Atopobium fossor (DSM 15642, ATCC 43386, CCUG 45424)

Name: Atopobium fossor (DSM 15642, ATCC 43386, CCUG 45424)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 3042

Type strain

Culture col. no. DSM 15642 ATCC 43386 CCUG 45424 CIP 106638 JCM 9981 2 more

NCBI tax ID(s) 1121023 39487

Special Collections DSMZ CCUG JCM CIP

History DSMZ <- Y. Benno, JCM <- STAFF 1023 <- ATCC <- D. N. Love and G. D. Bailey; VPB 2127 JCM <-- STAFF 1023 <-- ATCC 43386 <-- D. N. Love and G. D. Bailey VPB 2127. CIP <- 2000, JCM <- STAFF 1023 <- ATCC <- D.N. Love and G.D. Bailey: strain VPB 2127, Eubacterium fossor

Links

Atopobium fossor DSM 15642 is an obligate anaerobe, Gram-positive, coccus-shaped animal pathogen that was isolated from horse, submandilar abscess.

Gram-positive coccus-shaped obligate anaerobe animal pathogen genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 46048

ATCC 43386,JCM 9981,CCUG 45424,NCTC 11919,CIP 106638,DSM 15642

@ref 20215

Last LPSN update 2026-05-29 08:25:37

Domain Bacteria

Phylum Actinomycetota

Class Coriobacteriia

Order Coriobacteriales

Family Atopobiaceae

Genus Atopobium

Species Atopobium fossor

Full scientific name Atopobium fossor (Bailey and Love 1986) Kageyama et al. 1999

Synonyms (1)

Eubacterium fossor

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Confidence
119440	positive	coccus-shaped
125438			92.5
125439	negative		99.539

Colony morphology

119440

Hemolysis ability0

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
6012	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

Culture temp

@ref	Growth	Type	Temperature (°C)
6012	positive	growth	37
67770	positive	growth	37
119440	positive	growth	37
119440	negative	growth	10
119440	negative	growth	30
119440	negative	growth	35
119440	negative	growth	41
119440	negative	growth	45

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
6012	obligate anaerobe
125439	obligate aerobe	90.719

Spore formation

@ref	Spore formation	Confidence
125439		99.989

Halophily

@ref	Salt	Growth	Tested relation	Concentration
119440	NaCl		growth	6.5 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68380	29016 ChEBI	arginine	+	hydrolysis	from API rID32A
68380	16024 ChEBI	D-mannose	-	fermentation	from API rID32A
119440	4853 ChEBI	esculin	-	hydrolysis
119440	606565 ChEBI	hippurate	+	hydrolysis
68380	29985 ChEBI	L-glutamate	-	degradation	from API rID32A
119440	17632 ChEBI	nitrate	-	reduction
68380	17632 ChEBI	nitrate	-	reduction	from API rID32A
119440	16301 ChEBI	nitrite	-	reduction
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	Voges-proskauer-test
119440	15688 ChEBI	acetoin		-
68380	35581 ChEBI	indole	-		from API rID32A

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
68380	alanine arylamidase	+	3.4.11.2	from API rID32A
119440	alcohol dehydrogenase	-	1.1.1.1
68382	alkaline phosphatase	-	3.1.3.1	from API zym
68380	alkaline phosphatase	+	3.1.3.1	from API rID32A
68380	alpha-arabinosidase	-	3.2.1.55	from API rID32A
68382	alpha-chymotrypsin	-	3.4.21.1	from API zym
68382	alpha-fucosidase	-	3.2.1.51	from API zym
68380	alpha-fucosidase	-	3.2.1.51	from API rID32A
68382	alpha-galactosidase	-	3.2.1.22	from API zym
68380	alpha-galactosidase	-	3.2.1.22	from API rID32A
68382	alpha-glucosidase	-	3.2.1.20	from API zym
68380	alpha-glucosidase	-	3.2.1.20	from API rID32A
68382	alpha-mannosidase	-	3.2.1.24	from API zym
68380	arginine dihydrolase	+	3.5.3.6	from API rID32A
68382	beta-galactosidase	-	3.2.1.23	from API zym
119440	beta-galactosidase	-	3.2.1.23
68380	beta-galactosidase	-	3.2.1.23	from API rID32A
68380	beta-Galactosidase 6-phosphate	-		from API rID32A
68382	beta-glucosidase	-	3.2.1.21	from API zym
68380	beta-glucosidase	-	3.2.1.21	from API rID32A
68382	beta-glucuronidase	+	3.2.1.31	from API zym
68380	beta-glucuronidase	-	3.2.1.31	from API rID32A
119440	catalase	+	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
119440	gamma-glutamyltransferase	-	2.3.2.2
68380	glutamate decarboxylase	-	4.1.1.15	from API rID32A
68380	glutamyl-glutamate arylamidase	-		from API rID32A
68380	L-arginine arylamidase	+		from API rID32A
68382	leucine arylamidase	+	3.4.11.1	from API zym
68380	leucine arylamidase	+	3.4.11.1	from API rID32A
68382	lipase (C 14)	-		from API zym
119440	lysine decarboxylase	-	4.1.1.18
68382	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API zym
68380	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API rID32A
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
119440	ornithine decarboxylase	-	4.1.1.17
119440	oxidase	-
68380	pyrrolidonyl arylamidase	-	3.4.19.3	from API rID32A
68382	trypsin	-	3.4.21.4	from API zym
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
68382	valine arylamidase	-		from API zym

API zym

@ref	Control	Alkaline phosphatase	Esterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	Lipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	Trypsin	alpha- Chymotrypsin	Acid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	alpha- Galactosidase	beta- Galactosidase	beta- Glucuronidase	alpha- Glucosidase	beta- Glucosidase	N-acetyl-beta- glucosaminidase	alpha- Mannosidase	alpha- Fucosidase
119440	-	-	+	+	-	+	-	-	-	-	+	+	-	-	+	-	-	-	-	-

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
6012	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	+	+/-	+/-	+/-	+	-	+	+	+/-	+/-	-	+/-

API biotype100

@ref	ControlQ	D-glucose as carbon sourceGLU	D-fructose as carbon sourceFRU	D-galactose as carbon sourceGAL	D-trehalose as carbon sourceTRE	D-mannose as carbon sourceMNE	L-sorbose as carbon sourceSBE	D-melibiose as carbon sourceMEL	sucrose as carbon sourceSAC	D-raffinose as carbon sourceRAF	maltotriose as carbon sourceMTE	maltose as carbon sourceMAL	lactose as carbon sourceLAC	lactulose as carbon sourceLTE	1-O-methyl-beta-galactopyranoside as carbon sourceMbGa	1-O-methyl-alpha-galactopyranoside as carbon sourceMaGa	D-cellobiose as carbon sourceCEL	gentiobiose as carbon sourceGEN	1-O-methyl-beta-D-glucopyranoside as carbon sourceMbGu	esculin as carbon sourceESC	D-ribose as carbon sourceRIB	L-arabinose as carbon sourceARA	D-xylose as carbon sourceXYL	palatinose as carbon sourcePLE	L-rhamnose as carbon sourceRHA	L-fucose as carbon sourceFUC	D-melezitose as carbon sourceMLZ	D-arabitol as carbon sourceDARL	L-arabitol as carbon sourceLARL	xylitol as carbon sourceXLT	dulcitol as carbon sourceDUL	D-tagatose as carbon sourceTAG	glycerol as carbon sourceGLY	myo-inositol as carbon sourceINO	D-mannitol as carbon sourceMAN	maltitol as carbon sourceMTL	D-turanose as carbon sourceTUR	D-sorbitol as carbon sourceSOR	adonitol as carbon sourceADO	hydroxyquinoline-beta-glucuronide as carbon sourceHBG	D-lyxose as carbon sourceLYX	i-erythritol as carbon sourceERY	1-O-methyl-alpha-D-glucoside as carbon sourceMDG	3-O-methyl-D-glucose as carbon source3MDG	D-saccharate as carbon sourceSAT	mucate as carbon sourceMUC	L-tartrate as carbon sourceLTAT	D-tartrate as carbon sourceDTAT	meso-tartrate as carbon sourceMTAT	D-malate as carbon sourceDMLT	L-malate as carbon sourceLMLT	cis-aconitate as carbon sourceCATE	trans-aconitate as carbon sourceTATE	tricarballylate as carbon sourceTTE	citrate as carbon sourceCIT	D-glucuronate as carbon sourceGRT	D-galacturonate as carbon sourceGAT	2-ketogluconate as carbon source2KG	5-ketogluconate as carbon source5KG	tryptophan as carbon sourceTRY	N-acetyl-D-glucosamine as carbon sourceNAG	D-gluconate as carbon sourceGNT	phenylacetate as carbon sourcePAC	protocatechuate as carbon sourcePAT	4-hydroxybenzoate as carbon sourcepOBE	quinate as carbon sourceQAT	gentisate as carbon sourceGTE	3-hydroxybenzoate as carbon sourcemOBE	benzoate as carbon sourceBAT	3-phenylpropionate as carbon sourcePPAT	m-coumarate as carbon sourceCMT	trigonelline as carbon sourceTGE	betaine as carbon sourceBET	putrescine as carbon sourcePCE	4-aminobutyrate as carbon sourceABT	histamine as carbon sourceHIN	DL-lactate as carbon sourceLAT	caprate as carbon sourceCAP	caprylate as carbon sourceCYT	L-histidine as carbon sourceHIS	succinate as carbon sourceSUC	fumarate as carbon sourceFUM	glutarate as carbon sourceGRE	DL-glycerate as carbon sourceGYT	5-aminovalerate as carbon sourceAVT	ethanolamine as carbon sourceETN	tryptamine as carbon sourceTTN	D-glucosamine as carbon sourceGLN	itaconate as carbon sourceITA	3-hydroxybutyrate as carbon source3OBU	L-aspartate as carbon sourceAPT	L-glutamate as carbon sourceGTT	L-proline as carbon sourcePRO	D-alanine as carbon sourceDALA	L-alanine as carbon sourceLALA	L-serine as carbon sourceSER	malonate as carbon sourceMNT	propionate as carbon sourcePROP	L-tyrosine as carbon sourceTYR	2-ketoglutarate as carbon source2KT
119440	not determinedn.d.	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Mammals	#Equidae (Horse)
#Host Body-Site	#Oral cavity and airways	-

Isolation

@ref	Sample type	Country	Country ISO 3 Code	Continent
6012	horse, submandilar abscess	Australia	AUS	Australia and Oceania
56775	Horse submindilar abscess	Australia	AUS	Australia and Oceania
67770	Submandibular abscess in horse	Australia	AUS	Australia and Oceania
119440	Animal, Horse, submandilar abscess	Australia	AUS	Australia and Oceania

Interaction and safety

Risk assessment

@ref	Pathogenicity animal	Biosafety level	Biosafety level comment
6012		2	Risk group (German classification) According to TRBA 466
119440		1	Risk group (French 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	Atopobium fossor DSM 15642	contig		1121023.3		1121023	79
67770	ASM48312v1 assembly for Atopobium fossor DSM 15642	scaffold	GCA_000483125	1121023.4	2523231056	1121023	77.23

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Atopobium fossor strain ATCC 43386 16S ribosomal RNA gene, partial sequence	L34620	1469	39487
20218	Eubacterium fossor gene for 16S rRNA	AB015945	1475	39487
67770	Atopobium fossor gene for 16S ribosomal RNA, partial sequence, strain: JCM 9981	LC037224	1480	39487

GC content

67770

GC-content (mol%)44

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Atopobium fossor DSM 15642
BV-BRC: 1121023.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	90.72	no
125439	gram_stain	BacteriaNetⓘ	negative	99.54	no
125439	motility	BacteriaNetⓘ	yes	76.96	no
125439	spore_formation	BacteriaNetⓘ	no	99.99	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Atopobium fossor DSM 15642
PATRIC: 1121023.4

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	80.18	no
125438	anaerobic	anaerobicⓘ	yes	87.78	yes
125438	spore-forming	spore-formingⓘ	no	84.17	no
125438	aerobic	aerobicⓘ	no	96.12	no
125438	thermophilic	thermophileⓘ	no	92.43	yes
125438	flagellated	motile2+ⓘ	no	92.50	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Biochemical characterization and X-ray structural and mutagenic analyses of the putative autolysin CdCwlT33800 catalytic domain from Clostridioides difficile.	Sekiya H, Nonaka Y, Kamitori S, Tamai E.	Appl Environ Microbiol	10.1128/aem.01216-25	2025
	Biochemical Characterizations of the Putative Endolysin Ecd09610 Catalytic Domain from Clostridioides difficile.	Sekiya H, Yamaji H, Yoshida A, Matsunami R, Kamitori S, Tamai E.	Antibiotics (Basel)	10.3390/antibiotics11081131	2022
Enzymology	Sepsis with an Atopobium-like species in a patient with Fournier's gangrene.	Oyaert M, Cools P, Breyne J, Heyvaert G, Vandewiele A, Vaneechoutte M, Vervaeke S, De Laere E.	J Clin Microbiol	10.1128/jcm.02310-13	2014
Phylogeny	Phylogenic and phenotypic evidence for the transfer of Eubacterium fossor to the genus Atopobium as Atopobium fossor comb. nov.	Kageyama A, Benno Y, Nakase T.	Microbiol Immunol	10.1111/j.1348-0421.1999.tb02421.x	1999
	Characterization of microbial communities found in the human vagina by analysis of terminal restriction fragment length polymorphisms of 16S rRNA genes.	Coolen MJ, Post E, Davis CC, Forney LJ.	Appl Environ Microbiol	10.1128/aem.71.12.8729-8737.2005	2005
Genetics	Genome-Based Taxonomic Classification of the Phylum Actinobacteria.	Nouioui I, Carro L, Garcia-Lopez M, Meier-Kolthoff JP, Woyke T, Kyrpides NC, Pukall R, Klenk HP, Goodfellow M, Goker M.	Front Microbiol	10.3389/fmicb.2018.02007	2018
Genetics	Two new bacteria isolated from vagina of a patient with vaginosis: Atopobium massiliense sp. nov. and Butyricimonas vaginalis sp. nov.	Bordigoni A, Lo CI, Yimagou EK, Nicaise B, Diop K, Raoult D, Desnues C, Fenollar F.	New Microbes New Infect	10.1016/j.nmni.2020.100771	2020
Genetics	Noncontiguous finished genome sequence and description of Raoultibacter massiliensis gen. nov., sp. nov. and Raoultibacter timonensis sp. nov, two new bacterial species isolated from the human gut.	Traore SI, Bilen M, Beye M, Diop A, Mbogning Fonkou MD, Tall ML, Michelle C, Yasir M, Ibraheem Azhar E, Bibi F, Bittar F, Jiman-Fatani AA, Daoud Z, Cadoret F, Fournier PE, Edouard S.	Microbiologyopen	10.1002/mbo3.758	2019

References

#6012	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 15642
#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 )
#56775	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 45424
#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 .
#68382	Automatically annotated from API zym .
#119440	Collection of Institut Pasteur ; Curators of the CIP; CIP 106638
#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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Atopobium fossor (DSM 15642, ATCC 43386, CCUG 45424)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

API zym

API rID32A

API biotype100

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000483125

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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