Eubacterium barkeri (DSM 1223, ATCC 25849, NCIB 10623)

Name: Eubacterium barkeri (DSM 1223, ATCC 25849, NCIB 10623)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 5414

Type strain

Culture col. no. DSM 1223 ATCC 25849 NCIB 10623 VKM B-1775 VPI 5359 5 more

NCBI tax ID(s) 1528

Special Collections DSMZ JCM

History <- ATCC <- L.DS. Smith, VPI 5359 <- I. Pastan ATCC 25849 <-- L. DS. Smith VPI 5359.

Links

Eubacterium barkeri DSM 1223 is an anaerobe bacterium that was isolated from mud.

anaerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 38696

ATCC 25849,DSM 1223,NCIB 10623,VKM B-1775,JCM 1389,CCRC 14473,NCIMB 10623,BCRC 14473,CIP 104307

@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 barkeri

Full scientific name Eubacterium barkeri (Stadtman et al. 1972) Collins et al. 1994

Synonyms (1)

Clostridium barkeri

Morphology

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
587	NICOTINIC ACID MEDIUM (DSMZ Medium 152)		Medium recipe at MediaDive	Name: NICOTINIC ACID MEDIUM (DSMZ Medium 152) Composition: Yeast extract 10.0 g/l Nicotinic acid 5.0 g/l L-Cysteine HCl x H2O 0.5 g/l NaHCO3 0.4 g/l NaCl 0.08 g/l K2HPO4 0.04 g/l KH2PO4 0.04 g/l CaCl2 x 2 H2O 0.008 g/l MgSO4 x 7 H2O 0.008 g/l Distilled water
587	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)
587	positive	growth	30-37
67770	positive	growth	30

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
587	anaerobe
125439	anaerobe	99.8

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Mud (Sludge)

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
587	mud	Potomac river	USA	USA	North America
67770	Mud	Potomac River	USA	USA	North America

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
587	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
67770	IMG-taxon 2642422543 annotated assembly for Eubacterium barkeri VPI 5359	scaffold	GCA_900107125	1528.7	2642422543	1528	65.85

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
587	Eubacterium barkeri strain ATCC 25849 16S ribosomal RNA gene, partial sequence	M23927	1527		1528
67770	Eubacterium barkeri gene for 16S ribosomal RNA, partial sequence, strain: JCM 1389	LC036314	1486		1528

GC content

@ref	GC-content (mol%)	Method
587	45.0
67770	45	thermal denaturation, midpoint method (Tm)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Eubacterium barkeri VPI 5359
NCBI: GCA_900107125

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	yes	68.30	no
125439	motility	BacteriaNetⓘ	yes	66.40	no
125439	gram_stain	BacteriaNetⓘ	positive	67.00	no
125439	oxygen_tolerance	BacteriaNetⓘ	anaerobe	99.80	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Eubacterium barkeri strain VPI 5359
PATRIC: 1528.7

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	81.15	no
125438	anaerobic	anaerobicⓘ	yes	87.59	no
125438	spore-forming	spore-formingⓘ	no	63.21	no
125438	aerobic	aerobicⓘ	no	97.67	yes
125438	thermophilic	thermophileⓘ	no	89.79	yes
125438	flagellated	motile2+ⓘ	no	82.92	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Metabolism	Characterization and Genome Analysis of a Nicotine and Nicotinic Acid-Degrading Strain Pseudomonas putida JQ581 Isolated from Marine.	Li A, Qiu J, Chen D, Ye J, Wang Y, Tong L, Jiang J, Chen J.	Mar Drugs	10.3390/md15060156	2017
Metabolism	Restricted distribution of the butyrate kinase pathway among butyrate-producing bacteria from the human colon.	Louis P, Duncan SH, McCrae SI, Millar J, Jackson MS, Flint HJ.	J Bacteriol	10.1128/jb.186.7.2099-2106.2004	2004
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
	FBS-based cryoprotective compositions for effective cryopreservation of gut microbiota and key intestinal microorganisms.	Zalomova LV, Fesenko EE.	BMC Res Notes	10.1186/s13104-024-06836-2	2024
Genetics	Effect of rainfall on metagenomics in a sewage environment in Hongta District, Yuxi city, Yunnan Province.	Jia S, Gu W, Jiang L, Zhang Y, Fu X, Yin J, Zhou Y.	PeerJ	10.7717/peerj.20199	2025
	Functional Annotation of LigU as a 1,3-Allylic Isomerase during the Degradation of Lignin in the Protocatechuate 4,5-Cleavage Pathway from the Soil Bacterium Sphingobium sp. SYK-6.	Hogancamp TN, Raushel FM.	Biochemistry	10.1021/acs.biochem.8b00295	2018
Enzymology	Structural, Mechanistic, and Functional Insights into an Arthrobacter nicotinovorans Molybdenum Hydroxylase Involved in Nicotine Degradation.	Wang L, Mu X, Li W, Xu Q, Xu P, Zhang L, Zhang Y, Wu G.	Molecules	10.3390/molecules26144387	2021
Metabolism	Clostridioides difficile exploits xanthine and uric acid as nutrients by utilizing a selenium-dependent catabolic pathway.	Johnstone MA, Self WT.	Microbiol Spectr	10.1128/spectrum.00844-24	2024
Enzymology	Crystal structure and putative mechanism of 3-methylitaconate-delta-isomerase from Eubacterium barkeri.	Velarde M, Macieira S, Hilberg M, Broker G, Tu SM, Golding BT, Pierik AJ, Buckel W, Messerschmidt A.	J Mol Biol	10.1016/j.jmb.2009.06.052	2009
Genetics	Gut Microbiota Eubacterium callanderi Exerts Anti-Colorectal Cancer Activity.	Ryu SW, Kim JS, Oh BS, Choi WJ, Yu SY, Bak JE, Park SH, Kang SW, Lee J, Jung WY, Lee JS, Lee JH.	Microbiol Spectr	10.1128/spectrum.02531-22	2022
Metabolism	Lactobacillus paracasei CCFM1229 and Lactobacillus rhamnosus CCFM1228 Alleviated Depression- and Anxiety-Related Symptoms of Chronic Stress-Induced Depression in Mice by Regulating Xanthine Oxidase Activity in the Brain.	Xu M, Tian P, Zhu H, Zou R, Zhao J, Zhang H, Wang G, Chen W.	Nutrients	10.3390/nu14061294	2022
	Cloning, heterologous expression, and functional characterization of the nicotinate dehydrogenase gene from Pseudomonas putida KT2440.	Yang Y, Yuan S, Chen T, Ma P, Shang G, Dai Y.	Biodegradation	10.1007/s10532-008-9243-x	2009
Metabolism	Structural and kinetic properties of a beta-hydroxyacid dehydrogenase involved in nicotinate fermentation.	Reitz S, Alhapel A, Essen LO, Pierik AJ.	J Mol Biol	10.1016/j.jmb.2008.07.050	2008
Enzymology	The crystal structure of enamidase: a bifunctional enzyme of the nicotinate catabolism.	Kress D, Alhapel A, Pierik AJ, Essen LO.	J Mol Biol	10.1016/j.jmb.2008.09.002	2008
Enzymology	Searching for intermediates in the carbon skeleton rearrangement of 2-methyleneglutarate to (R)-3-methylitaconate catalyzed by coenzyme B12-dependent 2-methyleneglutarate mutase from Eubacterium barkeri.	Pierik AJ, Ciceri D, Lopez RF, Kroll F, Broker G, Beatrix B, Buckel W, Golding BT.	Biochemistry	10.1021/bi050049n	2005
	Biochemical and Genetic Analysis of 4-Hydroxypyridine Catabolism in Arthrobacter sp. Strain IN13.	Vaitekunas J, Gasparaviciute R, Stankeviciute J, Urbelis G, Meskys R.	Microorganisms	10.3390/microorganisms8060888	2020
Metabolism	Unravelling lactate-acetate and sugar conversion into butyrate by intestinal Anaerobutyricum and Anaerostipes species by comparative proteogenomics.	Shetty SA, Boeren S, Bui TPN, Smidt H, de Vos WM.	Environ Microbiol	10.1111/1462-2920.15269	2020
Metabolism	Rotation of the exo-methylene group of (R)-3-methylitaconate catalyzed by coenzyme B(12)-dependent 2-methyleneglutarate mutase from Eubacterium barkeri.	Pierik AJ, Ciceri D, Broker G, Edwards CH, McFarlane W, Winter J, Buckel W, Golding BT.	J Am Chem Soc	10.1021/ja020340f	2002
	A complete nicotinate degradation pathway in the microbial eukaryote Aspergillus nidulans.	Bokor E, Amon J, Varga M, Szekeres A, Hegedus Z, Jakusch T, Szakonyi Z, Flipphi M, Vagvolgyi C, Gacser A, Scazzocchio C, Hamari Z.	Commun Biol	10.1038/s42003-022-03684-3	2022
Enzymology	Impact of the Dimethyl Sulfoxide Reductase Superfamily on the Evolution of Biogeochemical Cycles.	Wells M, Kim M, Akob DM, Basu P, Stolz JF.	Microbiol Spectr	10.1128/spectrum.04145-22	2023
Enzymology	Selenium-containing xanthine dehydrogenase from Eubacterium barkeri.	Schrader T, Rienhofer A, Andreesen JR.	Eur J Biochem	10.1046/j.1432-1327.1999.00678.x	1999
Metabolism	Cloning of a novel 6-chloronicotinic acid chlorohydrolase from the newly isolated 6-chloronicotinic acid mineralizing Bradyrhizobiaceae strain SG-6C.	Shettigar M, Pearce S, Pandey R, Khan F, Dorrian SJ, Balotra S, Russell RJ, Oakeshott JG, Pandey G.	PLoS One	10.1371/journal.pone.0051162	2012
Genetics	The Characterization of Novel Tissue Microbiota Using an Optimized 16S Metagenomic Sequencing Pipeline.	Lluch J, Servant F, Paisse S, Valle C, Valiere S, Kuchly C, Vilchez G, Donnadieu C, Courtney M, Burcelin R, Amar J, Bouchez O, Lelouvier B.	PLoS One	10.1371/journal.pone.0142334	2015
Metabolism	Transcriptome analysis of genes and metabolic pathways associated with nicotine degradation in Aspergillus oryzae 112822.	He C, Huang Y, Liu P, Wei J, Yang Y, Xu L, Xiao M.	BMC Genomics	10.1186/s12864-019-5446-2	2019
Metabolism	Genome organization and evolution of a eukaryotic nicotinate co-inducible pathway.	Bokor E, Flipphi M, Kocsube S, Amon J, Vagvolgyi C, Scazzocchio C, Hamari Z.	Open Biol	10.1098/rsob.210099	2021
Metabolism	The Mo-Se active site of nicotinate dehydrogenase.	Wagener N, Pierik AJ, Ibdah A, Hille R, Dobbek H.	Proc Natl Acad Sci U S A	10.1073/pnas.0902210106	2009
	The complete genome sequence of Eubacterium limosum SA11, a metabolically versatile rumen acetogen.	Kelly WJ, Henderson G, Pacheco DM, Li D, Reilly K, Naylor GE, Janssen PH, Attwood GT, Altermann E, Leahy SC.	Stand Genomic Sci	10.1186/s40793-016-0147-9	2016
Phylogeny	The phylogeny of the genus Clostridium: proposal of five new genera and eleven new species combinations.	Collins MD, Lawson PA, Willems A, Cordoba JJ, Fernandez-Garayzabal J, Garcia P, Cai J, Hippe H, Farrow JA.	Int J Syst Bacteriol	10.1099/00207713-44-4-812	1994
Metabolism	Molecular and functional analysis of nicotinate catabolism in Eubacterium barkeri.	Alhapel A, Darley DJ, Wagener N, Eckel E, Elsner N, Pierik AJ.	Proc Natl Acad Sci U S A	10.1073/pnas.0601635103	2006
Enzymology	A preliminary crystallographic study of recombinant NicX, an Fe(2+)-dependent 2,5-dihydroxypyridine dioxygenase from Pseudomonas putida KT2440.	Jimenez JI, Acebron I, Garcia JL, Diaz E, Mancheno JM.	Acta Crystallogr Sect F Struct Biol Cryst Commun	10.1107/s174430911001119x	2010
Metabolism	A selenium-dependent xanthine dehydrogenase triggers biofilm proliferation in Enterococcus faecalis through oxidant production.	Srivastava M, Mallard C, Barke T, Hancock LE, Self WT.	J Bacteriol	10.1128/jb.01063-10	2011
Metabolism	Ustilago maydis produces itaconic acid via the unusual intermediate trans-aconitate.	Geiser E, Przybilla SK, Friedrich A, Buckel W, Wierckx N, Blank LM, Bolker M.	Microb Biotechnol	10.1111/1751-7915.12329	2016
Enzymology	Periplasmic Nicotine Dehydrogenase NdhAB Utilizes Pseudoazurin as Its Physiological Electron Acceptor in Agrobacterium tumefaciens S33.	Yu W, Wang R, Huang H, Xie H, Wang S.	Appl Environ Microbiol	10.1128/aem.01050-17	2017
Enzymology	A eukaryotic nicotinate-inducible gene cluster: convergent evolution in fungi and bacteria.	Amon J, Fernandez-Martin R, Bokor E, Cultrone A, Kelly JM, Flipphi M, Scazzocchio C, Hamari Z.	Open Biol	10.1098/rsob.170199	2017
Enzymology	Orphan SelD proteins and selenium-dependent molybdenum hydroxylases.	Haft DH, Self WT.	Biol Direct	10.1186/1745-6150-3-4	2008
Enzymology	Biochemical and structural studies of uncharacterized protein PA0743 from Pseudomonas aeruginosa revealed NAD+-dependent L-serine dehydrogenase.	Tchigvintsev A, Singer A, Brown G, Flick R, Evdokimova E, Tan K, Gonzalez CF, Savchenko A, Yakunin AF.	J Biol Chem	10.1074/jbc.m111.294561	2012
Metabolism	Selenium-dependent metabolism of purines: A selenium-dependent purine hydroxylase and xanthine dehydrogenase were purified from Clostridium purinolyticum and characterized.	Self WT, Stadtman TC.	Proc Natl Acad Sci U S A	10.1073/pnas.97.13.7208	2000
Enzymology	Molecular characterization of a Clostridium difficile bacteriophage and its cloned biologically active endolysin.	Mayer MJ, Narbad A, Gasson MJ.	J Bacteriol	10.1128/jb.00686-08	2008
Metabolism	Characterization of the protocatechuate 4,5-cleavage pathway operon in Comamonas sp. strain E6 and discovery of a novel pathway gene.	Kamimura N, Aoyama T, Yoshida R, Takahashi K, Kasai D, Abe T, Mase K, Katayama Y, Fukuda M, Masai E.	Appl Environ Microbiol	10.1128/aem.01863-10	2010
Metabolism	The three-dimensional crystal structure of the PrpF protein of Shewanella oneidensis complexed with trans-aconitate: insights into its biological function.	Garvey GS, Rocco CJ, Escalante-Semerena JC, Rayment I.	Protein Sci	10.1110/ps.072801907	2007
Metabolism	Purine catabolism in Escherichia coli and function of xanthine dehydrogenase in purine salvage.	Xi H, Schneider BL, Reitzer L.	J Bacteriol	10.1128/jb.182.19.5332-5341.2000	2000
Metabolism	Flexible community structure correlates with stable community function in methanogenic bioreactor communities perturbed by glucose.	Fernandez AS, Hashsham SA, Dollhopf SL, Raskin L, Glagoleva O, Dazzo FB, Hickey RF, Criddle CS, Tiedje JM.	Appl Environ Microbiol	10.1128/aem.66.9.4058-4067.2000	2000
Metabolism	Comparative genomic analyses of nickel, cobalt and vitamin B12 utilization.	Zhang Y, Rodionov DA, Gelfand MS, Gladyshev VN.	BMC Genomics	10.1186/1471-2164-10-78	2009
	Identification and Characterization of Two Novel Members of the Family Eubacteriaceae, Anaerofustis butyriciformans sp. nov. and Pseudoramibacter faecis sp. nov., Isolated from Human Feces.	Wang XM, Huang HJ, Sun XW, Wei RQ, Chen HY, Liu C, Liu SJ.	Microorganisms	10.3390/microorganisms13040916	2025
Phylogeny	Anaerovorax odorimutans gen. nov., sp. nov., a putrescine-fermenting, strictly anaerobic bacterium.	Matthies C, Evers S, Ludwig W, Schink B.	Int J Syst Evol Microbiol	10.1099/00207713-50-4-1591	2000
	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
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

References

#587	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 1223
#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 )
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#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 )

Rate our new design

Content

About us

Eubacterium barkeri (DSM 1223, ATCC 25849, NCIB 10623)

Name and taxonomic classification

Morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_900107125

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

Help

Social Media