Name: Geosporobacter subterraneus VNs68
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 2867

Type strain:

Species: Geosporobacter subterraneus

Strain Designation: VNs68

Culture col. no.: DSM 17957, JCM 14037, CIP 109751

Strain history: M.-L. Fardeau VNs68.

NCBI tax ID(s): 1121919 (strain), 390806 (species)

SI-ID 293890

DSM 17957, JCM 14037, CIP 109751

Section

Geosporobacter subterraneus VNs68 is an anaerobe, spore-forming, thermophilic bacterium that was isolated from water-producing deep artesian well.

Gram-positive
rod-shaped
spore-forming
anaerobe
thermophilic
16S sequence
Bacteria
genome sequence

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Bacillota*
	Class	*Clostridia*
	Order	*Eubacteriales*
	Family	*Clostridiaceae*
	Genus	*Geosporobacter*
	Species	**Geosporobacter subterraneus**
	Full Scientific Name (LPSN)	Geosporobacter subterraneus Klouche et al. 2007

Information on morphological and physiological properties Morphology

[Ref.: #31914]	Gram stain	positive
[Ref.: #69480]	Gram stain	positive Confidence in %100

[Ref.: #31914]	Cell length	3.0-5.0 µm

[Ref.: #31914]	Cell width	0.5 µm

[Ref.: #31914]	Cell shape	rod-shaped

[Ref.: #31914]	Motility	no
[Ref.: #69480]	Motility	yes Confidence in %90.292

Information on culture and growth conditions Culture and growth conditions

[Ref.: #7290]

Culture medium

PY + X MEDIUM (DSMZ Medium 104b)

[Ref.: #7290]

Culture medium growth

[Ref.: #7290]

Culture medium link

Medium recipe at MediaDive

[Ref.: #7290]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #7290]	growth	40 °C
[Ref.: #31914]	growth	22-55 °C
[Ref.: #31914]	optimum	42 °C
[Ref.: #67770]	growth	42 °C

[Ref.: #7290]	Temperature range	thermophilic
[Ref.: #31914]	Temperature range	thermophilic
[Ref.: #67770]	Temperature range	thermophilic
[Ref.: #69480]	Temperature range	thermophilic Confidence in %91.699

	pH	Kind of pH		pH
[Ref.: #31914]			optimum	7.3
[Ref.: #31914]			growth	5.6-8.4

Information on physiology and metabolism Physiology and metabolism

[Ref.: #7290]	Oxygen tolerance	anaerobe
[Ref.: #31914]	Oxygen tolerance	anaerobe
[Ref.: #69480]	Oxygen tolerance	anaerobe Confidence in %99.411

[Ref.: #31914]	Ability of spore formation	yes
[Ref.: #69481]	Ability of spore formation	yes Confidence in %100
[Ref.: #69480]	Ability of spore formation	yes Confidence in %100

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #31914]	alanine ChEBI	+	carbon source
[Ref.: #31914]	arginine ChEBI	+	carbon source
[Ref.: #31914]	asparagine ChEBI	+	carbon source
[Ref.: #31914]	aspartate ChEBI	+	carbon source
[Ref.: #31914]	cellobiose ChEBI	+	carbon source
[Ref.: #31914]	fructose ChEBI	+	carbon source
[Ref.: #31914]	glucose ChEBI	+	carbon source
[Ref.: #31914]	glutamate ChEBI	+	carbon source
[Ref.: #31914]	histidine ChEBI	+	carbon source
[Ref.: #31914]	ribose ChEBI	+	carbon source
[Ref.: #31914]	serine ChEBI	+	carbon source
[Ref.: #31914]	xylose ChEBI	+	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	gluconeogenesis	100	8 of 8
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	C4 and CAM-carbon fixation	100	8 of 8
[Ref.: #66794]	L-lactaldehyde degradation	100	3 of 3
[Ref.: #66794]	cardiolipin biosynthesis	100	7 of 7
[Ref.: #66794]	ethanol fermentation	100	2 of 2
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	starch degradation	100	10 of 10
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	aminopropanol phosphate biosynthesis	100	2 of 2
[Ref.: #66794]	reductive acetyl coenzyme A pathway	100	7 of 7
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	threonine metabolism	90	9 of 10
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	aspartate and asparagine metabolism	88.89	8 of 9
[Ref.: #66794]	glutamate and glutamine metabolism	85.71	24 of 28
[Ref.: #66794]	citric acid cycle	85.71	12 of 14
[Ref.: #66794]	ubiquinone biosynthesis	85.71	6 of 7
[Ref.: #66794]	vitamin B12 metabolism	85.29	29 of 34
[Ref.: #66794]	vitamin B1 metabolism	84.62	11 of 13
[Ref.: #66794]	phenylalanine metabolism	84.62	11 of 13
[Ref.: #66794]	NAD metabolism	83.33	15 of 18
[Ref.: #66794]	glycolate and glyoxylate degradation	83.33	5 of 6
[Ref.: #66794]	glycolysis	82.35	14 of 17
[Ref.: #66794]	pentose phosphate pathway	81.82	9 of 11
[Ref.: #66794]	degradation of sugar alcohols	81.25	13 of 16
[Ref.: #66794]	cellulose degradation	80	4 of 5
[Ref.: #66794]	lipoate biosynthesis	80	4 of 5
[Ref.: #66794]	glycine betaine biosynthesis	80	4 of 5
[Ref.: #66794]	hydrogen production	80	4 of 5
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	propionate fermentation	80	8 of 10
[Ref.: #66794]	alanine metabolism	79.31	23 of 29
[Ref.: #66794]	purine metabolism	78.72	74 of 94
[Ref.: #66794]	photosynthesis	78.57	11 of 14
[Ref.: #66794]	serine metabolism	77.78	7 of 9
[Ref.: #66794]	valine metabolism	77.78	7 of 9
[Ref.: #66794]	CO2 fixation in Crenarchaeota	77.78	7 of 9
[Ref.: #66794]	pyrimidine metabolism	77.78	35 of 45
[Ref.: #66794]	molybdenum cofactor biosynthesis	77.78	7 of 9
[Ref.: #66794]	isoleucine metabolism	75	6 of 8
[Ref.: #66794]	butanoate fermentation	75	3 of 4
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
[Ref.: #66794]	sulfopterin metabolism	75	3 of 4
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	CMP-KDO biosynthesis	75	3 of 4
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	flavin biosynthesis	73.33	11 of 15
[Ref.: #66794]	histidine metabolism	72.41	21 of 29
[Ref.: #66794]	heme metabolism	71.43	10 of 14
[Ref.: #66794]	tetrahydrofolate metabolism	71.43	10 of 14
[Ref.: #66794]	propanol degradation	71.43	5 of 7
[Ref.: #66794]	arginine metabolism	70.83	17 of 24
[Ref.: #66794]	Entner Doudoroff pathway	70	7 of 10
[Ref.: #66794]	methionine metabolism	69.23	18 of 26
[Ref.: #66794]	leucine metabolism	69.23	9 of 13
[Ref.: #66794]	urea cycle	69.23	9 of 13
[Ref.: #66794]	cyanate degradation	66.67	2 of 3
[Ref.: #66794]	selenocysteine biosynthesis	66.67	4 of 6
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	formaldehyde oxidation	66.67	2 of 3
[Ref.: #66794]	oxidative phosphorylation	61.54	56 of 91
[Ref.: #66794]	cysteine metabolism	61.11	11 of 18
[Ref.: #66794]	myo-inositol biosynthesis	60	6 of 10
[Ref.: #66794]	methylglyoxal degradation	60	3 of 5
[Ref.: #66794]	factor 420 biosynthesis	60	3 of 5
[Ref.: #66794]	phenylacetate degradation (aerobic)	60	3 of 5
[Ref.: #66794]	glycogen metabolism	60	3 of 5
[Ref.: #66794]	metabolism of amino sugars and derivatives	60	3 of 5
[Ref.: #66794]	lipid metabolism	58.06	18 of 31
[Ref.: #66794]	glutathione metabolism	57.14	8 of 14
[Ref.: #66794]	d-mannose degradation	55.56	5 of 9
[Ref.: #66794]	tryptophan metabolism	55.26	21 of 38
[Ref.: #66794]	non-pathway related	55.26	21 of 38
[Ref.: #66794]	proline metabolism	54.55	6 of 11
[Ref.: #66794]	metabolism of disaccharids	54.55	6 of 11
[Ref.: #66794]	lysine metabolism	52.38	22 of 42
[Ref.: #66794]	degradation of sugar acids	52	13 of 25
[Ref.: #66794]	lactate fermentation	50	2 of 4
[Ref.: #66794]	degradation of hexoses	50	9 of 18
[Ref.: #66794]	ketogluconate metabolism	50	4 of 8
[Ref.: #66794]	kanosamine biosynthesis II	50	1 of 2
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	isoprenoid biosynthesis	50	13 of 26
[Ref.: #66794]	quinate degradation	50	1 of 2
[Ref.: #66794]	degradation of pentoses	46.43	13 of 28
[Ref.: #66794]	nitrate assimilation	44.44	4 of 9
[Ref.: #66794]	lipid A biosynthesis	44.44	4 of 9
[Ref.: #66794]	tyrosine metabolism	42.86	6 of 14
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
[Ref.: #66794]	ethylmalonyl-CoA pathway	40	2 of 5
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	sulfate reduction	38.46	5 of 13
[Ref.: #66794]	dTDPLrhamnose biosynthesis	37.5	3 of 8
[Ref.: #66794]	d-xylose degradation	36.36	4 of 11
[Ref.: #66794]	polyamine pathway	34.78	8 of 23
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	octane oxidation	33.33	1 of 3
[Ref.: #66794]	enterobactin biosynthesis	33.33	1 of 3
[Ref.: #66794]	pantothenate biosynthesis	33.33	2 of 6
[Ref.: #66794]	ascorbate metabolism	31.82	7 of 22
[Ref.: #66794]	coenzyme M biosynthesis	30	3 of 10
[Ref.: #66794]	phenol degradation	30	6 of 20
[Ref.: #66794]	4-hydroxyphenylacetate degradation	30	3 of 10
[Ref.: #66794]	benzoyl-CoA degradation	28.57	2 of 7
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
[Ref.: #66794]	methanogenesis from CO2	25	3 of 12
[Ref.: #66794]	carnitine metabolism	25	2 of 8
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	vitamin E metabolism	25	1 of 4
[Ref.: #66794]	bile acid biosynthesis, neutral pathway	23.53	4 of 17
[Ref.: #66794]	carotenoid biosynthesis	22.73	5 of 22
[Ref.: #66794]	4-hydroxymandelate degradation	22.22	2 of 9
		Only first 10 entries are displayed. Click here to see all.

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #7290]	Sample type/isolated from	water-producing deep artesian well
[Ref.: #7290]	Geographic location (country and/or sea, region)	Paris Basin
[Ref.: #7290]	Country	France
[Ref.: #7290]	Country ISO 3 Code	FRA
[Ref.: #7290]	Continent	Europe

[Ref.: #67770]	Sample type/isolated from	Well-water from a deep aquifer at a depth of 800 m in the Paris Basin
[Ref.: #67770]	Country	France
[Ref.: #67770]	Country ISO 3 Code	FRA
[Ref.: #67770]	Continent	Europe
* marker position based on {}

Isolation sources categories

#Environmental

#Aquatic

What are isolation sources categories?

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #7290]

Biosafety level

Risk group (German classification)
According to TRBA 466

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #7290]	Geosporobacter subterraneus strain VNs68 16S ribosomal RNA gene, partial sequence	DQ643978	1627	ENA	390806 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Geosporobacter subterraneus DSM 17957	GCA_900142145	scaffold	GenBank	1121919 tax ID
[Ref.: #66792]	Geosporobacter subterraneus DSM 17957	1121919.3	wgs	PATRIC	1121919 tax ID	*
[Ref.: #66792]	Geosporobacter subterraneus DSM 17957	2585428170	draft	JGI IMG/M	1121919 tax ID	*

[Ref.: #7290]	GC-content	42.2 mol%
[Ref.: #67770]	GC-content	42.2 mol%	high performance liquid chromatography (HPLC)

Data predicted using genome information as a basis Genome-based predictions

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Geosporobacter subterraneus DSM 17957 DSM 17957 NCBI: GCA_900142145.1
[Ref.: #69481]	spore-forming	yes	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Geosporobacter subterraneus DSM 17957 PATRIC: 1121919.3
[Ref.: #69480]	motile	yes	83.186	yes
[Ref.: #69480]	flagellated	yes	52.751	no
[Ref.: #69480]	gram-positive	no	50	no
[Ref.: #69480]	anaerobic	yes	99.175	yes
[Ref.: #69480]	halophile	no	82.529	no
[Ref.: #69480]	spore-forming	yes	93.799	yes
[Ref.: #69480]	thermophile	yes	85.789	yes
[Ref.: #69480]	glucose-util	yes	91.022	yes
[Ref.: #69480]	aerobic	no	98.505	yes
[Ref.: #69480]	glucose-ferment	yes	51.221	no

Availability in culture collections External links

[Ref.: #7290]

Culture collection no.

DSM 17957, JCM 14037, CIP 109751

[Ref.: #72391]

SI-ID 293890

Literature:

Topic	Title	Authors	Journal	DOI	Year
Metabolism	Comparative genomic analysis of Geosporobacter ferrireducens and its versatility of anaerobic energy metabolism.	Jung MY, Kim SJ, Kim JG, Hong H, Gwak JH, Park SJ, Kim YH, Rhee SK	J Microbiol	10.1007/s12275-018-7451-6	2018	*
Phylogeny	Anaerosolibacter carboniphilus gen. nov., sp. nov., a strictly anaerobic iron-reducing bacterium isolated from coal-contaminated soil.	Hong H, Kim SJ, Min UG, Lee YJ, Kim SG, Roh SW, Kim JG, Na JG, Rhee SK	Int J Syst Evol Microbiol	10.1099/ijs.0.000124	2015	*
Phylogeny	Geosporobacter ferrireducens sp. nov., an anaerobic iron-reducing bacterium isolated from an oil-contaminated site.	Hong H, Kim SJ, Min UG, Lee YJ, Kim SG, Jung MY, Seo YS, Rhee SK	Antonie Van Leeuwenhoek	10.1007/s10482-015-0389-3	2015	*
Phylogeny	Thermotalea metallivorans gen. nov., sp. nov., a thermophilic, anaerobic bacterium from the Great Artesian Basin of Australia aquifer.	Ogg CD, Patel BK	Int J Syst Evol Microbiol	10.1099/ijs.0.004218-0	2009	*
Phylogeny	Geosporobacter subterraneus gen. nov., sp. nov., a spore-forming bacterium isolated from a deep subsurface aquifer.	Klouche N, Fardeau ML, Lascourreges JF, Cayol JL, Hacene H, Thomas P, Magot M	Int J Syst Evol Microbiol	10.1099/ijs.0.64642-0	2007	*

References

#7290

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 17957

#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 )

#31914

Barberan A, Caceres Velazquez H, Jones S, Fierer N.: Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information. mSphere 2: 2017 ( DOI 10.1128/mSphere.00237-17 , PubMed 28776041 ) - originally annotated from #28171 (see below)

#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 )

#67770 Japan Collection of Microorganism (JCM) ; Curators of the JCM;

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

#72391

Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.: StrainInfo: A central database for resolving microbial strain identifiers . ( DOI 10.60712/SI-ID293890.1 )

#28171

IJSEM 1757 2007 ( DOI 10.1099/ijs.0.64642-0 , PubMed 17684251 )

* These data were automatically processed and therefore are not curated

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Geosporobacter subterraneus DSM 17957 DSM 17957

Geosporobacter subterraneus DSM 17957

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