Eubacterium brachy (DSM 3990, ATCC 33089, CIP 104210)

Name: Eubacterium brachy (DSM 3990, ATCC 33089, CIP 104210)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 5418

Type strain

Strain Designation D6B-23

Culture col. no. DSM 3990 ATCC 33089 CIP 104210 D6B-23 JCM 11020

NCBI tax ID(s) 1321814 35517

Special Collections DSMZ CIP JCM

History <- ATCC <- VPI, D6B-23 CIP <- 1994, ATCC <- VPI: strain D6B-23

Links

Eubacterium brachy D6B-23 is an anaerobe, Gram-positive, rod-shaped bacterium that was isolated from subgingival region of mouth.

Gram-positive rod-shaped anaerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 46746

ATCC 33089,CIP 104210,DSM 3990,JCM 11020

@ref 20215

Last LPSN update 2026-02-09 11:18:57

Domain Bacteria

Phylum Bacillota

Class Clostridia

Order Eubacteriales

Family Eubacteriaceae

Genus Eubacterium

Species Eubacterium brachy

Full scientific name Eubacterium brachy Holdeman et al. 1980

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Motility
116988	positive	rod-shaped

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
1560	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
34045	MEDIUM 6 - Columbia agar with 10 % horse blood		Distilled water make up to (1000.000 ml);Columbia agar (39.000 g);Horseblood (100.000 ml)
116988	CIP Medium 187	Medium recipe at CIP
116988	CIP Medium 6	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
1560	positive	growth	37
34045	positive	growth	37

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
1560	anaerobe
125438	anaerobe	96.246
125439	anaerobe	99.7

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
116988	17632 ChEBI	nitrate	-	reduction
116988	16301 ChEBI	nitrite	-	reduction

Metabolite production

@ref	Chebi-ID	Metabolite	Production
116988	35581 ChEBI	indole

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	-	3.1.3.2	from API zym
68382	alkaline phosphatase	-	3.1.3.1	from API zym
68382	alpha-chymotrypsin	-	3.4.21.1	from API zym
68382	alpha-fucosidase	-	3.2.1.51	from API zym
68382	alpha-galactosidase	-	3.2.1.22	from API zym
68382	alpha-glucosidase	+	3.2.1.20	from API zym
68382	alpha-mannosidase	-	3.2.1.24	from API zym
68382	beta-galactosidase	-	3.2.1.23	from API zym
68382	beta-glucosidase	-	3.2.1.21	from API zym
68382	beta-glucuronidase	-	3.2.1.31	from API zym
116988	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
68382	leucine arylamidase	-	3.4.11.1	from API zym
68382	lipase (C 14)	-		from API zym
68382	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
116988	oxidase	-
68382	trypsin	-	3.4.21.4	from API zym
116988	urease	-	3.5.1.5
68382	valine arylamidase	-		from API zym

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	aspartate and asparagine metabolism	100	9 of 9
66794	coenzyme A metabolism	100	4 of 4
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	suberin monomers biosynthesis	100	2 of 2
66794	palmitate biosynthesis	100	22 of 22
66794	folate polyglutamylation	100	1 of 1
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	L-lactaldehyde degradation	100	3 of 3
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	peptidoglycan biosynthesis	86.67	13 of 15
66794	NAD metabolism	83.33	15 of 18
66794	photosynthesis	78.57	11 of 14
66794	chorismate metabolism	77.78	7 of 9
66794	vitamin B1 metabolism	76.92	10 of 13
66794	phenylalanine metabolism	76.92	10 of 13
66794	ppGpp biosynthesis	75	3 of 4
66794	acetate fermentation	75	3 of 4
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	threonine metabolism	70	7 of 10
66794	acetoin degradation	66.67	2 of 3
66794	formaldehyde oxidation	66.67	2 of 3
66794	octane oxidation	66.67	2 of 3
66794	C4 and CAM-carbon fixation	62.5	5 of 8
66794	gluconeogenesis	62.5	5 of 8
66794	alanine metabolism	62.07	18 of 29
66794	hydrogen production	60	3 of 5
66794	flavin biosynthesis	60	9 of 15
66794	pyrimidine metabolism	60	27 of 45
66794	glycolysis	58.82	10 of 17
66794	purine metabolism	58.51	55 of 94
66794	propanol degradation	57.14	4 of 7
66794	serine metabolism	55.56	5 of 9
66794	CO2 fixation in Crenarchaeota	55.56	5 of 9
66794	cysteine metabolism	55.56	10 of 18
66794	ethanol fermentation	50	1 of 2
66794	phenylmercury acetate degradation	50	1 of 2
66794	selenocysteine biosynthesis	50	3 of 6
66794	glutamate and glutamine metabolism	50	14 of 28
66794	sulfopterin metabolism	50	2 of 4
66794	adipate degradation	50	1 of 2
66794	butanoate fermentation	50	2 of 4
66794	leucine metabolism	46.15	6 of 13
66794	methionine metabolism	46.15	12 of 26
66794	tetrahydrofolate metabolism	42.86	6 of 14
66794	propionate fermentation	40	4 of 10
66794	arachidonate biosynthesis	40	2 of 5
66794	factor 420 biosynthesis	40	2 of 5
66794	glycine metabolism	40	4 of 10
66794	oxidative phosphorylation	39.56	36 of 91
66794	tryptophan metabolism	39.47	15 of 38
66794	isoprenoid biosynthesis	38.46	10 of 26
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	37.5	3 of 8
66794	ketogluconate metabolism	37.5	3 of 8
66794	vitamin B6 metabolism	36.36	4 of 11
66794	pentose phosphate pathway	36.36	4 of 11
66794	citric acid cycle	35.71	5 of 14
66794	non-pathway related	34.21	13 of 38
66794	degradation of aromatic, nitrogen containing compounds	33.33	4 of 12
66794	enterobactin biosynthesis	33.33	1 of 3
66794	IAA biosynthesis	33.33	1 of 3
66794	d-mannose degradation	33.33	3 of 9
66794	glycolate and glyoxylate degradation	33.33	2 of 6
66794	molybdenum cofactor biosynthesis	33.33	3 of 9
66794	pantothenate biosynthesis	33.33	2 of 6
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	phenylpropanoid biosynthesis	30.77	4 of 13
66794	sulfate reduction	30.77	4 of 13
66794	coenzyme M biosynthesis	30	3 of 10
66794	lipid metabolism	29.03	9 of 31
66794	reductive acetyl coenzyme A pathway	28.57	2 of 7
66794	lysine metabolism	28.57	12 of 42
66794	tyrosine metabolism	28.57	4 of 14
66794	proline metabolism	27.27	3 of 11
66794	isoleucine metabolism	25	2 of 8
66794	toluene degradation	25	1 of 4
66794	cyclohexanol degradation	25	1 of 4
66794	lactate fermentation	25	1 of 4
66794	degradation of sugar alcohols	25	4 of 16
66794	glycogen biosynthesis	25	1 of 4
66794	biotin biosynthesis	25	1 of 4
66794	CMP-KDO biosynthesis	25	1 of 4
66794	histidine metabolism	24.14	7 of 29
66794	urea cycle	23.08	3 of 13
66794	ascorbate metabolism	22.73	5 of 22
66794	lipid A biosynthesis	22.22	2 of 9
66794	degradation of hexoses	22.22	4 of 18
66794	valine metabolism	22.22	2 of 9
66794	glutathione metabolism	21.43	3 of 14
66794	arginine metabolism	20.83	5 of 24

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
116988	-	-	+	+	-	-	-	-	-	-	-	+	-	-	-	+	-	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host Body-Site	#Oral cavity and airways	#Mouth
#Host Body-Site	#Oral cavity and airways	#Gingiva

Isolation

@ref	Sample type	Isolation date
1560	subgingival region of mouth
116988	Human, Subgingival region of mouth	1978

Taxonmaps

69479

Global distribution of 16S sequence U13038 (>99% sequence identity) for [Eubacterium] brachy subclade from Microbeatlas

Aquatic Samples	761
Soil Samples	466
Animal Samples	40350
Plant Samples	242
Total Samples	41819

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
1560	2	Risk group (German classification) According to TRBA 466
116988	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	ASM48885v1 assembly for Eubacterium brachy ATCC 33089	scaffold	GCA_000488855	1321814.3	2558860285	1321814	46.95

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
20218	Eubacterium brachy 16S ribosomal RNA subunit, partial sequence	U13038	1438		35517
20218	E.brachy (ATCC 33089) gene for ribosomal RNA	Z36272	1500		35517

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Eubacterium brachy ATCC 33089
NCBI: GCA_000488855

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	yes	79.70	no
125439	motility	BacteriaNetⓘ	yes	75.40	no
125439	gram_stain	BacteriaNetⓘ	variable	81.00	no
125439	oxygen_tolerance	BacteriaNetⓘ	anaerobe	99.70	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Eubacterium brachy ATCC 33089 ATCC 33089
NCBI: GCA_000488855.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	71.51	no
125438	anaerobic	anaerobicⓘ	yes	96.25	yes
125438	aerobic	aerobicⓘ	no	99.02	yes
125438	spore-forming	spore-formingⓘ	no	73.64	no
125438	thermophilic	thermophileⓘ	no	88.63	yes
125438	flagellated	motile2+ⓘ	no	88.48	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Association of nine pathobionts with periodontitis in four South American and European countries.	Alvarez G, Arredondo A, Isabal S, Teughels W, Laleman I, Contreras MJ, Isbej L, Huapaya E, Mendoza G, Mor C, Nart J, Blanc V, Leon R.	J Oral Microbiol	10.1080/20002297.2023.2188630	2023
Genetics	Complete genome sequence of Eubacterium brachy GTC20104 isolated from a human pleural effusion.	Yonetamari J, Hayashi M, Muto Y, Tanaka K.	Microbiol Resour Announc	10.1128/mra.00747-25	2025
	Fecal microbiota transplantation improves bile acid malabsorption in patients with inflammatory bowel disease: results of microbiota and metabolites from two cohort studies.	Lu G, Zhang S, Wang R, Wu X, Chen Y, Wen Q, Cui B, Zhang F, Li P.	BMC Med	10.1186/s12916-025-04353-y	2025
	Impact of HIV on the Oral Microbiome of Children Living in Sub-Saharan Africa, Determined by Using an rpoC Gene Fragment Metataxonomic Approach.	Mann AE, O'Connell LM, Osagie E, Akhigbe P, Obuekwe O, Omoigberale A, Kelly C, DOMHaIN Study Team, Coker MO, Richards VP.	Microbiol Spectr	10.1128/spectrum.00871-23	2023
Enzymology	Detection of unculturable bacteria in periodontal health and disease by PCR.	Harper-Owen R, Dymock D, Booth V, Weightman AJ, Wade WG.	J Clin Microbiol	10.1128/jcm.37.5.1469-1473.1999	1999
Phylogeny	A fluorescent Gram stain for flow cytometry and epifluorescence microscopy.	Mason DJ, Shanmuganathan S, Mortimer FC, Gant VA.	Appl Environ Microbiol	10.1128/aem.64.7.2681-2685.1998	1998
Enzymology	Reaction of human sera with Eubacterium brachy: isolation and characterization of an extracellular antigen.	Vincent JW, Falkler WA, Dalessandro NF, Miller RA, Heath JR.	Infect Immun	10.1128/iai.47.3.592-597.1985	1985
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
Phylogeny	Molecular identification of microorganisms from endodontic infections.	Rolph HJ, Lennon A, Riggio MP, Saunders WP, MacKenzie D, Coldero L, Bagg J.	J Clin Microbiol	10.1128/jcm.39.9.3282-3289.2001	2001
	Design and evaluation of useful bacterium-specific PCR primers that amplify genes coding for bacterial 16S rRNA.	Marchesi JR, Sato T, Weightman AJ, Martin TA, Fry JC, Hiom SJ, Dymock D, Wade WG.	Appl Environ Microbiol	10.1128/aem.64.2.795-799.1998	1998
Metabolism	The metabolism of phenylalanine and leucine by a cell suspension of Eubacterium brachy and the effects of metronidazole on metabolism.	Hamid MA, Iwaku M, Hoshino E	Arch Oral Biol	10.1016/0003-9969(94)90080-9	1994

References

#1560	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 3990
#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 )
#34045	; Curators of the CIP;
#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) .
#66794	Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg: BRENDA, the ELIXIR core data resource in 2021: new developments and updates. Nucleic Acids Res. 49: D498 - D508 2020 ( DOI 10.1093/nar/gkaa1025 , PubMed 33211880 )
#68382	Automatically annotated from API zym .
#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 .
#116988	Collection of Institut Pasteur ; Curators of the CIP; CIP 104210
#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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Eubacterium brachy (DSM 3990, ATCC 33089, CIP 104210)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Metabolite utilization

Metabolite production

Enzymes

Pathway annotation

API zym

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000488855

16S sequences

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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