Clostridium cylindrosporum (DSM 605, ATCC 7905, IMG 1641)

Name: Clostridium cylindrosporum (DSM 605, ATCC 7905, IMG 1641)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 2577

Type strain

Strain Designation HC-1

Culture col. no. DSM 605 ATCC 7905 IMG 1641 HC-1

NCBI tax ID(s) 1121307 1495

Special Collections DSMZ

History DSMZ <- Institut für Mikrobiologie, Universität Göttingen (IMG), Germany; IMG 1641 <- G. Gottschalk <- H. A. Barker and J. V. Beck, University of California, Berkeley, USA; HC-1

Links

Clostridium cylindrosporum HC-1 is an anaerobe bacterium that was isolated from soil.

anaerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 34889

ATCC 7905,DSM 605,NCIMB 12822,IFO 13695,LMD 46.96,NCCB 46096,NBRC 13695,BCRC 14476,CCRC 14476

@ref 20215

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

Domain Bacteria

Phylum Bacillota

Class Clostridia

Order Eubacteriales

Family Clostridiaceae

Genus Clostridium

Species Clostridium cylindrosporum

Full scientific name Clostridium cylindrosporum (ex Barker and Beck 1942) Andreesen et al. 1985

BacDive ID	Other strains from **Clostridium cylindrosporum** (3)	Type strain
2540	C. cylindrosporum MBJ-2, DSM 10160
2579	C. cylindrosporum MJ-6, DSM 10162
2581	C. cylindrosporum NOA-2, DSM 10164

Morphology

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
317	GOTTSCHALKIA MEDIUM (DSMZ Medium 76)		Medium recipe at MediaDive	Name: GOTTSCHALKIA MEDIUM (DSMZ Medium 76) Composition: Uric acid 2.0 g/l Na2CO3 1.5 g/l Yeast extract 1.0 g/l K2HPO4 0.91 g/l KOH 0.67 g/l Na-thioglycolate 0.5 g/l MgSO4 x 7 H2O 0.25 g/l CaCl2 x 2 H2O 0.015 g/l FeSO4 x 7 H2O 0.006 g/l HCl 0.0025 g/l FeCl2 x 4 H2O 0.0015 g/l Sodium resazurin 0.0005 g/l NaOH 0.0005 g/l CoCl2 x 6 H2O 0.00019 g/l MnCl2 x 4 H2O 0.0001 g/l ZnCl2 7e-05 g/l Na2MoO4 x 2 H2O 3.6e-05 g/l NiCl2 x 6 H2O 2.4e-05 g/l H3BO3 6e-06 g/l Na2WO4 x 2 H2O 4e-06 g/l Na2SeO3 x 5 H2O 3e-06 g/l CuCl2 x 2 H2O 2e-06 g/l Distilled water

Culture temp

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

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
317	anaerobe
125439	anaerobe	96.34

Compound production

317

Compoundxanthine dehydrogenase

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	formaldehyde oxidation	100	3 of 3
66794	coenzyme A metabolism	100	4 of 4
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	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	lipoate biosynthesis	100	5 of 5
66794	palmitate biosynthesis	100	22 of 22
66794	folate polyglutamylation	100	1 of 1
66794	L-lactaldehyde degradation	100	3 of 3
66794	biotin biosynthesis	100	4 of 4
66794	reductive acetyl coenzyme A pathway	100	7 of 7
66794	chorismate metabolism	88.89	8 of 9
66794	vitamin B12 metabolism	88.24	30 of 34
66794	photosynthesis	85.71	12 of 14
66794	vitamin B1 metabolism	84.62	11 of 13
66794	NAD metabolism	83.33	15 of 18
66794	peptidoglycan biosynthesis	80	12 of 15
66794	threonine metabolism	80	8 of 10
66794	hydrogen production	80	4 of 5
66794	tetrahydrofolate metabolism	78.57	11 of 14
66794	heme metabolism	78.57	11 of 14
66794	molybdenum cofactor biosynthesis	77.78	7 of 9
66794	valine metabolism	77.78	7 of 9
66794	pyrimidine metabolism	77.78	35 of 45
66794	phenylalanine metabolism	76.92	10 of 13
66794	sulfopterin metabolism	75	3 of 4
66794	acetate fermentation	75	3 of 4
66794	C4 and CAM-carbon fixation	75	6 of 8
66794	ppGpp biosynthesis	75	3 of 4
66794	alanine metabolism	72.41	21 of 29
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	purine metabolism	70.21	66 of 94
66794	methionine metabolism	69.23	18 of 26
66794	acetoin degradation	66.67	2 of 3
66794	selenocysteine biosynthesis	66.67	4 of 6
66794	nitrate assimilation	66.67	6 of 9
66794	d-mannose degradation	66.67	6 of 9
66794	aspartate and asparagine metabolism	66.67	6 of 9
66794	octane oxidation	66.67	2 of 3
66794	cyanate degradation	66.67	2 of 3
66794	flavin biosynthesis	66.67	10 of 15
66794	proline metabolism	63.64	7 of 11
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
66794	isoleucine metabolism	62.5	5 of 8
66794	histidine metabolism	62.07	18 of 29
66794	glutamate and glutamine metabolism	60.71	17 of 28
66794	glycine betaine biosynthesis	60	3 of 5
66794	factor 420 biosynthesis	60	3 of 5
66794	methylglyoxal degradation	60	3 of 5
66794	glycolysis	58.82	10 of 17
66794	degradation of aromatic, nitrogen containing compounds	58.33	7 of 12
66794	arginine metabolism	58.33	14 of 24
66794	oxidative phosphorylation	58.24	53 of 91
66794	cysteine metabolism	55.56	10 of 18
66794	serine metabolism	55.56	5 of 9
66794	pentose phosphate pathway	54.55	6 of 11
66794	sulfate reduction	53.85	7 of 13
66794	tryptophan metabolism	50	19 of 38
66794	glycine metabolism	50	5 of 10
66794	adipate degradation	50	1 of 2
66794	ethanol fermentation	50	1 of 2
66794	kanosamine biosynthesis II	50	1 of 2
66794	lysine metabolism	50	21 of 42
66794	gluconeogenesis	50	4 of 8
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	Entner Doudoroff pathway	50	5 of 10
66794	citric acid cycle	50	7 of 14
66794	non-pathway related	50	19 of 38
66794	butanoate fermentation	50	2 of 4
66794	phenylmercury acetate degradation	50	1 of 2
66794	glycogen biosynthesis	50	2 of 4
66794	toluene degradation	50	2 of 4
66794	suberin monomers biosynthesis	50	1 of 2
66794	lipid metabolism	48.39	15 of 31
66794	isoprenoid biosynthesis	46.15	12 of 26
66794	leucine metabolism	46.15	6 of 13
66794	urea cycle	46.15	6 of 13
66794	CO2 fixation in Crenarchaeota	44.44	4 of 9
66794	propanol degradation	42.86	3 of 7
66794	glutathione metabolism	42.86	6 of 14
66794	tyrosine metabolism	42.86	6 of 14
66794	propionate fermentation	40	4 of 10
66794	arachidonate biosynthesis	40	2 of 5
66794	polyamine pathway	39.13	9 of 23
66794	phosphatidylethanolamine bioynthesis	38.46	5 of 13
66794	ketogluconate metabolism	37.5	3 of 8
66794	dTDPLrhamnose biosynthesis	37.5	3 of 8
66794	glycolate and glyoxylate degradation	33.33	2 of 6
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	pantothenate biosynthesis	33.33	2 of 6
66794	IAA biosynthesis	33.33	1 of 3
66794	enterobactin biosynthesis	33.33	1 of 3
66794	lipid A biosynthesis	33.33	3 of 9
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	carotenoid biosynthesis	31.82	7 of 22
66794	phenol degradation	30	6 of 20
66794	ubiquinone biosynthesis	28.57	2 of 7
66794	degradation of pentoses	28.57	8 of 28
66794	chlorophyll metabolism	27.78	5 of 18
66794	vitamin B6 metabolism	27.27	3 of 11
66794	metabolism of disaccharids	27.27	3 of 11
66794	lactate fermentation	25	1 of 4
66794	cyclohexanol degradation	25	1 of 4
66794	CMP-KDO biosynthesis	25	1 of 4
66794	androgen and estrogen metabolism	25	4 of 16
66794	degradation of sugar alcohols	25	4 of 16
66794	degradation of hexoses	22.22	4 of 18
66794	4-hydroxymandelate degradation	22.22	2 of 9

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Soil

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
317	soil	California	USA	USA	North America

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
317	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	ASM104737v1 assembly for Clostridium cylindrosporum DSM 605	contig	GCA_001047375	1121307.3	2630968942	1121307	71.23

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
317	Clostridium cylindrosporum 16S rRNA gene, partial, strain DSM 605	Y18179	1479		1495

GC content

317

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: ASM104737v1 assembly for Clostridium cylindrosporum DSM 605
NCBI: GCA_001047375

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	anaerobe	96.34	no
125439	gram_stain	BacteriaNetⓘ	variable	54.28	no
125439	motility	BacteriaNetⓘ	yes	74.04	no
125439	spore_formation	BacteriaNetⓘ	yes	72.19	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Clostridium cylindrosporum DSM 605
PATRIC: 1121307.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	64.65	no
125438	anaerobic	anaerobicⓘ	yes	84.37	yes
125438	spore-forming	spore-formingⓘ	yes	72.45	no
125438	aerobic	aerobicⓘ	no	97.13	yes
125438	thermophilic	thermophileⓘ	no	86.06	yes
125438	flagellated	motile2+ⓘ	yes	72.85	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Genome Sequence of Uric Acid-Fermenting Eubacterium angustum DSM 1989T (MK-1).	Poehlein A, Galperin MY, Andreesen JR, Daniel R.	Genome Announc	10.1128/genomea.01439-16	2017
	Co-cultivation of the strictly anaerobic methanogen Methanosarcina barkeri with aerobic methanotrophs in an oxygen-limited membrane bioreactor.	In 't Zandt MH, van den Bosch TJM, Rijkers R, van Kessel MAHJ, Jetten MSM, Welte CU.	Appl Microbiol Biotechnol	10.1007/s00253-018-9038-x	2018
	The Multifunctional Sactipeptide Ruminococcin C1 Displays Potent Antibacterial Activity In Vivo as Well as Other Beneficial Properties for Human Health.	Roblin C, Chiumento S, Jacqueline C, Pinloche E, Nicoletti C, Olleik H, Courvoisier-Dezord E, Amouric A, Basset C, Dru L, Ollivier M, Bogey-Lambert A, Vidal N, Atta M, Maresca M, Devillard E, Duarte V, Perrier J, Lafond M.	Int J Mol Sci	10.3390/ijms22063253	2021
	Microbial formation of caparrapidiol and derivatives from trans-nerolidol.	Abraham WR.	World J Microbiol Biotechnol	10.1007/bf00383071	1993
Enzymology	Purification and comparative studies of dihydrolipoamide dehydrogenases from the anaerobic, glycine-utilizing bacteria Peptostreptococcus glycinophilus, Clostridium cylindrosporum, and Clostridium sporogenes.	Dietrichs D, Andreesen JR.	J Bacteriol	10.1128/jb.172.1.243-251.1990	1990
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
Enzymology	Isolation of an atypically small lipoamide dehydrogenase involved in the glycine decarboxylase complex from Eubacterium acidaminophilum.	Freudenberg W, Dietrichs D, Lebertz H, Andreesen JR.	J Bacteriol	10.1128/jb.171.3.1346-1354.1989	1989
Phylogeny	Different fecal microbiotas and volatile organic compounds in treated and untreated children with celiac disease.	Di Cagno R, Rizzello CG, Gagliardi F, Ricciuti P, Ndagijimana M, Francavilla R, Guerzoni ME, Crecchio C, Gobbetti M, De Angelis M.	Appl Environ Microbiol	10.1128/aem.02793-08	2009
Metabolism	Purine and glycine metabolism by purinolytic clostridia.	Durre P, Andreesen JR.	J Bacteriol	10.1128/jb.154.1.192-199.1983	1983
Enzymology	Catalytic properties and classification of cellobiose dehydrogenases from ascomycetes.	Harreither W, Sygmund C, Augustin M, Narciso M, Rabinovich ML, Gorton L, Haltrich D, Ludwig R.	Appl Environ Microbiol	10.1128/aem.02052-10	2011
Metabolism	Duodenal and faecal microbiota of celiac children: molecular, phenotype and metabolome characterization.	Di Cagno R, De Angelis M, De Pasquale I, Ndagijimana M, Vernocchi P, Ricciuti P, Gagliardi F, Laghi L, Crecchio C, Guerzoni ME, Gobbetti M, Francavilla R.	BMC Microbiol	10.1186/1471-2180-11-219	2011
Metabolism	Carbon monoxide oxidation by Clostridium thermoaceticum and Clostridium formicoaceticum.	Diekert GB, Thauer RK.	J Bacteriol	10.1128/jb.136.2.597-606.1978	1978
Enzymology	Recovery and analysis of formyltetrahydrofolate synthetase gene sequences from natural populations of acetogenic bacteria.	Leaphart AB, Lovell CR.	Appl Environ Microbiol	10.1128/aem.67.3.1392-1395.2001	2001
	Ferredoxin and formyltetrahydrofolate synthetase: comparative studies with Clostridium acidiurici, Clostridium cylindrosporum, and newly isolated anaerobic uric acid-fermenting strains.	Champion AB, Rabinowitz JC.	J Bacteriol	10.1128/jb.132.3.1003-1020.1977	1977
Genetics	Draft Genome Sequence of Purine-Degrading Clostridium cylindrosporum HC-1 (DSM 605).	Poehlein A, Montoya Solano JD, Bengelsdorf FR, Schiel-Bengelsdorf B, Daniel R, Durre P	Genome Announc	10.1128/genomeA.00917-15	2015
	Sporulation of Clostridium cylindrosporum on a Defined, Low-Manganese Medium.	Sacks LE, Smith MR	Appl Environ Microbiol	10.1128/aem.53.7.1696-1698.1987	1987

References

#317	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 605
#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) .
#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 )
#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 cylindrosporum (DSM 605, ATCC 7905, IMG 1641)

Name and taxonomic classification

Morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Compound production

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_001047375

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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