #44797]	Incubation period	<1 day

Information on culture and growth conditions Culture and growth conditions

[Ref.: #8363]

Culture medium

CHOPPED MEAT MEDIUM WITH CARBOHYDRATES (DSMZ Medium 110)

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Culture medium growth

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Culture medium link

Medium recipe at MediaDive

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Culture medium composition

expand / minimize

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Culture medium

COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)

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Culture medium growth

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Culture medium link

Medium recipe at MediaDive

[Ref.: #8363]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #8363]			growth	37 °C
[Ref.: #67770]			growth	37 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #8363]	Oxygen tolerance	anaerobe
[Ref.: #44797]	Oxygen tolerance	anaerobe

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #68380]	arginine ChEBI	-	hydrolysis	* from API rID32A
[Ref.: #68380]	L-glutamate ChEBI	-	degradation	* from API rID32A
[Ref.: #68380]	nitrate ChEBI	-	reduction	* from API rID32A
[Ref.: #68380]	raffinose ChEBI	-	fermentation	* from API rID32A
[Ref.: #68380]	tryptophan ChEBI	+	energy source	* from API rID32A
[Ref.: #68380]	urea ChEBI	-	hydrolysis	* from API rID32A

	Metabolite production	Metabolite	Production
[Ref.: #68380]		indole ChEBI	yes	* from API rID32A

	Physiological tests	Metabolite	Indole test
[Ref.: #68380]		indole ChEBI	+	* from API rID32A

	Enzyme	Enzyme activity	EC number
[Ref.: #68380]	alanine arylamidase	-	3.4.11.2	* from API rID32A
[Ref.: #68380]	alkaline phosphatase	-	3.1.3.1	* from API rID32A
[Ref.: #68380]	alpha-arabinosidase	-	3.2.1.55	* from API rID32A
[Ref.: #68380]	alpha-fucosidase	-	3.2.1.51	* from API rID32A
[Ref.: #68380]	alpha-galactosidase	-	3.2.1.22	* from API rID32A
[Ref.: #68380]	alpha-glucosidase	-	3.2.1.20	* from API rID32A
[Ref.: #68380]	arginine dihydrolase	-	3.5.3.6	* from API rID32A
[Ref.: #68380]	beta-galactosidase	-	3.2.1.23	* from API rID32A
[Ref.: #68380]	beta-Galactosidase 6-phosphate	-		* from API rID32A
[Ref.: #68380]	beta-glucosidase	-	3.2.1.21	* from API rID32A
[Ref.: #68380]	beta-glucuronidase	-	3.2.1.31	* from API rID32A
[Ref.: #68380]	glutamate decarboxylase	-	4.1.1.15	* from API rID32A
[Ref.: #68380]	glutamyl-glutamate arylamidase	-		* from API rID32A
[Ref.: #68380]	glycin arylamidase	-		* from API rID32A
[Ref.: #68380]	histidine arylamidase	-		* from API rID32A
[Ref.: #68380]	L-arginine arylamidase	-		* from API rID32A
[Ref.: #68380]	leucine arylamidase	-	3.4.11.1	* from API rID32A
[Ref.: #68380]	leucyl glycin arylamidase	-	3.4.11.1	* from API rID32A
[Ref.: #68380]	N-acetyl-beta-glucosaminidase	-	3.2.1.52	* from API rID32A
[Ref.: #68380]	phenylalanine arylamidase	-		* from API rID32A
[Ref.: #68380]	proline-arylamidase	-	3.4.11.5	* from API rID32A
[Ref.: #68380]	pyrrolidonyl arylamidase	+	3.4.19.3	* from API rID32A
[Ref.: #68380]	serine arylamidase	-		* from API rID32A
[Ref.: #68380]	tryptophan deaminase	+	4.1.99.1	* from API rID32A
[Ref.: #68380]	tyrosine arylamidase	-		* from API rID32A
[Ref.: #68380]	urease	-	3.5.1.5	* from API rID32A
	Only first 10 entries are displayed. Click here to see all.

API® rID32A:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	Urease/urea hydrolysisURE	Arginine dihydrolaseADH (Arg)	alpha-Galactosidasealpha GAL	beta-Galactosidasebeta GAL	beta-Galactosidase 6-phosphatebeta GP	alpha-Glucosidasealpha GLU	beta-Glucosidasebeta GLU	alpha-Arabinosidasealpha ARA	beta-Glucuronidasebeta GUR	beta-N-Acetyl-beta-glucosaminidasebeta NAG	Fermentation of D-mannoseMNE	Fermentation of raffinoseRAF	Glutamate decarboxylaseGDC	alpha-Fucosidasealpha FUC	Reduction of nitrateNIT	Indole productionIND	Alkaline phosphatasePAL	L-arginine arylamidaseArgA	Proline arylamidaseProA	Leucyl glycin arylamidaseLGA	Phenylalanine arylamidasePheA	Leucine arylamidaseLeuA	Pyrrolidonyl arylamidasePyrA	Tyrosine arylamidaseTyrA	Alanine arylamidaseAlaA	Glycin arylamidaseGlyA	Histidine arylamidaseHisA	Glutamyl-glutamate arylamidaseGGA	Serine arylamidaseSerA
[Ref.: #8363]	13388	-	-	-	-	-	-	-	-	-	-	+/-	-	-	-	-	+	-	-	-	-	-	-	+	-	-	-	-	-	-
[Ref.: #44797]	3972	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	-	-	-	-	+	-	-	-	-	-	-
[Ref.: #8363]	12402	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	-	-	-	-	+	-	-	-	-	-	-

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #8363]	Sample type/isolated from	human faeces

[Ref.: #44797]	Sample type/isolated from	Human feces
* marker position based on {}

Isolation sources categories

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

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AB640694 (>99% sequence identity) for Fusobacterium from Microbeatlas

Aquatic Samples	2796
Soil Samples	1169
Animal Samples	50429
Plant Samples	432
Total Samples	54826

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #8363]	Pathogenicity (human)	yes
[Ref.: #8363]	Pathogenicity (animal)	yes
[Ref.: #8363]	Biosafety level	2	Risk group (German classification) According to TRBA 466

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

Only first 5 entries are displayed. Click here to see all.

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #8363]	Fusobacterium varium strain ATCC 8501 16S ribosomal RNA gene, partial sequence; internal transcribed spacer 1, complete sequence; and 23S ribosomal RNA gene, partial sequence	AF342854	778	GenBank ENA	856 tax ID
[Ref.: #67770]	Fusobacterium varium gene for 16S ribosomal RNA, partial sequence, strain: JCM 6320	AB640694	1469	GenBank ENA	856 tax ID
[Ref.: #124043]	Fusobacterium varium partial 16S rRNA gene, strain CCUG 4858	LT594100	1372	GenBank ENA	856 tax ID	*
[Ref.: #20218]	Fusobacterium varium 16S rRNA gene, strain ATCC 8501	AJ867036	1493	GenBank ENA	856 tax ID	*
[Ref.: #20218]	Fusobacterium varium strain ATCC 8501 16S ribosomal RNA gene, partial sequence; internal transcribed spacer 1, complete sequence; and 23S ribosomal RNA gene, partial sequence	AF342853	778	GenBank ENA	856 tax ID	*
[Ref.: #20218]	Fusobacterium varium strain CCUG 4858 clone 2 16S-23S ribosomal RNA intergenic spacer, partial sequence	GQ496444	170	GenBank ENA	856 tax ID	*
[Ref.: #20218]	Fusobacterium varium strain CCUG 4858 clone 9 16S-23S ribosomal RNA intergenic spacer, partial sequence	GQ496445	170	GenBank ENA	856 tax ID	*
[Ref.: #20218]	Fusobacterium varium rRNA small subunit	X55413	1333	GenBank ENA	856 tax ID	*
[Ref.: #20218]	Fusobacterium varium small subunit rRNA sequence	M58686	1454	GenBank ENA	856 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Fusobacterium varium NCTC10560	GCA_900637705	complete	GenBank ENA	856 tax ID	*
[Ref.: #66792]	Fusobacterium varium strain NCTC10560	856.21	complete	PATRIC	856 tax ID	*
[Ref.: #66792]	Fusobacterium varium NCTC10560	2847458331	complete	JGI IMG/M	856 tax ID	*

Data predicted using genome information as a basis Genome-based predictions

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Fusobacterium varium strain NCTC10560 PATRIC: 856.21
[Ref.: #69481]	spore-forming	spore-formingⓘ	yes	62	no

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Fusobacterium varium NCTC10560 NCBI: GCA_900637705.1
[Ref.: #69480]	gram-positive	gram-positiveⓘ	no	83.456	no
[Ref.: #69480]	anaerobic	anaerobicⓘ	yes	86.213	no
[Ref.: #69480]	aerobic	aerobicⓘ	no	94.37	no
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	72.923	no
[Ref.: #69480]	thermophilic	thermophileⓘ	no	93.147	no
[Ref.: #69480]	flagellated	motile2+ⓘ	no	74.268	no

Availability in culture collections External links

[Ref.: #8363]

Culture collection no.

DSM 19868, ATCC 8501, CCUG 4858, NCTC 10560, JCM 6320, BCRC 17682

[Ref.: #75253]

SI-ID 34971

Literature:

Topic	Title	Authors	Journal	DOI	Year
Metabolism	Corticotropin-releasing factor secretion from dendritic cells stimulated by commensal bacteria.	Hojo M, Ohkusa T, Tomeoku H, Koido S, Asaoka D, Nagahara A, Watanabe S	World J Gastroenterol	10.3748/wjg.v17.i35.4017	2011	*
Pathogenicity	Seroprevalence 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 H	FEMS Immunol Med Microbiol	10.1111/j.1574-695X.2009.00550.x	2009	*
Phylogeny	Comparison 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 T	J Vet Med Sci	10.1292/jvms.64.285	2002	*

References

#8363

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 19868

#20215

Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.: List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ. IJSEM ( DOI 10.1099/ijsem.0.004332 )

#20218

Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 )

#44797 Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 4858

#66792

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#67770 Japan Collection of Microorganism (JCM) ; Curators of the JCM;

#68380

Automatically annotated from API rID32A .

#69479

João 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.: MicrobeAtlas 1.0 beta .

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

#75253

Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.: StrainInfo: A central database for resolving microbial strain identifiers . ( DOI 10.60712/SI-ID34971.1 )

#124043

Dr. Isabel Schober, Dr. Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .

* These data were automatically processed and therefore are not curated

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Fusobacterium varium strain NCTC10560

Fusobacterium varium NCTC10560

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