Desulfoscipio gibsoniae (DSM 7213, NBRC 112754, Groll)

Name: Desulfoscipio gibsoniae (DSM 7213, NBRC 112754, Groll)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 11825

Type strain

Strain Designation Groll

Culture col. no. DSM 7213 NBRC 112754 Groll

NCBI tax ID(s) 767817 102134

Special Collections DSMZ

History <- K.-H. Blotevogel, Univ. Oldenburg, Germany; Groll <- J. Küver, Max-Planck-Inst. Marine Microbiology, Bremen, Germany {1991}

Links

Desulfoscipio gibsoniae Groll is an anaerobe bacterium that was isolated from freshwater mud.

anaerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 48385

NBRC 112754,DSM 7213

@ref 20215

Last LPSN update 2026-02-09 11:20:40

Domain Bacteria

Phylum Bacillota

Class Clostridia

Order Eubacteriales

Family Peptococcaceae

Genus Desulfoscipio

Species Desulfoscipio gibsoniae

Full scientific name Desulfoscipio gibsoniae (Kuever et al. 1999) Watanabe et al. 2021

Synonyms (2)

Desulfotomaculum gibsoniae
Desulfallas gibsoniae

Morphology

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
3053	DESULFOFARCIMEN MEDIUM (DSMZ Medium 124)		Medium recipe at MediaDive	Name: DESULFOFARCIMEN MEDIUM (DSMZ Medium 124; with strain-specific modifications) Composition: NaHCO3 4.48654 g/l Na2SO4 2.83151 g/l NaCl 1.1665 g/l Yeast extract 0.997009 g/l Na-benzoate 0.598205 g/l Na2S x 9 H2O 0.398804 g/l MgCl2 x 6 H2O 0.398804 g/l KCl 0.299103 g/l NH4Cl 0.269192 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 Sodium resazurin 0.000498504 g/l NaOH 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 Calcium D-(+)-pantothenate 4.98504e-05 g/l p-Aminobenzoic acid 4.98504e-05 g/l Nicotinic acid 4.98504e-05 g/l Riboflavin 4.98504e-05 g/l Thiamine HCl 4.98504e-05 g/l (DL)-alpha-Lipoic 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)
3053	positive	growth	35

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
3053	anaerobe
125439	anaerobe	93.1

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	C4 and CAM-carbon fixation	100	8 of 8
66794	denitrification	100	2 of 2
66794	adipate degradation	100	2 of 2
66794	biotin biosynthesis	100	4 of 4
66794	L-lactaldehyde degradation	100	3 of 3
66794	coenzyme A metabolism	100	4 of 4
66794	formaldehyde oxidation	100	3 of 3
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	reductive acetyl coenzyme A pathway	100	7 of 7
66794	cardiolipin biosynthesis	100	7 of 7
66794	hydrogen production	100	5 of 5
66794	palmitate biosynthesis	100	22 of 22
66794	acetate fermentation	100	4 of 4
66794	ppGpp biosynthesis	100	4 of 4
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	toluene degradation	100	4 of 4
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	vitamin B1 metabolism	92.31	12 of 13
66794	propionate fermentation	90	9 of 10
66794	aspartate and asparagine metabolism	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	vitamin B12 metabolism	88.24	30 of 34
66794	gluconeogenesis	87.5	7 of 8
66794	isoleucine metabolism	87.5	7 of 8
66794	alanine metabolism	86.21	25 of 29
66794	glutamate and glutamine metabolism	85.71	24 of 28
66794	propanol degradation	85.71	6 of 7
66794	ubiquinone biosynthesis	85.71	6 of 7
66794	benzoyl-CoA degradation	85.71	6 of 7
66794	leucine metabolism	84.62	11 of 13
66794	NAD metabolism	83.33	15 of 18
66794	1,4-dihydroxy-6-naphthoate biosynthesis	83.33	5 of 6
66794	peptidoglycan biosynthesis	80	12 of 15
66794	threonine metabolism	80	8 of 10
66794	cellulose degradation	80	4 of 5
66794	glycine betaine biosynthesis	80	4 of 5
66794	phenylacetate degradation (aerobic)	80	4 of 5
66794	methylglyoxal degradation	80	4 of 5
66794	citric acid cycle	78.57	11 of 14
66794	photosynthesis	78.57	11 of 14
66794	serine metabolism	77.78	7 of 9
66794	pyrimidine metabolism	77.78	35 of 45
66794	valine metabolism	77.78	7 of 9
66794	CO2 fixation in Crenarchaeota	77.78	7 of 9
66794	molybdenum cofactor biosynthesis	77.78	7 of 9
66794	phenylalanine metabolism	76.92	10 of 13
66794	sulfopterin metabolism	75	3 of 4
66794	glycogen biosynthesis	75	3 of 4
66794	flavin biosynthesis	73.33	11 of 15
66794	pentose phosphate pathway	72.73	8 of 11
66794	purine metabolism	71.28	67 of 94
66794	glycolysis	70.59	12 of 17
66794	starch degradation	70	7 of 10
66794	coenzyme M biosynthesis	70	7 of 10
66794	oxidative phosphorylation	69.23	63 of 91
66794	IAA biosynthesis	66.67	2 of 3
66794	selenocysteine biosynthesis	66.67	4 of 6
66794	octane oxidation	66.67	2 of 3
66794	d-mannose degradation	66.67	6 of 9
66794	acetoin degradation	66.67	2 of 3
66794	glycolate and glyoxylate degradation	66.67	4 of 6
66794	nitrate assimilation	66.67	6 of 9
66794	methionine metabolism	65.38	17 of 26
66794	heme metabolism	64.29	9 of 14
66794	tetrahydrofolate metabolism	64.29	9 of 14
66794	proline metabolism	63.64	7 of 11
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
66794	histidine metabolism	62.07	18 of 29
66794	isoprenoid biosynthesis	61.54	16 of 26
66794	sulfate reduction	61.54	8 of 13
66794	lipid metabolism	61.29	19 of 31
66794	glycogen metabolism	60	3 of 5
66794	factor 420 biosynthesis	60	3 of 5
66794	lipoate biosynthesis	60	3 of 5
66794	degradation of aromatic, nitrogen containing compounds	58.33	7 of 12
66794	non-pathway related	57.89	22 of 38
66794	tryptophan metabolism	57.89	22 of 38
66794	arginine metabolism	54.17	13 of 24
66794	lactate fermentation	50	2 of 4
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	lysine metabolism	50	21 of 42
66794	butanoate fermentation	50	2 of 4
66794	glutathione metabolism	50	7 of 14
66794	phenol degradation	50	10 of 20
66794	ketogluconate metabolism	50	4 of 8
66794	vitamin E metabolism	50	2 of 4
66794	ethanol fermentation	50	1 of 2
66794	glycine metabolism	50	5 of 10
66794	cysteine metabolism	50	9 of 18
66794	degradation of sugar alcohols	50	8 of 16
66794	urea cycle	46.15	6 of 13
66794	degradation of hexoses	44.44	8 of 18
66794	androgen and estrogen metabolism	43.75	7 of 16
66794	tyrosine metabolism	42.86	6 of 14
66794	Entner Doudoroff pathway	40	4 of 10
66794	myo-inositol biosynthesis	40	4 of 10
66794	ethylmalonyl-CoA pathway	40	2 of 5
66794	arachidonate biosynthesis	40	2 of 5
66794	vitamin K metabolism	40	2 of 5
66794	polyamine pathway	39.13	9 of 23
66794	dTDPLrhamnose biosynthesis	37.5	3 of 8
66794	vitamin B6 metabolism	36.36	4 of 11
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	methane metabolism	33.33	1 of 3
66794	cyanate degradation	33.33	1 of 3
66794	pantothenate biosynthesis	33.33	2 of 6
66794	lipid A biosynthesis	33.33	3 of 9
66794	enterobactin biosynthesis	33.33	1 of 3
66794	degradation of pentoses	32.14	9 of 28
66794	phosphatidylethanolamine bioynthesis	30.77	4 of 13
66794	4-hydroxyphenylacetate degradation	30	3 of 10
66794	bile acid biosynthesis, neutral pathway	29.41	5 of 17
66794	d-xylose degradation	27.27	3 of 11
66794	cholesterol biosynthesis	27.27	3 of 11
66794	metabolism of disaccharids	27.27	3 of 11
66794	3-phenylpropionate degradation	26.67	4 of 15
66794	CMP-KDO biosynthesis	25	1 of 4
66794	carnitine metabolism	25	2 of 8
66794	cyclohexanol degradation	25	1 of 4
66794	methanogenesis from CO2	25	3 of 12
66794	ascorbate metabolism	22.73	5 of 22
66794	4-hydroxymandelate degradation	22.22	2 of 9

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Freshwater
#Environmental	#Terrestrial	#Mud (Sludge)

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
3053	freshwater mud	Bremen	Germany	DEU	Europe

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
3053	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	ASM23371v3 assembly for Desulfoscipio gibsoniae DSM 7213	complete	GCA_000233715	767817.3	2508501002	767817	95.42

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
20218	Desulfotomaculum sp. 16S rRNA gene, DSM 7213	Y11576	1450		41211
3053	Desulfotomaculum sp. DSM 7213 16S rRNA gene, strain DSM 7213, clone 14	AJ294433	1485		767817

GC content

3053

GC-content (mol%)42.1

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Desulfallas gibsoniae Groll, DSM 7213
IMG: 2508501002

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	yes	70.00	no
125439	motility	BacteriaNetⓘ	yes	60.10	no
125439	gram_stain	BacteriaNetⓘ	variable	63.80	no
125439	oxygen_tolerance	BacteriaNetⓘ	anaerobe	93.10	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Desulfoscipio gibsoniae DSM 7213 DSM 7213
NCBI: GCA_000233715.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	56.84	no
125438	anaerobic	anaerobicⓘ	yes	83.57	no
125438	aerobic	aerobicⓘ	no	86.60	no
125438	spore-forming	spore-formingⓘ	yes	80.52	no
125438	thermophilic	thermophileⓘ	no	73.36	yes
125438	flagellated	motile2+ⓘ	yes	68.86	no

Literature

Title	Authors	Journal	DOI	Year
The hindgut microbiota of coconut rhinoceros beetles (Oryctes rhinoceros) in relation to their geographical populations.	Han C-J, Huang J-P, Chiang M-R, Jean OSM, Nand N, Etebari K, Shelomi M.	Appl Environ Microbiol	10.1128/aem.00987-24	2024

References

#3053	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 7213
#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 )
#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 gibsoniae (DSM 7213, NBRC 112754, Groll)

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_000233715

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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