Clostridium intestinale (DSM 6191, ATCC 49213, JCM 7506)

Name: Clostridium intestinale (DSM 6191, ATCC 49213, JCM 7506)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 2755

Type strain

Strain Designation Catt39

Culture col. no. DSM 6191 ATCC 49213 JCM 7506 Catt39 VTT E-032440

NCBI tax ID(s) 1121320 36845

Special Collections DSMZ JCM

History DSMZ <- ATCC <- T. Mitsuoka, Catt39 JCM <-- W.-K. Lee strain Catt 39.

Links

Clostridium intestinale Catt39 is an anaerobe bacterium that was isolated from faeces of cattle.

anaerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 42355

ATCC 49213,JCM 7506,DSM 6191,VTT E-032440

@ref 20215

Last LPSN update 2026-05-29 08:25:32

Domain Bacteria

Phylum Bacillota

Class Clostridia

Order Eubacteriales

Family Clostridiaceae

Genus Clostridium

Species Clostridium intestinale

Full scientific name Clostridium intestinale corrig. Lee et al. 1989

Synonyms (1)

Clostridium intestinalis

BacDive ID	Other strains from **Clostridium intestinale** (1)	Type strain
2756	C. intestinale RC, DSM 16614

Morphology

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
2519	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

Culture temp

@ref	Growth	Type	Temperature (°C)
2519	positive	growth	37
67770	positive	growth	37

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
2519	anaerobe
125439	anaerobe	97.998

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Mammals	#Bovinae (Cow, Cattle)
#Host Body Product	#Gastrointestinal tract	#Feces (Stool)

Isolation

@ref	Sample type	Country	Country ISO 3 Code	Continent
2519	faeces of cattle	Japan	JPN	Asia
67770	Cat feces

Taxonmaps

69479

Global distribution of 16S sequence X76740 (>99% sequence identity) for Clostridium intestinale subclade from Microbeatlas

Aquatic Samples	625
Soil Samples	990
Animal Samples	4023
Plant Samples	309
Total Samples	5947

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
2519	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
66792	IMG-taxon 2585428084 annotated assembly for Clostridium intestinale DSM 6191	scaffold	GCA_900130055	1121320.3	2585428084	1121320	68.54

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
2519	Clostridium intestinale 16S rRNA gene., type strain DSM 6191T	X76740	1385		36845
67770	Clostridium intestinale gene for 16S ribosomal RNA, partial sequence, strain: JCM 7506	LC037210	1482		36845

GC content

@ref	GC-content (mol%)
2519	27.0
67770	27

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: IMG-taxon 2585428084 annotated assembly for Clostridium intestinale DSM 6191
NCBI: GCA_900130055

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	anaerobe	98.00	no
125439	gram_stain	BacteriaNetⓘ	variable	50.53	no
125439	motility	BacteriaNetⓘ	yes	70.81	no
125439	spore_formation	BacteriaNetⓘ	yes	72.53	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Clostridium intestinale DSM 6191 DSM 6191
NCBI: GCA_900130055.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	60.61	no
125438	anaerobic	anaerobicⓘ	yes	83.25	no
125438	aerobic	aerobicⓘ	no	94.47	no
125438	spore-forming	spore-formingⓘ	yes	79.03	no
125438	thermophilic	thermophileⓘ	no	91.75	yes
125438	flagellated	motile2+ⓘ	yes	86.71	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Enzymology	Molecular Characterization of a Novel Lytic Enzyme LysC from Clostridium intestinale URNW and Its Antibacterial Activity Mediated by Positively Charged N-Terminal Extension.	Plotka M, Szadkowska M, Hakansson M, Kovacic R, Al-Karadaghi S, Walse B, Werbowy O, Kaczorowska AK, Kaczorowski T.	Int J Mol Sci	10.3390/ijms21144894	2020
	Differential modulation of post-antibiotic colonization resistance to Clostridioides difficile by two probiotic Lactobacillus strains.	Foley MH, McMillan AS, O'Flaherty S, Thanissery R, Vanhoy ME, Fuller MG, Barrangou R, Theriot CM.	mBio	10.1128/mbio.01468-25	2025
	The human intestinal bacterium Eggerthella lenta influences gut metabolomes in gnotobiotic mice	Viehof A, Haange S, Streidl T, Schubert K, Engelmann B, Haller D, Rolle-Kampczyk U, von Bergen M, Clavel T.	Microbiome Res Rep		2024
	A consortium of seven commensal bacteria promotes gut microbiota recovery and strengthens ecological barrier against vancomycin-resistant enterococci.	Jan A, Bayle P, Mohellibi N, Lemoine C, Pepke F, Beguet-Crespel F, Jouanin I, Tremblay-Franco M, Laroche B, Serror P, Rigottier-Gois L.	Microbiome	10.1186/s40168-025-02127-5	2025
	The microbial-derived bile acid lithocholate and its epimers inhibit Clostridioides difficile growth and pathogenicity while sparing members of the gut microbiota.	Kisthardt SC, Thanissery R, Pike CM, Foley MH, Theriot CM.	J Bacteriol	10.1128/jb.00180-23	2023
	Characterization of antibiotic resistance genes in the species of the rumen microbiota.	Sabino YNV, Santana MF, Oyama LB, Santos FG, Moreira AJS, Huws SA, Mantovani HC.	Nat Commun	10.1038/s41467-019-13118-0	2019
	Gut colonisation with multidrug-resistant Klebsiella pneumoniae worsens Pseudomonas aeruginosa lung infection.	Le Guern R, Grandjean T, Stabler S, Bauduin M, Gosset P, Kipnis E, Dessein R.	Nat Commun	10.1038/s41467-022-35767-4	2023
Metabolism	The gut bacterium Extibacter muris produces secondary bile acids and influences liver physiology in gnotobiotic mice.	Streidl T, Karkossa I, Segura Munoz RR, Eberl C, Zaufel A, Plagge J, Schmaltz R, Schubert K, Basic M, Schneider KM, Afify M, Trautwein C, Tolba R, Stecher B, Doden HL, Ridlon JM, Ecker J, Moustafa T, von Bergen M, Ramer-Tait AE, Clavel T.	Gut Microbes	10.1080/19490976.2020.1854008	2021
Phylogeny	Sequence and cultivation study of Muribaculaceae reveals novel species, host preference, and functional potential of this yet undescribed family.	Lagkouvardos I, Lesker TR, Hitch TCA, Galvez EJC, Smit N, Neuhaus K, Wang J, Baines JF, Abt B, Stecher B, Overmann J, Strowig T, Clavel T.	Microbiome	10.1186/s40168-019-0637-2	2019
Metabolism	Novel Lytic Enzyme of Prophage Origin from Clostridium botulinum E3 Strain Alaska E43 with Bactericidal Activity against Clostridial Cells.	Morzywolek A, Plotka M, Kaczorowska AK, Szadkowska M, Kozlowski LP, Wyrzykowski D, Makowska J, Waters JJ, Swift SM, Donovan DM, Kaczorowski T.	Int J Mol Sci	10.3390/ijms22179536	2021
	Draft Genome Sequence of the Hydrogen- and Ethanol-Producing Bacterium Clostridium intestinale Strain URNW.	Lal S, Ramachandran U, Zhang X, Sparling R, Levin DB.	Genome Announc	10.1128/genomea.00871-13	2013
Phylogeny	Bacteremia caused by Clostridium intestinale.	Elsayed S, Zhang K.	J Clin Microbiol	10.1128/jcm.43.4.2018-2020.2005	2005
Phylogeny	Isolation and characterization of a hydrogen- and ethanol-producing Clostridium sp. strain URNW.	Ramachandran U, Wrana N, Cicek N, Sparling R, Levin DB	Can J Microbiol	10.1139/W11-005	2011

References

#2519	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 6191
#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 )
#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;
#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 intestinale (DSM 6191, ATCC 49213, JCM 7506)

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_900130055

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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