Clostridium scindens (DSM 100975, BL-389-WT-3D)

Name: Clostridium scindens (DSM 100975, BL-389-WT-3D)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 159178

Type strain

Strain Designation BL-389-WT-3D

Culture col. no. DSM 100975 BL-389-WT-3D

NCBI tax ID(s) 29347

Special Collections DSMZ Pig DZIF

Links

Clostridium scindens BL-389-WT-3D is a mesophilic prokaryote that was isolated from feces; pig, 8 weeks old, wild type.

mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 406717

DSM 100975

@ref 20215

Last LPSN update 2025-12-16 10:08:11

Domain Bacillati

Phylum Bacillota

Class Clostridia

Order Eubacteriales

Family Clostridiaceae

Genus Clostridium

Species Clostridium scindens

Full scientific name Clostridium scindens Morris et al. 1985

BacDive ID	Other strains from **Clostridium scindens** (7)	Type strain
2748	C. scindens 19, CCUG 45363, JCM 6567, CIP 106687, DSM ... (type strain)
160948	C. scindens JCM 10418, VPI 12708
160949	C. scindens JCM 10419
160951	C. scindens JCM 10420
160952	C. scindens JCM 10421
160953	C. scindens JCM 10422
160954	C. scindens JCM 10423

Morphology

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
66001	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)	Range
66001	positive	growth	37	mesophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125438	anaerobe	92.327
125439	anaerobe	99.8

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	alpha-galactosidase	-	3.2.1.22	from API rID32A
68380	alpha-glucosidase	-	3.2.1.20	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	beta-glucuronidase	-	3.2.1.31	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
66001	-	-	-	+/-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	-	-	-	-	-	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host Body Product	#Gastrointestinal tract	#Feces (Stool)
#Host	#Mammals	#Suidae (Pig,Swine)

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
66001	feces; pig, 8 weeks old, wild type	Kranzberg (Bavaria)	Germany	DEU	Europe

Taxonmaps

69479

Global distribution of 16S sequence MN537450 (>99% sequence identity) for [Clostridium] scindens subclade from Microbeatlas

Aquatic Samples	837
Soil Samples	346
Animal Samples	78797
Plant Samples	225
Total Samples	80205

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
66001	1	Risk group (German classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
124043	ASM969641v1 assembly for [Clostridium] scindens BL-389-WT-3D	contig	GCA_009696415	29347.24	8067701361	29347	55.89

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
66001	[Clostridium] scindens strain DSM 100975 16S ribosomal RNA gene, partial sequence	MN537450	1487		29347

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: [Clostridium] scindens strain BL-389-WT-3D
PATRIC: 29347.24

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	yes	73.90	no
125439	motility	BacteriaNetⓘ	yes	80.60	no
125439	gram_stain	BacteriaNetⓘ	variable	69.90	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: [Clostridium] scindens strain BL-389-WT-3D
PATRIC: 29347.24

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	77.26	no
125438	anaerobic	anaerobicⓘ	yes	92.33	no
125438	spore-forming	spore-formingⓘ	yes	53.14	no
125438	aerobic	aerobicⓘ	no	97.34	no
125438	thermophilic	thermophileⓘ	no	91.11	no
125438	flagellated	motile2+ⓘ	no	82.81	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Clostridium scindens: history and current outlook for a keystone species in the mammalian gut involved in bile acid and steroid metabolism.	Daniel SL, Ridlon JM.	FEMS Microbiol Rev	10.1093/femsre/fuaf016	2025
Metabolism	The Hylemon-Björkhem pathway of bile acid 7-dehydroxylation: history, biochemistry, and microbiology.	Ridlon JM, Daniel SL, Gaskins HR.	J Lipid Res	10.1016/j.jlr.2023.100392	2023
Phylogeny	A collection of bacterial isolates from the pig intestine reveals functional and taxonomic diversity.	Wylensek D, Hitch TCA, Riedel T, Afrizal A, Kumar N, Wortmann E, Liu T, Devendran S, Lesker TR, Hernandez SB, Heine V, Buhl EM, M D'Agostino P, Cumbo F, Fischoder T, Wyschkon M, Looft T, Parreira VR, Abt B, Doden HL, Ly L, Alves JMP, Reichlin M, Flisikowski K, Suarez LN, Neumann AP, Suen G, de Wouters T, Rohn S, Lagkouvardos I, Allen-Vercoe E, Sproer C, Bunk B, Taverne-Thiele AJ, Giesbers M, Wells JM, Neuhaus K, Schnieke A, Cava F, Segata N, Elling L, Strowig T, Ridlon JM, Gulder TAM, Overmann J, Clavel T.	Nat Commun	10.1038/s41467-020-19929-w	2020

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 )
#66001	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 100975
#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 .
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#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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Clostridium scindens (DSM 100975, BL-389-WT-3D)

Name and taxonomic classification

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_009696415

16S sequences

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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