Clostridium symbiosum (DSM 29356, SRB539-5-G-R)

Name: Clostridium symbiosum (DSM 29356, SRB539-5-G-R)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 130933

Type strain

Strain Designation SRB539-5-G-R

Culture col. no. DSM 29356 SRB539-5-G-R

NCBI tax ID(s) 1512

Special Collections DSMZ Mouse DZIF

History DSMZ <- T. Clavel, TU Munich, Freising-Weihenstephan, Germany; SRB539-5-G-R

Links

Clostridium symbiosum SRB539-5-G-R is an anaerobe bacterium that was isolated from mouse gut.

anaerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 408137

DSM 29356

@ref 20215

Last LPSN update 2026-05-29 08:37:30

Domain Bacteria

Phylum Bacillota

Class Clostridia

Order Eubacteriales

Family Clostridiaceae

Genus Clostridium

Species Clostridium symbiosum

Full scientific name Clostridium symbiosum (Stevens 1956) Kaneuchi et al. 1976 (Approved Lists 1980)

Synonyms (1)

"Bacteroides symbiosus"

BacDive ID	Other strains from **Clostridium symbiosum** (10)	Type strain
2721	C. symbiosum 2, DSM 934, ATCC 14940, LSU (M. Sebald), ... (type strain)
150600	C. symbiosum CCUG 41715
152023	C. symbiosum CCUG 45577 B
153376	C. symbiosum CCUG 49377
153644	C. symbiosum CCUG 50474
153779	C. symbiosum CCUG 50960
155139	C. symbiosum CCUG 56568
156494	C. symbiosum CCUG 62167 Q
157675	C. symbiosum LT0011, DSM 108250
158919	C. symbiosum H4_29, DSM 108200

Morphology

Colony morphology

22225

Incubation period2-3 days

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
22225	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
22225	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)
22225	positive	growth	37

Physiology and metabolism

Oxygen tolerance

22225

Oxygen toleranceanaerobe

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
22225	-	-	-	+/-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Mammals	#Muridae (Mouse/Rat)
#Host Body-Site	#Gastrointestinal tract	-

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
22225	mouse gut	Freising	Germany	DEU	Europe

Taxonmaps

69479

Global distribution of 16S sequence KR364763 (>99% sequence identity) for [Clostridium] symbiosum subclade from Microbeatlas

Aquatic Samples	3039
Soil Samples	1377
Animal Samples	184529
Plant Samples	554
Total Samples	189499

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
22225	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	ASM2462270v1 assembly for [Clostridium] symbiosum DSM 29356	contig	GCA_024622705	1512.173	8067772417	1512	57.28

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
22225	[Clostridium] symbiosum strain SRB539-5-G-R 16S ribosomal RNA gene, partial sequence	KR364763	1430		1512

Genome-based predictions

Predictions

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: [Clostridium] symbiosum DSM 29356
NCBI: GCA_024622705.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	61.90	no
125438	anaerobic	anaerobicⓘ	yes	88.44	yes
125438	aerobic	aerobicⓘ	no	96.37	no
125438	spore-forming	spore-formingⓘ	yes	67.93	no
125438	thermophilic	thermophileⓘ	no	93.05	no
125438	flagellated	motile2+ⓘ	yes	68.89	no

Literature

Title	Authors	Journal	DOI	Year
A toolbox for genetic manipulation in intestinal Clostridium symbiosum.	Yang P, Tian J, Zhang L, Zhang H, Yang G, Ren Y, Fang J, Gu Y, Jiang W.	Synth Syst Biotechnol	10.1016/j.synbio.2023.12.005	2024

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 )
#22225	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 29356
#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 )
#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 symbiosum (DSM 29356, SRB539-5-G-R)

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_024622705

16S sequences

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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