Name: Staphylothermus marinus F1
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 4201

Type strain:

Species: Staphylothermus marinus

Strain Designation: F1

Culture col. no.: DSM 3639, JCM 9404, ATCC 43588

Strain history: DSM 3639 <-- K. O. Stetter and G. Fiala F1.

NCBI tax ID(s): 399550 (strain), 2280 (species)

SI-ID 47743

ATCC 43588, DSM 3639, JCM 9404

Special Collections

DSMZ
JCM

Other strains from Staphylothermus marinus

Section

Staphylothermus marinus F1 is an anaerobe, Gram-negative archaeon that was isolated from geothermally heated marine sediment.

Gram-negative
anaerobe
16S sequence
Archaea
genome sequence

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

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Archaea"
	Phylum	*Thermoproteota*
	Class	*Thermoprotei*
	Order	*Desulfurococcales*
	Family	*Desulfurococcaceae*
	Genus	*Staphylothermus*
	Species	**Staphylothermus marinus**
	Full Scientific Name (LPSN)	Staphylothermus marinus Stetter and Fiala 1986

Information on culture and growth conditions Culture and growth conditions

[Ref.: #1429]

Culture medium

PYROCOCCUS MEDIUM (DSMZ Medium 377)

[Ref.: #1429]

Culture medium growth

[Ref.: #1429]

Culture medium link

Medium recipe at MediaDive

[Ref.: #1429]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #1429]			growth	88 °C
[Ref.: #67770]			growth	90 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #1429]	Oxygen tolerance	anaerobe
[Ref.: #69480]	Oxygen tolerance	anaerobe Confidence in %93.039

[Ref.: #69480]

Ability of spore formation

no Confidence in %92.263

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	teichoic acid biosynthesis	100	1 of 1
[Ref.: #66794]	pantothenate biosynthesis	100	6 of 6
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	ribulose monophosphate pathway	100	2 of 2
[Ref.: #66794]	mannosylglycerate biosynthesis	100	2 of 2
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	flavin biosynthesis	93.33	14 of 15
[Ref.: #66794]	cellulose degradation	80	4 of 5
[Ref.: #66794]	starch degradation	80	8 of 10
[Ref.: #66794]	aspartate and asparagine metabolism	77.78	7 of 9
[Ref.: #66794]	molybdenum cofactor biosynthesis	77.78	7 of 9
[Ref.: #66794]	palmitate biosynthesis	77.27	17 of 22
[Ref.: #66794]	vitamin B1 metabolism	76.92	10 of 13
[Ref.: #66794]	glycolysis	76.47	13 of 17
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	coenzyme A metabolism	75	3 of 4
[Ref.: #66794]	pyrimidine metabolism	68.89	31 of 45
[Ref.: #66794]	glutamate and glutamine metabolism	67.86	19 of 28
[Ref.: #66794]	glycolate and glyoxylate degradation	66.67	4 of 6
[Ref.: #66794]	L-lactaldehyde 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]	enterobactin biosynthesis	66.67	2 of 3
[Ref.: #66794]	serine metabolism	66.67	6 of 9
[Ref.: #66794]	formaldehyde oxidation	66.67	2 of 3
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	photosynthesis	64.29	9 of 14
[Ref.: #66794]	purine metabolism	62.77	59 of 94
[Ref.: #66794]	lipoate biosynthesis	60	3 of 5
[Ref.: #66794]	glycogen metabolism	60	3 of 5
[Ref.: #66794]	ubiquinone biosynthesis	57.14	4 of 7
[Ref.: #66794]	propanol degradation	57.14	4 of 7
[Ref.: #66794]	degradation of sugar alcohols	56.25	9 of 16
[Ref.: #66794]	oxidative phosphorylation	56.04	51 of 91
[Ref.: #66794]	NAD metabolism	55.56	10 of 18
[Ref.: #66794]	methionine metabolism	53.85	14 of 26
[Ref.: #66794]	lipid metabolism	51.61	16 of 31
[Ref.: #66794]	suberin monomers biosynthesis	50	1 of 2
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	degradation of hexoses	50	9 of 18
[Ref.: #66794]	acetate fermentation	50	2 of 4
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	50	1 of 2
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	dolichol and dolichyl phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	cis-vaccenate biosynthesis	50	1 of 2
[Ref.: #66794]	polyamine pathway	47.83	11 of 23
[Ref.: #66794]	sulfate reduction	46.15	6 of 13
[Ref.: #66794]	alanine metabolism	44.83	13 of 29
[Ref.: #66794]	non-pathway related	44.74	17 of 38
[Ref.: #66794]	cysteine metabolism	44.44	8 of 18
[Ref.: #66794]	valine metabolism	44.44	4 of 9
[Ref.: #66794]	glutathione metabolism	42.86	6 of 14
[Ref.: #66794]	tyrosine metabolism	42.86	6 of 14
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
[Ref.: #66794]	propionate fermentation	40	4 of 10
[Ref.: #66794]	vitamin K metabolism	40	2 of 5
[Ref.: #66794]	hydrogen production	40	2 of 5
[Ref.: #66794]	3-chlorocatechol degradation	40	2 of 5
[Ref.: #66794]	phenylalanine metabolism	38.46	5 of 13
[Ref.: #66794]	urea cycle	38.46	5 of 13
[Ref.: #66794]	isoprenoid biosynthesis	38.46	10 of 26
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	37.5	3 of 8
[Ref.: #66794]	ketogluconate metabolism	37.5	3 of 8
[Ref.: #66794]	C4 and CAM-carbon fixation	37.5	3 of 8
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	36.36	4 of 11
[Ref.: #66794]	pentose phosphate pathway	36.36	4 of 11
[Ref.: #66794]	metabolism of disaccharids	36.36	4 of 11
[Ref.: #66794]	lysine metabolism	35.71	15 of 42
[Ref.: #66794]	tryptophan metabolism	34.21	13 of 38
[Ref.: #66794]	lipid A biosynthesis	33.33	3 of 9
[Ref.: #66794]	CO2 fixation in Crenarchaeota	33.33	3 of 9
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	octane oxidation	33.33	1 of 3
[Ref.: #66794]	chlorophyll metabolism	33.33	6 of 18
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	myo-inositol biosynthesis	30	3 of 10
[Ref.: #66794]	phenol degradation	30	6 of 20
[Ref.: #66794]	threonine metabolism	30	3 of 10
[Ref.: #66794]	arginine metabolism	29.17	7 of 24
[Ref.: #66794]	citric acid cycle	28.57	4 of 14
[Ref.: #66794]	cardiolipin biosynthesis	28.57	2 of 7
[Ref.: #66794]	mevalonate metabolism	28.57	2 of 7
[Ref.: #66794]	degradation of pentoses	28.57	8 of 28
[Ref.: #66794]	vitamin B6 metabolism	27.27	3 of 11
[Ref.: #66794]	peptidoglycan biosynthesis	26.67	4 of 15
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	gluconeogenesis	25	2 of 8
[Ref.: #66794]	sulfopterin metabolism	25	1 of 4
[Ref.: #66794]	biotin biosynthesis	25	1 of 4
[Ref.: #66794]	catecholamine biosynthesis	25	1 of 4
[Ref.: #66794]	ppGpp biosynthesis	25	1 of 4
[Ref.: #66794]	CMP-KDO biosynthesis	25	1 of 4
[Ref.: #66794]	methanogenesis from CO2	25	3 of 12
[Ref.: #66794]	butanoate fermentation	25	1 of 4
[Ref.: #66794]	isoleucine metabolism	25	2 of 8
[Ref.: #66794]	leucine metabolism	23.08	3 of 13
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	23.08	3 of 13
[Ref.: #66794]	ascorbate metabolism	22.73	5 of 22
[Ref.: #66794]	nitrate assimilation	22.22	2 of 9
[Ref.: #66794]	histidine metabolism	20.69	6 of 29
		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.: #1429]	Sample type/isolated from	geothermally heated marine sediment
[Ref.: #1429]	Geographic location (country and/or sea, region)	Vulcano island
[Ref.: #1429]	Country	Italy
[Ref.: #1429]	Country ISO 3 Code	ITA
[Ref.: #1429]	Continent	Europe

[Ref.: #67770]	Sample type/isolated from	Geothermally heated sea floor at Vulcano
[Ref.: #67770]	Country	Italy
[Ref.: #67770]	Country ISO 3 Code	ITA
[Ref.: #67770]	Continent	Europe
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Marine
#Environmental	#Aquatic	#Sediment

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence X99560 (>99% sequence identity) for Staphylothermus marinus subclade from Microbeatlas

Aquatic Samples	1
Soil Samples
Animal Samples
Plant Samples
Total Samples	1

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

[Ref.: #1429]

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]	S.marinus 16S rRNA gene	X99560	1442	GenBank ENA	399550 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Staphylothermus marinus F1	GCA_000015945	complete	GenBank ENA	399550 tax ID	*
[Ref.: #66792]	Staphylothermus marinus F1, DSM 3639	640069332	complete	JGI IMG/M	399550 tax ID	*
[Ref.: #66792]	Staphylothermus marinus F1	399550.11	complete	PATRIC	399550 tax ID	*

[Ref.: #1429]	GC-content	35.0 mol%
[Ref.: #67770]	GC-content	35.3 mol%	high performance liquid chromatography (HPLC)
[Ref.: #67770]	GC-content	34.9 mol%	thermal denaturation, midpoint method (Tm)

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

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Staphylothermus marinus F1 F1 NCBI: GCA_000015945.1
[Ref.: #69480]	gram-positive	gram-positiveⓘ	no	71.211	no
[Ref.: #69480]	anaerobic	anaerobicⓘ	yes	93.039	yes
[Ref.: #69480]	aerobic	aerobicⓘ	no	91.866	yes
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	92.263	no
[Ref.: #69480]	thermophilic	thermophileⓘ	yes	85.553	yes
[Ref.: #69480]	flagellated	motile2+ⓘ	no	73.607	no

Availability in culture collections External links

[Ref.: #1429]

Culture collection no.

DSM 3639, JCM 9404, ATCC 43588

[Ref.: #73701]

SI-ID 47743

References

#1429

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 3639

#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 )

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

#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) .

#73701

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-ID47743.1 )

* These data were automatically processed and therefore are not curated

Change proposal

You found an error in BacDive? Please tell us about it!

Note that changes will be reviewed and judged. If your changes are legitimate, changes will occur within the next BacDive update. Only proposed changes supported by the according reference will be reviewed. The BacDive team reserves the right to reject proposed changes.

Search for species Staphylothermus marinus in external resources:
SILVA
BRENDA
PANGAEA
GBIF

Staphylothermus marinus F1 F1

Change proposal

Change proposal