Fusobacterium varium (DSM 19868, ATCC 8501, CCUG 4858)

Name: Fusobacterium varium (DSM 19868, ATCC 8501, CCUG 4858)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 5774

Type strain

Culture col. no. DSM 19868 ATCC 8501 CCUG 4858 NCTC 10560 JCM 6320 1 more

NCBI tax ID(s) 856

Special Collections DSMZ CCUG JCM

Links

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

anaerobe mesophilic human pathogen genome sequence 16S sequence

Name and taxonomic classification

SI-ID 34971

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

@ref 20215

Last LPSN update 2025-12-16 09:48:09

Domain Fusobacteriati

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 (2)

Fusobacterium pseudonecrophorum
"Bacteroides varius"

BacDive ID	Other strains from **Fusobacterium varium** (5)	Type strain
148256	F. varium CCUG 35114
153497	F. varium CCUG 49763
164785	F. varium JCM 3721
164786	F. varium JCM 3722, ATCC 51644, KCTC 15083
164787	F. varium JCM 3723

Morphology

Colony morphology

@ref	Incubation period
8363	2-3 days
44797	<1 day

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
8363	CHOPPED MEAT MEDIUM WITH CARBOHYDRATES (DSMZ Medium 110)		Medium recipe at MediaDive	Name: 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
8363	COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)		Medium recipe at MediaDive	Name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar base

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
8363	positive	growth	37	mesophilic
67770	positive	growth	37	mesophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
8363	anaerobe
44797	anaerobe
125439	anaerobe	98.8

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68380	29016 ChEBI	arginine	-	hydrolysis	from API rID32A
68380	29985 ChEBI	L-glutamate	-	degradation	from API rID32A
68380	17632 ChEBI	nitrate	-	reduction	from API rID32A
68380	16634 ChEBI	raffinose	-	fermentation	from API rID32A
68380	27897 ChEBI	tryptophan	+	energy source	from API rID32A
68380	16199 ChEBI	urea	-	hydrolysis	from API rID32A

Metabolite production

@ref	Chebi-ID	Metabolite	Production
68380	35581 ChEBI	indole		from API rID32A

Metabolite tests

@ref	Chebi-ID	Metabolite	Indole test
68380	35581 ChEBI	indole	+	from API rID32A

Enzymes

@ref	Value	Activity	Ec
68380	alanine arylamidase	-	3.4.11.2	from API rID32A
68380	alkaline phosphatase	-	3.1.3.1	from API rID32A
68380	alpha-arabinosidase	-	3.2.1.55	from API rID32A
68380	alpha-fucosidase	-	3.2.1.51	from API rID32A
68380	alpha-galactosidase	-	3.2.1.22	from API rID32A
68380	alpha-glucosidase	-	3.2.1.20	from API rID32A
68380	arginine dihydrolase	-	3.5.3.6	from API rID32A
68380	beta-galactosidase	-	3.2.1.23	from API rID32A
68380	beta-Galactosidase 6-phosphate	-		from API rID32A
68380	beta-glucosidase	-	3.2.1.21	from API rID32A
68380	beta-glucuronidase	-	3.2.1.31	from API rID32A
68380	glutamate decarboxylase	-	4.1.1.15	from API rID32A
68380	glutamyl-glutamate arylamidase	-		from API rID32A
68380	glycin arylamidase	-		from API rID32A
68380	histidine arylamidase	-		from API rID32A
68380	L-arginine arylamidase	-		from API rID32A
68380	leucine arylamidase	-	3.4.11.1	from API rID32A
68380	leucyl glycin arylamidase	-	3.4.11.1	from API rID32A
68380	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API rID32A
68380	phenylalanine arylamidase	-		from API rID32A
68380	proline-arylamidase	-	3.4.11.5	from API rID32A
68380	pyrrolidonyl arylamidase	+	3.4.19.3	from API rID32A
68380	serine arylamidase	-		from API rID32A
68380	tryptophan deaminase	+	4.1.99.1	from API rID32A
68380	tyrosine arylamidase	-		from API rID32A
68380	urease	-	3.5.1.5	from API rID32A

API rID32A

@ref	URE	ADH (Arg)	alpha GAL	beta GAL	beta-Galactosidase 6-phosphatebeta GP	alpha GLU	beta GLU	alpha ARA	beta GUR	beta-N-Acetyl-beta-glucosaminidasebeta NAG	MNE	RAF	GDC	alpha FUC	Reduction of nitrateNIT	IND	PAL	L-arginine arylamidaseArgA	ProA	LGA	Phenylalanine arylamidasePheA	Leucine arylamidaseLeuA	PyrA	Tyrosine arylamidaseTyrA	Alanine arylamidaseAlaA	Glycin arylamidaseGlyA	Histidine arylamidaseHisA	Glutamyl-glutamate arylamidaseGGA	Serine arylamidaseSerA
8363	-	-	-	-	-	-	-	-	-	-	+/-	-	-	-	-	+	-	-	-	-	-	-	+	-	-	-	-	-	-
44797	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	-	-	-	-	+	-	-	-	-	-	-
8363	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	-	-	-	-	+	-	-	-	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Human	-
#Host Body Product	#Gastrointestinal tract	#Feces (Stool)

Isolation

@ref	Sample type
8363	human faeces
44797	Human feces

Taxonmaps

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

Interaction and safety

Risk assessment

@ref	Pathogenicity human	Pathogenicity animal	Biosafety level	Biosafety level comment
8363			2	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	52451_E01 assembly for Fusobacterium varium NCTC10560	complete	GCA_900637705	856.21	2847458331	856	65.26

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
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	856
20218	Fusobacterium varium 16S rRNA gene, strain ATCC 8501	AJ867036	1493	856
20218	Fusobacterium varium small subunit rRNA sequence	M58686	1454	856
20218	Fusobacterium varium rRNA small subunit	X55413	1333	856
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	856
67770	Fusobacterium varium gene for 16S ribosomal RNA, partial sequence, strain: JCM 6320	AB640694	1469	856
124043	Fusobacterium varium partial 16S rRNA gene, strain CCUG 4858	LT594100	1372	856

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Fusobacterium varium strain NCTC10560
PATRIC: 856.21

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	yes	58.30	no
125439	motility	BacteriaNetⓘ	yes	71.80	no
125439	gram_stain	BacteriaNetⓘ	positive	80.50	no
125439	oxygen_tolerance	BacteriaNetⓘ	anaerobe	98.80	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Fusobacterium varium NCTC10560
NCBI: GCA_900637705.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	83.46	no
125438	anaerobic	anaerobicⓘ	yes	86.21	no
125438	aerobic	aerobicⓘ	no	94.37	no
125438	spore-forming	spore-formingⓘ	no	72.92	no
125438	thermophilic	thermophileⓘ	no	93.15	no
125438	flagellated	motile2+ⓘ	no	74.27	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	The Regulation of Nucleic Acid Vaccine Responses by the Microbiome.	Johnson AMF, Hager K, Alameh MG, Van P, Potchen N, Mayer-Blackwell K, Fiore-Gartland A, Minot S, Lin PJC, Tam YK, Weissman D, Kublin JG.	J Immunol	10.4049/jimmunol.2300196	2023
Metabolism	Human skin microbiota is a rich source of bacteriocin-producing staphylococci that kill human pathogens.	O'Sullivan JN, Rea MC, O'Connor PM, Hill C, Ross RP.	FEMS Microbiol Ecol	10.1093/femsec/fiy241	2019
	Unexpected finding of Fusobacterium varium as the dominant Fusobacterium species in cattle rumen: potential implications for liver abscess etiology and interventions.	Schwarz C, Mathieu J, Gomez JL, Miller MR, Tikhonova M, Nagaraja TG, Alvarez PJJ.	J Anim Sci	10.1093/jas/skad130	2023
Transcriptome	Characterization of Fusobacterium varium Fv113-g1 isolated from a patient with ulcerative colitis based on complete genome sequence and transcriptome analysis.	Sekizuka T, Ogasawara Y, Ohkusa T, Kuroda M.	PLoS One	10.1371/journal.pone.0189319	2017
	Association of germ-free mice with a simplified human intestinal microbiota results in a shortened intestine.	Slezak K, Krupova Z, Rabot S, Loh G, Levenez F, Descamps A, Lepage P, Dore J, Bellier S, Blaut M.	Gut Microbes	10.4161/gmic.28203	2014
Pathogenicity	In vitro activity of tomopenem (CS-023/RO4908463) against anaerobic bacteria.	Tanaka K, Mikamo H, Nakao K, Ichiishi T, Goto T, Yamagishi Y, Watanabe K.	Antimicrob Agents Chemother	10.1128/aac.00595-08	2009
Pathogenicity	In vitro antimicrobial activity of razupenem (SMP-601, PTZ601) against anaerobic bacteria.	Tran CM, Tanaka K, Yamagishi Y, Goto T, Mikamo H, Watanabe K.	Antimicrob Agents Chemother	10.1128/aac.01038-10	2011
Pathogenicity	The Use of Defined Microbial Communities To Model Host-Microbe Interactions in the Human Gut.	Elzinga J, van der Oost J, de Vos WM, Smidt H.	Microbiol Mol Biol Rev	10.1128/mmbr.00054-18	2019
	In vitro and in vivo antibacterial activities of TAK-083, an agent for treatment of Helicobacter pylori infection.	Kanamaru T, Nakano Y, Toyoda Y, Miyagawa KI, Tada M, Kaisho T, Nakao M.	Antimicrob Agents Chemother	10.1128/aac.45.9.2455-2459.2001	2001
Pathogenicity	In vitro activities of gatifloxacin, two other quinolones, and five nonquinolone antimicrobials against obligately anaerobic bacteria.	Schaumann R, Ackermann G, Pless B, Claros MC, Rodloff AC.	Antimicrob Agents Chemother	10.1128/aac.43.11.2783	1999
Phylogeny	Quantification of different Eubacterium spp. in human fecal samples with species-specific 16S rRNA-targeted oligonucleotide probes.	Schwiertz A, Le Blay G, Blaut M.	Appl Environ Microbiol	10.1128/aem.66.1.375-382.2000	2000
Pathogenicity	In vitro antianaerobic activity of DX-619, a new des-fluoro(6) quinolone.	Tanaka K, Mikamo H, Nakao K, Watanabe K.	Antimicrob Agents Chemother	10.1128/aac.00639-06	2006
Enzymology	Abilities of the mCP Agar method and CRENAME alpha toxin-specific real-time PCR assay to detect Clostridium perfringens spores in drinking water.	Maheux AF, Berube E, Boudreau DK, Villeger R, Cantin P, Boissinot M, Bissonnette L, Bergeron MG.	Appl Environ Microbiol	10.1128/aem.02791-13	2013
Pathogenicity	In vitro activity of FK037, a new parenteral cephalosporin, against anaerobic bacteria.	Kato N, Kato H, Tanaka Y, Bando K, Watanabe K, Ueno K.	Antimicrob Agents Chemother	10.1128/aac.37.5.957	1993
Phylogeny	PCR assay for species-specific identification of Bacteroides thetaiotaomicron.	Teng LJ, Hsueh PR, Tsai JC, Chiang FL, Chen CY, Ho SW, Luh KT.	J Clin Microbiol	10.1128/jcm.38.4.1672-1675.2000	2000
Phylogeny	Use of PCR and sodium dodecyl sulfate-polyacrylamide gel electrophoresis techniques for differentiation of Prevotella intermedia sensu stricto and Prevotella nigrescens.	Premaraj T, Kato N, Fukui K, Kato H, Watanabe K.	J Clin Microbiol	10.1128/jcm.37.4.1057-1061.1999	1999
	Polysaccharide-mediated protection against abscess formation in experimental intra-abdominal sepsis.	Tzianabos AO, Kasper DL, Cisneros RL, Smith RS, Onderdonk AB.	J Clin Invest	10.1172/jci118340	1995
	Cellular fatty acids in Fusobacterium species as a tool for identification.	Tuner K, Baron EJ, Summanen P, Finegold SM.	J Clin Microbiol	10.1128/jcm.30.12.3225-3229.1992	1992
	Morphology of bacteriophage-like particles from Fusobacterium symbiosum.	Foglesong MA, Markovetz AJ.	J Bacteriol	10.1128/jb.119.1.325-329.1974	1974
	Antimicrobial activity of DU-6681a, a parent compound of novel oral carbapenem DZ-2640.	Tanaka M, Hohmura M, Nishi T, Sato K, Hayakawa I.	Antimicrob Agents Chemother	10.1128/aac.41.6.1260	1997
Pathogenicity	Comparison of the activity of ionophores with other antibacterial agents against anaerobes.	Watanabe K, Watanabe J, Kuramitsu S, Maruyama HB.	Antimicrob Agents Chemother	10.1128/aac.19.4.519	1981
Phylogeny	Rapid and correct identification of intestinal Bacteroides spp. with chromosomal DNA probes by whole-cell dot blot hybridization.	Morotomi M, Ohno T, Mutai M.	Appl Environ Microbiol	10.1128/aem.54.5.1158-1162.1988	1988
Pathogenicity	In vitro and in vivo antibacterial activities of AT-4140, a new broad-spectrum quinolone.	Nakamura S, Minami A, Nakata K, Kurobe N, Kouno K, Sakaguchi Y, Kashimoto S, Yoshida H, Kojima T, Ohue T.	Antimicrob Agents Chemother	10.1128/aac.33.8.1167	1989
Pathogenicity	Ceftizoxime (FK 749), a new parenteral cephalosporin: in vitro and in vivo antibacterial activities.	Kamimura T, Matsumoto Y, Okada N, Mine Y, Nishida M, Goto S, Kuwahara S.	Antimicrob Agents Chemother	10.1128/aac.16.5.540	1979
Pathogenicity	Antimicrobial and beta-lactamase inhibitory activities of carpetimycins A and B, new carbapenem antibiotics.	Kobayashi F, Saino Y, Koshi T, Hattori Y, Nakayama M, Iwasaki A, Mori T, Mitsuhashi S.	Antimicrob Agents Chemother	10.1128/aac.21.4.536	1982
	Quantitative gas chromatographic analysis of volatile fatty acids in spent culture media and body fluids.	van den Bogaard AE, Hazen MJ, Van Boven CP.	J Clin Microbiol	10.1128/jcm.23.3.523-530.1986	1986
Phylogeny	Evaluation of simplified dichotomous schemata for the identification of anaerobic bacteria from clinical material.	Porschen RK, Stalons DR.	J Clin Microbiol	10.1128/jcm.3.2.161-171.1976	1976
	Gut microbiota composition in male rat models under different nutritional status and physical activity and its association with serum leptin and ghrelin levels.	Queipo-Ortuno MI, Seoane LM, Murri M, Pardo M, Gomez-Zumaquero JM, Cardona F, Casanueva F, Tinahones FJ.	PLoS One	10.1371/journal.pone.0065465	2013
Phylogeny	Gut microbiota in children with type 1 diabetes differs from that in healthy children: a case-control study.	Murri M, Leiva I, Gomez-Zumaquero JM, Tinahones FJ, Cardona F, Soriguer F, Queipo-Ortuno MI.	BMC Med	10.1186/1741-7015-11-46	2013
Enzymology	Specific detection of Mycobacterium paratuberculosis by DNA hybridisation with a fragment of the insertion element IS900.	Moss MT, Green EP, Tizard ML, Malik ZP, Hermon-Taylor J.	Gut	10.1136/gut.32.4.395	1991
	Compilation of small ribosomal subunit RNA structures.	Neefs JM, Van de Peer Y, De Rijk P, Chapelle S, De Wachter R.	Nucleic Acids Res	10.1093/nar/21.13.3025	1993
	Metabolite-mediated interactions and direct contact between Fusobacterium varium and Faecalibacterium prausnitzii.	Hosomi K, Maruyama S, Matsuoka T, Furuta M, Tojima Y, Uchiyama K, Morita M, Kawashima H, Kobayashi T, Kunisawa J.	Microbiome	10.1186/s40168-025-02168-w	2025
	Isolation and Evaluation of Potential Use of Prebiotics-Utilizing Butyrate-Producing Bacteria in Nibea coibor.	Li Z, Tran NT, Zhang M, Li Z, Yang W, Wang S, Hu Z, Li S.	Aquac Nutr	10.1155/anu/4679037	2025
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 .
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#125438	Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 )
#125439	Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy: deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 .
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

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Fusobacterium varium (DSM 19868, ATCC 8501, CCUG 4858)

Name and taxonomic classification

Morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

API rID32A

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_900637705

16S sequences

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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