Enterocloster clostridioformis (DSM 26114, YL32)

Name: Enterocloster clostridioformis (DSM 26114, YL32)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 130916

Type strain

Strain Designation YL32

Culture col. no. DSM 26114 YL32

NCBI tax ID(s) 1531

Special Collections DSMZ Mouse DZIF

History <- B. Stecher, Max von Pettenkofer-Inst., Munich; YL32

Links

Enterocloster clostridioformis YL32 is an anaerobe bacterium that was isolated from C57Bl/6J wildtype mouse.

anaerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 406137

DSM 26114

@ref 20215

Last LPSN update 2026-02-09 11:31:20

Domain Bacteria

Phylum Bacillota

Class Clostridia

Order Eubacteriales

Family Lachnospiraceae

Genus Enterocloster

Species Enterocloster clostridioformis

Full scientific name Enterocloster clostridioformis (Burri and Ankersmit 1906) Haas and Blanchard 2020

Synonyms (4)

"Bacteroides clostridiiformis"
"Bacterium clostridiiforme"
Clostridium clostridioforme
Clostridium clostridiiforme

BacDive ID	Other strains from **Enterocloster clostridioformis** (2)	Type strain
2569	E. clostridioformis T90, DSM 933, ATCC 25537, CCUG 16791, NCTC ... (type strain)
158909	E. clostridioformis H4_30, DSM 108191

Morphology

Colony morphology

22208

Incubation period1-2 days

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
22208	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
22208	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

Culture temp

@ref	Growth	Type	Temperature (°C)
22208	positive	growth	37

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
22208	anaerobe
125439	anaerobe	99.9

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68380	29016 ChEBI	arginine	-	hydrolysis	from API rID32A
68380	16024 ChEBI	D-mannose	-	fermentation	from API rID32A
68380	29985 ChEBI	L-glutamate	-	degradation	from API rID32A
68380	17632 ChEBI	nitrate	-	reduction	from API rID32A
68380	16634 ChEBI	raffinose	-	fermentation	from API rID32A
68380	27897 ChEBI	tryptophan	-	energy source	from API rID32A
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
68380	alkaline phosphatase	-	3.1.3.1	from API rID32A
68380	alpha-arabinosidase	-	3.2.1.55	from API rID32A
68380	alpha-fucosidase	-	3.2.1.51	from API rID32A
68380	arginine dihydrolase	-	3.5.3.6	from API rID32A
68380	beta-Galactosidase 6-phosphate	-		from API rID32A
68380	beta-glucosidase	-	3.2.1.21	from API rID32A
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
68380	phenylalanine arylamidase	-		from API rID32A
68380	proline-arylamidase	-	3.4.11.5	from API rID32A
68380	pyrrolidonyl arylamidase	-	3.4.19.3	from API rID32A
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

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
22208	-	-	-	-	-	-	-	-	+/-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-
22208	-	-	+	+	-	-	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-
22208	-	-	+	+	-	+	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Mammals	#Muridae (Mouse/Rat)

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
22208	C57Bl/6J wildtype mouse	Zurich	Switzerland	CHE	Europe

Taxonmaps

69479

Global distribution of 16S sequence KR364750 (>99% sequence identity) for Enterocloster clostridioformis subclade from Microbeatlas

Aquatic Samples	1136
Soil Samples	492
Animal Samples	71851
Plant Samples	358
Total Samples	73837

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
22208	2	Risk group (German classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM1669678v1 assembly for Enterocloster clostridioformis YL32	chromosome	GCA_016696785	1531.148	8002801866	1531	55.64
66792	ASM222154v1 assembly for Enterocloster clostridioformis YL32	contig	GCA_002221545	1531.13	2857266821	1531	46.33
66792	ASM1020618v1 assembly for Enterocloster clostridioformis YL32	contig	GCA_010206185	1531.125		1531

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
22208	Enterocloster clostridioformis strain YL32 16S ribosomal RNA gene, partial sequence	KR364750	1444		1531

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Enterocloster clostridioformis YL32
NCBI: GCA_002221545

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	yes	76.90	no
125439	motility	BacteriaNetⓘ	yes	78.70	no
125439	gram_stain	BacteriaNetⓘ	positive	66.80	no
125439	oxygen_tolerance	BacteriaNetⓘ	anaerobe	99.90	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Enterocloster clostridioformis YL32
NCBI: GCA_016696785.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	61.57	no
125438	anaerobic	anaerobicⓘ	yes	84.46	no
125438	aerobic	aerobicⓘ	no	95.82	yes
125438	spore-forming	spore-formingⓘ	yes	63.91	no
125438	thermophilic	thermophileⓘ	no	93.49	yes
125438	flagellated	motile2+ⓘ	yes	72.26	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Metabolism	Sulfoquinovose is exclusively metabolized by the gut microbiota and degraded differently in mice and humans.	Krasenbrink J, Hanson BT, Weiss AS, Borusak S, Tanabe TS, Lang M, Aichinger G, Hausmann B, Berry D, Richter A, Marko D, Mussmann M, Schleheck D, Stecher B, Loy A.	Microbiome	10.1186/s40168-025-02175-x	2025
	The human intestinal bacterium Eggerthella lenta influences gut metabolomes in gnotobiotic mice	Viehof A, Haange S, Streidl T, Schubert K, Engelmann B, Haller D, Rolle-Kampczyk U, von Bergen M, Clavel T.	Microbiome Res Rep		2024
	A standardized gnotobiotic mouse model harboring a minimal 15-member mouse gut microbiota recapitulates SOPF/SPF phenotypes.	Darnaud M, De Vadder F, Bogeat P, Boucinha L, Bulteau AL, Bunescu A, Couturier C, Delgado A, Dugua H, Elie C, Mathieu A, Novotna T, Ouattara DA, Planel S, Saliou A, Srutkova D, Yansouni J, Stecher B, Schwarzer M, Leulier F, Tamellini A.	Nat Commun	10.1038/s41467-021-26963-9	2021
Metabolism	The gut bacterium Extibacter muris produces secondary bile acids and influences liver physiology in gnotobiotic mice.	Streidl T, Karkossa I, Segura Munoz RR, Eberl C, Zaufel A, Plagge J, Schmaltz R, Schubert K, Basic M, Schneider KM, Afify M, Trautwein C, Tolba R, Stecher B, Doden HL, Ridlon JM, Ecker J, Moustafa T, von Bergen M, Ramer-Tait AE, Clavel T.	Gut Microbes	10.1080/19490976.2020.1854008	2021
	Nutritional and host environments determine community ecology and keystone species in a synthetic gut bacterial community.	Weiss AS, Niedermeier LS, von Strempel A, Burrichter AG, Ring D, Meng C, Kleigrewe K, Lincetto C, Hubner J, Stecher B.	Nat Commun	10.1038/s41467-023-40372-0	2023
	Bacteriophages targeting protective commensals impair resistance against Salmonella Typhimurium infection in gnotobiotic mice.	von Strempel A, Weiss AS, Wittmann J, Salvado Silva M, Ring D, Wortmann E, Clavel T, Debarbieux L, Kleigrewe K, Stecher B.	PLoS Pathog	10.1371/journal.ppat.1011600	2023

References

#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 )
#22208	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 26114
#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) .
#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 .
#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 )

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Enterocloster clostridioformis (DSM 26114, YL32)

Name and taxonomic classification

Morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

API rID32A

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_016696785

16S sequences

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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