Name: Eubacterium limosum DSM 20543
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 5432

Type strain:

Species: Eubacterium limosum

Culture col. no.: DSM 20543, ATCC 8486, NCIB 9763, CCUG 16793, JCM 6421, BCRC 14401, CIP 104169, JCM 9978, KCTC 3266, NCIMB 9763

Strain history: CIP <- 1994, ATCC <- A.H. Eggerth, Bacteroides limosus

NCBI tax ID(s): 1736 (species)

SI-ID 34969

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

Other strains from Eubacterium limosum

E. limosum 2A, DSM 2593, JCM 10283, CCUG 16794
E. limosum llA, DSM 2594
E. limosum CCUG 2228
E. limosum CCUG 17367
E. limosum CCUG 51363
E. limosum G14, DSM 107592
E. limosum JCM 6501, VPI 1939

Section

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

anaerobe
human pathogen
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 limosum**
	Full Scientific Name (LPSN)	Eubacterium limosum (Eggerth 1935) Prévot 1938 (Approved Lists 1980)

	Synonym	"Butyribacterium* limosum"*
	Synonym	"Bacteroides* limosus"*

Information on morphological and physiological properties Morphology

[Ref.: #69480]	Gram stain	positive Confidence in %100

[Ref.: #69480]	Motility	no Confidence in %91.29

Information on culture and growth conditions Culture and growth conditions

[Ref.: #8772]

Culture medium

PYG MEDIUM (MODIFIED) (DSMZ Medium 104)

[Ref.: #8772]

Culture medium growth

[Ref.: #8772]

Culture medium link

Medium recipe at MediaDive

[Ref.: #8772]

Culture medium composition

expand / minimize

[Ref.: #41025]

Culture medium

MEDIUM 187 - for anaerobic bacteria

[Ref.: #41025]

Culture medium growth

[Ref.: #41025]

Culture medium composition

expand / minimize

[Ref.: #120605]

Culture medium

CIP Medium 187

[Ref.: #120605]

Culture medium growth

[Ref.: #120605]

Culture medium link

Medium recipe provided by DSMZ

		Temperature
[Ref.: #8772]	growth	37 °C
[Ref.: #41025]	growth	37 °C
[Ref.: #46528]	growth	37 °C
[Ref.: #67770]	growth	37 °C

[Ref.: #8772]	Temperature range	mesophilic
[Ref.: #41025]	Temperature range	mesophilic
[Ref.: #46528]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #8772]	Oxygen tolerance	anaerobe
[Ref.: #46528]	Oxygen tolerance	anaerobe
[Ref.: #69480]	Oxygen tolerance	anaerobe Confidence in %99.071

[Ref.: #69481]	Ability of spore formation	no Confidence in %94
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.671

[Ref.: #8772]	Murein short key	B04
[Ref.: #8772]	Murein types	B2alpha {L-Ser} [L-Orn] D-Glu-D-Lys(D-Orn)

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #68380]	arginine ChEBI	-	hydrolysis	* from API rID32A
[Ref.: #68379]	D-mannitol ChEBI	+	fermentation	* from API Coryne
[Ref.: #68380]	D-mannose ChEBI	-	fermentation	* from API rID32A
[Ref.: #68379]	D-ribose ChEBI	+	fermentation	* from API Coryne
[Ref.: #68379]	D-xylose ChEBI	-	fermentation	* from API Coryne
[Ref.: #68379]	esculin ChEBI	-	hydrolysis	* from API Coryne
[Ref.: #68379]	gelatin ChEBI	-	hydrolysis	* from API Coryne
[Ref.: #68379]	glycogen ChEBI	-	fermentation	* from API Coryne
[Ref.: #68380]	L-glutamate ChEBI	+	degradation	* from API rID32A
[Ref.: #68379]	lactose ChEBI	-	fermentation	* from API Coryne
[Ref.: #68379]	maltose ChEBI	-	fermentation	* from API Coryne
[Ref.: #68379]	nitrate ChEBI	-	reduction	* from API Coryne, API rID32A
[Ref.: #68380]	raffinose ChEBI	-	fermentation	* from API rID32A
[Ref.: #68379]	sucrose ChEBI	-	fermentation	* from API Coryne
[Ref.: #68380]	tryptophan ChEBI	-	energy source	* from API rID32A
[Ref.: #68379]	urea ChEBI	-	hydrolysis	* from API Coryne, API rID32A
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #68380]		indole ChEBI	no	* from API rID32A

	Physiological tests	Metabolite	Indole test
[Ref.: #68380]		indole ChEBI	-	* from API rID32A

	Enzyme	Enzyme activity	EC number
[Ref.: #68380]	alanine arylamidase	-	3.4.11.2	* from API rID32A
[Ref.: #68379]	alkaline phosphatase	-	3.1.3.1	* from API Coryne
[Ref.: #68380]	alpha-arabinosidase	-	3.2.1.55	* from API rID32A
[Ref.: #68380]	alpha-fucosidase	-	3.2.1.51	* from API rID32A
[Ref.: #68380]	alpha-galactosidase	-	3.2.1.22	* from API rID32A
[Ref.: #68380]	alpha-glucosidase	-	3.2.1.20	* from API rID32A, API Coryne
[Ref.: #68380]	arginine dihydrolase	-	3.5.3.6	* from API rID32A
[Ref.: #68380]	beta-galactosidase	-	3.2.1.23	* from API rID32A, API Coryne
[Ref.: #68380]	beta-Galactosidase 6-phosphate	-		* from API rID32A
[Ref.: #68380]	beta-glucosidase	-	3.2.1.21	* from API rID32A, API Coryne
[Ref.: #68380]	beta-glucuronidase	-	3.2.1.31	* from API rID32A, API Coryne
[Ref.: #68379]	catalase	-	1.11.1.6	* from API Coryne
[Ref.: #68379]	gelatinase	-		* from API Coryne
[Ref.: #68380]	glutamate decarboxylase	+	4.1.1.15	* from API rID32A
[Ref.: #68380]	glutamyl-glutamate arylamidase	-		* from API rID32A
[Ref.: #68380]	glycin arylamidase	-		* from API rID32A
[Ref.: #68380]	histidine arylamidase	-		* from API rID32A
[Ref.: #68380]	L-arginine arylamidase	-		* from API rID32A
[Ref.: #68380]	leucine arylamidase	-	3.4.11.1	* from API rID32A
[Ref.: #68380]	leucyl glycin arylamidase	+	3.4.11.1	* from API rID32A
[Ref.: #68380]	N-acetyl-beta-glucosaminidase	-	3.2.1.52	* from API rID32A, API Coryne
[Ref.: #68380]	phenylalanine arylamidase	-		* from API rID32A
[Ref.: #68380]	proline-arylamidase	-	3.4.11.5	* from API rID32A
[Ref.: #68379]	pyrazinamidase	-	3.5.1.B15	* from API Coryne
[Ref.: #68380]	pyrrolidonyl arylamidase	-	3.4.19.3	* from API rID32A, API Coryne
[Ref.: #68380]	serine arylamidase	-		* from API rID32A
[Ref.: #68380]	tryptophan deaminase	-	4.1.99.1	* from API rID32A
[Ref.: #68380]	tyrosine arylamidase	-		* from API rID32A
[Ref.: #68380]	urease	-	3.5.1.5	* from API rID32A, API Coryne
	Only first 10 entries are displayed. Click here to see all.

API® Coryne:

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

	API ID	Reduction of nitrateNIT	PyrazinamidasePYZ	Pyrrolidonyl arylamidasePYRA	Alkaline phosphatasePAL	beta-Glucuronidasebeta GUR	beta-Galactosidasebeta GAL	alpha-Glucosidasealpha GLU	N-Acetyl-beta-Glucosidasebeta NAG	Esculin hydrolysis/beta-GlucosidaseESC	Urease/urea hydrolysisURE	Gelatinase/gelatin hydrolysisGEL	Control fermentationControl	Fermentation of D-glucoseGLU	Fermentation of D-riboseRIB	Fermentation of D-xyloseXYL	Fermentation of D-mannitolMAN	Fermentation of maltoseMAL	Fermentation of lactoseLAC	Fermentation of sucroseSAC	Fermentation of glycogenGLYG	CatalaseCAT
[Ref.: #46528]	782	-	-	-	-	-	-	-	-	-	-	-	-	not determinedn.d.	+	-	+	-	-	-	-	-

API® rID32A:

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

	API ID	Urease/urea hydrolysisURE	Arginine dihydrolaseADH (Arg)	alpha-Galactosidasealpha GAL	beta-Galactosidasebeta GAL	beta-Galactosidase 6-phosphatebeta GP	alpha-Glucosidasealpha GLU	beta-Glucosidasebeta GLU	alpha-Arabinosidasealpha ARA	beta-Glucuronidasebeta GUR	beta-N-Acetyl-beta-glucosaminidasebeta NAG	Fermentation of D-mannoseMNE	Fermentation of raffinoseRAF	Glutamate decarboxylaseGDC	alpha-Fucosidasealpha FUC	Reduction of nitrateNIT	Indole productionIND	Alkaline phosphatasePAL	L-arginine arylamidaseArgA	Proline arylamidaseProA	Leucyl glycin arylamidaseLGA	Phenylalanine arylamidasePheA	Leucine arylamidaseLeuA	Pyrrolidonyl arylamidasePyrA	Tyrosine arylamidaseTyrA	Alanine arylamidaseAlaA	Glycin arylamidaseGlyA	Histidine arylamidaseHisA	Glutamyl-glutamate arylamidaseGGA	Serine arylamidaseSerA
[Ref.: #8772]	12717	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	-	-	-	-	+	-	-	-	-	-	-	-	-	-
[Ref.: #8772]	12716	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	-	+/-	-	-	+	-	-	-	-	-	-	-	-	-

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

[Ref.: #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

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

[Ref.: #8772]	Pathogenicity (human)	yes, in single cases
[Ref.: #8772]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #120605]	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.: #67770]	Eubacterium limosum gene for 16S ribosomal RNA, partial sequence, strain: JCM 9978	LC019782	1425	ENA	1736 tax ID
[Ref.: #20218]	Eubacterium limosum strain ATCC 8486 16S ribosomal RNA gene, partial sequence	M59120	1525	ENA	1736 tax ID	*
[Ref.: #20218]	Eubacterium limosum gene for 16S ribosomal RNA, partial sequence, strain: JCM 6421	AB595134	1484	ENA	1736 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Eubacterium limosum ATCC 8486	GCA_000807675	complete	GenBank	1736 tax ID	*
[Ref.: #66792]	Eubacterium limosum ATCC 8480	1736.3	wgs	PATRIC	1736 tax ID	*
[Ref.: #66792]	Eubacterium limosum ATCC 8486	2814123220	complete	JGI IMG/M	1736 tax ID	*

[Ref.: #8772]	GC-content	47.8 mol%
[Ref.: #67770]	GC-content	47.8 mol%	thermal denaturation, midpoint method (Tm)

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 limosum ATCC 8486 NCBI: GCA_000807675.2
[Ref.: #69481]	spore-forming	no	94	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Eubacterium limosum ATCC 8486 NCBI: GCA_000807675.1
[Ref.: #69480]	motile	no	86.594	no
[Ref.: #69480]	flagellated	no	92.042	no
[Ref.: #69480]	gram-positive	yes	87.289	no
[Ref.: #69480]	anaerobic	yes	99.491	yes
[Ref.: #69480]	aerobic	no	97.982	yes
[Ref.: #69480]	halophile	no	86.392	no
[Ref.: #69480]	spore-forming	no	57.851	no
[Ref.: #69480]	thermophile	no	99.196	yes
[Ref.: #69480]	glucose-util	yes	78.808	no
[Ref.: #69480]	glucose-ferment	yes	54.622	no
[Ref.: #69480]	motile	no	86.594	no
[Ref.: #69480]	flagellated	no	92.042	no
[Ref.: #69480]	gram-positive	yes	87.289	no
[Ref.: #69480]	anaerobic	yes	99.491	yes
[Ref.: #69480]	aerobic	no	97.982	yes
[Ref.: #69480]	halophile	no	86.392	no
[Ref.: #69480]	spore-forming	no	57.851	no
[Ref.: #69480]	glucose-util	yes	78.808	no
[Ref.: #69480]	thermophile	no	99.196	yes
[Ref.: #69480]	glucose-ferment	yes	54.622	no

Availability in culture collections External links

[Ref.: #8772]

Culture collection no.

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

[Ref.: #74920]

SI-ID 34969

Literature:

Only first 10 entries are displayed. Click here to see all.

Topic	Title	Authors	Journal	DOI	Year
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	*
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	*
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	*
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	*
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	*
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	*
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	*
	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	*
	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	*

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 .

#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 )

#74920

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-ID34969.1 )

#120605 Collection of Institut Pasteur ; Curators of the CIP; CIP 104169
* These data were automatically processed and therefore are not curated

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Eubacterium limosum ATCC 8486

Eubacterium limosum ATCC 8486

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