Clostridium colinum (DSM 6011, ATCC 27770, JCM 5831)

Name: Clostridium colinum (DSM 6011, ATCC 27770, JCM 5831)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 2754

Type strain

Strain Designation 72042

Culture col. no. DSM 6011 ATCC 27770 JCM 5831 CCUG 21927 72042 1 more

NCBI tax ID(s) 36835

Special Collections DSMZ CCUG JCM

History <- ATCC; ATCC 27770 <- H. A. Berkhoff; 72042 ATCC 27770 <-- G. A. Berkhoff 72042.

Links

Clostridium colinum 72042 is an anaerobe animal pathogen that was isolated from chicken with ulcerative enteritis.

anaerobe animal pathogen genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 39168

ATCC 27770,DSM 6011,JCM 5831,CCM 3932,CCUG 21927

@ref 20215

Last LPSN update 2026-02-09 11:18:21

Domain Bacteria

Phylum Bacillota

Class Clostridia

Order Eubacteriales

Family Clostridiaceae

Genus Clostridium

Species Clostridium colinum

Full scientific name Clostridium colinum (ex Berkhoff et al. 1974) Berkhoff 1985

Synonyms (1)

"Tyzzerella colina"

Morphology

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
2418	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

Culture temp

@ref	Growth	Type	Temperature (°C)
2418	positive	growth	37
47519	positive	growth	37
67770	positive	growth	37

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
2418	anaerobe
47519	anaerobe
125438	anaerobe	94.347

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-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	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

Fatty acid profile

Metadata FA analysis

@ref

47519

Fatty acid	Percentage	ECL
C20:0	45.2	20
C10:0	26.6	10
C18:0	8	18
C12:0	5.9	12
C14:0	3.2	14
C18:2 ω6,9c/C18:0 ANTE	3.2	17.724
C20:1 ω9c	2.7	19.77
C18:1 ω9c	2.2	17.769
Unidentified	2
C20:2 ω6,9c	0.9	19.735

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
2418	-	-	-	-	-	+	+	-	+	-	+	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Infection	#Disease	-
#Host	#Birds	#Chicken
#Host	#Microbial	#Bacteria

Isolation

@ref	Sample type
2418	chicken with ulcerative enteritis
47519	Chicken with ulcerative enteritis
67770	Chicken with ulcerative enteritis

Taxonmaps

69479

Global distribution of 16S sequence X76748 (>99% sequence identity) for [Clostridium] colinum subclade from Microbeatlas

Aquatic Samples	8
Soil Samples	4
Animal Samples	890
Plant Samples	4
Total Samples	906

Interaction and safety

Risk assessment

@ref	Pathogenicity animal	Biosafety level	Biosafety level comment
2418		2	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	DSM6011 assembly for [Clostridium] colinum DSM 6011	complete	GCA_940677205	36835.4	8045689594	36835	92.94

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Clostridium colinum strain DSM 6011 16S ribosomal RNA gene, partial sequence	HM245938	842	36835
2418	Clostridium colinum 16S rRNA gene, type strain DSM 6011T	X76748	1473	36835
67770	[Clostridium] colinum gene for 16S ribosomal RNA, partial sequence, strain: JCM 5831	LC011040	1481	36835

GC content

@ref	GC-content (mol%)	Method
2418	43.0
67770	43	thermal denaturation, midpoint method (Tm)

Genome-based predictions

Predictions

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: [Clostridium] colinum DSM 6011
NCBI: GCA_940677205.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	aerobic	aerobicⓘ	no	99.02	no
125438	gram-positive	gram-positiveⓘ	yes	66.87	no
125438	anaerobic	anaerobicⓘ	yes	94.35	yes
125438	spore-forming	spore-formingⓘ	no	55.65	no
125438	thermophilic	thermophileⓘ	no	84.12	yes
125438	flagellated	motile2+ⓘ	yes	65.18	no

Literature

Title	Authors	Journal	DOI	Year
Agglutinins to bacteria in Crohn's disease.	Matthews N, Mayberry JF, Rhodes J, Neale L, Munro J, Wensinck F, Lawson GH, Rowland AC, Berkhoff GA, Barthold SW.	Gut	10.1136/gut.21.5.376	1980
Anaeropeptidivorans aminofermentans gen. nov., sp. nov., a mesophilic proteolytic salt-tolerant bacterium isolated from a laboratory-scale biogas fermenter, and emended description of Clostridium colinum.	Koller N, Hahnke S, Zverlov V, Wibberg D, Klingl A, Busche T, Klocke M, Puhler A, Schluter A, Liebl W, Maus I.	Int J Syst Evol Microbiol	10.1099/ijsem.0.005668	2022

References

#2418	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 6011
#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 )
#47519	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 21927
#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 .
#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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Clostridium colinum (DSM 6011, ATCC 27770, JCM 5831)

Name and taxonomic classification

Morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

Fatty acid profile

API rID32A

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_940677205

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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