Paraclostridium bifermentans (DSM 29423, G7K1R3-PYG-90)

Name: Paraclostridium bifermentans (DSM 29423, G7K1R3-PYG-90)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 130915

Type strain

Strain Designation G7K1R3-PYG-90

Culture col. no. DSM 29423 G7K1R3-PYG-90

NCBI tax ID(s) 1490

Special Collections DSMZ Mouse DZIF

Links

Paraclostridium bifermentans G7K1R3-PYG-90 is an anaerobe, mesophilic human pathogen that was isolated from caecal content; wildtype C57BL/6 mouse.

anaerobe mesophilic human pathogen genome sequence 16S sequence

Name and taxonomic classification

SI-ID 402142

DSM 29423

@ref 20215

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

Domain Bacillati

Phylum Bacillota

Class Clostridia

Order Peptostreptococcales

Family Peptostreptococcaceae

Genus Paraclostridium

Species Paraclostridium bifermentans

Full scientific name Paraclostridium bifermentans (Weinberg and Séguin 1918) Sasi Jyothsna et al. 2016

Synonyms (2)

"Bacillus bifermentans"
Clostridium bifermentans

BacDive ID	Other strains from **Paraclostridium bifermentans** (11)	Type strain
2556	P. bifermentans DSM 630
2557	P. bifermentans 701, Beerens, DSM 631
2558	P. bifermentans TYR6, DSM 13560, CIP 106673
132447	P. bifermentans F1, DSM 103419, CN 4781, WDCM 00079, NCTC ...
134757	P. bifermentans Tissier, CIP 60.14, ATCC 19299, CCUG 9279, ...
137111	P. bifermentans TM, CIP 60.56
146782	P. bifermentans CCUG 32113
147220	P. bifermentans CCUG 33082
148369	P. bifermentans CCUG 35297
148501	P. bifermentans CCUG 35556 A
151269	P. bifermentans CCUG 43592

Morphology

Colony morphology

22207

Incubation period2-3 days

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
22207	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
22207	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
22207	positive	growth	37	mesophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance
22207	anaerobe
125438	anaerobe

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
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-galactosidase	-	3.2.1.22	from API rID32A
68380	alpha-glucosidase	-	3.2.1.20	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	leucyl glycin arylamidase	-	3.4.11.1	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
22207	-	-	-	-	-	-	-	-	-	+/-	-	-	-	-	-	+	-	-	+	-	-	+/-	-	-	-	-	-	-	-
22207	-	+/-	-	-	-	-	-	-	-	+	-	-	-	-	-	+	+/-	-	+	-	-	+	-	-	-	-	-	-	-
22207	-	+/-	-	-	-	-	-	-	-	+	-	-	-	-	-	+	+/-	-	+	-	-	+	-	-	-	-	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Mammals	#Muridae (Mouse/Rat)
#Host Body-Site	#Gastrointestinal tract	#Large intestine
#Host Body Product	#Gastrointestinal tract	#Caecal content

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
22207	caecal content; wildtype C57BL/6 mouse	Freising	Germany	DEU	Europe

Taxonmaps

69479

Global distribution of 16S sequence KR364757 (>99% sequence identity) for Paeniclostridium from Microbeatlas

Aquatic Samples	9424
Soil Samples	14269
Animal Samples	25127
Plant Samples	2734
Total Samples	51554

Interaction and safety

Risk assessment

@ref	Pathogenicity human	Pathogenicity animal	Biosafety level	Biosafety level comment
22207			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	ASM2462208v1 assembly for Paraclostridium bifermentans DSM 29423	contig	GCA_024622085	1490.111	8065551808	1490	73.47

Genome browser: GCA_024622085

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
22207	Clostridium sp. G7K1R3-PYG-90 16S ribosomal RNA gene, partial sequence	KR364757	1402		1796624

Genome-based predictions

Predictions

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Paraclostridium bifermentans DSM 29423
NCBI: GCA_024622085.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	72.84	no
125438	anaerobic	anaerobicⓘ	yes	90.94	yes
125438	aerobic	aerobicⓘ	no	96.42	yes
125438	spore-forming	spore-formingⓘ	yes	73.38	no
125438	thermophilic	thermophileⓘ	no	92.72	yes
125438	flagellated	motile2+ⓘ	yes	76.94	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 )
#22207	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 29423
#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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