Paraclostridium bifermentans subsp. bifermentans (DSM 14991, ATCC 638, JCM 1386)

Name: Paraclostridium bifermentans subsp. bifermentans (DSM 14991, ATCC 638, JCM 1386)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 2559

Type strain

Strain Designation 76, 10028

Culture col. no. DSM 14991 ATCC 638 JCM 1386 CCUG 36626 NCIMB 10716 7 more

NCBI tax ID(s) 1490 2663174

Special Collections DSMZ CCUG JCM CIP

History DSMZ <- JCM; JCM 1386 <- ATCC; ATCC 638 <- I. C. Hall; 76 JCM <-- ATCC 638 <-- I. C. Hall 76. CIP <- 1994, J.P. Carlier, Inst. Pasteur, Paris, France: strain 10028 <- ATCC <- I.C. Hall: strain 76, Bacillus centrosporogenes

Links

Paraclostridium bifermentans subsp. bifermentans 76 is an anaerobe, spore-forming, Gram-positive human pathogen that was isolated from soil.

spore-forming Gram-positive motile rod-shaped anaerobe human pathogen genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 34627

ATCC 638,CCUG 36626,NCIMB 10716,CIP 104309,JCM 1386,CCRC 14542,DSM 14991,BCRC 14542,NCTC 13019,NRRL B-41229,VTT E-042450

@ref 20215

Last LPSN update 2026-05-29 08:25:30

Domain Bacteria

Phylum Bacillota

Class Clostridia

Order Peptostreptococcales

Family Peptostreptococcaceae

Genus Paraclostridium

Species Paraclostridium bifermentans subsp. bifermentans

Full scientific name Paraclostridium bifermentans subsp. bifermentans (Weinberg and Séguin 1918) Kutsuna et al. 2019

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Motility
116804	positive	rod-shaped

Colony morphology

116804

Hemolysis ability1

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
5658	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
5658	FASTIDIOUS ANAEROBE BROTH (DSMZ Medium 1203a)	Medium recipe at MediaDive	Name: FASTIDIOUS ANAEROBE BROTH (DSMZ Medium 1203a) Composition: Fastidious Anaerobe Basal Broth 35.4 g/l Deionized water
5658	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
41797	MEDIUM 20 - for Anaerobic bacteria		Agar (15.000 g);Glucose (5.000 g);Yeast extract (20.000 g);Tryptone (30.000 g);Cysteine hydrochloride (0.500 g);distilled water (1000.000 ml);Hemin solution -M00149 (25.000 ml)
116804	CIP Medium 20	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
5658	positive	growth	37
41797	positive	growth	37
67770	positive	growth	37

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
5658	anaerobe
125439	facultative anaerobe	97.826

Spore formation

116804

Spore formationyes

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
116804	4853 ChEBI	esculin	+	hydrolysis
68380	29985 ChEBI	L-glutamate	-	degradation	from API rID32A
68380	17632 ChEBI	nitrate	-	reduction	from API rID32A
116804	17632 ChEBI	nitrate	+	reduction
116804	16301 ChEBI	nitrite	+	reduction
68380	16634 ChEBI	raffinose	-	fermentation	from API rID32A
116804	132112 ChEBI	sodium thiosulfate	+	builds gas from
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
116804	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Indole test
68380	35581 ChEBI	indole	+	from API rID32A

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
68380	alanine arylamidase	-	3.4.11.2	from API rID32A
116804	alcohol dehydrogenase	-	1.1.1.1
68382	alkaline phosphatase	+	3.1.3.1	from API zym
68380	alkaline phosphatase	-	3.1.3.1	from API rID32A
68380	alpha-arabinosidase	-	3.2.1.55	from API rID32A
68382	alpha-chymotrypsin	-	3.4.21.1	from API zym
68382	alpha-fucosidase	-	3.2.1.51	from API zym
68380	alpha-fucosidase	-	3.2.1.51	from API rID32A
68382	alpha-galactosidase	-	3.2.1.22	from API zym
68380	alpha-galactosidase	-	3.2.1.22	from API rID32A
68382	alpha-glucosidase	+	3.2.1.20	from API zym
68380	alpha-glucosidase	-	3.2.1.20	from API rID32A
68382	alpha-mannosidase	-	3.2.1.24	from API zym
68380	arginine dihydrolase	-	3.5.3.6	from API rID32A
68382	beta-galactosidase	-	3.2.1.23	from API zym
68380	beta-galactosidase	-	3.2.1.23	from API rID32A
68380	beta-Galactosidase 6-phosphate	-		from API rID32A
68382	beta-glucosidase	-	3.2.1.21	from API zym
68380	beta-glucosidase	-	3.2.1.21	from API rID32A
68382	beta-glucuronidase	-	3.2.1.31	from API zym
68380	beta-glucuronidase	-	3.2.1.31	from API rID32A
116804	catalase	-	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
116804	DNase	+
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
116804	gelatinase	-
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
116804	lecithinase	+
68382	leucine arylamidase	+	3.4.11.1	from API zym
68380	leucine arylamidase	-	3.4.11.1	from API rID32A
68380	leucyl glycin arylamidase	-	3.4.11.1	from API rID32A
68382	lipase (C 14)	-		from API zym
116804	lysine decarboxylase	-	4.1.1.18
68382	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API zym
68380	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API rID32A
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
116804	ornithine decarboxylase	-	4.1.1.17
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
68382	trypsin	-	3.4.21.4	from API zym
68380	tryptophan deaminase	+	4.1.99.1	from API rID32A
68380	tyrosine arylamidase	-		from API rID32A
116804	urease	-	3.5.1.5
68380	urease	-	3.5.1.5	from API rID32A
68382	valine arylamidase	-		from API zym

API zym

@ref	Control	Alkaline phosphatase	Esterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	Lipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	Trypsin	alpha- Chymotrypsin	Acid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	alpha- Galactosidase	beta- Galactosidase	beta- Glucuronidase	alpha- Glucosidase	beta- Glucosidase	N-acetyl-beta- glucosaminidase	alpha- Mannosidase	alpha- Fucosidase
116804	-	+	+	+	-	+	-	-	-	-	+	+	-	-	-	+	-	-	-	-

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
5658	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	+	-	-	-	-	-	-	-	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Soil

Isolation

@ref	Sample type
5658	soil
53282	Soil
67770	Soil

Interaction and safety

Risk assessment

@ref	Pathogenicity human	Pathogenicity animal	Biosafety level	Biosafety level comment
5658			2	Risk group (German classification) According to TRBA 466
116804			2	Risk group (French classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	Paraclostridium bifermentans strain DSM 14991	complete		1490.78		1490	97.76
66792	Paraclostridium bifermentans strain DSM 14991	complete		1490.81		1490	97.76
66792	Paraclostridium bifermentans strain DSM 14991	complete		1490.75		1490	97.76
66792	ASM1991602v1 assembly for Paraclostridium bifermentans DSM 14991	complete	GCA_019916025	1490.72	8065351417	1490	97.12
67770	ASM45224v2 assembly for Paraclostridium bifermentans ATCC 638 = DSM 14991	contig	GCA_000452245	1233171.3	2541047518	1233171	73.92
67770	ASM680287v1 assembly for Paraclostridium bifermentans ATCC 638	scaffold	GCA_006802875	1490.25	8118849419	1490	58.94

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Paraclostridium bifermentans gene for 16S rRNA, partial sequence, strain: ATCC 638	AB075769	1476	1490
20218	Paraclostridium bifermentans gene for 16S ribosomal RNA, partial cds, strain: JCM 1386	AB618787	1463	1490
20218	Clostridium bifermentans strain DSM 14991 16S ribosomal RNA gene, partial sequence	HM245932	841	1490
20218	Clostridium bifermentans 16S rRNA gene	X75906	1451	1490
5658	Clostridium bifermentans 16S rRNA gene, strain DSM 10716	X73437	1498	1490
124043	Paraclostridium bifermentans strain ATCC 638 16S ribosomal RNA gene, partial sequence.	ON078500	1397	1490
124043	Paraclostridium bifermentans strain DSM 14991 16S ribosomal RNA gene, partial sequence.	ON078501	1394	1490
124043	Paraclostridium bifermentans strain ATCC 638 16S ribosomal RNA gene, partial sequence.	MH173799	913	1490

GC content

@ref	GC-content (mol%)	Method
5658	27	thermal denaturation, midpoint method (Tm)
67770	29.2	high performance liquid chromatography (HPLC)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Paraclostridium bifermentans strain DSM 14991
BV-BRC: 1490.75

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	facultative anaerobe	97.83	no
125439	gram_stain	BacteriaNetⓘ	positive	81.08	no
125439	motility	BacteriaNetⓘ	yes	66.02	no
125439	spore_formation	BacteriaNetⓘ	yes	60.40	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Paraclostridium bifermentans DSM 14991
NCBI: GCA_019916025.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	71.95	no
125438	anaerobic	anaerobicⓘ	yes	89.94	yes
125438	aerobic	aerobicⓘ	no	96.85	yes
125438	spore-forming	spore-formingⓘ	yes	70.70	no
125438	thermophilic	thermophileⓘ	no	92.66	no
125438	flagellated	motile2+ⓘ	yes	76.44	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Complete Genome Sequence of Paraclostridium bifermentans DSM 14991.	Little GT, Selles Vidal L, Steadman M, Leyden-Preece R, Taylor GM, Heap JT.	Microbiol Resour Announc	10.1128/mra.00103-22	2022
	In-Depth Analysis of an Obligate Anaerobe Paraclostridium bifermentans Isolated from Uterus of Bubalus bubalis.	Gohil P, Patel K, Patel S, Pandit R, Suthar V, Duggirala S, Joshi M, Patil D, Joshi C.	Animals (Basel)	10.3390/ani12141765	2022
Genetics	Profiling of the intestinal community of Clostridia: taxonomy and evolutionary analysis.	Candeliere F, Musmeci E, Amaretti A, Sola L, Raimondi S, Rossi M.	Microbiome Res Rep	10.20517/mrr.2022.19	2023
	The small acid-soluble proteins of spore-forming organisms: similarities and differences in function.	Nerber HN, Sorg JA.	Anaerobe	10.1016/j.anaerobe.2024.102844	2024
Metabolism	In vivo commensal control of Clostridioides difficile virulence.	Girinathan BP, DiBenedetto N, Worley JN, Peltier J, Arrieta-Ortiz ML, Immanuel SRC, Lavin R, Delaney ML, Cummins CK, Hoffman M, Luo Y, Gonzalez-Escalona N, Allard M, Onderdonk AB, Gerber GK, Sonenshein AL, Baliga NS, Dupuy B, Bry L.	Cell Host Microbe	10.1016/j.chom.2021.09.007	2021
	Arsenic Mobilization and Transformation by Ammonium-Generating Bacteria Isolated from High Arsenic Groundwater in Hetao Plain, China.	Jiang Z, Shen X, Shi B, Cui M, Wang Y, Li P.	Int J Environ Res Public Health	10.3390/ijerph19159606	2022
	Identification of a family of peptidoglycan transpeptidases reveals that Clostridioides difficile requires noncanonical cross-links for viability.	Bollinger KW, Muh U, Ocius KL, Apostolos AJ, Pires MM, Helm RF, Popham DL, Weiss DS, Ellermeier CD.	Proc Natl Acad Sci U S A	10.1073/pnas.2408540121	2024
Genetics	Culture and genome-based analysis of four soil Clostridium isolates reveal their potential for antimicrobial production.	Pahalagedara ASNW, Jauregui R, Maclean P, Altermann E, Flint S, Palmer J, Brightwell G, Gupta TB.	BMC Genomics	10.1186/s12864-021-08005-2	2021
	Silver and Copper Complexes with Ibuprofen and Caffeine-Preparation and Evaluation of Their Selected Biological Effects.	Borowka A, Sieroslawska A, Baier A, Rymuszka A, Olszewska E.	Molecules	10.3390/molecules29020506	2024
Pathogenicity	A neurotoxin that specifically targets Anopheles mosquitoes.	Contreras E, Masuyer G, Qureshi N, Chawla S, Dhillon HS, Lee HL, Chen J, Stenmark P, Gill SS.	Nat Commun	10.1038/s41467-019-10732-w	2019
Enzymology	In vivo evaluation of Clostridioides difficile enoyl-ACP reductase II (FabK) inhibition by phenylimidazole unveils a promising narrow-spectrum antimicrobial strategy.	Dureja C, Rutherford JT, Pavel FB, Norseeda K, Prah I, Sun D, Hevener KE, Hurdle JG.	Antimicrob Agents Chemother	10.1128/aac.01222-23	2024
	Antimicrobial Activity of Soil Clostridium Enriched Conditioned Media Against Bacillus mycoides, Bacillus cereus, and Pseudomonas aeruginosa.	Pahalagedara ASNW, Flint S, Palmer J, Subbaraj A, Brightwell G, Gupta TB.	Front Microbiol	10.3389/fmicb.2020.608998	2020
Pathogenicity	Using a Novel Lysin To Help Control Clostridium difficile Infections.	Wang Q, Euler CW, Delaune A, Fischetti VA.	Antimicrob Agents Chemother	10.1128/aac.01357-15	2015
	Species-specific oligonucleotide probes for rRNA of Clostridium difficile and related species.	Wilson KH, Blitchington R, Hindenach B, Greene RC.	J Clin Microbiol	10.1128/jcm.26.12.2484-2488.1988	1988
Phylogeny	Taxonomic implications of spore fine structure in Clostridium bifermentans.	Rode LJ, Smith LD.	J Bacteriol	10.1128/jb.105.1.349-354.1971	1971
Enzymology	Cloning and expression of the phospholipase C gene from Clostridium perfringens and Clostridium bifermentans.	Tso JY, Siebel C.	Infect Immun	10.1128/iai.57.2.468-476.1989	1989
Metabolism	Expression and delivery of an endolysin to combat Clostridium perfringens.	Gervasi T, Horn N, Wegmann U, Dugo G, Narbad A, Mayer MJ.	Appl Microbiol Biotechnol	10.1007/s00253-013-5128-y	2014
Metabolism	Biohydrogenation of C20 polyunsaturated fatty acids by anaerobic bacteria.	Sakurama H, Kishino S, Mihara K, Ando A, Kita K, Takahashi S, Shimizu S, Ogawa J	J Lipid Res	10.1194/jlr.M045450	2014
Phenotype	Correlative properties for a differentiation of two Clostridium sordellii phenotypes and their distinction from Clostridium bifermentans.	Roggentin P, Gutschker-Gdaniec G, Schauer R, Hobrecht R	Zentralbl Bakteriol Mikrobiol Hyg A	10.1016/s0176-6724(85)80020-1	1985
Phylogeny	Description of Paraclostridium bifermentans subsp. muricolitidis subsp. nov., emended description of Paraclostridium bifermentans (Sasi Jyothsna et al., 2016), and creation of Paraclostridium bifermentans subsp. bifermentans subsp. nov.	Kutsuna R, Miyoshi-Akiyama T, Mori K, Hayashi M, Tomida J, Morita Y, Tanaka K, Kawamura Y	Microbiol Immunol	10.1111/1348-0421.12663	2019
Phylogeny	Paraclostridium benzoelyticum gen. nov., sp. nov., isolated from marine sediment and reclassification of Clostridium bifermentans as Paraclostridium bifermentans comb. nov. Proposal of a new genus Paeniclostridium gen. nov. to accommodate Clostridium sordellii and Clostridium ghonii.	Sasi Jyothsna TS, Tushar L, Sasikala C, Ramana CV	Int J Syst Evol Microbiol	10.1099/ijsem.0.000874	2016

References

#5658	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 14991
#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 )
#20218	Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 )
#41797	; Curators of the CIP;
#53282	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 36626
#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) .
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#68380	Automatically annotated from API rID32A .
#68382	Automatically annotated from API zym .
#116804	Collection of Institut Pasteur ; Curators of the CIP; CIP 104309
#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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Paraclostridium bifermentans subsp. bifermentans (DSM 14991, ATCC 638, JCM 1386)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

API zym

API rID32A

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_019916025

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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