Name: Hyperthermus butylicus PLM1-5
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 13524

Type strain:

Species: Hyperthermus butylicus

Strain Designation: PLM1-5

Culture col. no.: DSM 5456, JCM 9403

Strain history: DSM 5456 <-- W. Zillig PLM1-5.

NCBI tax ID(s): 415426 (strain), 54248 (species)

SI-ID 92326

DSM 5456, JCM 9403, ATCC 700455

Section

Hyperthermus butylicus PLM1-5 is an anaerobe, hyperthermophilic, Gram-negative archaeon that was isolated from solfataric sea floor sediment.

Gram-negative
anaerobe
hyperthermophilic
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	*Pyrodictiaceae*
	Genus	*Hyperthermus*
	Species	**Hyperthermus butylicus**
	Full Scientific Name (LPSN)	Hyperthermus butylicus Zillig et al. 1991

Information on morphological and physiological properties Morphology

[Ref.: #69480]	Gram stain	negative Confidence in %99.967

[Ref.: #69480]	Motility	yes Confidence in %90.214

Information on culture and growth conditions Culture and growth conditions

[Ref.: #2171]

Culture medium

HYPERTHERMUS BUTYLICUS MEDIUM (DSMZ Medium 491)

[Ref.: #2171]

Culture medium growth

[Ref.: #2171]

Culture medium link

Medium recipe at MediaDive

[Ref.: #2171]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #2171]			growth	99 °C
[Ref.: #67770]			growth	95 °C

[Ref.: #2171]	Temperature range	hyperthermophilic
[Ref.: #67770]	Temperature range	hyperthermophilic
[Ref.: #69480]	Temperature range	thermophilic Confidence in %100

Information on physiology and metabolism Physiology and metabolism

[Ref.: #2171]	Oxygen tolerance	anaerobe
[Ref.: #69480]	Oxygen tolerance	anaerobe Confidence in %99.05

[Ref.: #69480]

Ability of spore formation

no Confidence in %99.852

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	sulfopterin metabolism	100	4 of 4
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	ribulose monophosphate pathway	100	2 of 2
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	87.5	7 of 8
[Ref.: #66794]	flavin biosynthesis	86.67	13 of 15
[Ref.: #66794]	ubiquinone biosynthesis	85.71	6 of 7
[Ref.: #66794]	hydrogen production	80	4 of 5
[Ref.: #66794]	molybdenum cofactor biosynthesis	77.78	7 of 9
[Ref.: #66794]	NAD metabolism	77.78	14 of 18
[Ref.: #66794]	palmitate biosynthesis	77.27	17 of 22
[Ref.: #66794]	coenzyme A metabolism	75	3 of 4
[Ref.: #66794]	pyrimidine metabolism	73.33	33 of 45
[Ref.: #66794]	photosynthesis	71.43	10 of 14
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	aspartate and asparagine metabolism	66.67	6 of 9
[Ref.: #66794]	d-mannose degradation	66.67	6 of 9
[Ref.: #66794]	pantothenate biosynthesis	66.67	4 of 6
[Ref.: #66794]	glycolysis	64.71	11 of 17
[Ref.: #66794]	heme metabolism	64.29	9 of 14
[Ref.: #66794]	glutamate and glutamine metabolism	64.29	18 of 28
[Ref.: #66794]	C4 and CAM-carbon fixation	62.5	5 of 8
[Ref.: #66794]	gluconeogenesis	62.5	5 of 8
[Ref.: #66794]	urea cycle	61.54	8 of 13
[Ref.: #66794]	polyamine pathway	60.87	14 of 23
[Ref.: #66794]	oxidative phosphorylation	60.44	55 of 91
[Ref.: #66794]	lipoate biosynthesis	60	3 of 5
[Ref.: #66794]	cellulose degradation	60	3 of 5
[Ref.: #66794]	threonine metabolism	60	6 of 10
[Ref.: #66794]	methionine metabolism	57.69	15 of 26
[Ref.: #66794]	nitrate assimilation	55.56	5 of 9
[Ref.: #66794]	serine metabolism	55.56	5 of 9
[Ref.: #66794]	pentose phosphate pathway	54.55	6 of 11
[Ref.: #66794]	purine metabolism	54.26	51 of 94
[Ref.: #66794]	vitamin B1 metabolism	53.85	7 of 13
[Ref.: #66794]	alanine metabolism	51.72	15 of 29
[Ref.: #66794]	denitrification	50	1 of 2
[Ref.: #66794]	dolichol and dolichyl phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	cysteine metabolism	50	9 of 18
[Ref.: #66794]	kanosamine biosynthesis II	50	1 of 2
[Ref.: #66794]	myo-inositol biosynthesis	50	5 of 10
[Ref.: #66794]	cis-vaccenate biosynthesis	50	1 of 2
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	50	1 of 2
[Ref.: #66794]	glycolate and glyoxylate degradation	50	3 of 6
[Ref.: #66794]	acetate fermentation	50	2 of 4
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	50	6 of 12
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	selenocysteine biosynthesis	50	3 of 6
[Ref.: #66794]	lysine metabolism	47.62	20 of 42
[Ref.: #66794]	sulfate reduction	46.15	6 of 13
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	45.45	5 of 11
[Ref.: #66794]	reductive acetyl coenzyme A pathway	42.86	3 of 7
[Ref.: #66794]	creatinine degradation	40	2 of 5
[Ref.: #66794]	coenzyme M biosynthesis	40	4 of 10
[Ref.: #66794]	factor 420 biosynthesis	40	2 of 5
[Ref.: #66794]	phenylalanine 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]	non-pathway related	36.84	14 of 38
[Ref.: #66794]	tetrahydrofolate metabolism	35.71	5 of 14
[Ref.: #66794]	tyrosine metabolism	35.71	5 of 14
[Ref.: #66794]	citric acid cycle	35.71	5 of 14
[Ref.: #66794]	lipid metabolism	35.48	11 of 31
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	cyanate degradation	33.33	1 of 3
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	CO2 fixation in Crenarchaeota	33.33	3 of 9
[Ref.: #66794]	formaldehyde oxidation	33.33	1 of 3
[Ref.: #66794]	valine metabolism	33.33	3 of 9
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	octane oxidation	33.33	1 of 3
[Ref.: #66794]	tryptophan metabolism	31.58	12 of 38
[Ref.: #66794]	isoprenoid biosynthesis	30.77	8 of 26
[Ref.: #66794]	propionate fermentation	30	3 of 10
[Ref.: #66794]	Entner Doudoroff pathway	30	3 of 10
[Ref.: #66794]	propanol degradation	28.57	2 of 7
[Ref.: #66794]	mevalonate metabolism	28.57	2 of 7
[Ref.: #66794]	glutathione metabolism	28.57	4 of 14
[Ref.: #66794]	cardiolipin biosynthesis	28.57	2 of 7
[Ref.: #66794]	aclacinomycin biosynthesis	28.57	2 of 7
[Ref.: #66794]	degradation of hexoses	27.78	5 of 18
[Ref.: #66794]	metabolism of disaccharids	27.27	3 of 11
[Ref.: #66794]	vitamin B6 metabolism	27.27	3 of 11
[Ref.: #66794]	proline metabolism	27.27	3 of 11
[Ref.: #66794]	peptidoglycan biosynthesis	26.67	4 of 15
[Ref.: #66794]	phenol degradation	25	5 of 20
[Ref.: #66794]	CMP-KDO biosynthesis	25	1 of 4
[Ref.: #66794]	carnitine metabolism	25	2 of 8
[Ref.: #66794]	biotin biosynthesis	25	1 of 4
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	isoleucine metabolism	25	2 of 8
[Ref.: #66794]	ppGpp biosynthesis	25	1 of 4
[Ref.: #66794]	catecholamine biosynthesis	25	1 of 4
[Ref.: #66794]	butanoate fermentation	25	1 of 4
[Ref.: #66794]	methanogenesis from CO2	25	3 of 12
[Ref.: #66794]	glycogen biosynthesis	25	1 of 4
[Ref.: #66794]	lipid A biosynthesis	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.: #2171]	Sample type/isolated from	solfataric sea floor sediment
[Ref.: #2171]	Geographic location (country and/or sea, region)	San Miguel island
[Ref.: #2171]	Country	Azores
[Ref.: #2171]	Country ISO 3 Code	PRT

[Ref.: #67770]	Sample type/isolated from	Solfataric sea floor on the beach of the São Miguel Island
[Ref.: #67770]	Geographic location (country and/or sea, region)	Azores
[Ref.: #67770]	Country	Portugal
[Ref.: #67770]	Country ISO 3 Code	PRT
[Ref.: #67770]	Continent	Europe
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Marine
#Environmental	#Aquatic	#Sediment
#Environmental	#Terrestrial	#Volcanic

What are isolation sources categories?

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

[Ref.: #2171]

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]	H.butylicus 16S rRNA gene	X99553	1311	ENA	415426 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Hyperthermus butylicus DSM 5456	GCA_000015145	complete	GenBank	415426 tax ID	*
[Ref.: #66792]	Hyperthermus butylicus DSM 5456	640069314	complete	JGI IMG/M	415426 tax ID	*
[Ref.: #66792]	Hyperthermus butylicus DSM 5456	415426.13	complete	PATRIC	415426 tax ID	*

[Ref.: #2171]

GC-content

55.6 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: Hyperthermus butylicus DSM 5456 DSM 5456 NCBI: GCA_000015145.1
[Ref.: #69481]	spore-forming	yes	83	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Hyperthermus butylicus DSM 5456 DSM 5456 NCBI: GCA_000015145.1
[Ref.: #69480]	motile	no	62.344	no
[Ref.: #69480]	flagellated	no	90.043	no
[Ref.: #69480]	gram-positive	no	97.412	no
[Ref.: #69480]	anaerobic	yes	99.055	no
[Ref.: #69480]	halophile	no	77.957	no
[Ref.: #69480]	spore-forming	no	96.488	no
[Ref.: #69480]	thermophile	yes	100	yes
[Ref.: #69480]	glucose-util	yes	74.797	no
[Ref.: #69480]	aerobic	no	96.633	yes
[Ref.: #69480]	glucose-ferment	no	62.251	no

Availability in culture collections External links

[Ref.: #2171]

Culture collection no.

DSM 5456, JCM 9403

[Ref.: #82715]

SI-ID 92326

References

#2171

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 5456

#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;

#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 )

#82715

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-ID92326.1 )

* These data were automatically processed and therefore are not curated

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Hyperthermus butylicus DSM 5456 DSM 5456

Hyperthermus butylicus DSM 5456 DSM 5456

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