Clostridium fimetarium (DSM 9179, CIP 105360, Z-2189)

Name: Clostridium fimetarium (DSM 9179, CIP 105360, Z-2189)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 2788

Type strain

Strain Designation Z-2189

Culture col. no. DSM 9179 CIP 105360 Z-2189

NCBI tax ID(s) 1121311 99656

Special Collections DSMZ CIP

History <- O. R. Kotsyurbenko, Z-2189 CIP <- 1997, DSM <- O.R. Kotsyurbenko: strain Z-2189

Links

Clostridium fimetarium Z-2189 is an anaerobe, Gram-positive, rod-shaped bacterium that was isolated from cattle manure.

Gram-positive rod-shaped anaerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 48590

DSM 9179,CIP 105360

@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 fimetarium

Full scientific name Clostridium fimetarium Kotsyurbenko et al. 1997

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Motility
119350	positive	rod-shaped

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
3505	CLOSTRIDIUM (GV) MEDIUM (DSMZ Medium 500)	Medium recipe at MediaDive	Name: CLOSTRIDIUM (GV) MEDIUM (DSMZ Medium 500) Composition: D-Glucose 4.97512 g/l NaHCO3 2.98507 g/l NaCl 2.23881 g/l Yeast extract 0.995025 g/l NH4Cl 0.497512 g/l MgSO4 x 7 H2O 0.497512 g/l K2HPO4 0.348259 g/l Na2S x 9 H2O 0.298507 g/l L-Cysteine HCl x H2O 0.298507 g/l CaCl2 x 2 H2O 0.248756 g/l KH2PO4 0.228856 g/l HCl 0.00248756 g/l FeSO4 x 7 H2O 0.00199005 g/l FeCl2 x 4 H2O 0.00149254 g/l NaOH 0.000497512 g/l Sodium resazurin 0.000497512 g/l CoCl2 x 6 H2O 0.000189055 g/l MnCl2 x 4 H2O 9.95025e-05 g/l Pyridoxine hydrochloride 9.95025e-05 g/l ZnCl2 6.96517e-05 g/l p-Aminobenzoic acid 4.97512e-05 g/l (DL)-alpha-Lipoic acid 4.97512e-05 g/l Calcium D-(+)-pantothenate 4.97512e-05 g/l Nicotinic acid 4.97512e-05 g/l Riboflavin 4.97512e-05 g/l Thiamine HCl 4.97512e-05 g/l Na2MoO4 x 2 H2O 3.58209e-05 g/l NiCl2 x 6 H2O 2.38806e-05 g/l Folic acid 1.99005e-05 g/l Biotin 1.99005e-05 g/l H3BO3 5.97015e-06 g/l Na2WO4 x 2 H2O 3.9801e-06 g/l Na2SeO3 x 5 H2O 2.98507e-06 g/l CuCl2 x 2 H2O 1.99005e-06 g/l Vitamin B12 9.95025e-07 g/l Distilled water
36600	MEDIUM 424 - for Clostridium fimetarium		Sodium hydrogen carbonate (3.000 g);Distilled water make up to (990.000 ml);Sodium chloride (2.250 g);Iron (II) sulphate heptahydrate (2.000 g);Magnesium sulphate heptahydrate (0.500 g);Calcium chloride dihydrate (0.250 g);Yeast extract (1.000 g);Potassiu
119350	CIP Medium 424	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
3505	positive	growth	20
36600	positive	growth	20

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
3505	anaerobe
125439	anaerobe	98

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	cardiolipin biosynthesis	100	7 of 7
66794	coenzyme A metabolism	100	4 of 4
66794	threonine metabolism	100	10 of 10
66794	C4 and CAM-carbon fixation	100	8 of 8
66794	gluconeogenesis	100	8 of 8
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	L-lactaldehyde degradation	100	3 of 3
66794	suberin monomers biosynthesis	100	2 of 2
66794	methylglyoxal degradation	100	5 of 5
66794	ppGpp biosynthesis	100	4 of 4
66794	palmitate biosynthesis	100	22 of 22
66794	folate polyglutamylation	100	1 of 1
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	vitamin B1 metabolism	92.31	12 of 13
66794	starch degradation	90	9 of 10
66794	serine 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	NAD metabolism	88.89	16 of 18
66794	glycolysis	88.24	15 of 17
66794	pyrimidine metabolism	86.67	39 of 45
66794	propanol degradation	85.71	6 of 7
66794	phenylalanine metabolism	84.62	11 of 13
66794	pentose phosphate pathway	81.82	9 of 11
66794	Entner Doudoroff pathway	80	8 of 10
66794	hydrogen production	80	4 of 5
66794	peptidoglycan biosynthesis	80	12 of 15
66794	cellulose degradation	80	4 of 5
66794	flavin biosynthesis	80	12 of 15
66794	glycine betaine biosynthesis	80	4 of 5
66794	metabolism of amino sugars and derivatives	80	4 of 5
66794	glutamate and glutamine metabolism	78.57	22 of 28
66794	valine metabolism	77.78	7 of 9
66794	d-mannose degradation	77.78	7 of 9
66794	molybdenum cofactor biosynthesis	77.78	7 of 9
66794	purine metabolism	76.6	72 of 94
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	vitamin E metabolism	75	3 of 4
66794	acetate fermentation	75	3 of 4
66794	glycogen biosynthesis	75	3 of 4
66794	sulfopterin metabolism	75	3 of 4
66794	ketogluconate metabolism	75	6 of 8
66794	butanoate fermentation	75	3 of 4
66794	tetrahydrofolate metabolism	71.43	10 of 14
66794	photosynthesis	71.43	10 of 14
66794	reductive acetyl coenzyme A pathway	71.43	5 of 7
66794	degradation of sugar alcohols	68.75	11 of 16
66794	formaldehyde oxidation	66.67	2 of 3
66794	glycolate and glyoxylate degradation	66.67	4 of 6
66794	octane oxidation	66.67	2 of 3
66794	methane metabolism	66.67	2 of 3
66794	selenocysteine biosynthesis	66.67	4 of 6
66794	enterobactin biosynthesis	66.67	2 of 3
66794	cyanate degradation	66.67	2 of 3
66794	CO2 fixation in Crenarchaeota	66.67	6 of 9
66794	acetoin degradation	66.67	2 of 3
66794	methionine metabolism	65.38	17 of 26
66794	heme metabolism	64.29	9 of 14
66794	degradation of sugar acids	64	16 of 25
66794	oxidative phosphorylation	63.74	58 of 91
66794	d-xylose degradation	63.64	7 of 11
66794	isoleucine metabolism	62.5	5 of 8
66794	alanine metabolism	62.07	18 of 29
66794	histidine metabolism	62.07	18 of 29
66794	lysine metabolism	61.9	26 of 42
66794	sulfate reduction	61.54	8 of 13
66794	leucine metabolism	61.54	8 of 13
66794	glycogen metabolism	60	3 of 5
66794	tryptophan metabolism	57.89	22 of 38
66794	citric acid cycle	57.14	8 of 14
66794	polyamine pathway	56.52	13 of 23
66794	cysteine metabolism	55.56	10 of 18
66794	proline metabolism	54.55	6 of 11
66794	non-pathway related	52.63	20 of 38
66794	lipid metabolism	51.61	16 of 31
66794	dTDPLrhamnose biosynthesis	50	4 of 8
66794	pantothenate biosynthesis	50	3 of 6
66794	adipate degradation	50	1 of 2
66794	ethanol fermentation	50	1 of 2
66794	ribulose monophosphate pathway	50	1 of 2
66794	degradation of hexoses	50	9 of 18
66794	degradation of aromatic, nitrogen containing compounds	50	6 of 12
66794	urea cycle	46.15	6 of 13
66794	vitamin B6 metabolism	45.45	5 of 11
66794	ascorbate metabolism	45.45	10 of 22
66794	metabolism of disaccharids	45.45	5 of 11
66794	nitrate assimilation	44.44	4 of 9
66794	ubiquinone biosynthesis	42.86	3 of 7
66794	arginine metabolism	41.67	10 of 24
66794	propionate fermentation	40	4 of 10
66794	factor 420 biosynthesis	40	2 of 5
66794	myo-inositol biosynthesis	40	4 of 10
66794	arachidonate biosynthesis	40	2 of 5
66794	glycine metabolism	40	4 of 10
66794	degradation of pentoses	39.29	11 of 28
66794	isoprenoid biosynthesis	38.46	10 of 26
66794	phenylpropanoid biosynthesis	38.46	5 of 13
66794	androgen and estrogen metabolism	37.5	6 of 16
66794	phenol degradation	35	7 of 20
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	IAA biosynthesis	33.33	1 of 3
66794	lipid A biosynthesis	33.33	3 of 9
66794	phosphatidylethanolamine bioynthesis	30.77	4 of 13
66794	coenzyme M biosynthesis	30	3 of 10
66794	aclacinomycin biosynthesis	28.57	2 of 7
66794	tyrosine metabolism	28.57	4 of 14
66794	glutathione metabolism	28.57	4 of 14
66794	arachidonic acid metabolism	27.78	5 of 18
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	methanogenesis from CO2	25	3 of 12
66794	lactate fermentation	25	1 of 4
66794	cyclohexanol degradation	25	1 of 4
66794	CMP-KDO biosynthesis	25	1 of 4
66794	toluene degradation	25	1 of 4
66794	biotin biosynthesis	25	1 of 4
66794	4-hydroxymandelate degradation	22.22	2 of 9

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
3505	cattle manure	Russia	RUS
119350	Cattle manure	Russian Federation	RUS	Europe

Taxonmaps

69479

Global distribution of 16S sequence AF126687 (>99% sequence identity) for [Clostridium] fimetarium subclade from Microbeatlas

Aquatic Samples	727
Soil Samples	643
Animal Samples	2428
Plant Samples	79
Total Samples	3877

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
3505	1	Risk group (German classification) According to TRBA 466
119350	2	Risk group (French 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 2675903166 annotated assembly for [Clostridium] fimetarium DSM 9179	contig	GCA_900111235	99656.3	2675903166	99656	67.02

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
3505	Clostridium fimetarium 16S ribosomal RNA gene, partial sequence	AF126687	1497		99656

GC content

@ref	GC-content (mol%)	Method
3505	35.6	thermal denaturation, midpoint method (Tm)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: [Clostridium] fimetarium DSM 9179
NCBI: GCA_900111235

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	yes	86.80	no
125439	motility	BacteriaNetⓘ	yes	78.00	no
125439	gram_stain	BacteriaNetⓘ	positive	70.60	no
125439	oxygen_tolerance	BacteriaNetⓘ	anaerobe	98.00	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: [Clostridium] fimetarium strain DSM 9179
PATRIC: 99656.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	66.80	no
125438	anaerobic	anaerobicⓘ	yes	89.93	yes
125438	aerobic	aerobicⓘ	no	93.48	yes
125438	spore-forming	spore-formingⓘ	yes	61.52	no
125438	thermophilic	thermophileⓘ	no	91.69	yes
125438	flagellated	motile2+ⓘ	yes	75.08	no

Literature

References

#3505	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 9179
#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 )
#36600	; Curators of the CIP;
#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 )
#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 .
#119350	Collection of Institut Pasteur ; Curators of the CIP; CIP 105360
#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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