Clostridium cocleatum (CCUG 46310, CCUG 45854, DSM 1551)

Name: Clostridium cocleatum (CCUG 46310, CCUG 45854, DSM 1551)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 2575

Type strain

Strain Designation I50

Culture col. no. CCUG 46310 CCUG 45854 DSM 1551 ATCC 29902 NCTC 11210 4 more

NCBI tax ID(s) 1121304 69824

Special Collections DSMZ CCUG JCM Mouse DZIF

History <- C. Kaneuchi, Institute of Physical and Chemical Research, Komagome Branch, Tokyo, Japan; I50 <- C. Kaneuchi; {1975} C. Kaneuchi I 50 <-- K. Itoh 50.

Links

Clostridium cocleatum I50 is an anaerobe, mesophilic prokaryote that was isolated from caecal content; wildtype C57BL/6 mouse.

anaerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 39795

ATCC 29902,NCTC 11210,DSM 1551,JCM 1397,CCM 6166,CCRC 14465,CCUG45854,CCUG 46310,BCRC 14465

@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 cocleatum

Full scientific name Clostridium cocleatum Kaneuchi et al. 1979 (Approved Lists 1980)

Synonyms (1)

Thomasclavelia cocleata

Morphology

Colony morphology

818

Incubation period1-2 days

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
818	CMC MEDIUM (N2/CO2) (DSMZ Medium 110a)		Medium recipe at MediaDive	Name: CMC MEDIUM (N2/CO2) (DSMZ Medium 110a) Composition: Ground beef 500.0 g/l Casitone 30.0 g/l Yeast extract 5.0 g/l K2HPO4 5.0 g/l D-Glucose 4.0 g/l Na2CO3 1.5 g/l Cellobiose 1.0 g/l Maltose 1.0 g/l Starch 1.0 g/l L-Cysteine HCl x H2O 0.5 g/l Sodium resazurin 0.0005 g/l NaOH Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
818	positive	growth	37	mesophilic
57145	positive	growth	37	mesophilic
67770	positive	growth	37	mesophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
818	anaerobe
57145	anaerobe
125439	anaerobe	98.2

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	cardiolipin biosynthesis	100	7 of 7
66794	teichoic acid biosynthesis	100	1 of 1
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	L-lactaldehyde degradation	100	3 of 3
66794	coenzyme A metabolism	100	4 of 4
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	folate polyglutamylation	100	1 of 1
66794	palmitate biosynthesis	90.91	20 of 22
66794	threonine metabolism	90	9 of 10
66794	valine metabolism	88.89	8 of 9
66794	aspartate and asparagine metabolism	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	glycine betaine biosynthesis	80	4 of 5
66794	peptidoglycan biosynthesis	80	12 of 15
66794	hydrogen production	80	4 of 5
66794	NAD metabolism	77.78	14 of 18
66794	vitamin B1 metabolism	76.92	10 of 13
66794	acetate fermentation	75	3 of 4
66794	CMP-KDO biosynthesis	75	3 of 4
66794	glycogen biosynthesis	75	3 of 4
66794	ppGpp biosynthesis	75	3 of 4
66794	C4 and CAM-carbon fixation	75	6 of 8
66794	photosynthesis	71.43	10 of 14
66794	glycolysis	70.59	12 of 17
66794	phenylalanine metabolism	69.23	9 of 13
66794	pyrimidine metabolism	68.89	31 of 45
66794	serine metabolism	66.67	6 of 9
66794	flavin biosynthesis	66.67	10 of 15
66794	acetoin degradation	66.67	2 of 3
66794	d-mannose degradation	66.67	6 of 9
66794	formaldehyde oxidation	66.67	2 of 3
66794	octane oxidation	66.67	2 of 3
66794	purine metabolism	65.96	62 of 94
66794	tetrahydrofolate metabolism	64.29	9 of 14
66794	isoleucine metabolism	62.5	5 of 8
66794	methionine metabolism	61.54	16 of 26
66794	leucine metabolism	61.54	8 of 13
66794	methylglyoxal degradation	60	3 of 5
66794	starch degradation	60	6 of 10
66794	O-antigen biosynthesis	60	3 of 5
66794	glycogen metabolism	60	3 of 5
66794	alanine metabolism	58.62	17 of 29
66794	glutamate and glutamine metabolism	57.14	16 of 28
66794	propanol degradation	57.14	4 of 7
66794	polyamine pathway	56.52	13 of 23
66794	histidine metabolism	55.17	16 of 29
66794	proline metabolism	54.55	6 of 11
66794	arginine metabolism	54.17	13 of 24
66794	suberin monomers biosynthesis	50	1 of 2
66794	dTDPLrhamnose biosynthesis	50	4 of 8
66794	Entner Doudoroff pathway	50	5 of 10
66794	cysteine metabolism	50	9 of 18
66794	glycolate and glyoxylate degradation	50	3 of 6
66794	sulfopterin metabolism	50	2 of 4
66794	dolichol and dolichyl phosphate biosynthesis	50	1 of 2
66794	ethanol fermentation	50	1 of 2
66794	butanoate fermentation	50	2 of 4
66794	biotin biosynthesis	50	2 of 4
66794	adipate degradation	50	1 of 2
66794	gluconeogenesis	50	4 of 8
66794	ketogluconate metabolism	50	4 of 8
66794	ribulose monophosphate pathway	50	1 of 2
66794	oxidative phosphorylation	49.45	45 of 91
66794	lysine metabolism	47.62	20 of 42
66794	tryptophan metabolism	47.37	18 of 38
66794	non-pathway related	47.37	18 of 38
66794	urea cycle	46.15	6 of 13
66794	pentose phosphate pathway	45.45	5 of 11
66794	lipid metabolism	45.16	14 of 31
66794	molybdenum cofactor biosynthesis	44.44	4 of 9
66794	CO2 fixation in Crenarchaeota	44.44	4 of 9
66794	ubiquinone biosynthesis	42.86	3 of 7
66794	citric acid cycle	42.86	6 of 14
66794	reductive acetyl coenzyme A pathway	42.86	3 of 7
66794	myo-inositol biosynthesis	40	4 of 10
66794	metabolism of amino sugars and derivatives	40	2 of 5
66794	factor 420 biosynthesis	40	2 of 5
66794	bacilysin biosynthesis	40	2 of 5
66794	arachidonate biosynthesis	40	2 of 5
66794	degradation of hexoses	38.89	7 of 18
66794	isoprenoid biosynthesis	38.46	10 of 26
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	37.5	3 of 8
66794	vitamin B6 metabolism	36.36	4 of 11
66794	d-xylose degradation	36.36	4 of 11
66794	metabolism of disaccharids	36.36	4 of 11
66794	lipid A biosynthesis	33.33	3 of 9
66794	cyanate degradation	33.33	1 of 3
66794	sphingosine metabolism	33.33	2 of 6
66794	IAA biosynthesis	33.33	1 of 3
66794	degradation of aromatic, nitrogen containing compounds	33.33	4 of 12
66794	enterobactin biosynthesis	33.33	1 of 3
66794	selenocysteine biosynthesis	33.33	2 of 6
66794	ascorbate metabolism	31.82	7 of 22
66794	phenylpropanoid biosynthesis	30.77	4 of 13
66794	propionate fermentation	30	3 of 10
66794	coenzyme M biosynthesis	30	3 of 10
66794	glycine metabolism	30	3 of 10
66794	tyrosine metabolism	28.57	4 of 14
66794	degradation of pentoses	28.57	8 of 28
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	carnitine metabolism	25	2 of 8
66794	lactate fermentation	25	1 of 4
66794	cyclohexanol degradation	25	1 of 4
66794	degradation of sugar alcohols	25	4 of 16
66794	vitamin E metabolism	25	1 of 4
66794	sulfate reduction	23.08	3 of 13
66794	phosphatidylethanolamine bioynthesis	23.08	3 of 13
66794	4-hydroxymandelate degradation	22.22	2 of 9
66794	nitrate assimilation	22.22	2 of 9
66794	glutathione metabolism	21.43	3 of 14

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
818	caecal content; wildtype C57BL/6 mouse	Miyazaki	Japan	JPN	Asia
57145	Mouse cecum		Japan	JPN	Asia
67770	Cecum of mouse

Taxonmaps

69479

Global distribution of 16S sequence Y18188 (>99% sequence identity) for [Clostridium] cocleatum subclade from Microbeatlas

Aquatic Samples	565
Soil Samples	695
Animal Samples	62316
Plant Samples	163
Total Samples	63739

Interaction and safety

Risk assessment

@ref	Pathogenicity human	Biosafety level	Biosafety level comment
818	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
66792	ASM2462289v1 assembly for Thomasclavelia cocleata DSM 1551	contig	GCA_024622895	69824.31	8067364886	69824	66.26
66792	Erysipelatoclostridium cocleatum ATCC 29902	contig			2574179769	69824	65.06
67770	ASM280340v1 assembly for Thomasclavelia cocleata ATCC 29902	scaffold	GCA_002803405	69824.4		69824	58.92
67770	IMG-taxon 2634166354 annotated assembly for Thomasclavelia cocleata DSM 1551	scaffold	GCA_900102365	69824.3	2634166354	69824	57.33

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
20218	[Clostridium] cocleatum gene for 16S ribosomal RNA, partial sequence	AB910744	1488		69824
818	Clostridium cocleatum 16S rRNA gene, partial, strain DSM 1551	Y18188	1489		69824

GC content

818

GC-content (mol%)27.9

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Thomasclavelia cocleata DSM 1551
NCBI: GCA_900102365

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	yes	71.80	no
125439	motility	BacteriaNetⓘ	yes	56.60	no
125439	gram_stain	BacteriaNetⓘ	positive	89.20	no
125439	oxygen_tolerance	BacteriaNetⓘ	anaerobe	98.20	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Antimicrobial Activity of Processed Spices Used in Traditional Southern Italian Sausage Processing	De Candia S, Quintieri L, Caputo L, Baruzzi F.	Journal of food processing and preservation.	10.1111/jfpp.13022	2017
	In Silico Screening of Bacteriocin Gene Clusters within a Set of Marine Bacillota Genomes.	Teber R, Asakawa S.	Int J Mol Sci	10.3390/ijms25052566	2024
	Production of polyhydroxyalkanoate (PHA) biopolymer from crop residue using bacteria as an alternative to plastics: a review.	Chouhan A, Tiwari A.	RSC Adv	10.1039/d4ra08505a	2025
Metabolism	Functional analysis of multiple nifB genes of Paenibacillus strains in synthesis of Mo-, Fe- and V-nitrogenases.	Li Q, Zhang H, Zhang L, Chen S.	Microb Cell Fact	10.1186/s12934-021-01629-9	2021
	A standardized gnotobiotic mouse model harboring a minimal 15-member mouse gut microbiota recapitulates SOPF/SPF phenotypes.	Darnaud M, De Vadder F, Bogeat P, Boucinha L, Bulteau AL, Bunescu A, Couturier C, Delgado A, Dugua H, Elie C, Mathieu A, Novotna T, Ouattara DA, Planel S, Saliou A, Srutkova D, Yansouni J, Stecher B, Schwarzer M, Leulier F, Tamellini A.	Nat Commun	10.1038/s41467-021-26963-9	2021
Metabolism	Footprint area analysis of binary imaged Cupriavidus necator cells to study PHB production at balanced, transient, and limited growth conditions in a cascade process.	Vadlja D, Koller M, Novak M, Braunegg G, Horvat P.	Appl Microbiol Biotechnol	10.1007/s00253-016-7844-6	2016
Metabolism	Quorum-sensing regulation of constitutive plantaricin by Lactobacillus plantarum strains under a model system for vegetables and fruits.	Rizzello CG, Filannino P, Di Cagno R, Calasso M, Gobbetti M.	Appl Environ Microbiol	10.1128/aem.03224-13	2014
Metabolism	Lactic acid fermentation as a tool to enhance the functional features of Echinacea spp.	Rizzello CG, Coda R, Macias DS, Pinto D, Marzani B, Filannino P, Giuliani G, Paradiso VM, Di Cagno R, Gobbetti M.	Microb Cell Fact	10.1186/1475-2859-12-44	2013
	Experimental evaluation of the importance of colonization history in early-life gut microbiota assembly.	Martinez I, Maldonado-Gomez MX, Gomes-Neto JC, Kittana H, Ding H, Schmaltz R, Joglekar P, Cardona RJ, Marsteller NL, Kembel SW, Benson AK, Peterson DA, Ramer-Tait AE, Walter J.	Elife	10.7554/elife.36521	2018
Metabolism	Paenibacillus taohuashanense sp. nov., a nitrogen-fixing species isolated from rhizosphere soil of the root of Caragana kansuensis Pojark.	Xie JB, Zhang LH, Zhou YG, Liu HC, Chen SF.	Antonie Van Leeuwenhoek	10.1007/s10482-012-9773-4	2012
Phylogeny	Paenibacillus typhae sp. nov., isolated from roots of Typha angustifolia L.	Kong BH, Liu QF, Liu M, Liu Y, Liu L, Li CL, Yu R, Li YH.	Int J Syst Evol Microbiol	10.1099/ijs.0.042747-0	2013
Phylogeny	Description of Christensenella minuta gen. nov., sp. nov., isolated from human faeces, which forms a distinct branch in the order Clostridiales, and proposal of Christensenellaceae fam. nov.	Morotomi M, Nagai F, Watanabe Y.	Int J Syst Evol Microbiol	10.1099/ijs.0.026989-0	2012
Phylogeny	Paenibacillus sophorae sp. nov., a nitrogen-fixing species isolated from the rhizosphere of Sophora japonica.	Jin HJ, Lv J, Chen SF.	Int J Syst Evol Microbiol	10.1099/ijs.0.021709-0	2011

References

#818	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 1551
#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 )
#57145	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 46310
#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) .
#66794	Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg: BRENDA, the ELIXIR core data resource in 2021: new developments and updates. Nucleic Acids Res. 49: D498 - D508 2020 ( DOI 10.1093/nar/gkaa1025 , PubMed 33211880 )
#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 .
#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 cocleatum (CCUG 46310, CCUG 45854, DSM 1551)

Name and taxonomic classification

Morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_024622895

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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