Name: Spirochaeta thermophila Z-1203
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 14323

Type strain:

Species: Spirochaeta thermophila

Strain Designation: Z-1203

Culture col. no.: DSM 6578, ATCC 700085

Strain history: <- F. A. Rainey; Z-1203 <- H. Y. Aksenova

NCBI tax ID(s): 869211 (strain), 154 (species)

SI-ID 43763

ATCC 700085, DSM 6578

Other strains from Spirochaeta thermophila

S. thermophila RI 19.B1, DSM 6192, ATCC 49972

Section

Spirochaeta thermophila Z-1203 is an anaerobe, thermophilic, Gram-negative bacterium that was isolated from marine hot spring.

Gram-negative
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	*Spirochaetota*
	Class	*Spirochaetia*
	Order	*Spirochaetales*
	Family	*Spirochaetaceae*
	Genus	*Spirochaeta*
	Species	**Spirochaeta thermophila**
	Full Scientific Name (LPSN)	Spirochaeta thermophila Aksenova et al. 1992

Information on morphological and physiological properties Morphology

[Ref.: #69480]	Gram stain	negative Confidence in %99.901

Multimedia content

[Ref.: #66793]

Caption:

electron microscopic image

[Ref.: #66793]

Intellectual property rights:

Information on culture and growth conditions Culture and growth conditions

[Ref.: #2738]

Culture medium

SPIROCHAETA THERMOPHILA MEDIUM (DSMZ Medium 509)

[Ref.: #2738]

Culture medium growth

[Ref.: #2738]

Culture medium link

Medium recipe at MediaDive

[Ref.: #2738]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #2738]			growth	65 °C

[Ref.: #2738]	Temperature range	thermophilic
[Ref.: #69480]	Temperature range	thermophilic Confidence in %98.476

Information on physiology and metabolism Physiology and metabolism

[Ref.: #2738]	Oxygen tolerance	anaerobe
[Ref.: #69480]	Oxygen tolerance	anaerobe Confidence in %99.998

[Ref.: #69480]

Ability of spore formation

no Confidence in %99.984

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	cellulose degradation	100	5 of 5
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	lipoate biosynthesis	100	5 of 5
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	cardiolipin biosynthesis	100	7 of 7
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	sulfopterin metabolism	100	4 of 4
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	ceramide biosynthesis	100	1 of 1
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	threonine metabolism	90	9 of 10
[Ref.: #66794]	starch degradation	90	9 of 10
[Ref.: #66794]	valine metabolism	88.89	8 of 9
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	glycolate and glyoxylate degradation	83.33	5 of 6
[Ref.: #66794]	degradation of sugar alcohols	81.25	13 of 16
[Ref.: #66794]	Entner Doudoroff pathway	80	8 of 10
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	glycogen metabolism	80	4 of 5
[Ref.: #66794]	NAD metabolism	77.78	14 of 18
[Ref.: #66794]	d-mannose degradation	77.78	7 of 9
[Ref.: #66794]	aspartate and asparagine metabolism	77.78	7 of 9
[Ref.: #66794]	phenylalanine metabolism	76.92	10 of 13
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	gluconeogenesis	75	6 of 8
[Ref.: #66794]	C4 and CAM-carbon fixation	75	6 of 8
[Ref.: #66794]	isoleucine metabolism	75	6 of 8
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	pyrimidine metabolism	73.33	33 of 45
[Ref.: #66794]	flavin biosynthesis	73.33	11 of 15
[Ref.: #66794]	pentose phosphate pathway	72.73	8 of 11
[Ref.: #66794]	reductive acetyl coenzyme A pathway	71.43	5 of 7
[Ref.: #66794]	photosynthesis	71.43	10 of 14
[Ref.: #66794]	tetrahydrofolate metabolism	71.43	10 of 14
[Ref.: #66794]	vitamin B1 metabolism	69.23	9 of 13
[Ref.: #66794]	purine metabolism	68.09	64 of 94
[Ref.: #66794]	degradation of pentoses	67.86	19 of 28
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	serine metabolism	66.67	6 of 9
[Ref.: #66794]	cyanate degradation	66.67	2 of 3
[Ref.: #66794]	formaldehyde oxidation	66.67	2 of 3
[Ref.: #66794]	acetyl CoA biosynthesis	66.67	2 of 3
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	isoprenoid biosynthesis	65.38	17 of 26
[Ref.: #66794]	glycolysis	64.71	11 of 17
[Ref.: #66794]	glutamate and glutamine metabolism	64.29	18 of 28
[Ref.: #66794]	d-xylose degradation	63.64	7 of 11
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
[Ref.: #66794]	degradation of hexoses	61.11	11 of 18
[Ref.: #66794]	non-pathway related	60.53	23 of 38
[Ref.: #66794]	hydrogen production	60	3 of 5
[Ref.: #66794]	ubiquinone biosynthesis	57.14	4 of 7
[Ref.: #66794]	heme metabolism	57.14	8 of 14
[Ref.: #66794]	propanol degradation	57.14	4 of 7
[Ref.: #66794]	CO2 fixation in Crenarchaeota	55.56	5 of 9
[Ref.: #66794]	sulfate reduction	53.85	7 of 13
[Ref.: #66794]	leucine metabolism	53.85	7 of 13
[Ref.: #66794]	oxidative phosphorylation	53.85	49 of 91
[Ref.: #66794]	urea cycle	53.85	7 of 13
[Ref.: #66794]	alanine metabolism	51.72	15 of 29
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	dTDPLrhamnose biosynthesis	50	4 of 8
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	butanoate fermentation	50	2 of 4
[Ref.: #66794]	propionate fermentation	50	5 of 10
[Ref.: #66794]	CMP-KDO biosynthesis	50	2 of 4
[Ref.: #66794]	cyclohexanol degradation	50	2 of 4
[Ref.: #66794]	suberin monomers biosynthesis	50	1 of 2
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	adipate degradation	50	1 of 2
[Ref.: #66794]	cysteine metabolism	50	9 of 18
[Ref.: #66794]	histidine metabolism	48.28	14 of 29
[Ref.: #66794]	polyamine pathway	47.83	11 of 23
[Ref.: #66794]	lysine metabolism	47.62	20 of 42
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	46.15	6 of 13
[Ref.: #66794]	methionine metabolism	46.15	12 of 26
[Ref.: #66794]	arginine metabolism	45.83	11 of 24
[Ref.: #66794]	metabolism of disaccharids	45.45	5 of 11
[Ref.: #66794]	proline metabolism	45.45	5 of 11
[Ref.: #66794]	tryptophan metabolism	44.74	17 of 38
[Ref.: #66794]	nitrate assimilation	44.44	4 of 9
[Ref.: #66794]	citric acid cycle	42.86	6 of 14
[Ref.: #66794]	methylglyoxal degradation	40	2 of 5
[Ref.: #66794]	factor 420 biosynthesis	40	2 of 5
[Ref.: #66794]	glycine metabolism	40	4 of 10
[Ref.: #66794]	myo-inositol biosynthesis	40	4 of 10
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	lipid metabolism	38.71	12 of 31
[Ref.: #66794]	ketogluconate metabolism	37.5	3 of 8
[Ref.: #66794]	degradation of sugar acids	36	9 of 25
[Ref.: #66794]	tyrosine metabolism	35.71	5 of 14
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	arachidonic acid metabolism	33.33	6 of 18
[Ref.: #66794]	molybdenum cofactor biosynthesis	33.33	3 of 9
[Ref.: #66794]	selenocysteine biosynthesis	33.33	2 of 6
[Ref.: #66794]	lipid A biosynthesis	33.33	3 of 9
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	33.33	4 of 12
[Ref.: #66794]	ascorbate metabolism	31.82	7 of 22
[Ref.: #66794]	coenzyme M biosynthesis	30	3 of 10
[Ref.: #66794]	glutathione metabolism	28.57	4 of 14
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	androgen and estrogen metabolism	25	4 of 16
[Ref.: #66794]	phenylpropanoid biosynthesis	23.08	3 of 13
[Ref.: #66794]	chlorophyll metabolism	22.22	4 of 18
[Ref.: #66794]	vitamin B12 metabolism	20.59	7 of 34
		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.: #2738]	Sample type/isolated from	marine hot spring
[Ref.: #2738]	Geographic location (country and/or sea, region)	Kurils, Shiashkoten island
[Ref.: #2738]	Country	Russia
[Ref.: #2738]	Country ISO 3 Code	RUS
[Ref.: #2738]	Continent	Europe
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Marine
#Environmental	#Aquatic	#Thermal spring
#Condition	#Thermophilic (>45°C)	-

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence FR749903 (>99% sequence identity) for Spirochaeta thermophila subclade from Microbeatlas

Aquatic Samples	191
Soil Samples	56
Animal Samples	727
Plant Samples	40
Total Samples	1014

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

[Ref.: #2738]

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.: #20218]	Spirochaeta thermophila partial 16S rRNA gene, type strain DSM 6578T	FR749903	1538	ENA	154 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Spirochaeta thermophila DSM 6578	GCA_000184345	complete	GenBank	869211 tax ID	*
[Ref.: #66792]	Spirochaeta thermophila DSM 6578	869211.3	wgs	PATRIC	869211 tax ID	*
[Ref.: #66792]	Spirochaeta thermophila Z-1203, DSM 6578	2506381022	complete	JGI IMG/M	869211 tax ID	*

[Ref.: #2738]

GC-content

60.9 mol%

sequence analysis

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: Spirochaeta thermophila DSM 6578 DSM 6578 NCBI: GCA_000184345.2
[Ref.: #69481]	spore-forming	yes	70	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Spirochaeta thermophila DSM 6578 DSM 6578 NCBI: GCA_000184345.2
[Ref.: #69480]	motile	yes	89.463	no
[Ref.: #69480]	flagellated	no	70.26	no
[Ref.: #69480]	gram-positive	no	94.022	no
[Ref.: #69480]	anaerobic	yes	98.949	yes
[Ref.: #69480]	aerobic	no	97.253	yes
[Ref.: #69480]	halophile	no	79.28	no
[Ref.: #69480]	spore-forming	no	90.121	no
[Ref.: #69480]	thermophile	yes	98.39	yes
[Ref.: #69480]	glucose-util	yes	87.749	no
[Ref.: #69480]	glucose-ferment	yes	55.207	no

Availability in culture collections External links

[Ref.: #2738]

Culture collection no.

DSM 6578, ATCC 700085

[Ref.: #83472]

SI-ID 43763

Literature:

Topic	Title	Authors	Journal	DOI	Year
Enzymology	Insight into the potential factors influencing the catalytic direction in cellobiose 2-epimerase by crystallization and mutagenesis.	Feng Y, Hua X, Shen Q, Matthews M, Zhang Y, Fisher AJ, Lyu X, Yang R	Acta Crystallogr D Struct Biol	10.1107/S205979832001222X	2020	*
Metabolism	Glucose catabolism by Spirochaeta thermophila RI 19.B1.	Janssen PH, Morgan HW	J Bacteriol	10.1128/jb.174.8.2449-2453.1992	1992	*

References

#2738

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 6578

#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) .

#66793

Mukherjee et al.: GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life. 35: 676 - 683 2017 ( DOI 10.1038/nbt.3886 , PubMed 28604660 )

#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 )

#83472

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-ID43763.1 )

* These data were automatically processed and therefore are not curated

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Spirochaeta thermophila DSM 6578 DSM 6578

Spirochaeta thermophila DSM 6578 DSM 6578

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