Name: Eubacterium brachy D6B-23
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 5418

Type strain:

Species: Eubacterium brachy

Strain Designation: D6B-23

Culture col. no.: DSM 3990, ATCC 33089, CIP 104210, JCM 11020

Strain history: CIP <- 1994, ATCC <- VPI: strain D6B-23

NCBI tax ID(s): 1321814 (strain), 35517 (species)

SI-ID 46746

ATCC 33089, CIP 104210, DSM 3990, JCM 11020

Section

Eubacterium brachy D6B-23 is an anaerobe, mesophilic bacterium that was isolated from subgingival region of mouth.

anaerobe
mesophilic
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	*Bacillota*
	Class	*Clostridia*
	Order	*Eubacteriales*
	Family	*Eubacteriaceae*
	Genus	*Eubacterium*
	Species	**Eubacterium brachy**
	Full Scientific Name (LPSN)	Eubacterium brachy Holdeman et al. 1980

Information on morphological and physiological properties Morphology

[Ref.: #116988]	Gram stain	positive
[Ref.: #69480]	Gram stain	positive Confidence in %99.719

[Ref.: #116988]	Cell shape	rod-shaped

[Ref.: #116988]	Motility	no
[Ref.: #69480]	Motility	no Confidence in %92.718

Information on culture and growth conditions Culture and growth conditions

[Ref.: #1560]

Culture medium

CHOPPED MEAT MEDIUM WITH CARBOHYDRATES (DSMZ Medium 110)

[Ref.: #1560]

Culture medium growth

[Ref.: #1560]

Culture medium link

Medium recipe at MediaDive

[Ref.: #1560]

Culture medium composition

expand / minimize

[Ref.: #34045]

Culture medium

MEDIUM 6 - Columbia agar with 10 % horse blood

[Ref.: #34045]

Culture medium growth

[Ref.: #34045]

Culture medium composition

expand / minimize

[Ref.: #116988]

Culture medium

CIP Medium 187

[Ref.: #116988]

Culture medium growth

[Ref.: #116988]

Culture medium link

Medium recipe provided by DSMZ

[Ref.: #116988]

Culture medium

CIP Medium 6

[Ref.: #116988]

Culture medium growth

[Ref.: #116988]

Culture medium link

Medium recipe provided by DSMZ

	Temperatures	Kind of temperature		Temperature
[Ref.: #1560]			growth	37 °C
[Ref.: #34045]			growth	37 °C

[Ref.: #1560]	Temperature range	mesophilic
[Ref.: #34045]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #1560]	Oxygen tolerance	anaerobe
[Ref.: #69480]	Oxygen tolerance	anaerobe Confidence in %99.238

[Ref.: #69480]

Ability of spore formation

no Confidence in %99.99

	Metabolite utilization	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #116988]		nitrate ChEBI	-	reduction
[Ref.: #116988]		nitrite ChEBI	-	reduction

	Metabolite production	Metabolite	Production
[Ref.: #116988]		indole ChEBI	no

	Enzyme	Enzyme activity	EC number
[Ref.: #68382]	acid phosphatase	-	3.1.3.2	* from API zym
[Ref.: #68382]	alkaline phosphatase	-	3.1.3.1	* from API zym
[Ref.: #68382]	alpha-chymotrypsin	-	3.4.21.1	* from API zym
[Ref.: #68382]	alpha-fucosidase	-	3.2.1.51	* from API zym
[Ref.: #68382]	alpha-galactosidase	-	3.2.1.22	* from API zym
[Ref.: #68382]	alpha-glucosidase	+	3.2.1.20	* from API zym
[Ref.: #68382]	alpha-mannosidase	-	3.2.1.24	* from API zym
[Ref.: #68382]	beta-galactosidase	-	3.2.1.23	* from API zym
[Ref.: #68382]	beta-glucosidase	-	3.2.1.21	* from API zym
[Ref.: #68382]	beta-glucuronidase	-	3.2.1.31	* from API zym
[Ref.: #116988]	catalase	-	1.11.1.6
[Ref.: #68382]	cystine arylamidase	-	3.4.11.3	* from API zym
[Ref.: #68382]	esterase (C 4)	+		* from API zym
[Ref.: #68382]	esterase lipase (C 8)	+		* from API zym
[Ref.: #68382]	leucine arylamidase	-	3.4.11.1	* from API zym
[Ref.: #68382]	lipase (C 14)	-		* from API zym
[Ref.: #68382]	N-acetyl-beta-glucosaminidase	-	3.2.1.52	* from API zym
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	+		* from API zym
[Ref.: #116988]	oxidase	-
[Ref.: #68382]	trypsin	-	3.4.21.4	* from API zym
[Ref.: #116988]	urease	-	3.5.1.5
[Ref.: #68382]	valine arylamidase	-		* from API zym
	Only first 10 entries are displayed. Click here to see all.

API® zym:

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

	API ID	Control	2-naphthyl phosphateAlkaline phosphatase	2-naphthyl butyrateEsterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	2-naphthyl myristateLipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	N-benzoyl-DL-arginine-2-naphthylamideTrypsin	N-glutaryl-phenylalanine-2-naphthylamidealpha- Chymotrypsin	2-naphthyl phosphateAcid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	6-Br-2-naphthyl-alphaD-galactpyranosidealpha- Galactosidase	2-naphthyl-betaD-galactpyranosidebeta- Galactosidase	Naphthol-AS-BI-betaD-glucuronidebeta- Glucuronidase	2-naphthyl-alphaD-glucopyranosidealpha- Glucosidase	6-Br-2-naphthyl-betaD-glucopyranosidebeta- Glucosidase	1-naphthyl-N-acetyl-betaD-glucosaminideN-acetyl-beta- glucosaminidase	6-Br-2-naphthyl-alphaD-mannopyranosidealpha- Mannosidase	2-naphthyl-alphaL-fucopyranosidealpha- Fucosidase
[Ref.: #116988]	7840	-	-	+	+	-	-	-	-	-	-	-	+	-	-	-	+	-	-	-	-

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

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

[Ref.: #1560]	Sample type/isolated from	subgingival region of mouth

[Ref.: #116988]	Sample type/isolated from	Human, Subgingival region of mouth
[Ref.: #116988]	Isolation date	1978
* marker position based on {}

Isolation sources categories

#Host Body-Site	#Oral cavity and airways	#Mouth
#Host Body-Site	#Oral cavity and airways	#Gingiva

What are isolation sources categories?

[Ref.: #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

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

[Ref.: #1560]	Biosafety level	2	Risk group (German classification) According to TRBA 466
[Ref.: #116988]	Biosafety level	1	Risk group (French classification)

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

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #20218]	Eubacterium brachy 16S ribosomal RNA subunit, partial sequence	U13038	1438	ENA	35517 tax ID	*
[Ref.: #20218]	E.brachy (ATCC 33089) gene for ribosomal RNA	Z36272	1500	ENA	35517 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Eubacterium brachy ATCC 33089	GCA_000488855	scaffold	GenBank	1321814 tax ID	*
[Ref.: #66792]	Eubacterium brachy ATCC 33089	1321814.3	wgs	PATRIC	1321814 tax ID	*
[Ref.: #66792]	Eubacterium brachy ATCC 33089	2558860285	draft	JGI IMG/M	1321814 tax ID	*

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

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Eubacterium brachy ATCC 33089 ATCC 33089 NCBI: GCA_000488855.1
[Ref.: #69481]	spore-forming	yes	83	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Eubacterium brachy ATCC 33089 ATCC 33089 NCBI: GCA_000488855.1
[Ref.: #69480]	motile	no	91.868	no
[Ref.: #69480]	flagellated	no	98.048	no
[Ref.: #69480]	gram-positive	yes	68.671	no
[Ref.: #69480]	anaerobic	yes	98.77	no
[Ref.: #69480]	aerobic	no	98.975	no
[Ref.: #69480]	halophile	yes	53.468	no
[Ref.: #69480]	spore-forming	no	86.718	no
[Ref.: #69480]	thermophile	no	94.485	yes
[Ref.: #69480]	glucose-util	yes	71.348	no
[Ref.: #69480]	glucose-ferment	yes	51.755	no

Availability in culture collections External links

[Ref.: #1560]

Culture collection no.

DSM 3990, ATCC 33089, CIP 104210, JCM 11020

[Ref.: #74907]

SI-ID 46746

Literature:

Topic	Title	Authors	Journal	DOI	Year
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 .

#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 )

#74907

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-ID46746.1 )

#116988 Collection of Institut Pasteur ; Curators of the CIP; CIP 104210
* These data were automatically processed and therefore are not curated

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Eubacterium brachy ATCC 33089 ATCC 33089

Eubacterium brachy ATCC 33089 ATCC 33089

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