Clostridium beijerinckii (DSM 105335, WB01-NA02)

Name: Clostridium beijerinckii (DSM 105335, WB01-NA02)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 158905

Type strain

Strain Designation WB01-NA02

Culture col. no. DSM 105335 WB01-NA02

NCBI tax ID(s) 1520

Special Collections DSMZ Pig DZIF

History <- E. Allen-Vercoe, Univ. Guelph, Ontario, Canada;

Links

Clostridium beijerinckii WB01-NA02 is a mesophilic prokaryote that was isolated from wild boar.

mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 398119

DSM 105335

@ref 20215

Last LPSN update 2026-02-09 11:38:27

Domain Bacteria

Phylum Bacillota

Class Clostridia

Order Eubacteriales

Family Clostridiaceae

Genus Clostridium

Species Clostridium beijerinckii

Full scientific name Clostridium beijerinckii Donker 1926 (Approved Lists 1980)

Synonyms (1)

Clostridium diolis

BacDive ID	Other strains from **Clostridium beijerinckii** (30)	Type strain
2548	C. beijerinckii E. McCoy A-67, L.S. McClung 1671, 10026, ... (type strain)
2547	C. beijerinckii DSM 552, VKM B-1773
2549	C. beijerinckii N.O. Sjolander and McCoy, 67, 7, N.O. Sjolander ...
2550	C. beijerinckii 2287, McClung, A-14, 2287, McClung, DSM 1739, ...
2551	C. beijerinckii DSM 51, ATCC 17797 (1969)
2552	C. beijerinckii 34, Ng 34, DSM 53, ATCC 14949, NCIMB 9503, ...
2553	C. beijerinckii A-39, DSM 6422, NRRL B-592
2554	C. beijerinckii A-21, DSM 6423, NRRL B-593
2555	C. beijerinckii KT-1P, DSM 13821
2692	C. beijerinckii C8, DSM 11329, IAM 19232, JCM 7847
2819	C. beijerinckii 88-273, SH1, DSM 15410, ATCC BAA-557, DSM ...
165626	C. beijerinckii JCM 7833, IAM 19015
165630	C. beijerinckii JCM 7837, IAM 19225
165631	C. beijerinckii JCM 7838, IAM 19240, IFO 3859, NBRC 3859, ...
165632	C. beijerinckii JCM 7839, IAM 19092
165633	C. beijerinckii JCM 7840, IAM 19108
165685	C. beijerinckii JCM 7986, IAM 19046
165689	C. beijerinckii JCM 7990, IAM 19050
165696	C. beijerinckii JCM 7997, IAM 19060
165721	C. beijerinckii JCM 8023, ATCC 14823, ATCC 6014, IAM 19002, ...
165722	C. beijerinckii JCM 8024, IAM 19006
165723	C. beijerinckii JCM 8025, IAM 19007, NRRL B-591
165724	C. beijerinckii JCM 8026, IAM 19008, NRRL B592
165725	C. beijerinckii JCM 8027, IAM 19093
165726	C. beijerinckii JCM 8028, IAM 19105
165727	C. beijerinckii JCM 8030, IAM 19091
165728	C. beijerinckii JCM 8031, IAM 19106
165729	C. beijerinckii JCM 8032, IAM 19094
165730	C. beijerinckii JCM 8033, IAM 19095
165731	C. beijerinckii JCM 8034, IAM 19098

Morphology

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
65727	WILKINS-CHALGREN ANAEROBE BROTH (DSMZ Medium 339)		Medium recipe at MediaDive	Name: WILKINS-CHALGREN ANAEROBE BROTH (DSMZ Medium 339) Composition: dehydrated Wilkins-Chalgren medium 33.0 g/l L-Cysteine HCl 0.3 g/l Sodium resazurin 0.0005 g/l Distilled water
65727	COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)		Medium recipe at MediaDive	Name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar base

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
65727	positive	growth	37	mesophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	anaerobe	97.7

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-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
65727	-	-	-	+/-	+/-	+	+	+	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Mammals	#Suidae (Pig,Swine)

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
65727	wild boar	Stratford, Ontario	Canada	CAN	North America

Taxonmaps

69479

Global distribution of 16S sequence MN537489 (>99% sequence identity) for Clostridium from Microbeatlas

Aquatic Samples	1977
Soil Samples	1985
Animal Samples	5931
Plant Samples	442
Total Samples	10335

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
65727	1	Risk group (German classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	NCBI tax ID	Score
66792	ASM1284396v1 assembly for Clostridium beijerinckii WB01_NA02	contig	GCA_012843965	1520.347	1520	43

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
65727	Clostridium sp. strain DSM 105335 16S ribosomal RNA gene, partial sequence	MN537489	1418		1506

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Clostridium beijerinckii WB01_NA02
NCBI: GCA_012843965

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	yes	84.60	no
125439	motility	BacteriaNetⓘ	yes	81.60	no
125439	gram_stain	BacteriaNetⓘ	positive	73.80	no
125439	oxygen_tolerance	BacteriaNetⓘ	anaerobe	97.70	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Clostridium beijerinckii WB01_NA02
NCBI: GCA_012843965.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	54.94	no
125438	anaerobic	anaerobicⓘ	yes	86.86	no
125438	aerobic	aerobicⓘ	no	93.38	no
125438	spore-forming	spore-formingⓘ	yes	80.93	no
125438	thermophilic	thermophileⓘ	no	97.38	yes
125438	flagellated	motile2+ⓘ	yes	77.67	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 )
#65727	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 105335
#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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