Clostridium putrefaciens (DSM 1291, ATCC 25786, NCTC 9836)

Name: Clostridium putrefaciens (DSM 1291, ATCC 25786, NCTC 9836)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 2652

Type strain

Culture col. no. DSM 1291 ATCC 25786 NCTC 9836 CCUG 30534 VPI 5395 3 more

NCBI tax ID(s) 99675

Special Collections DSMZ CCUG JCM

History <- ATCC; ATCC 25786 <- L. DS. Smith, Virginia Polytechnical Institute and State University (VPI), Blacksburg, V., USA; VPI 5395 <- NCTC; NCTC 9836 <- E. M. Barnes, Low Temperature Research Station, Cambridge, England, U.K.; {1956} ATCC 25786 <-- L. DS. Smith VPI 5395 <-- NCTC 9836 <-- E. M. Barnes.

Links

Clostridium putrefaciens DSM 1291 is an anaerobe bacterium that was isolated from ham.

anaerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 92909

ATCC 25786,CCUG 30534,DSM 1291,NCTC 9836,NCIB 11406,JCM 1431,CCRC 14480,NCIMB 11406,BCRC 14480

@ref 20215

Last LPSN update 2026-02-09 11:18:19

Domain Bacteria

Phylum Bacillota

Class Clostridia

Order Eubacteriales

Family Clostridiaceae

Genus Clostridium

Species Clostridium putrefaciens

Full scientific name Clostridium putrefaciens (McBryde 1911) Sturges and Drake 1927 (Approved Lists 1980)

Synonyms (1)

"Bacillus putrefaciens"

Morphology

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
622	CMC MEDIUM (N2/CO2) (DSMZ Medium 110a)		Medium recipe at MediaDive	Name: CMC MEDIUM (N2/CO2) (DSMZ Medium 110a) Composition: Ground beef 495.049 g/l Casitone 29.703 g/l Yeast extract 4.9505 g/l K2HPO4 4.9505 g/l D-Glucose 3.9604 g/l Na2CO3 1.48515 g/l Cellobiose 0.990099 g/l D-Maltose 0.990099 g/l Starch 0.990099 g/l L-Cysteine HCl x H2O 0.49505 g/l Sodium resazurin 0.00049505 g/l NaOH Distilled water
622	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)
622	positive	growth	25
50134	positive	growth	26
50134	positive	growth	37
67770	positive	growth	26

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
622	anaerobe
50134	anaerobe
125438	anaerobe	91.835
125439	anaerobe	99.5

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Food production	#Meat

Isolation

@ref	Sample type	Country	Country ISO 3 Code	Continent
622	ham	United Kingdom	GBR	Europe
50134	Spoiled cured ham
67770	Spoiled ham

Taxonmaps

69479

Global distribution of 16S sequence Y18177 (>99% sequence identity) for Clostridium from Microbeatlas

Aquatic Samples	3822
Soil Samples	4363
Animal Samples	10663
Plant Samples	861
Total Samples	19709

Interaction and safety

Risk assessment

@ref	Pathogenicity human	Biosafety level	Biosafety level comment
622	yes, in single cases	1	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
67770	52654_E01 assembly for Clostridium putrefaciens NCTC9836	contig	GCA_900461105	99675.3	2808606539	99675	75.26

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Clostridium putrifaciens 16S rRNA gene, partial, strain DSM 1291	Y18177	1480	99675
20218	Clostridium putrefaciens gene for 16S ribosomal RNA, partial cds, strain: JCM 1431	AB618788	1473	99675
622	Clostridium putrefaciens 16S ribosomal RNA gene, partial sequence	AF127024	1487	99675

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Clostridium putrefaciens NCTC9836
NCBI: GCA_900461105

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	yes	80.10	no
125439	motility	BacteriaNetⓘ	yes	77.70	no
125439	gram_stain	BacteriaNetⓘ	positive	84.80	no
125439	oxygen_tolerance	BacteriaNetⓘ	anaerobe	99.50	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Clostridium putrefaciens strain NCTC9836
PATRIC: 99675.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	72.08	no
125438	anaerobic	anaerobicⓘ	yes	91.84	yes
125438	aerobic	aerobicⓘ	no	97.28	yes
125438	spore-forming	spore-formingⓘ	yes	71.53	no
125438	thermophilic	thermophileⓘ	no	89.73	no
125438	flagellated	motile2+ⓘ	yes	77.19	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Taxonogenomic description of four new Clostridium species isolated from human gut: 'Clostridium amazonitimonense', 'Clostridium merdae', 'Clostridium massilidielmoense' and 'Clostridium nigeriense'.	Alou MT, Ndongo S, Fregere L, Labas N, Andrieu C, Richez M, Couderc C, Baudoin JP, Abrahao J, Brah S, Diallo A, Sokhna C, Cassir N, La Scola B, Cadoret F, Raoult D.	New Microbes New Infect	10.1016/j.nmni.2017.11.003	2018
Enzymology	N2O-producing microorganisms in the gut of the earthworm Aporrectodea caliginosa are indicative of ingested soil bacteria.	Ihssen J, Horn MA, Matthies C, Gossner A, Schramm A, Drake HL.	Appl Environ Microbiol	10.1128/aem.69.3.1655-1661.2003	2003
	Hydrophobicity of Bacillus and Clostridium spores.	Wiencek KM, Klapes NA, Foegeding PM.	Appl Environ Microbiol	10.1128/aem.56.9.2600-2605.1990	1990
Genetics	Development of the human infant intestinal microbiota.	Palmer C, Bik EM, DiGiulio DB, Relman DA, Brown PO.	PLoS Biol	10.1371/journal.pbio.0050177	2007
	Bacterial species diversity of traditionally ripened sheep legs from the Faroe Islands (skerpikjøt).	Charmpi C, Thamsborg KKM, Mikalsen SO, Magnussen E, Sosa Fajardo A, Van der Veken D, Leisner JJ, Leroy F.	Int J Food Microbiol	10.1016/j.ijfoodmicro.2022.110023	2023
Metabolism	Exploring the functional diversity and metabolic activities of the human gut microbiome in Thai adults in response to a prebiotic diet.	Kingkaw A, Patumcharoenpol P, Suratannon N, Nakphaichit M, Roytrakul S, Vongsangnak W.	Microbiol Spectr	10.1128/spectrum.01599-24	2025
Enzymology	Kinetic and structural characterization of carboxyspermidine dehydrogenase of polyamine biosynthesis.	Lee DF, Atencio N, Bouchey S, Shoemaker MR, Dodd JS, Satre M, Miller KA, McFarlane JS.	J Biol Chem	10.1016/j.jbc.2023.105033	2023
Genetics	Bacterial community changes in strawberry fruits (Fragaria × ananassa variety "Monterey") from farm field to retail market stands, an indicator of postharvest contamination.	Tenea GN, Reyes P.	Front Microbiol	10.3389/fmicb.2024.1348316	2024
	Acupoint Massage Therapy Alters the Composition of Gut Microbiome in Functional Constipation Patients.	Chen H, Tan PS, Li CP, Chen BZ, Xu YQ, He YQ, Ke X.	Evid Based Complement Alternat Med	10.1155/2021/1416236	2021
	Occurrence of genes encoding spore germination in Clostridium species that cause meat spoilage.	Burgess SA, Palevich FP, Gardner A, Mills J, Brightwell G, Palevich N.	Microb Genom	10.1099/mgen.0.000767	2022
Enzymology	Detection of cold-tolerant clostridia other than Clostridium estertheticum in raw vacuum-packed chill-stored meat.	Cavill L, Renteria-Monterrubio AL, Helps CR, Corry JE.	Food Microbiol	10.1016/j.fm.2011.01.003	2011
	In silico characterization and structural modeling of bacterial metalloprotease of family M4.	Hasan R, Rony MNH, Ahmed R.	J Genet Eng Biotechnol	10.1186/s43141-020-00105-y	2021
Enzymology	Sources of psychrophilic and psychrotolerant clostridia causing spoilage of vacuum-packed chilled meats, as determined by PCR amplification procedure.	Broda DM, Boerema JA, Brightwell G.	J Appl Microbiol	10.1111/j.1365-2672.2009.04193.x	2009
Phylogeny	Identification of Clostridium spp. derived from a sheep and cattle slaughterhouse by matrix-assisted laser desorption and ionization-time of flight mass spectrometry (MALDI-TOF MS) and 16S rDNA sequencing.	Bakhtiary F, Sayevand HR, Remely M, Hippe B, Indra A, Hosseini H, Haslberger AG.	J Food Sci Technol	10.1007/s13197-018-3255-2	2018
	Gut microbiota in regulatory T cell generation and function: mechanisms and health implications.	Sharma A, Sharma G, Im SH.	Gut Microbes	10.1080/19490976.2025.2516702	2025
Enzymology	Unraveling the Genotypic and Phenotypic Diversity of the Psychrophilic Clostridium estertheticum Complex, a Meat Spoilage Agent.	Wambui J, Stevens MJA, Cernela N, Stephan R.	Front Microbiol	10.3389/fmicb.2022.856810	2022
	Dietary L-Tryptophan Modulates the Structural and Functional Composition of the Intestinal Microbiome in Weaned Piglets.	Liang H, Dai Z, Liu N, Ji Y, Chen J, Zhang Y, Yang Y, Li J, Wu Z, Wu G.	Front Microbiol	10.3389/fmicb.2018.01736	2018
Metabolism	The presence of antibody-coated anaerobic bacteria in asymptomatic bacteriuria during pregnancy.	Meijer-Severs GJ, Aarnoudse JG, Mensink WF, Dankert J.	J Infect Dis	10.1093/infdis/140.5.653	1979

References

#622	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 1291
#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 )
#50134	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 30534
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#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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Clostridium putrefaciens (DSM 1291, ATCC 25786, NCTC 9836)

Name and taxonomic classification

Morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_900461105

16S sequences

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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