Clostridium ramosum (DSM 29357, SRB509-5-F-B)

Name: Clostridium ramosum (DSM 29357, SRB509-5-F-B)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 130927

Type strain

Strain Designation SRB509-5-F-B

Culture col. no. DSM 29357 SRB509-5-F-B

NCBI tax ID(s) 1547

Special Collections DSMZ Mouse DZIF

Links

Clostridium ramosum SRB509-5-F-B is an anaerobe, mesophilic prokaryote that was isolated from ileal mucosa; TNF^deltaARE/+ C57BL/6 mouse.

anaerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 406436

DSM 29357

@ref 20215

Last LPSN update 2025-12-16 10:01:07

Domain Bacillati

Phylum Bacillota

Class Clostridia

Order Eubacteriales

Family Clostridiaceae

Genus Clostridium

Species Clostridium ramosum

Full scientific name Clostridium ramosum (Veillon and Zuber 1898) Holdeman et al. 1971 (Approved Lists 1980)

Synonyms (3)

Thomasclavelia ramosa
"Erysipelatoclostridium ramosum"
"Bacillus ramosus"

BacDive ID	Other strains from **Clostridium ramosum** (8)	Type strain
148490	C. ramosum CCUG 35540
148608	C. ramosum CCUG 35705
150967	C. ramosum CCUG 42893
151816	C. ramosum CCUG 44972
151840	C. ramosum CCUG 45030
152520	C. ramosum CCUG 46995
154479	C. ramosum CCUG 53777
165123	C. ramosum JCM 5235, ATCC 13937, NCTC 10474

Morphology

Cell morphology

@ref	Gram stain	Confidence
125439	positive	91.2

Colony morphology

22219

Incubation period2-3 days

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
22219	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
22219	FASTIDIOUS ANAEROBE AGAR (DSMZ Medium 1203)	Medium recipe at MediaDive	Name: FASTIDIOUS ANAEROBE AGAR (DSMZ Medium 1203) Composition: Horse blood 100.0 g/l Fastidious Anaerobe Agar 45.7 g/l Distilled water
22219	CHOPPED MEAT MEDIUM (DSMZ Medium 78)	Medium recipe at MediaDive	Name: CHOPPED MEAT MEDIUM (DSMZ Medium 78) Composition: Ground beef 500.0 g/l Casitone 30.0 g/l Agar 15.0 g/l Ethanol 9.5 g/l (optional) K2HPO4 5.0 g/l Yeast extract 5.0 g/l L-Cysteine HCl 0.5 g/l Haemin 0.005 g/l (optional) Resazurin 0.001 g/l Vitamin K3 0.0005 g/l (optional) Vitamin K1 (optional) NaOH (optional) Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
22219	positive	growth	37	mesophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance
22219	anaerobe
125439	facultative anaerobe

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	alpha-arabinosidase	-	3.2.1.55	from API rID32A
68380	alpha-fucosidase	-	3.2.1.51	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	+	3.2.1.23	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	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
22219	-	-	+/-	+	+	+	+	-	-	+	+	+	-	-	-	-	+	-	-	+	-	-	-	-	-	-	-	-	-
22219	-	-	-	+	+	+	+	-	-	+	+	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-
22219	-	-	-	+	+	+	+	-	-	+	+	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-

Isolation, sampling and environmental information

Isolation source categories

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

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
22219	ileal mucosa; TNF^deltaARE/+ C57BL/6 mouse	Freising	Germany	DEU	Europe

Taxonmaps

69479

Global distribution of 16S sequence KR364754 (>99% sequence identity) for Erysipelatoclostridium ramosum subclade from Microbeatlas

Aquatic Samples	2108
Soil Samples	626
Animal Samples	103847
Plant Samples	377
Total Samples	106958

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
22219	2	Risk group (German classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	NCBI tax ID	Score
124043	ASM1676685v1 assembly for Thomasclavelia ramosa FDAARGOS_1106	chromosome	GCA_016766855	1547.131	1547	88.64
66792	ASM2462280v1 assembly for Thomasclavelia ramosa DSM 29357	contig	GCA_024622805	1547.317	1547	68.39

Genome browser: GCA_016766855

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
22219	Thomasclavelia ramosa strain SRB509-5-F-B 16S ribosomal RNA gene, partial sequence	KR364754	1417		1547

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Thomasclavelia ramosa DSM 29357
NCBI: GCA_024622805

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	yes	62.10	no
125439	motility	BacteriaNetⓘ	yes	65.30	no
125439	gram_stain	BacteriaNetⓘ	positive	91.20	no
125439	oxygen_tolerance	BacteriaNetⓘ	facultative anaerobe	97.80	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Erysipelatoclostridium ramosum strain FDAARGOS_1106 strain Not applicable
PATRIC: 1547.131

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	79.88	no
125438	anaerobic	anaerobicⓘ	yes	88.42	no
125438	spore-forming	spore-formingⓘ	no	59.41	no
125438	aerobic	aerobicⓘ	no	98.65	no
125438	thermophilic	thermophileⓘ	no	92.51	yes
125438	flagellated	motile2+ⓘ	no	81.27	no

Literature

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 )
#22219	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 29357
#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 .
#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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