Eubacterium limosum (DSM 20543, ATCC 8486, NCIB 9763)

Name: Eubacterium limosum (DSM 20543, ATCC 8486, NCIB 9763)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 5432

Type strain

Culture col. no. DSM 20543 ATCC 8486 NCIB 9763 CCUG 16793 JCM 6421 5 more

NCBI tax ID(s) 1736

Special Collections DSMZ CCUG JCM KCTC CIP

History <- ATCC <- A.H. Eggerth (Bacteroides limosus) T. Mitsuoka <-- ATCC 8486 <-- A. H. Eggerth ("Bacteroides limosum"). CIP <- 1994, ATCC <- A.H. Eggerth, Bacteroides limosus

Links

Eubacterium limosum DSM 20543 is an anaerobe, mesophilic prokaryote of the family Eubacteriaceae.

anaerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 34969

ATCC 8486,NCIB 9763,CCUG 16793,DSM 20543,CIP 104169,JCM 6421,CCRC 14401,NCIMB 9763,JCM 9978,KCTC 3266,BCRC 14401,LMG 28910

@ref 20215

Last LPSN update 2025-12-16 09:48:04

Domain Bacillati

Phylum Bacillota

Class Clostridia

Order Eubacteriales

Family Eubacteriaceae

Genus Eubacterium

Species Eubacterium limosum

Full scientific name Eubacterium limosum (Eggerth 1935) Prévot 1938 (Approved Lists 1980)

Synonyms (2)

"Butyribacterium limosum"
"Bacteroides limosus"

BacDive ID	Other strains from **Eubacterium limosum** (7)	Type strain
5430	E. limosum 2A, DSM 2593, JCM 10283, CCUG 16794
5431	E. limosum llA, DSM 2594
141485	E. limosum CCUG 2228
143136	E. limosum CCUG 17367
153852	E. limosum CCUG 51363
157742	E. limosum G14, DSM 107592
165411	E. limosum JCM 6501, VPI 1939

Morphology

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
8772	PYG MEDIUM (MODIFIED) (DSMZ Medium 104)	Medium recipe at MediaDive	Name: PYG MEDIUM (modified) (DSMZ Medium 104) Composition: Yeast extract 10.0 g/l Peptone 5.0 g/l Trypticase peptone 5.0 g/l Beef extract 5.0 g/l Glucose 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 MgSO4 x 7 H2O 0.02 g/l CaCl2 x 2 H2O 0.01 g/l Hemin 0.005 g/l Ethanol 0.0038 g/l Resazurin 0.001 g/l Tween 80 Vitamin K1 NaOH Distilled water
41025	MEDIUM 187 - for anaerobic bacteria		Distilled water make up to (1000.000 ml);Glucose (5.000 g);Yeast extract(20.000 g);Tryptone (30.000 g);Cysteine hydrochloride (0.500 g);Hemin solution - M00149(25.000 ml)
120605	CIP Medium 187	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
8772	positive	growth	37	mesophilic
41025	positive	growth	37	mesophilic
46528	positive	growth	37	mesophilic
67770	positive	growth	37	mesophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
8772	anaerobe
46528	anaerobe
125438	anaerobe	90.954
125439	anaerobe	99.6

Murein

@ref	Murein short key	Type
8772	B04	B2alpha {L-Ser} [L-Orn] D-Glu-D-Lys(D-Orn)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68380	29016 ChEBI	arginine	-	hydrolysis	from API rID32A
68379	16899 ChEBI	D-mannitol	+	fermentation	from API Coryne
68380	16024 ChEBI	D-mannose	-	fermentation	from API rID32A
68379	16988 ChEBI	D-ribose	+	fermentation	from API Coryne
68379	65327 ChEBI	D-xylose	-	fermentation	from API Coryne
68379	4853 ChEBI	esculin	-	hydrolysis	from API Coryne
68379	5291 ChEBI	gelatin	-	hydrolysis	from API Coryne
68379	28087 ChEBI	glycogen	-	fermentation	from API Coryne
68380	29985 ChEBI	L-glutamate	+	degradation	from API rID32A
68379	17716 ChEBI	lactose	-	fermentation	from API Coryne
68379	17306 ChEBI	maltose	-	fermentation	from API Coryne
68379	17632 ChEBI	nitrate	-	reduction	from API Coryne
68380	17632 ChEBI	nitrate	-	reduction	from API rID32A
68380	16634 ChEBI	raffinose	-	fermentation	from API rID32A
68379	17992 ChEBI	sucrose	-	fermentation	from API Coryne
68380	27897 ChEBI	tryptophan	-	energy source	from API rID32A
68379	16199 ChEBI	urea	-	hydrolysis	from API Coryne
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
68380	35581 ChEBI	indole	-	from API rID32A

Enzymes

@ref	Value	Activity	Ec
68380	alanine arylamidase	-	3.4.11.2	from API rID32A
68379	alkaline phosphatase	-	3.1.3.1	from API Coryne
68380	alpha-arabinosidase	-	3.2.1.55	from API rID32A
68380	alpha-fucosidase	-	3.2.1.51	from API rID32A
68380	alpha-galactosidase	-	3.2.1.22	from API rID32A
68380	alpha-glucosidase	-	3.2.1.20	from API rID32A
68379	alpha-glucosidase	-	3.2.1.20	from API Coryne
68380	arginine dihydrolase	-	3.5.3.6	from API rID32A
68380	beta-galactosidase	-	3.2.1.23	from API rID32A
68379	beta-galactosidase	-	3.2.1.23	from API Coryne
68380	beta-Galactosidase 6-phosphate	-		from API rID32A
68379	beta-glucosidase	-	3.2.1.21	from API Coryne
68380	beta-glucosidase	-	3.2.1.21	from API rID32A
68380	beta-glucuronidase	-	3.2.1.31	from API rID32A
68379	beta-glucuronidase	-	3.2.1.31	from API Coryne
68379	catalase	-	1.11.1.6	from API Coryne
68379	gelatinase	-		from API Coryne
68380	glutamate decarboxylase	+	4.1.1.15	from API rID32A
68380	glutamyl-glutamate arylamidase	-		from API rID32A
68380	glycin arylamidase	-		from API rID32A
68380	histidine arylamidase	-		from API rID32A
68380	L-arginine arylamidase	-		from API rID32A
68380	leucine arylamidase	-	3.4.11.1	from API rID32A
68380	leucyl glycin arylamidase	+	3.4.11.1	from API rID32A
68380	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API rID32A
68379	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API Coryne
68380	phenylalanine arylamidase	-		from API rID32A
68380	proline-arylamidase	-	3.4.11.5	from API rID32A
68379	pyrazinamidase	-	3.5.1.B15	from API Coryne
68380	pyrrolidonyl arylamidase	-	3.4.19.3	from API rID32A
68379	pyrrolidonyl arylamidase	-	3.4.19.3	from API Coryne
68380	serine arylamidase	-		from API rID32A
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
68379	urease	-	3.5.1.5	from API Coryne

API coryne

@ref	Reduction of nitrateNIT	PYZ	PYRA	PAL	beta GUR	beta GAL	alpha GLU	beta NAG	ESC	URE	GEL	Control fermentationControl	GLU	RIB	XYL	MAN	MAL	LAC	SAC	GLYG	CAT
46528	-	-	-	-	-	-	-	-	-	-	-	-	not determinedn.d.	+	-	+	-	-	-	-	-

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
8772	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	-	-	-	-	+	-	-	-	-	-	-	-	-	-
8772	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	-	+/-	-	-	+	-	-	-	-	-	-	-	-	-

Isolation, sampling and environmental information

Taxonmaps

69479

Global distribution of 16S sequence LC019782 (>99% sequence identity) for Eubacterium from Microbeatlas

Aquatic Samples	2430
Soil Samples	550
Animal Samples	38820
Plant Samples	312
Total Samples	42112

Interaction and safety

Risk assessment

@ref	Pathogenicity human	Biosafety level	Biosafety level comment
8772	yes, in single cases	1	Risk group (German classification) According to TRBA 466
120605		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	ASM80767v2 assembly for Eubacterium limosum ATCC 8486	complete	GCA_000807675	1736.46	2814123220	1736	98.86
66792	Eubacterium limosum ATCC 8480	contig		1736.3		1736	70.6

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Eubacterium limosum strain ATCC 8486 16S ribosomal RNA gene, partial sequence	M59120	1525	1736
20218	Eubacterium limosum gene for 16S ribosomal RNA, partial sequence, strain: JCM 6421	AB595134	1484	1736
67770	Eubacterium limosum gene for 16S ribosomal RNA, partial sequence, strain: JCM 9978	LC019782	1425	1736

GC content

@ref	GC-content (mol%)	Method
8772	47.8
67770	47.8	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 limosum ATCC 8486
IMG: 2814123220

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	yes	78.30	no
125439	motility	BacteriaNetⓘ	yes	63.00	no
125439	gram_stain	BacteriaNetⓘ	positive	53.00	no
125439	oxygen_tolerance	BacteriaNetⓘ	anaerobe	99.60	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Eubacterium limosum ATCC 8486
NCBI: GCA_000807675.2

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	72.93	no
125438	anaerobic	anaerobicⓘ	yes	90.95	yes
125438	aerobic	aerobicⓘ	no	94.26	no
125438	spore-forming	spore-formingⓘ	no	50.97	no
125438	thermophilic	thermophileⓘ	no	90.06	yes
125438	flagellated	motile2+ⓘ	no	56.40	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Metabolism	Alternative pathway for dopamine production by acetogenic gut bacteria that O-Demethylate 3-Methoxytyramine, a metabolite of catechol O-Methyltransferase.	Rich BE, Jackson JC, de Ora LO, Long ZG, Uyeda KS, Bess EN.	J Appl Microbiol	10.1111/jam.15682	2022
	Refining and illuminating acetogenic Eubacterium strains for reclassification and metabolic engineering.	Flaiz M, Poehlein A, Wilhelm W, Mook A, Daniel R, Durre P, Bengelsdorf FR.	Microb Cell Fact	10.1186/s12934-024-02301-8	2024
	The extent of nitrogen isotopic fractionation in rumen bacteria is associated with changes in rumen nitrogen metabolism.	Cantalapiedra-Hijar G, Martinez-Fernandez G, Forano E, Denman SE, Morgavi D, McSweeney CS.	PLoS One	10.1371/journal.pone.0291243	2023
	GABA Production by Human Intestinal Bacteroides spp.: Prevalence, Regulation, and Role in Acid Stress Tolerance.	Otaru N, Ye K, Mujezinovic D, Berchtold L, Constancias F, Cornejo FA, Krzystek A, de Wouters T, Braegger C, Lacroix C, Pugin B.	Front Microbiol	10.3389/fmicb.2021.656895	2021
Metabolism	Transcriptome and translatome of CO₂ fixing acetogens under heterotrophic and autotrophic conditions.	Song Y, Bae J, Shin J, Jin S, Lee JK, Kim SC, Cho S, Cho BK.	Sci Data	10.1038/s41597-021-00837-7	2021
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
	CO₂ fixation by anaerobic non-photosynthetic mixotrophy for improved carbon conversion.	Jones SW, Fast AG, Carlson ED, Wiedel CA, Au J, Antoniewicz MR, Papoutsakis ET, Tracy BP.	Nat Commun	10.1038/ncomms12800	2016
Metabolism	A cobalamin-dependent pathway of choline demethylation from the human gut acetogen Eubacterium limosum.	Jiang R, Kountz DJ, Zhang L, Krzycki JA.	J Biol Chem	10.1016/j.jbc.2025.108524	2025
Genetics	Genome sequence of Eubacterium callanderi AM6, isolated from a Parkinson's disease patient.	Kumar M, Sayavedra L, Baker DJ, Shouche YS, Narbad A.	Microbiol Resour Announc	10.1128/mra.00039-25	2025
	Storage of the vital metal tungsten in a dominant SCFA-producing human gut microbe Eubacterium limosum and implications for other gut microbes.	Shao N, Zhou D, Schut GJ, Poole FL, Coffey SB, Donaghy AP, Putumbaka S, Thorgersen MP, Chen L, Rose J, Wang B-C, Adams MWW.	mBio	10.1128/mbio.02605-24	2025
	Deletion of biofilm synthesis in Eubacterium limosum ATCC 8486 improves handling and transformation efficiency.	Sanford PA, Miller KG, Hoyt KO, Woolston BM.	FEMS Microbiol Lett	10.1093/femsle/fnad030	2023
Genetics	Development of a Recombineering System for the Acetogen Eubacterium limosum with Cas9 Counterselection for Markerless Genome Engineering.	Sanford PA, Woolston BM.	ACS Synth Biol	10.1021/acssynbio.4c00253	2024
Phylogeny	Genome-Based Reclassification of Strain KIST612, Previously Classified as Eubacterium limosum, into a New Strain of Eubacterium callanderi.	Kim JY, Kang B, Oh S, Gil Y, Choi IG, Chang IS.	J Microbiol Biotechnol	10.4014/jmb.2304.04011	2023
	Exploitation of a Type 1 Toxin-Antitoxin System as an Inducible Counter-Selective Marker for Genome Editing in the Acetogen Eubacterium limosum.	Millard J, Agius A, Zhang Y, Soucaille P, Minton NP.	Microorganisms	10.3390/microorganisms11051256	2023
	Carotenoid productivity in human intestinal bacteria Eubacterium limosum and Leuconostoc mesenteroides with functional analysis of their carotenoid biosynthesis genes.	Matsumoto W, Takemura M, Nanaura H, Ami Y, Maoka T, Shindo K, Kurihara S, Misawa N.	Eng Microbiol	10.1016/j.engmic.2024.100147	2024
Enzymology	Tungsten is utilized for lactate consumption and SCFA production by a dominant human gut microbe Eubacterium limosum.	Putumbaka S, Schut GJ, Thorgersen MP, Poole FL, Shao N, Rodionov DA, Adams MWW.	Proc Natl Acad Sci U S A	10.1073/pnas.2411809121	2025
Genetics	Genome Sequence of Eubacterium limosum B2 and Evolution for Growth on a Mineral Medium with Methanol and CO₂ as Sole Carbon Sources.	Pregnon G, Minton NP, Soucaille P.	Microorganisms	10.3390/microorganisms10091790	2022
	Developing a genetic engineering method for Acetobacterium wieringae to expand one-carbon valorization pathways.	Moreira JPC, Heap JT, Alves JI, Domingues L.	Biotechnol Biofuels Bioprod	10.1186/s13068-023-02259-6	2023
Metabolism	The MttB superfamily member MtyB from the human gut symbiont Eubacterium limosum is a cobalamin-dependent gamma-butyrobetaine methyltransferase.	Ellenbogen JB, Jiang R, Kountz DJ, Zhang L, Krzycki JA.	J Biol Chem	10.1016/j.jbc.2021.101327	2021
Metabolism	Gut symbiont-derived ursodeoxycholic acid promotes fatty acid oxidation to protect against renal ischemia-reperfusion injury.	Xie M, Zheng J, Yu Y, Yang Q, Zhou Z, Xue J, Wang B, Qiu Y, Zhu Z, Sun Q, Shi X, Shangguan W, Li L, Zou Z, Zhao J, Wu P.	Cell Rep Med	10.1016/j.xcrm.2025.102373	2025
	Expanding the genetic engineering toolbox for the metabolically flexible acetogen Eubacterium limosum.	Sanford PA, Woolston BM.	J Ind Microbiol Biotechnol	10.1093/jimb/kuac019	2022
	Genome-wide CRISPRi screen identifies enhanced autolithotrophic phenotypes in acetogenic bacterium Eubacterium limosum.	Shin J, Bae J, Lee H, Kang S, Jin S, Song Y, Cho S, Cho BK.	Proc Natl Acad Sci U S A	10.1073/pnas.2216244120	2023
Phylogeny	Reclassification of Catabacter hongkongensis as Christensenella hongkongensis comb. nov. based on whole genome analysis.	Liu X, Sutter JL, de la Cuesta-Zuluaga J, Waters JL, Youngblut ND, Ley RE.	Int J Syst Evol Microbiol	10.1099/ijsem.0.004774	2021
	Genome Sequence of Eubacterium callanderi AMC0717, Isolated from the Colonic Mucosa of an 11-Year-Old Organ Donor.	Marsh AJ, Chandrashekhar K, Ng S, Roach J, Magness ST, Azcarate-Peril MA.	Microbiol Resour Announc	10.1128/mra.00995-20	2020
Metabolism	Genome-scale analysis of syngas fermenting acetogenic bacteria reveals the translational regulation for its autotrophic growth.	Song Y, Shin J, Jin S, Lee JK, Kim DR, Kim SC, Cho S, Cho BK.	BMC Genomics	10.1186/s12864-018-5238-0	2018
	Genomic potential and physiological characteristics of C1 metabolism in novel acetogenic bacteria.	Yu J, Park MJ, Lee J, Kwon SJ, Lim JK, Lee HS, Kang SG, Lee JH, Kwon KK, Kim YJ.	Front Microbiol	10.3389/fmicb.2023.1279544	2023
Genetics	Targeted curation of the gut microbial gene content modulating human cardiovascular disease.	Borton MA, Shaffer M, Hoyt DW, Jiang R, Ellenbogen JB, Purvine S, Nicora CD, Eder EK, Wong AR, Smulian AG, Lipton MS, Krzycki JA, Wrighton KC.	mBio	10.1128/mbio.01511-23	2023
	Harnessing acetogenic bacteria for one-carbon valorization toward sustainable chemical production.	Bae J, Park C, Jung H, Jin S, Cho BK.	RSC Chem Biol	10.1039/d4cb00099d	2024
	Bioinformatics and metabolic flux analysis highlight a new mechanism involved in lactate oxidation in Clostridium tyrobutyricum.	Munier E, Licandro H, Beuvier E, Cachon R.	Int Microbiol	10.1007/s10123-022-00316-y	2023
Enzymology	Anaerobic bacteria in the intestinal microbiota of Brazilian children.	Talarico ST, Santos FE, Brandt KG, Martinez MB, Taddei CR.	Clinics (Sao Paulo)	10.6061/clinics/2017(03)05	2017
	Comparative genomics and proteomics of Eubacterium maltosivorans: functional identification of trimethylamine methyltransferases and bacterial microcompartments in a human intestinal bacterium with a versatile lifestyle.	Feng Y, Bui TPN, Stams AJM, Boeren S, Sanchez-Andrea I, de Vos WM.	Environ Microbiol	10.1111/1462-2920.15886	2022
Metabolism	Determination of Butyrate Synthesis Capacity in Gut Microbiota: Quantification of but Gene Abundance by qPCR in Fecal Samples.	Daskova N, Heczkova M, Modos I, Videnska P, Splichalova P, Pelantova H, Kuzma M, Gojda J, Cahova M.	Biomolecules	10.3390/biom11091303	2021
	Microbiome- and Host Inflammasome-Targeting Inhibitor Nanoligomers Are Therapeutic in the Murine Colitis Model.	Sharma S, Gilberto VS, Levens CL, Chatterjee A, Kuhn KA, Nagpal P.	ACS Pharmacol Transl Sci	10.1021/acsptsci.4c00102	2024
Enzymology	Reduction, evolutionary pattern and positive selection of genes encoding formate dehydrogenase in Wood-Ljungdahl pathway of gastrointestinal acetogens suggests their adaptation to formate-rich habitats.	Yao Y, Fu B, Han D, Zhang Y, Wei Z, Liu H.	Environ Microbiol Rep	10.1111/1758-2229.13129	2023
	Engineered phage with antibacterial CRISPR-Cas selectively reduce E. coli burden in mice.	Gencay YE, Jasinskyte D, Robert C, Semsey S, Martinez V, Petersen AO, Brunner K, de Santiago Torio A, Salazar A, Turcu IC, Eriksen MK, Koval L, Takos A, Pascal R, Schou TS, Bayer L, Bryde T, Johansen KC, Bak EG, Smrekar F, Doyle TB, Satlin MJ, Gram A, Carvalho J, Jessen L, Hallstrom B, Hink J, Damholt B, Troy A, Grove M, Clube J, Grondahl C, Haaber JK, van der Helm E, Zdravkovic M, Sommer MOA.	Nat Biotechnol	10.1038/s41587-023-01759-y	2024
Enzymology	RiboRid: A low cost, advanced, and ultra-efficient method to remove ribosomal RNA for bacterial transcriptomics.	Choe D, Szubin R, Poudel S, Sastry A, Song Y, Lee Y, Cho S, Palsson B, Cho BK.	PLoS Genet	10.1371/journal.pgen.1009821	2021
Metabolism	Tungsten enzymes play a role in detoxifying food and antimicrobial aldehydes in the human gut microbiome.	Schut GJ, Thorgersen MP, Poole FL, Haja DK, Putumbaka S, Adams MWW.	Proc Natl Acad Sci U S A	10.1073/pnas.2109008118	2021
Metabolism	The Sporomusa type Nfn is a novel type of electron-bifurcating transhydrogenase that links the redox pools in acetogenic bacteria.	Kremp F, Roth J, Muller V.	Sci Rep	10.1038/s41598-020-71038-2	2020
	Genome-Scale Analysis of Acetobacterium woodii Identifies Translational Regulation of Acetogenesis.	Shin J, Song Y, Kang S, Jin S, Lee JK, Kim DR, Cho S, Muller V, Cho BK.	mSystems	10.1128/msystems.00696-21	2021
	Recent insight and future techniques to enhance rumen fermentation in dairy goats.	Mamuad LL, Lee SS, Lee SS.	Asian-Australas J Anim Sci	10.5713/ajas.19.0323	2019
Pathogenicity	Gut microbial metabolite hyodeoxycholic acid targets the TLR4/MD2 complex to attenuate inflammation and protect against sepsis.	Li J, Chen Y, Li R, Zhang X, Chen T, Mei F, Liu R, Chen M, Ge Y, Hu H, Wei R, Chen Z, Fan H, Zeng Z, Deng Y, Luo H, Hu S, Cai S, Wu F, Shi N, Wang Z, Zeng Y, Xie M, Jiang Y, Chen Z, Jia W, Chen P.	Mol Ther	10.1016/j.ymthe.2023.01.018	2023
Metabolism	Effects of reductive acetogenic bacteria and lauric acid on in vivo ruminal fermentation, microbial populations, and methane mitigation in Hanwoo steers in South Korea.	Kim SH, Mamuad LL, Choi YJ, Sung HG, Cho KK, Lee SS.	J Anim Sci	10.1093/jas/sky266	2018
Metabolism	Rumen fermentation and acetogen population changes in response to an exogenous acetogen TWA4 strain and Saccharomyces cerevisiae fermentation product.	Yang CL, Guan LL, Liu JX, Wang JK.	J Zhejiang Univ Sci B	10.1631/jzus.b1500013	2015
	Application of Microalgal Stress Responses in Industrial Microalgal Production Systems.	Wang J, Wang Y, Wu Y, Fan Y, Zhu C, Fu X, Chu Y, Chen F, Sun H, Mou H.	Mar Drugs	10.3390/md20010030	2021
Pathogenicity	Microbiota-derived bile acids antagonize the host androgen receptor and drive anti-tumor immunity.	Jin WB, Xiao L, Jeong M, Han SJ, Zhang W, Yano H, Shi H, Arifuzzaman M, Lyu M, Wang D, Tang YA, Qiao S, JRI IBD Live Cell Bank Consortium, Yang X, Yang HS, Fu J, Sonnenberg GF, Collins N, Artis D, Guo CJ.	Cell	10.1016/j.cell.2025.02.029	2025
Genetics	Safety Evaluation of Oral Care Probiotics Weissella cibaria CMU and CMS1 by Phenotypic \|and Genotypic Analysis.	Kang MS, Yeu JE, Hong SP.	Int J Mol Sci	10.3390/ijms20112693	2019
Transcriptome	The Complete Genome Sequence of Clostridium aceticum: a Missing Link between Rnf- and Cytochrome-Containing Autotrophic Acetogens.	Poehlein A, Cebulla M, Ilg MM, Bengelsdorf FR, Schiel-Bengelsdorf B, Whited G, Andreesen JR, Gottschalk G, Daniel R, Durre P.	mBio	10.1128/mbio.01168-15	2015
Metabolism	Functional cooperation of the glycine synthase-reductase and Wood-Ljungdahl pathways for autotrophic growth of Clostridium drakei.	Song Y, Lee JS, Shin J, Lee GM, Jin S, Kang S, Lee JK, Kim DR, Lee EY, Kim SC, Cho S, Kim D, Cho BK.	Proc Natl Acad Sci U S A	10.1073/pnas.1912289117	2020
Enzymology	Formyltetrahydrofolate synthetase sequences from salt marsh plant roots reveal a diversity of acetogenic bacteria and other bacterial functional groups.	Leaphart AB, Friez MJ, Lovell CR.	Appl Environ Microbiol	10.1128/aem.69.1.693-696.2003	2003
Enzymology	PCR detection and quantitation of predominant anaerobic bacteria in human and animal fecal samples.	Wang RF, Cao WW, Cerniglia CE.	Appl Environ Microbiol	10.1128/aem.62.4.1242-1247.1996	1996
Pathogenicity	In Vitro Antibacterial Properties of Cefiderocol, a Novel Siderophore Cephalosporin, against Gram-Negative Bacteria.	Ito A, Sato T, Ota M, Takemura M, Nishikawa T, Toba S, Kohira N, Miyagawa S, Ishibashi N, Matsumoto S, Nakamura R, Tsuji M, Yamano Y.	Antimicrob Agents Chemother	10.1128/aac.01454-17	2018
	In vitro and in vivo antibacterial activities of TAK-083, an agent for treatment of Helicobacter pylori infection.	Kanamaru T, Nakano Y, Toyoda Y, Miyagawa KI, Tada M, Kaisho T, Nakao M.	Antimicrob Agents Chemother	10.1128/aac.45.9.2455-2459.2001	2001
Metabolism	Metabolism of the 18O-methoxy substituent of 3-methoxybenzoic acid and other unlabeled methoxybenzoic acids by anaerobic bacteria.	DeWeerd KA, Saxena A, Nagle DP, Suflita JM.	Appl Environ Microbiol	10.1128/aem.54.5.1237-1242.1988	1988
	In vitro enrofloxacin binding in human fecal slurries.	Ahn Y, Linder SW, Veach BT, Steve Yan S, Haydee Fernandez A, Pineiro SA, Cerniglia CE.	Regul Toxicol Pharmacol	10.1016/j.yrtph.2011.11.013	2012
Phylogeny	Development of cpn60-based real-time quantitative PCR assays for the detection of 14 Campylobacter species and application to screening of canine fecal samples.	Chaban B, Musil KM, Himsworth CG, Hill JE.	Appl Environ Microbiol	10.1128/aem.00101-09	2009
	Role of peptidoglycan subtypes in the pathogenesis of bacterial cell wall arthritis.	Simelyte E, Rimpilainen M, Zhang X, Toivanen P.	Ann Rheum Dis	10.1136/ard.62.10.976	2003
Enzymology	Detection of Clostridium proteoclasticum and closely related strains in the rumen by competitive PCR.	Reilly K, Attwood GT.	Appl Environ Microbiol	10.1128/aem.64.3.907-913.1998	1998
Phylogeny	Functional gene analysis suggests different acetogen populations in the bovine rumen and tammar wallaby forestomach.	Gagen EJ, Denman SE, Padmanabha J, Zadbuke S, Al Jassim R, Morrison M, McSweeney CS.	Appl Environ Microbiol	10.1128/aem.01679-10	2010
	Simplified gas chromatographic procedure for identification of bacterial metabolic products.	Carlsson J.	Appl Microbiol	10.1128/am.25.2.287-289.1973	1973
Enzymology	Development of a differential medium for bile salt hydrolase-active Lactobacillus spp.	Dashkevicz MP, Feighner SD.	Appl Environ Microbiol	10.1128/aem.55.1.11-16.1989	1989
	Mercury methylation and demethylation in anoxic lake sediments and by strictly anaerobic bacteria.	Pak KR, Bartha R.	Appl Environ Microbiol	10.1128/aem.64.3.1013-1017.1998	1998
Pathogenicity	In vitro and in vivo antibacterial activities of KRM-1648 and KRM-1657, new rifamycin derivatives.	Fujii K, Tsuji A, Miyazaki S, Yamaguchi K, Goto S.	Antimicrob Agents Chemother	10.1128/aac.38.5.1118	1994
Enzymology	Superoxide dismutase in anaerobes: survey.	Gregory EM, Moore WE, Holdeman LV.	Appl Environ Microbiol	10.1128/aem.35.5.988-991.1978	1978
	Antimicrobial activity of DU-6681a, a parent compound of novel oral carbapenem DZ-2640.	Tanaka M, Hohmura M, Nishi T, Sato K, Hayakawa I.	Antimicrob Agents Chemother	10.1128/aac.41.6.1260	1997
Pathogenicity	Comparison of the activity of ionophores with other antibacterial agents against anaerobes.	Watanabe K, Watanabe J, Kuramitsu S, Maruyama HB.	Antimicrob Agents Chemother	10.1128/aac.19.4.519	1981
Enzymology	Evaluation of an immunofluorescent-antibody test for rapid identification of Pseudomonas aeruginosa in blood cultures.	Counts GW, Schwartz RW, Ulness BK, Hamilton DJ, Rosok MJ, Cunningham MD, Tam MR, Darveau RP.	J Clin Microbiol	10.1128/jcm.26.6.1161-1165.1988	1988
Metabolism	Ammonia-hyperproducing bacteria from New Zealand ruminants.	Attwood GT, Klieve AV, Ouwerkerk D, Patel BK.	Appl Environ Microbiol	10.1128/aem.64.5.1796-1804.1998	1998
Pathogenicity	Lansoprazole, a novel benzimidazole proton pump inhibitor, and its related compounds have selective activity against Helicobacter pylori.	Iwahi T, Satoh H, Nakao M, Iwasaki T, Yamazaki T, Kubo K, Tamura T, Imada A.	Antimicrob Agents Chemother	10.1128/aac.35.3.490	1991
Cultivation	Comparison of media in the Anaerobe-Tek and Presumpto plate systems and evaluation of the Anaerobe-Tek system for identification of commonly encountered anaerobes.	Lombard GL, Whaley DN, Dowell VR.	J Clin Microbiol	10.1128/jcm.16.6.1066-1072.1982	1982
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
Metabolism	Importance of tetrahydrofolate and ATP in the anaerobic O-demethylation reaction for phenylmethylethers.	Berman MH, Frazer AC.	Appl Environ Microbiol	10.1128/aem.58.3.925-931.1992	1992
Pathogenicity	In vitro and in vivo antibacterial activities of AT-4140, a new broad-spectrum quinolone.	Nakamura S, Minami A, Nakata K, Kurobe N, Kouno K, Sakaguchi Y, Kashimoto S, Yoshida H, Kojima T, Ohue T.	Antimicrob Agents Chemother	10.1128/aac.33.8.1167	1989
Pathogenicity	Antimicrobial and beta-lactamase inhibitory activities of carpetimycins A and B, new carbapenem antibiotics.	Kobayashi F, Saino Y, Koshi T, Hattori Y, Nakayama M, Iwasaki A, Mori T, Mitsuhashi S.	Antimicrob Agents Chemother	10.1128/aac.21.4.536	1982
Phylogeny	Evaluation of simplified dichotomous schemata for the identification of anaerobic bacteria from clinical material.	Porschen RK, Stalons DR.	J Clin Microbiol	10.1128/jcm.3.2.161-171.1976	1976
Pathogenicity	Moxalactam (6059-S), a novel 1-oxa-beta-lactam with an expanded antibacterial spectrum: laboratory evaluation.	Yoshida T, Matsuura S, Mayama M, Kameda Y, Kuwahara S.	Antimicrob Agents Chemother	10.1128/aac.17.3.302	1980
Metabolism	Cytokine Response after Stimulation with Key Commensal Bacteria Differ in Post-Infectious Irritable Bowel Syndrome (PI-IBS) Patients Compared to Healthy Controls.	Sundin J, Rangel I, Repsilber D, Brummer RJ.	PLoS One	10.1371/journal.pone.0134836	2015
	Clostridium butyricum-altered lung microbiome is associated with enhanced anti-influenza effects via G-protein-coupled receptor120.	Hagihara M, Yamashita M, Ariyoshi T, Minemura A, Yoshida C, Higashi S, Oka K, Takahashi M, Ota A, Maenaka A, Iwasaki K, Hirai J, Shibata Y, Umemura T, Mori T, Kato H, Asai N, Mikamo H.	iScience	10.1016/j.isci.2025.113502	2025
	Isolation and characterization of reductive acetogens from rumen fluid samples of Murrah buffaloes.	Choudhury PK, Jena R, Puniya AK, Tomar SK.	3 Biotech	10.1007/s13205-023-03688-8	2023
	The Potential Impact of Probiotics on the Gut Microbiome of Athletes.	Wosinska L, Cotter PD, O'Sullivan O, Guinane C.	Nutrients	10.3390/nu11102270	2019
	Short-Chain Fatty Acids and Human Health: From Metabolic Pathways to Current Therapeutic Implications.	Facchin S, Bertin L, Bonazzi E, Lorenzon G, De Barba C, Barberio B, Zingone F, Maniero D, Scarpa M, Ruffolo C, Angriman I, Savarino EV.	Life (Basel)	10.3390/life14050559	2024
Metabolism	High methanol-to-formate ratios induce butanol production in Eubacterium limosum.	Wood JC, Marcellin E, Plan MR, Virdis B	Microb Biotechnol	10.1111/1751-7915.13963	2021
Metabolism	MtcB, a member of the MttB superfamily from the human gut acetogen Eubacterium limosum, is a cobalamin-dependent carnitine demethylase.	Kountz DJ, Behrman EJ, Zhang L, Krzycki JA	J Biol Chem	10.1074/jbc.RA120.012934	2020
	Adaptive Laboratory Evolution of Eubacterium limosum ATCC 8486 on Carbon Monoxide.	Kang S, Song Y, Jin S, Shin J, Bae J, Kim DR, Lee JK, Kim SC, Cho S, Cho BK	Front Microbiol	10.3389/fmicb.2020.00402	2020
Phylogeny	Reductive acetogens isolated from ruminants and their effect on in vitro methane mitigation and milk performance in Holstein cows.	Kim SH, Mamuad LL, Islam M, Lee SS	J Anim Sci Technol	10.5187/jast.2020.62.1.1	2020
Metabolism	MtpB, a member of the MttB superfamily from the human intestinal acetogen Eubacterium limosum, catalyzes proline betaine demethylation.	Picking JW, Behrman EJ, Zhang L, Krzycki JA	J Biol Chem	10.1074/jbc.RA119.009886	2019
Transcriptome	Determination of the Genome and Primary Transcriptome of Syngas Fermenting Eubacterium limosum ATCC 8486.	Song Y, Shin J, Jeong Y, Jin S, Lee JK, Kim DR, Kim SC, Cho S, Cho BK	Sci Rep	10.1038/s41598-017-14123-3	2017
Genetics	Draft Genome Sequence of Chemolithoautotrophic Acetogenic Butanol-Producing Eubacterium limosum ATCC 8486.	Song Y, Cho BK	Genome Announc	10.1128/genomeA.01564-14	2015
	Effect of Phytogenic Feed Additives in Soybean Meal on In vitro Swine Fermentation for Odor Reduction and Bacterial Community Comparison.	Alam MJ, Mamuad LL, Kim SH, Jeong CD, Sung HG, Cho SB, Jeon CO, Lee K, Lee SS	Asian-Australas J Anim Sci	10.5713/ajas.2012.12511	2013
Metabolism	Reductive dechlorination of methoxychlor and DDT by human intestinal bacterium Eubacterium limosum under anaerobic conditions.	Yim YJ, Seo J, Kang SI, Ahn JH, Hur HG	Arch Environ Contam Toxicol	10.1007/s00244-007-9044-y	2007
Metabolism	Biotransformation of the isoflavonoids biochanin A, formononetin, and glycitein by Eubacterium limosum.	Hur H, Rafii F	FEMS Microbiol Lett	10.1111/j.1574-6968.2000.tb09353.x	2000
Metabolism	Features of rumen and sewage sludge strains of Eubacterium limosum, a methanol- and H2-CO2-utilizing species.	Genthner BR, Davis CL, Bryant MP	Appl Environ Microbiol	10.1128/aem.42.1.12-19.1981	1981
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	Description of Absiella argi gen. nov., sp. nov., and transfer of Eubacterium dolichum and Eubacterium tortuosum to the genus Absiella as Absiella dolichum comb. nov. and Absiella tortuosum comb. nov.	Paek J, Shin Y, Kim JS, Kim H, Kook JK, Paek WK, Chang YH	Anaerobe	10.1016/j.anaerobe.2017.07.006	2017

References

#8772	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 20543
#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 )
#41025	; Curators of the CIP;
#46528	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 16793
#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;
#68379	Automatically annotated from API Coryne .
#68380	Automatically annotated from API rID32A .
#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 .
#120605	Collection of Institut Pasteur ; Curators of the CIP; CIP 104169
#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 limosum (DSM 20543, ATCC 8486, NCIB 9763)

Name and taxonomic classification

Morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Murein

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

API coryne

API rID32A

Isolation, sampling and environmental information

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000807675

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

Help

Social Media