Clostridium fervidum (DSM 5463, ATCC 43204, KCTC 15126)

Name: Clostridium fervidum (DSM 5463, ATCC 43204, KCTC 15126)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 2518

Type strain

Strain Designation Rt4-B1

Culture col. no. DSM 5463 ATCC 43204 KCTC 15126 Rt4-B1

NCBI tax ID(s) 1121261 29344

Special Collections DSMZ KCTC

History <- ATCC <- B.K.C. Patel, Rt4-B1 <- DSM <- ATCC <- BKC Patel, Rt4-B1

Links

Clostridium fervidum Rt4-B1 is an anaerobe, rod-shaped bacterium that was isolated from hot spring.

rod-shaped anaerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 41707

KCTC 15126,ATCC 43204,DSM 5463

@ref 20215

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

Domain Bacteria

Phylum Bacillota

Class Clostridia

Order Eubacteriales

Family Clostridiaceae

Genus Clostridium

Species Clostridium fervidum

Full scientific name Clostridium fervidum corrig. Patel et al. 1987

Synonyms (2)

Clostridium fervidus
Caloramator fervidus

Morphology

Cell morphology

@ref	Cell shape	Gram stain
67771	rod-shaped
67771		negative

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
2174	THERMOANAEROBACTER BROCKII MEDIUM (DSMZ Medium 144)		Medium recipe at MediaDive	Name: THERMOANAEROBACTER BROCKII MEDIUM (DSMZ Medium 144) Composition: Trypticase peptone 10.0 g/l D-Glucose 5.0 g/l Yeast extract 3.0 g/l K2HPO4 1.5 g/l Na2S x 9 H2O 1.0 g/l NH4Cl 0.9 g/l KH2PO4 0.75 g/l MgCl2 x 6 H2O 0.4 g/l Nitrilotriacetic acid 0.1152 g/l NaCl 0.009 g/l FeSO4 x 7 H2O 0.003 g/l FeCl2 x 4 H2O 0.0018 g/l CoCl2 x 6 H2O 0.00153 g/l MnCl2 x 4 H2O 0.0009 g/l CaCl2 x 2 H2O 0.0009 g/l ZnCl2 0.0009 g/l Sodium resazurin 0.0005 g/l NiCl2 x 6 H2O 0.00027 g/l Na2SeO3 x 5 H2O 0.00027 g/l CuCl2 0.00018 g/l H3BO3 9e-05 g/l Na2MoO4 x 2 H2O 9e-05 g/l Pyridoxine hydrochloride 5e-05 g/l p-Aminobenzoic acid 2.5e-05 g/l (DL)-alpha-Lipoic acid 2.5e-05 g/l Riboflavin 2.5e-05 g/l Calcium D-(+)-pantothenate 2.5e-05 g/l Thiamine HCl 2.5e-05 g/l Nicotinic acid 2.5e-05 g/l Biotin 1e-05 g/l Folic acid 1e-05 g/l Vitamin B12 5e-07 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
2174	positive	growth	65
67771	positive	growth	65

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
2174	anaerobe
67771	anaerobe
125438	anaerobe	92.373
125439	anaerobe	99.9

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	C4 and CAM-carbon fixation	100	8 of 8
66794	cardiolipin biosynthesis	100	7 of 7
66794	adipate degradation	100	2 of 2
66794	coenzyme A metabolism	100	4 of 4
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	L-lactaldehyde degradation	100	3 of 3
66794	suberin monomers biosynthesis	100	2 of 2
66794	folate polyglutamylation	100	1 of 1
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	chorismate metabolism	88.89	8 of 9
66794	gluconeogenesis	87.5	7 of 8
66794	palmitate biosynthesis	86.36	19 of 22
66794	photosynthesis	85.71	12 of 14
66794	peptidoglycan biosynthesis	80	12 of 15
66794	hydrogen production	80	4 of 5
66794	CO2 fixation in Crenarchaeota	77.78	7 of 9
66794	urea cycle	76.92	10 of 13
66794	vitamin B1 metabolism	76.92	10 of 13
66794	acetate fermentation	75	3 of 4
66794	butanoate fermentation	75	3 of 4
66794	ppGpp biosynthesis	75	3 of 4
66794	glycogen biosynthesis	75	3 of 4
66794	sulfopterin metabolism	75	3 of 4
66794	purine metabolism	74.47	70 of 94
66794	propanol degradation	71.43	5 of 7
66794	reductive acetyl coenzyme A pathway	71.43	5 of 7
66794	glycolysis	70.59	12 of 17
66794	threonine metabolism	70	7 of 10
66794	glutamate and glutamine metabolism	67.86	19 of 28
66794	NAD metabolism	66.67	12 of 18
66794	selenocysteine biosynthesis	66.67	4 of 6
66794	aspartate and asparagine metabolism	66.67	6 of 9
66794	octane oxidation	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	formaldehyde oxidation	66.67	2 of 3
66794	molybdenum cofactor biosynthesis	66.67	6 of 9
66794	pyrimidine metabolism	64.44	29 of 45
66794	tetrahydrofolate metabolism	64.29	9 of 14
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
66794	phenylalanine metabolism	61.54	8 of 13
66794	lipoate biosynthesis	60	3 of 5
66794	glycogen metabolism	60	3 of 5
66794	alanine metabolism	58.62	17 of 29
66794	lipid metabolism	58.06	18 of 31
66794	d-mannose degradation	55.56	5 of 9
66794	pentose phosphate pathway	54.55	6 of 11
66794	phosphatidylethanolamine bioynthesis	53.85	7 of 13
66794	glycolate and glyoxylate degradation	50	3 of 6
66794	dolichol and dolichyl phosphate biosynthesis	50	1 of 2
66794	CMP-KDO biosynthesis	50	2 of 4
66794	ethanol fermentation	50	1 of 2
66794	cis-vaccenate biosynthesis	50	1 of 2
66794	sphingosine metabolism	50	3 of 6
66794	isoleucine metabolism	50	4 of 8
66794	citric acid cycle	50	7 of 14
66794	ketogluconate metabolism	50	4 of 8
66794	phenylmercury acetate degradation	50	1 of 2
66794	oxidative phosphorylation	48.35	44 of 91
66794	histidine metabolism	48.28	14 of 29
66794	nitrate assimilation	44.44	4 of 9
66794	serine metabolism	44.44	4 of 9
66794	cysteine metabolism	44.44	8 of 18
66794	isoprenoid biosynthesis	42.31	11 of 26
66794	methionine metabolism	42.31	11 of 26
66794	tryptophan metabolism	42.11	16 of 38
66794	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
66794	cellulose degradation	40	2 of 5
66794	glycine metabolism	40	4 of 10
66794	metabolism of amino sugars and derivatives	40	2 of 5
66794	Entner Doudoroff pathway	40	4 of 10
66794	ethylmalonyl-CoA pathway	40	2 of 5
66794	coenzyme M biosynthesis	40	4 of 10
66794	starch degradation	40	4 of 10
66794	non-pathway related	39.47	15 of 38
66794	polyamine pathway	39.13	9 of 23
66794	lysine metabolism	38.1	16 of 42
66794	proline metabolism	36.36	4 of 11
66794	lipid A biosynthesis	33.33	3 of 9
66794	cyanate degradation	33.33	1 of 3
66794	degradation of hexoses	33.33	6 of 18
66794	IAA biosynthesis	33.33	1 of 3
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	valine metabolism	33.33	3 of 9
66794	pantothenate biosynthesis	33.33	2 of 6
66794	degradation of pentoses	32.14	9 of 28
66794	leucine metabolism	30.77	4 of 13
66794	phenylpropanoid biosynthesis	30.77	4 of 13
66794	sulfate reduction	30.77	4 of 13
66794	myo-inositol biosynthesis	30	3 of 10
66794	propionate fermentation	30	3 of 10
66794	arginine metabolism	29.17	7 of 24
66794	benzoyl-CoA degradation	28.57	2 of 7
66794	ubiquinone biosynthesis	28.57	2 of 7
66794	metabolism of disaccharids	27.27	3 of 11
66794	vitamin B6 metabolism	27.27	3 of 11
66794	ascorbate metabolism	27.27	6 of 22
66794	flavin biosynthesis	26.67	4 of 15
66794	biotin biosynthesis	25	1 of 4
66794	lactate fermentation	25	1 of 4
66794	cyclohexanol degradation	25	1 of 4
66794	toluene degradation	25	1 of 4
66794	phenol degradation	25	5 of 20
66794	methanogenesis from CO2	25	3 of 12
66794	tyrosine metabolism	21.43	3 of 14
66794	glutathione metabolism	21.43	3 of 14

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Thermal spring
#Condition	#Thermophilic (>45°C)	-

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
2174	hot spring	Kuiran Park	New Zealand	NZL	Australia and Oceania
67771	From hot spring	Kuiran Park	New Zealand	NZL	Australia and Oceania

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
2174	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 2599185232 annotated assembly for Caloramator fervidus DSM 5463	contig	GCA_900108045	29344.3	2599185232	29344	68.78

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
2174	Clostridium fervidus (ATCC 43204) 16S ribosomal RNA (16S rRNA) gene	L09187	1519		1121261
67771	Caloramator fervidus strain RT4. B1 16S ribosomal RNA, partial sequence	NR_025899	1519		29344

GC content

2174

GC-content (mol%)39.0

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Caloramator fervidus DSM 5463
NCBI: GCA_900108045

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	yes	80.20	no
125439	motility	BacteriaNetⓘ	yes	75.90	no
125439	gram_stain	BacteriaNetⓘ	variable	65.00	no
125439	oxygen_tolerance	BacteriaNetⓘ	anaerobe	99.90	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Caloramator fervidus strain DSM 5463
PATRIC: 29344.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	55.03	yes
125438	anaerobic	anaerobicⓘ	yes	92.37	yes
125438	spore-forming	spore-formingⓘ	yes	57.10	no
125438	aerobic	aerobicⓘ	no	98.25	yes
125438	thermophilic	thermophileⓘ	yes	67.19	yes
125438	flagellated	motile2+ⓘ	yes	67.99	no

Literature

References

#2174	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 5463
#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 )
#67771	Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;
#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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