Clostridium uliginosum (DSM 12992, ATCC BAA-53, CK55)

Name: Clostridium uliginosum (DSM 12992, ATCC BAA-53, CK55)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 2796

Type strain

Strain Designation CK55

Culture col. no. DSM 12992 ATCC BAA-53 CK55

NCBI tax ID(s) 1121343 119641

Special Collections DSMZ

History <- C. Matthies and C. H. Kuhner, Universität Bayreuth, Bayreuth, Germany; CK55 <- C. H. Kuhner {1994}

Links

Clostridium uliginosum CK55 is an anaerobe bacterium that was isolated from acidic peat bog.

anaerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 49385

DSM 12992,ATCC BAA-53

@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 uliginosum

Full scientific name Clostridium uliginosum Matthies et al. 2001

Morphology

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
4870	ANAEROBIC TRYPTIC SOY BROTH MEDIUM (DSMZ Medium 869)		Medium recipe at MediaDive	Name: ANAEROBIC TRYPTIC SOY BROTH MEDIUM (DSMZ Medium 869) Composition: Trypticase soy broth 5.5 g/l D-Glucose 2.0 g/l Resazurin 0.0005 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
4870	positive	growth	20

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
4870	anaerobe
125439	facultative anaerobe	97.6

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	metabolism of amino sugars and derivatives	100	5 of 5
66794	cardiolipin biosynthesis	100	7 of 7
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	starch degradation	100	10 of 10
66794	ethanol fermentation	100	2 of 2
66794	adipate degradation	100	2 of 2
66794	palmitate biosynthesis	100	22 of 22
66794	ppGpp biosynthesis	100	4 of 4
66794	methylglyoxal degradation	100	5 of 5
66794	L-lactaldehyde degradation	100	3 of 3
66794	formaldehyde oxidation	100	3 of 3
66794	coenzyme A metabolism	100	4 of 4
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	C4 and CAM-carbon fixation	100	8 of 8
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	suberin monomers biosynthesis	100	2 of 2
66794	folate polyglutamylation	100	1 of 1
66794	vitamin B1 metabolism	92.31	12 of 13
66794	pentose phosphate pathway	90.91	10 of 11
66794	myo-inositol biosynthesis	90	9 of 10
66794	gluconeogenesis	87.5	7 of 8
66794	tetrahydrofolate metabolism	85.71	12 of 14
66794	purine metabolism	84.04	79 of 94
66794	pyrimidine metabolism	82.22	37 of 45
66794	degradation of sugar alcohols	81.25	13 of 16
66794	glycogen metabolism	80	4 of 5
66794	flavin biosynthesis	80	12 of 15
66794	threonine metabolism	80	8 of 10
66794	glycine betaine biosynthesis	80	4 of 5
66794	vitamin B12 metabolism	79.41	27 of 34
66794	photosynthesis	78.57	11 of 14
66794	CO2 fixation in Crenarchaeota	77.78	7 of 9
66794	serine metabolism	77.78	7 of 9
66794	valine metabolism	77.78	7 of 9
66794	chorismate metabolism	77.78	7 of 9
66794	aspartate and asparagine metabolism	77.78	7 of 9
66794	glycolysis	76.47	13 of 17
66794	acetate fermentation	75	3 of 4
66794	butanoate fermentation	75	3 of 4
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	CMP-KDO biosynthesis	75	3 of 4
66794	glycogen biosynthesis	75	3 of 4
66794	ketogluconate metabolism	75	6 of 8
66794	isoleucine metabolism	75	6 of 8
66794	peptidoglycan biosynthesis	73.33	11 of 15
66794	NAD metabolism	72.22	13 of 18
66794	propanol degradation	71.43	5 of 7
66794	phosphatidylethanolamine bioynthesis	69.23	9 of 13
66794	phenylalanine metabolism	69.23	9 of 13
66794	alanine metabolism	68.97	20 of 29
66794	d-mannose degradation	66.67	6 of 9
66794	IAA biosynthesis	66.67	2 of 3
66794	molybdenum cofactor biosynthesis	66.67	6 of 9
66794	arginine metabolism	66.67	16 of 24
66794	octane oxidation	66.67	2 of 3
66794	methane metabolism	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	histidine metabolism	65.52	19 of 29
66794	heme metabolism	64.29	9 of 14
66794	glutamate and glutamine metabolism	64.29	18 of 28
66794	d-xylose degradation	63.64	7 of 11
66794	oxidative phosphorylation	61.54	56 of 91
66794	urea cycle	61.54	8 of 13
66794	lipid metabolism	61.29	19 of 31
66794	hydrogen production	60	3 of 5
66794	factor 420 biosynthesis	60	3 of 5
66794	cellulose degradation	60	3 of 5
66794	propionate fermentation	60	6 of 10
66794	glutathione metabolism	57.14	8 of 14
66794	citric acid cycle	57.14	8 of 14
66794	non-pathway related	55.26	21 of 38
66794	methionine metabolism	53.85	14 of 26
66794	sulfate reduction	53.85	7 of 13
66794	sulfopterin metabolism	50	2 of 4
66794	Entner Doudoroff pathway	50	5 of 10
66794	pantothenate biosynthesis	50	3 of 6
66794	toluene degradation	50	2 of 4
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	glycolate and glyoxylate degradation	50	3 of 6
66794	ribulose monophosphate pathway	50	1 of 2
66794	glycine metabolism	50	5 of 10
66794	biotin biosynthesis	50	2 of 4
66794	selenocysteine biosynthesis	50	3 of 6
66794	phenylmercury acetate degradation	50	1 of 2
66794	tryptophan metabolism	50	19 of 38
66794	cysteine metabolism	50	9 of 18
66794	degradation of pentoses	46.43	13 of 28
66794	leucine metabolism	46.15	6 of 13
66794	phenylpropanoid biosynthesis	46.15	6 of 13
66794	metabolism of disaccharids	45.45	5 of 11
66794	proline metabolism	45.45	5 of 11
66794	nitrate assimilation	44.44	4 of 9
66794	lysine metabolism	42.86	18 of 42
66794	reductive acetyl coenzyme A pathway	42.86	3 of 7
66794	ubiquinone biosynthesis	42.86	3 of 7
66794	tyrosine metabolism	42.86	6 of 14
66794	isoprenoid biosynthesis	42.31	11 of 26
66794	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
66794	arachidonate biosynthesis	40	2 of 5
66794	coenzyme M biosynthesis	40	4 of 10
66794	vitamin B6 metabolism	36.36	4 of 11
66794	polyamine pathway	34.78	8 of 23
66794	cyanate degradation	33.33	1 of 3
66794	arachidonic acid metabolism	33.33	6 of 18
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	lipid A biosynthesis	33.33	3 of 9
66794	enterobactin biosynthesis	33.33	1 of 3
66794	sphingosine metabolism	33.33	2 of 6
66794	1,4-dihydroxy-6-naphthoate biosynthesis	33.33	2 of 6
66794	androgen and estrogen metabolism	31.25	5 of 16
66794	4-hydroxyphenylacetate degradation	30	3 of 10
66794	benzoyl-CoA degradation	28.57	2 of 7
66794	degradation of hexoses	27.78	5 of 18
66794	ascorbate metabolism	27.27	6 of 22
66794	dTDPLrhamnose biosynthesis	25	2 of 8
66794	cyclohexanol degradation	25	1 of 4
66794	lactate fermentation	25	1 of 4
66794	carnitine metabolism	25	2 of 8
66794	4-hydroxymandelate degradation	22.22	2 of 9

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Wetland (Swamp)
#Condition	#Acidic	-

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
4870	acidic peat bog	East-central Germany, Fichtelgebirge near Bayreuth	Germany	DEU	Europe

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
4870	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 2675903229 annotated assembly for Clostridium uliginosum DSM 12992	scaffold	GCA_900112485	119641.3	2675903229	119641	62.71

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
4870	Clostridium uliginosum partial 16S rRNA gene, strain CK55	AJ276992	1437		119641

GC content

@ref	GC-content (mol%)	Method
4870	28	high performance liquid chromatography (HPLC)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Clostridium uliginosum DSM 12992
NCBI: GCA_900112485

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	yes	80.30	no
125439	motility	BacteriaNetⓘ	yes	81.90	no
125439	gram_stain	BacteriaNetⓘ	positive	84.30	no
125439	oxygen_tolerance	BacteriaNetⓘ	facultative anaerobe	97.60	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Clostridium uliginosum DSM 12992
NCBI: GCA_900112485.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	60.30	no
125438	anaerobic	anaerobicⓘ	yes	83.72	yes
125438	aerobic	aerobicⓘ	no	94.19	yes
125438	spore-forming	spore-formingⓘ	yes	72.93	no
125438	thermophilic	thermophileⓘ	no	92.70	yes
125438	flagellated	motile2+ⓘ	yes	76.25	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Evaluation of two fungal exopolysaccharides as potential biomaterials for wound healing applications.	Hamidi M, Okoro OV, Rashidi K, Salami MS, Mirzaei Seveiri R, Samadian H, Shavandi A.	World J Microbiol Biotechnol	10.1007/s11274-022-03459-2	2022
Enzymology	Identification of dehydrogenase, hydratase, and aldolase responsible for the propionyl residue removal in degradation of cholic acid C-17 side chain in Comamonas testosteroni TA441.	Horinouchi M.	Microbiol Spectr	10.1128/spectrum.00308-25	2025
	A two-stage metabolome refining pipeline for natural products discovery.	Zhang R, Wang B, Wang C, Huang K, Li Z, Yang J, Kuang J, Ren L, Wu M, Zhang K, Xie H, Liu Y, Wu M, Wu Y, Xu F.	Synth Syst Biotechnol	10.1016/j.synbio.2025.01.006	2025
Genetics	Draft Genome Sequence of the Oleaginous Yeast Apiotrichum porosum (syn. Trichosporon porosum) DSM 27194.	Gorte O, Aliyu H, Neumann A, Ochsenreither K.	J Genomics	10.7150/jgen.32210	2019
	First Insight into the Genome Sequence of Clostridium vincentii DSM 10228, Isolated from Sediment of the McMurdo Ice Shelf, Antarctica.	Poehlein A, Bolz S, Fischer B, Daniel R.	Genome Announc	10.1128/genomea.00334-18	2018
	Furaquinocins K and L: Novel Naphthoquinone-Based Meroterpenoids from Streptomyces sp. Je 1-369.	Tistechok S, Stierhof M, Myronovskyi M, Zapp J, Gromyko O, Luzhetskyy A.	Antibiotics (Basel)	10.3390/antibiotics11111587	2022
	Cyclic Tetrapeptides with Synergistic Antifungal Activity from the Fungus Aspergillus westerdijkiae Using LC-MS/MS-Based Molecular Networking.	Han J, Wang H, Zhang R, Dai H, Chen B, Wang T, Sun J, Wang W, Song F, Li E, Lyu Z, Liu H.	Antibiotics (Basel)	10.3390/antibiotics11020166	2022
Enzymology	Bioconversion of Phytosterols to 9-Hydroxy-3-Oxo-4,17-Pregadiene-20-Carboxylic Acid Methyl Ester by Enoyl-CoA Deficiency and Modifying Multiple Genes in Mycolicibacterium neoaurum.	Yuan C, Song S, He J, Zhang J, Liu X, Pena EL, Sun J, Shi J, Su Z, Zhang B.	Appl Environ Microbiol	10.1128/aem.01303-22	2022
	Exploring Verrucosidin Derivatives with Glucose-Uptake-Stimulatory Activity from Penicillium cellarum Using MS/MS-Based Molecular Networking.	Han J, Chen B, Zhang R, Zhang J, Dai H, Wang T, Sun J, Zhu G, Li W, Li E, Liu X, Yin W, Liu H.	J Fungi (Basel)	10.3390/jof8020143	2022
	Simultaneous Production of Multiple Antimicrobial Compounds by Bacillus velezensis ML122-2 Isolated From Assam Tea Leaf [Camellia sinensis var. assamica (J.W.Mast.) Kitam.].	Rungsirivanich P, Parlindungan E, O'Connor PM, Field D, Mahony J, Thongwai N, van Sinderen D.	Front Microbiol	10.3389/fmicb.2021.789362	2021
Genetics	Genomic insights into the lifestyles, functional capacities and oleagenicity of members of the fungal family Trichosporonaceae.	Aliyu H, Gorte O, de Maayer P, Neumann A, Ochsenreither K.	Sci Rep	10.1038/s41598-020-59672-2	2020
	Rapid physiological characterization of microorganisms by biosensor technique.	Riedel K, Kunze G.	Microbiol Res	10.1016/s0944-5013(97)80033-x	1997
Genetics	Identification of the Biosynthetic Gene Cluster of Thermoactinoamides and Discovery of New Congeners by Integrated Genome Mining and MS-Based Molecular Networking.	Della Sala G, Mangoni A, Costantino V, Teta R.	Front Chem	10.3389/fchem.2020.00397	2020
	Evaluation of Downstream Processing, Extraction, and Quantification Strategies for Single Cell Oil Produced by the Oleaginous Yeasts Saitozyma podzolica DSM 27192 and Apiotrichum porosum DSM 27194.	Gorte O, Hollenbach R, Papachristou I, Steinweg C, Silve A, Frey W, Syldatk C, Ochsenreither K.	Front Bioeng Biotechnol	10.3389/fbioe.2020.00355	2020
Genetics	Complete Genome Sequence of Clostridium estertheticum DSM 8809, a Microbe Identified in Spoiled Vacuum Packed Beef.	Yu Z, Gunn L, Brennan E, Reid R, Wall PG, Gaora PO, Hurley D, Bolton D, Fanning S.	Front Microbiol	10.3389/fmicb.2016.01764	2016
Enzymology	Quantification of fungal DNA by using fluorescence resonance energy transfer and the light cycler system.	Loeffler J, Henke N, Hebart H, Schmidt D, Hagmeyer L, Schumacher U, Einsele H.	J Clin Microbiol	10.1128/jcm.38.2.586-590.2000	2000
Phylogeny	Clostridium aquiflavi sp. nov., isolated from yellow water of Nongxiangxing baijiu in the Yibin region of China.	Sun S, Feng H, Liu R, Cheng J, Mu S, Liu Y, Gao Y, Yao S, Zhai L.	Int J Syst Evol Microbiol	10.1099/ijsem.0.006420	2024
Phylogeny	Blastococcus endophyticus sp. nov., an actinobacterium isolated from Camptotheca acuminata.	Zhu WY, Zhang JL, Qin YL, Xiong ZJ, Zhang DF, Klenk HP, Zhao LX, Xu LH, Li WJ.	Int J Syst Evol Microbiol	10.1099/ijs.0.049239-0	2013
Phylogeny	Gracilibacillus kekensis sp. nov., a moderate halophile isolated from Keke Salt Lake.	Gao M, Liu ZZ, Zhou YG, Liu HC, Ma YC, Wang L, Chen SF, Ji XC.	Int J Syst Evol Microbiol	10.1099/ijs.0.030858-0	2012
Enzymology	Micromonospora tulbaghiae sp. nov., isolated from the leaves of wild garlic, Tulbaghia violacea.	Kirby BM, Meyers PR.	Int J Syst Evol Microbiol	10.1099/ijs.0.013243-0	2010
Phylogeny	Clostridium uliginosum sp. nov., a novel acid-tolerant, anaerobic bacterium with connecting filaments.	Matthies C, Kuhner CH, Acker G, Drake HL	Int J Syst Evol Microbiol	10.1099/00207713-51-3-1119	2001

References

#4870	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 12992
#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 )

Rate our new design

Content

About us

Clostridium uliginosum (DSM 12992, ATCC BAA-53, CK55)

Name and taxonomic classification

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

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_900112485

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

Help

Social Media