Name: Clostridium tepidiprofundi DSM 19306
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 2845

Type strain:

Species: Clostridium tepidiprofundi

Culture col. no.: DSM 19306, VKM B-2459, SG 508

Strain history: <- G. B. Slobodkina, Winogradsky Inst. Microbiol., RAS, Moscow, Russia; SG 508 <- G. B. Slobodkina {2006}

NCBI tax ID(s): 1121338 (strain), 420412 (species)

SI-ID 404621

DSM 19306

Section

Clostridium tepidiprofundi DSM 19306 is an anaerobe, spore-forming, thermophilic bacterium that was isolated from deep-sea hydrothermal vent chimney.

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	*Clostridium*
	Species	**Clostridium tepidiprofundi**
	Full Scientific Name (LPSN)	Clostridium tepidiprofundi Slobodkina et al. 2008

Information on morphological and physiological properties Morphology

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

[Ref.: #32431]	Cell length	2.5 µm

[Ref.: #32431]	Cell width	0.5 µm

[Ref.: #32431]	Cell shape	rod-shaped

Information on culture and growth conditions Culture and growth conditions

[Ref.: #8027]

Culture medium

ANAEROBIC SEAWATER (SWM) MEDIUM (DSMZ Medium 504)

[Ref.: #8027]

Culture medium growth

[Ref.: #8027]

Culture medium link

Medium recipe at MediaDive

[Ref.: #8027]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #8027]	growth	50 °C
[Ref.: #32431]	growth	22-60 °C
[Ref.: #32431]	optimum	50 °C

[Ref.: #8027]	Temperature range	thermophilic
[Ref.: #32431]	Temperature range	thermophilic
[Ref.: #69480]	Temperature range	thermophilic Confidence in %96.817

	pH	Kind of pH		pH
[Ref.: #32431]			optimum	6.4
[Ref.: #32431]			growth	4-8.5

Information on physiology and metabolism Physiology and metabolism

[Ref.: #8027]	Oxygen tolerance	anaerobe
[Ref.: #32431]	Oxygen tolerance	anaerobe
[Ref.: #69480]	Oxygen tolerance	anaerobe Confidence in %100

[Ref.: #32431]	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

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #32431]		NaCl		growth	01-06	%
[Ref.: #32431]		NaCl		optimum	2.5	%

	Metabolite utilization	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #32431]		glucose ChEBI	+	carbon source
[Ref.: #32431]		maltose ChEBI	+	carbon source

	Metabolite production	Metabolite	Production
[Ref.: #32431]		hydrogen sulfide ChEBI	yes

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	C4 and CAM-carbon fixation	100	8 of 8
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	butanoate fermentation	100	4 of 4
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	L-lactaldehyde degradation	100	3 of 3
[Ref.: #66794]	palmitate biosynthesis	95.45	21 of 22
[Ref.: #66794]	vitamin B1 metabolism	92.31	12 of 13
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	gluconeogenesis	87.5	7 of 8
[Ref.: #66794]	glutamate and glutamine metabolism	82.14	23 of 28
[Ref.: #66794]	threonine metabolism	80	8 of 10
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	starch degradation	80	8 of 10
[Ref.: #66794]	lipoate biosynthesis	80	4 of 5
[Ref.: #66794]	vitamin B12 metabolism	79.41	27 of 34
[Ref.: #66794]	alanine metabolism	79.31	23 of 29
[Ref.: #66794]	photosynthesis	78.57	11 of 14
[Ref.: #66794]	citric acid cycle	78.57	11 of 14
[Ref.: #66794]	aspartate and asparagine metabolism	77.78	7 of 9
[Ref.: #66794]	CO2 fixation in Crenarchaeota	77.78	7 of 9
[Ref.: #66794]	NAD metabolism	77.78	14 of 18
[Ref.: #66794]	phenylalanine metabolism	76.92	10 of 13
[Ref.: #66794]	glycolysis	76.47	13 of 17
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
[Ref.: #66794]	lactate fermentation	75	3 of 4
[Ref.: #66794]	sulfopterin metabolism	75	3 of 4
[Ref.: #66794]	biotin biosynthesis	75	3 of 4
[Ref.: #66794]	flavin biosynthesis	73.33	11 of 15
[Ref.: #66794]	purine metabolism	72.34	68 of 94
[Ref.: #66794]	propanol degradation	71.43	5 of 7
[Ref.: #66794]	tetrahydrofolate metabolism	71.43	10 of 14
[Ref.: #66794]	propionate fermentation	70	7 of 10
[Ref.: #66794]	urea cycle	69.23	9 of 13
[Ref.: #66794]	pyrimidine metabolism	66.67	30 of 45
[Ref.: #66794]	serine metabolism	66.67	6 of 9
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	formaldehyde oxidation	66.67	2 of 3
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	d-mannose degradation	66.67	6 of 9
[Ref.: #66794]	selenocysteine biosynthesis	66.67	4 of 6
[Ref.: #66794]	oxidative phosphorylation	63.74	58 of 91
[Ref.: #66794]	hydrogen production	60	3 of 5
[Ref.: #66794]	glycogen metabolism	60	3 of 5
[Ref.: #66794]	cellulose degradation	60	3 of 5
[Ref.: #66794]	reductive acetyl coenzyme A pathway	57.14	4 of 7
[Ref.: #66794]	lipid metabolism	54.84	17 of 31
[Ref.: #66794]	histidine metabolism	51.72	15 of 29
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	CMP-KDO biosynthesis	50	2 of 4
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	dTDPLrhamnose biosynthesis	50	4 of 8
[Ref.: #66794]	heme metabolism	50	7 of 14
[Ref.: #66794]	toluene degradation	50	2 of 4
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	lysine metabolism	50	21 of 42
[Ref.: #66794]	cis-vaccenate biosynthesis	50	1 of 2
[Ref.: #66794]	non-pathway related	50	19 of 38
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	isoleucine metabolism	50	4 of 8
[Ref.: #66794]	tryptophan metabolism	47.37	18 of 38
[Ref.: #66794]	methionine metabolism	46.15	12 of 26
[Ref.: #66794]	isoprenoid biosynthesis	46.15	12 of 26
[Ref.: #66794]	cysteine metabolism	44.44	8 of 18
[Ref.: #66794]	cardiolipin biosynthesis	42.86	3 of 7
[Ref.: #66794]	ubiquinone biosynthesis	42.86	3 of 7
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
[Ref.: #66794]	metabolism of amino sugars and derivatives	40	2 of 5
[Ref.: #66794]	bacilysin biosynthesis	40	2 of 5
[Ref.: #66794]	ethylmalonyl-CoA pathway	40	2 of 5
[Ref.: #66794]	coenzyme M biosynthesis	40	4 of 10
[Ref.: #66794]	degradation of hexoses	38.89	7 of 18
[Ref.: #66794]	leucine metabolism	38.46	5 of 13
[Ref.: #66794]	ketogluconate metabolism	37.5	3 of 8
[Ref.: #66794]	arginine metabolism	37.5	9 of 24
[Ref.: #66794]	pentose phosphate pathway	36.36	4 of 11
[Ref.: #66794]	vitamin B6 metabolism	36.36	4 of 11
[Ref.: #66794]	polyamine pathway	34.78	8 of 23
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	1,4-dihydroxy-6-naphthoate biosynthesis	33.33	2 of 6
[Ref.: #66794]	lipid A biosynthesis	33.33	3 of 9
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	nitrate assimilation	33.33	3 of 9
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	valine metabolism	33.33	3 of 9
[Ref.: #66794]	glycolate and glyoxylate degradation	33.33	2 of 6
[Ref.: #66794]	molybdenum cofactor biosynthesis	33.33	3 of 9
[Ref.: #66794]	enterobactin biosynthesis	33.33	1 of 3
[Ref.: #66794]	degradation of pentoses	32.14	9 of 28
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	30.77	4 of 13
[Ref.: #66794]	phenylpropanoid biosynthesis	30.77	4 of 13
[Ref.: #66794]	sulfate reduction	30.77	4 of 13
[Ref.: #66794]	aclacinomycin biosynthesis	28.57	2 of 7
[Ref.: #66794]	benzoyl-CoA degradation	28.57	2 of 7
[Ref.: #66794]	tyrosine metabolism	28.57	4 of 14
[Ref.: #66794]	proline metabolism	27.27	3 of 11
[Ref.: #66794]	ascorbate metabolism	27.27	6 of 22
[Ref.: #66794]	metabolism of disaccharids	27.27	3 of 11
[Ref.: #66794]	degradation of sugar alcohols	25	4 of 16
[Ref.: #66794]	carnitine metabolism	25	2 of 8
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	methanogenesis from CO2	25	3 of 12
[Ref.: #66794]	glutathione metabolism	21.43	3 of 14
		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.: #8027]	Sample type/isolated from	deep-sea hydrothermal vent chimney
[Ref.: #8027]	Geographic location (country and/or sea, region)	North Pacific, East Pacific Rise, 13 N
[Ref.: #8027]	Country	International waters
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Hydrothermal vent
#Environmental	#Aquatic	#Marine
#Condition	#Thermophilic (>45°C)	-

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence EF197795 (>99% sequence identity) for Clostridium tepidiprofundi subclade from Microbeatlas

Aquatic Samples	357
Soil Samples	93
Animal Samples	624
Plant Samples	20
Total Samples	1094

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

[Ref.: #8027]

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.: #8027]	Clostridium tepidiprofundi strain SG 508 16S ribosomal RNA gene, partial sequence	EF197795	1464	ENA	1121338 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Clostridium tepidiprofundi DSM 19306	GCA_001594005	contig	GenBank	1121338 tax ID	*
[Ref.: #66792]	Clostridium tepidiprofundi DSM 19306	1121338.3	wgs	PATRIC	1121338 tax ID	*
[Ref.: #66792]	Clostridium tepidiprofundi DSM 19306	2684622633	draft	JGI IMG/M	1121338 tax ID	*

[Ref.: #8027]	GC-content	31 mol%	thermal denaturation, midpoint method (Tm)
[Ref.: #32431]	GC-content	30.9 mol%

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: Clostridium tepidiprofundi DSM 19306 PATRIC: 1121338.3
[Ref.: #69481]	spore-forming	yes	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Clostridium tepidiprofundi DSM 19306 PATRIC: 1121338.3
[Ref.: #69480]	motile	yes	87.942	no
[Ref.: #69480]	flagellated	no	63.094	no
[Ref.: #69480]	gram-positive	yes	60.149	no
[Ref.: #69480]	anaerobic	yes	99.727	yes
[Ref.: #69480]	aerobic	no	98.942	yes
[Ref.: #69480]	halophile	no	92.126	no
[Ref.: #69480]	spore-forming	yes	94.418	yes
[Ref.: #69480]	thermophile	yes	74.029	no
[Ref.: #69480]	glucose-util	yes	87.209	yes
[Ref.: #69480]	glucose-ferment	yes	55.617	no

Availability in culture collections External links

[Ref.: #8027]

Culture collection no.

DSM 19306, VKM B-2459, SG 508

[Ref.: #72369]

SI-ID 404621

Literature:

	Title	Authors	Journal	DOI	Year
Phylogeny	Haloimpatiens lingqiaonensis gen. nov., sp. nov., an anaerobic bacterium isolated from paper-mill wastewater.	Wu D, Zhang NF, Sun C, Zhang WW, Han SB, Pan J, Wu M, Th D, Zhu XF	Int J Syst Evol Microbiol	10.1099/ijsem.0.000765	2015	*
Phylogeny	Oceanirhabdus sediminicola gen. nov., sp. nov., an anaerobic bacterium isolated from sea sediment.	Pi RX, Zhang WW, Fang MX, Zhang YZ, Li TT, Wu M, Zhu XF	Int J Syst Evol Microbiol	10.1099/ijs.0.051243-0	2013	*
Phylogeny	Clostridium tepidiprofundi sp. nov., a moderately thermophilic bacterium from a deep-sea hydrothermal vent.	Slobodkina GB, Kolganova TV, Tourova TP, Kostrikina NA, Jeanthon C, Bonch-Osmolovskaya EA, Slobodkin AI	Int J Syst Evol Microbiol	10.1099/ijs.0.65485-0	2008	*
	First Insights into the Genome of the Moderately Thermophilic Bacterium Clostridium tepidiprofundi SG 508T.	Poehlein A, Friedrich I, Kruger L, Daniel R	Genome Announc	10.1128/genomeA.00379-16	2016	*

References

#8027

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 19306

#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 )

#32431

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 #28653 (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 )

#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 .

#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 )

#72369

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-ID404621.1 )

#28653

IJSEM 852 2008 ( DOI 10.1099/ijs.0.65485-0 , PubMed 18398181 )

* These data were automatically processed and therefore are not curated

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