Eubacterium aggregans (DSM 12183, SR12, KCTC 5834)

Name: Eubacterium aggregans (DSM 12183, SR12, KCTC 5834)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 5449

Type strain

Strain Designation SR12

Culture col. no. DSM 12183 SR12 KCTC 5834

NCBI tax ID(s) 81409

Special Collections DSMZ

History <- J.-L. Garcia; SR12

Links

Eubacterium aggregans SR12 is an anaerobe bacterium that was isolated from anaerobic digester fed with olive mill wastewater.

anaerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 49247

KCTC 5834,DSM 12183

@ref 20215

Last LPSN update 2026-02-09 11:18:58

Domain Bacteria

Phylum Bacillota

Class Clostridia

Order Eubacteriales

Family Eubacteriaceae

Genus Eubacterium

Species Eubacterium aggregans

Full scientific name Eubacterium aggregans Mechichi et al. 2000

Morphology

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
4636	EUBACTERIUM AGGREGANS MEDIUM (DSMZ Medium 711a)		Medium recipe at MediaDive	Name: EUBACTERIUM AGGREGANS MEDIUM (DSMZ Medium 711a) Composition: Fructose 4.98504 g/l Na2CO3 1.49551 g/l trans-3,4,5-trimethoxycinnamate 1.18644 g/l NH4Cl 0.997009 g/l Yeast extract 0.997009 g/l NaCl 0.598205 g/l Na2S x 9 H2O 0.299103 g/l K2HPO4 0.299103 g/l KH2PO4 0.299103 g/l L-Cysteine HCl x H2O 0.299103 g/l MgCl2 x 6 H2O 0.199402 g/l CaCl2 x 2 H2O 0.0997009 g/l KCl 0.0997009 g/l HCl 0.00373878 g/l FeCl2 x 4 H2O 0.00224327 g/l Sodium resazurin 0.000498504 g/l CoCl2 x 6 H2O 0.000284148 g/l MnCl2 x 4 H2O 0.000149551 g/l ZnCl2 0.000104686 g/l Pyridoxine hydrochloride 9.97009e-05 g/l Na2MoO4 x 2 H2O 5.38385e-05 g/l (DL)-alpha-Lipoic acid 4.98504e-05 g/l p-Aminobenzoic acid 4.98504e-05 g/l Calcium D-(+)-pantothenate 4.98504e-05 g/l Nicotinic acid 4.98504e-05 g/l Riboflavin 4.98504e-05 g/l Thiamine HCl 4.98504e-05 g/l NiCl2 x 6 H2O 3.58923e-05 g/l Folic acid 1.99402e-05 g/l Biotin 1.99402e-05 g/l H3BO3 8.97308e-06 g/l CuCl2 x 2 H2O 2.99103e-06 g/l Vitamin B12 9.97009e-07 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
4636	positive	growth	37

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
4636	anaerobe
125439	anaerobe	99.8

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	methylglyoxal degradation	100	5 of 5
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	coenzyme A metabolism	100	4 of 4
66794	cyanate degradation	100	3 of 3
66794	threonine metabolism	100	10 of 10
66794	aminopropanol phosphate biosynthesis	100	2 of 2
66794	adipate degradation	100	2 of 2
66794	ppGpp biosynthesis	100	4 of 4
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	L-lactaldehyde degradation	100	3 of 3
66794	palmitate biosynthesis	100	22 of 22
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	C4 and CAM-carbon fixation	100	8 of 8
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	suberin monomers biosynthesis	100	2 of 2
66794	folate polyglutamylation	100	1 of 1
66794	starch degradation	90	9 of 10
66794	chorismate metabolism	88.89	8 of 9
66794	CO2 fixation in Crenarchaeota	88.89	8 of 9
66794	valine metabolism	88.89	8 of 9
66794	gluconeogenesis	87.5	7 of 8
66794	isoleucine metabolism	87.5	7 of 8
66794	alanine metabolism	86.21	25 of 29
66794	reductive acetyl coenzyme A pathway	85.71	6 of 7
66794	propanol degradation	85.71	6 of 7
66794	vitamin B1 metabolism	84.62	11 of 13
66794	Entner Doudoroff pathway	80	8 of 10
66794	peptidoglycan biosynthesis	80	12 of 15
66794	lipoate biosynthesis	80	4 of 5
66794	phenylacetate degradation (aerobic)	80	4 of 5
66794	flavin biosynthesis	80	12 of 15
66794	heme metabolism	78.57	11 of 14
66794	photosynthesis	78.57	11 of 14
66794	serine metabolism	77.78	7 of 9
66794	molybdenum cofactor biosynthesis	77.78	7 of 9
66794	phenylalanine metabolism	76.92	10 of 13
66794	vitamin B12 metabolism	76.47	26 of 34
66794	glycogen biosynthesis	75	3 of 4
66794	acetate fermentation	75	3 of 4
66794	ketogluconate metabolism	75	6 of 8
66794	glutamate and glutamine metabolism	75	21 of 28
66794	degradation of sugar alcohols	75	12 of 16
66794	butanoate fermentation	75	3 of 4
66794	purine metabolism	73.4	69 of 94
66794	NAD metabolism	72.22	13 of 18
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	glycolysis	70.59	12 of 17
66794	methionine metabolism	69.23	18 of 26
66794	acetoin degradation	66.67	2 of 3
66794	glycolate and glyoxylate degradation	66.67	4 of 6
66794	methane metabolism	66.67	2 of 3
66794	enterobactin biosynthesis	66.67	2 of 3
66794	pyrimidine metabolism	66.67	30 of 45
66794	aspartate and asparagine metabolism	66.67	6 of 9
66794	octane oxidation	66.67	2 of 3
66794	formaldehyde oxidation	66.67	2 of 3
66794	histidine metabolism	65.52	19 of 29
66794	tetrahydrofolate metabolism	64.29	9 of 14
66794	pentose phosphate pathway	63.64	7 of 11
66794	tryptophan metabolism	63.16	24 of 38
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
66794	leucine metabolism	61.54	8 of 13
66794	urea cycle	61.54	8 of 13
66794	degradation of pentoses	60.71	17 of 28
66794	cellulose degradation	60	3 of 5
66794	metabolism of amino sugars and derivatives	60	3 of 5
66794	hydrogen production	60	3 of 5
66794	glycogen metabolism	60	3 of 5
66794	propionate fermentation	60	6 of 10
66794	non-pathway related	57.89	22 of 38
66794	citric acid cycle	57.14	8 of 14
66794	lysine metabolism	57.14	24 of 42
66794	d-mannose degradation	55.56	5 of 9
66794	oxidative phosphorylation	54.95	50 of 91
66794	proline metabolism	54.55	6 of 11
66794	vitamin B6 metabolism	54.55	6 of 11
66794	dTDPLrhamnose biosynthesis	50	4 of 8
66794	ribulose monophosphate pathway	50	1 of 2
66794	toluene degradation	50	2 of 4
66794	4-hydroxyphenylacetate degradation	50	5 of 10
66794	coenzyme M biosynthesis	50	5 of 10
66794	lactate fermentation	50	2 of 4
66794	sulfopterin metabolism	50	2 of 4
66794	ethanol fermentation	50	1 of 2
66794	glutathione metabolism	50	7 of 14
66794	tyrosine metabolism	50	7 of 14
66794	phenylmercury acetate degradation	50	1 of 2
66794	selenocysteine biosynthesis	50	3 of 6
66794	degradation of aromatic, nitrogen containing compounds	50	6 of 12
66794	cysteine metabolism	50	9 of 18
66794	arginine metabolism	50	12 of 24
66794	quinate degradation	50	1 of 2
66794	biotin biosynthesis	50	2 of 4
66794	lipid metabolism	45.16	14 of 31
66794	degradation of hexoses	44.44	8 of 18
66794	ubiquinone biosynthesis	42.86	3 of 7
66794	aclacinomycin biosynthesis	42.86	3 of 7
66794	ascorbate metabolism	40.91	9 of 22
66794	bacilysin biosynthesis	40	2 of 5
66794	arachidonate biosynthesis	40	2 of 5
66794	glycine metabolism	40	4 of 10
66794	isoprenoid biosynthesis	38.46	10 of 26
66794	sphingosine metabolism	33.33	2 of 6
66794	allantoin degradation	33.33	3 of 9
66794	lipid A biosynthesis	33.33	3 of 9
66794	sulfoquinovose degradation	33.33	1 of 3
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	IAA biosynthesis	33.33	1 of 3
66794	pantothenate biosynthesis	33.33	2 of 6
66794	sulfate reduction	30.77	4 of 13
66794	benzoyl-CoA degradation	28.57	2 of 7
66794	degradation of sugar acids	28	7 of 25
66794	metabolism of disaccharids	27.27	3 of 11
66794	d-xylose degradation	27.27	3 of 11
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	polyamine pathway	26.09	6 of 23
66794	cyclohexanol degradation	25	1 of 4
66794	CMP-KDO biosynthesis	25	1 of 4
66794	catecholamine biosynthesis	25	1 of 4
66794	carnitine metabolism	25	2 of 8
66794	bile acid biosynthesis, neutral pathway	23.53	4 of 17
66794	chlorophyll metabolism	22.22	4 of 18
66794	arachidonic acid metabolism	22.22	4 of 18
66794	nitrate assimilation	22.22	2 of 9
66794	4-hydroxymandelate degradation	22.22	2 of 9

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Biodegradation	#Anaerobic digestor
#Engineered	#Industrial	-
#Engineered	#Waste	#Industrial wastewater
#Condition	#Anoxic (anaerobic)	-

Isolation

@ref	Sample type	Country	Country ISO 3 Code	Continent
4636	anaerobic digester fed with olive mill wastewater	Tunisia	TUN	Africa

Taxonmaps

69479

Global distribution of 16S sequence AF073898 (>99% sequence identity) for Eubacterium aggregans subclade from Microbeatlas

Aquatic Samples	1316
Soil Samples	45
Animal Samples	175
Plant Samples	30
Total Samples	1566

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
4636	1	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	IMG-taxon 2642422588 annotated assembly for Eubacterium aggregans SR12	contig	GCA_900107815	81409.3	2642422588	81409	64.92

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
4636	Eubacterium aggregans 16S ribosomal RNA gene, partial sequence	AF073898	1509		81409

GC content

@ref	GC-content (mol%)	Method
4636	55	high performance liquid chromatography (HPLC)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Eubacterium aggregans SR12
NCBI: GCA_900107815

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	yes	71.60	no
125439	motility	BacteriaNetⓘ	yes	50.30	no
125439	gram_stain	BacteriaNetⓘ	positive	71.80	no
125439	oxygen_tolerance	BacteriaNetⓘ	anaerobe	99.80	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Metabolism	Using gas mixtures of CO, CO₂ and H₂ as microbial substrates: the do's and don'ts of successful technology transfer from laboratory to production scale.	Takors R, Kopf M, Mampel J, Bluemke W, Blombach B, Eikmanns B, Bengelsdorf FR, Weuster-Botz D, Durre P.	Microb Biotechnol	10.1111/1751-7915.13270	2018
Metabolism	Eubacterium maltosivorans sp. nov., a novel human intestinal acetogenic and butyrogenic bacterium with a versatile metabolism.	Feng Y, Stams AJM, Sanchez-Andrea I, de Vos WM	Int J Syst Evol Microbiol	10.1099/ijsem.0.003028	2018
Phylogeny	Eubacterium aggreganssp. nov., a new homoacetogenic bacterium from olive mill wastewater treatment digestor.	Mechichi T, Labat M, Woo TH, Thomas P, Garcia JL, Patel BK	Anaerobe	10.1006/anae.1998.0179	1998

References

#4636	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 12183
#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 )
#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 )
#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 .
#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 aggregans (DSM 12183, SR12, KCTC 5834)

Name and taxonomic classification

Morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_900107815

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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