Desulfoscipio geothermicus (DSM 3669, NBRC 112753, BSD)

Name: Desulfoscipio geothermicus (DSM 3669, NBRC 112753, BSD)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 11790

Type strain

Strain Designation BSD

Culture col. no. DSM 3669 NBRC 112753 BSD

NCBI tax ID(s) 1121426 39060

Special Collections DSMZ

History <- S. Daumas, Université de Provence, Marseille, France; BSD <- S. Daumas {1985}

Links

Desulfoscipio geothermicus BSD is an anaerobe bacterium that was isolated from anoxic geothermal ground-water.

anaerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 126041

NBRC 112753,DSM 3669,ATCC 49053,VTT E-061476

@ref 20215

Last LPSN update 2026-02-09 11:20:39

Domain Bacteria

Phylum Bacillota

Class Clostridia

Order Eubacteriales

Family Peptococcaceae

Genus Desulfoscipio

Species Desulfoscipio geothermicus

Full scientific name Desulfoscipio geothermicus (Daumas et al. 1990) Watanabe et al. 2021

Synonyms (2)

Desulfallas geothermicus
Desulfotomaculum geothermicum

Morphology

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
1450	DESULFOBACTER SP. MEDIUM (LACTATE) (DSMZ Medium 195c)		Medium recipe at MediaDive	Name: DESULFOBACTER SP. MEDIUM (LACTATE) (DSMZ Medium 195c) Composition: NaCl 20.9372 g/l Na2SO4 2.99103 g/l MgCl2 x 6 H2O 2.99103 g/l Na-L-lactate 2.49252 g/l Na2CO3 1.49551 g/l KCl 0.498504 g/l Na2S x 9 H2O 0.398804 g/l NH4Cl 0.299103 g/l KH2PO4 0.199402 g/l CaCl2 x 2 H2O 0.149551 g/l HCl 0.00249252 g/l FeCl2 x 4 H2O 0.00149551 g/l NaOH 0.000498504 g/l Sodium resazurin 0.000498504 g/l CoCl2 x 6 H2O 0.000189432 g/l Pyridoxine hydrochloride 9.97009e-05 g/l MnCl2 x 4 H2O 9.97009e-05 g/l ZnCl2 6.97906e-05 g/l p-Aminobenzoic acid 4.98504e-05 g/l (DL)-alpha-Lipoic acid 4.98504e-05 g/l Thiamine HCl 4.98504e-05 g/l Calcium D-(+)-pantothenate 4.98504e-05 g/l Riboflavin 4.98504e-05 g/l Nicotinic acid 4.98504e-05 g/l Na2MoO4 x 2 H2O 3.58923e-05 g/l NiCl2 x 6 H2O 2.39282e-05 g/l Biotin 1.99402e-05 g/l Folic acid 1.99402e-05 g/l H3BO3 5.98205e-06 g/l Na2WO4 x 2 H2O 3.98804e-06 g/l Na2SeO3 x 5 H2O 2.99103e-06 g/l CuCl2 x 2 H2O 1.99402e-06 g/l Vitamin B12 9.97009e-07 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
1450	positive	growth	50

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
1450	anaerobe
125438	anaerobe	92.41
125439	anaerobe	98.8

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	ppGpp biosynthesis	100	4 of 4
66794	reductive acetyl coenzyme A pathway	100	7 of 7
66794	methylglyoxal degradation	100	5 of 5
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	adipate degradation	100	2 of 2
66794	hydrogen production	100	5 of 5
66794	propanol degradation	100	7 of 7
66794	L-lactaldehyde degradation	100	3 of 3
66794	palmitate biosynthesis	100	22 of 22
66794	biotin biosynthesis	100	4 of 4
66794	coenzyme A metabolism	100	4 of 4
66794	denitrification	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	folate polyglutamylation	100	1 of 1
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	suberin monomers biosynthesis	100	2 of 2
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	sulfopterin metabolism	100	4 of 4
66794	C4 and CAM-carbon fixation	100	8 of 8
66794	aspartate and asparagine metabolism	88.89	8 of 9
66794	CO2 fixation in Crenarchaeota	88.89	8 of 9
66794	gluconeogenesis	87.5	7 of 8
66794	ubiquinone biosynthesis	85.71	6 of 7
66794	leucine metabolism	84.62	11 of 13
66794	selenocysteine biosynthesis	83.33	5 of 6
66794	1,4-dihydroxy-6-naphthoate biosynthesis	83.33	5 of 6
66794	glutamate and glutamine metabolism	82.14	23 of 28
66794	flavin biosynthesis	80	12 of 15
66794	threonine metabolism	80	8 of 10
66794	factor 420 biosynthesis	80	4 of 5
66794	starch degradation	80	8 of 10
66794	phenylacetate degradation (aerobic)	80	4 of 5
66794	ethylmalonyl-CoA pathway	80	4 of 5
66794	cellulose degradation	80	4 of 5
66794	citric acid cycle	78.57	11 of 14
66794	photosynthesis	78.57	11 of 14
66794	valine metabolism	77.78	7 of 9
66794	phenylalanine metabolism	76.92	10 of 13
66794	glycolysis	76.47	13 of 17
66794	alanine metabolism	75.86	22 of 29
66794	glycogen biosynthesis	75	3 of 4
66794	vitamin B12 metabolism	73.53	25 of 34
66794	peptidoglycan biosynthesis	73.33	11 of 15
66794	pentose phosphate pathway	72.73	8 of 11
66794	NAD metabolism	72.22	13 of 18
66794	tetrahydrofolate metabolism	71.43	10 of 14
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	propionate fermentation	70	7 of 10
66794	vitamin B1 metabolism	69.23	9 of 13
66794	glycolate and glyoxylate degradation	66.67	4 of 6
66794	octane oxidation	66.67	2 of 3
66794	formaldehyde oxidation	66.67	2 of 3
66794	serine metabolism	66.67	6 of 9
66794	chorismate metabolism	66.67	6 of 9
66794	acetoin degradation	66.67	2 of 3
66794	d-mannose degradation	66.67	6 of 9
66794	molybdenum cofactor biosynthesis	66.67	6 of 9
66794	heme metabolism	64.29	9 of 14
66794	purine metabolism	63.83	60 of 94
66794	isoleucine metabolism	62.5	5 of 8
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
66794	urea cycle	61.54	8 of 13
66794	glycogen metabolism	60	3 of 5
66794	coenzyme M biosynthesis	60	6 of 10
66794	lipoate biosynthesis	60	3 of 5
66794	4-hydroxyphenylacetate degradation	60	6 of 10
66794	pyrimidine metabolism	60	27 of 45
66794	histidine metabolism	58.62	17 of 29
66794	tryptophan metabolism	57.89	22 of 38
66794	non-pathway related	57.89	22 of 38
66794	isoprenoid biosynthesis	57.69	15 of 26
66794	oxidative phosphorylation	54.95	50 of 91
66794	arginine metabolism	54.17	13 of 24
66794	methionine metabolism	53.85	14 of 26
66794	sulfate reduction	53.85	7 of 13
66794	dTDPLrhamnose biosynthesis	50	4 of 8
66794	ethanol fermentation	50	1 of 2
66794	pantothenate biosynthesis	50	3 of 6
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	acetate fermentation	50	2 of 4
66794	ketogluconate metabolism	50	4 of 8
66794	degradation of sugar alcohols	50	8 of 16
66794	butanoate fermentation	50	2 of 4
66794	degradation of aromatic, nitrogen containing compounds	50	6 of 12
66794	toluene degradation	50	2 of 4
66794	glycine metabolism	50	5 of 10
66794	dolichol and dolichyl phosphate biosynthesis	50	1 of 2
66794	lipid metabolism	48.39	15 of 31
66794	proline metabolism	45.45	5 of 11
66794	nitrate assimilation	44.44	4 of 9
66794	cysteine metabolism	44.44	8 of 18
66794	polyamine pathway	43.48	10 of 23
66794	lysine metabolism	42.86	18 of 42
66794	benzoyl-CoA degradation	42.86	3 of 7
66794	Entner Doudoroff pathway	40	4 of 10
66794	creatinine degradation	40	2 of 5
66794	arachidonate biosynthesis	40	2 of 5
66794	phenol degradation	40	8 of 20
66794	metabolism of amino sugars and derivatives	40	2 of 5
66794	degradation of hexoses	38.89	7 of 18
66794	phosphatidylethanolamine bioynthesis	38.46	5 of 13
66794	androgen and estrogen metabolism	37.5	6 of 16
66794	metabolism of disaccharids	36.36	4 of 11
66794	tyrosine metabolism	35.71	5 of 14
66794	IAA biosynthesis	33.33	1 of 3
66794	methane metabolism	33.33	1 of 3
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	cyanate degradation	33.33	1 of 3
66794	sulfoquinovose degradation	33.33	1 of 3
66794	lipid A biosynthesis	33.33	3 of 9
66794	sphingosine metabolism	33.33	2 of 6
66794	degradation of pentoses	32.14	9 of 28
66794	ascorbate metabolism	31.82	7 of 22
66794	phenylpropanoid biosynthesis	30.77	4 of 13
66794	bile acid biosynthesis, neutral pathway	29.41	5 of 17
66794	glutathione metabolism	28.57	4 of 14
66794	d-xylose degradation	27.27	3 of 11
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	3-phenylpropionate degradation	26.67	4 of 15
66794	cyclohexanol degradation	25	1 of 4
66794	lactate fermentation	25	1 of 4
66794	CMP-KDO biosynthesis	25	1 of 4
66794	carnitine metabolism	25	2 of 8
66794	methanogenesis from CO2	25	3 of 12

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Groundwater
#Condition	#Anoxic (anaerobic)	-

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
1450	anoxic geothermal ground-water	Paris Basin	France	FRA	Europe

Taxonmaps

69479

Global distribution of 16S sequence Y11567 (>99% sequence identity) for Desulfallas geothermicus subclade from Microbeatlas

Aquatic Samples	170
Soil Samples	15
Animal Samples	43
Plant Samples
Total Samples	228

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
1450	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 2602042027 annotated assembly for Desulfoscipio geothermicus DSM 3669	scaffold	GCA_900115975	39060.4	2602042027	1121426	59.55

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	D.geothermicum 16S rRNA gene	X80789	1497	39060
20218	D.geothermicum 16S rRNA gene	Y11567	1567	39060
1450	Desulfotomaculum geothermicum 16S rRNA gene, strain DSM 3669	AJ294428	1468	1121426

GC content

@ref	GC-content (mol%)	Method
1450	49.9	sequence analysis

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Desulfoscipio geothermicus DSM 3669
NCBI: GCA_900115975

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	yes	73.80	no
125439	motility	BacteriaNetⓘ	yes	54.30	no
125439	gram_stain	BacteriaNetⓘ	variable	72.80	no
125439	oxygen_tolerance	BacteriaNetⓘ	anaerobe	98.80	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Desulfoscipio geothermicus DSM 3669 DSM 3669
NCBI: GCA_900115975.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	56.28	no
125438	anaerobic	anaerobicⓘ	yes	92.41	yes
125438	aerobic	aerobicⓘ	no	94.18	yes
125438	spore-forming	spore-formingⓘ	yes	81.50	no
125438	thermophilic	thermophileⓘ	yes	51.15	yes
125438	flagellated	motile2+ⓘ	yes	70.36	no

Literature

Title	Authors	Journal	DOI	Year
Discovery of a New Class of Aminoacyl Radical Enzymes Expands Nature's Known Radical Chemistry.	Fu B, Yang H, Kountz DJ, Lundahl MN, Beller HR, Broderick WE, Broderick JB, Hoffman BH, Balskus EP.	J Am Chem Soc	10.1021/jacs.4c10348	2024

References

#1450	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 3669
#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 )
#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 .
#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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Desulfoscipio geothermicus (DSM 3669, NBRC 112753, BSD)

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

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_900115975

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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