Name: Hydrogenothermus marinus VM1
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 514

Type strain:

Species: Hydrogenothermus marinus

Strain Designation: VM1

Culture col. no.: DSM 12046, JCM 10974, ATCC BAA-483

Strain history: M. Thomm VM1.

NCBI tax ID(s): 133270 (species)

SI-ID 49229

DSM 12046, JCM 10974, ATCC BAA-483

Section

Hydrogenothermus marinus VM1 is an anaerobe, thermophilic, motile bacterium of the family Hydrogenothermaceae.

motile
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	*Aquificota*
	Class	*Aquificia*
	Order	*Aquificales*
	Family	*Hydrogenothermaceae*
	Genus	*Hydrogenothermus*
	Species	**Hydrogenothermus marinus**
	Full Scientific Name (LPSN)	Hydrogenothermus marinus Stöhr et al. 2001

Information on morphological and physiological properties Morphology

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

[Ref.: #69480]	Motility	yes Confidence in %94.818

Information on culture and growth conditions Culture and growth conditions

[Ref.: #4588]

Culture medium

VM1 MEDIUM (DSMZ Medium 890)

[Ref.: #4588]

Culture medium growth

[Ref.: #4588]

Culture medium link

Medium recipe at MediaDive

[Ref.: #4588]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #4588]			growth	65 °C
[Ref.: #67770]			growth	65 °C

[Ref.: #4588]	Temperature range	thermophilic
[Ref.: #67770]	Temperature range	thermophilic
[Ref.: #69480]	Temperature range	thermophilic Confidence in %100

Information on physiology and metabolism Physiology and metabolism

[Ref.: #69480]

Oxygen tolerance

anaerobe Confidence in %94.575

[Ref.: #69480]

Ability of spore formation

no Confidence in %99.893

[Ref.: #67770]

Observation

quinones: MTK-7 analog

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	chorismate metabolism	100	9 of 9
[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]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	glycolate and glyoxylate degradation	100	6 of 6
[Ref.: #66794]	palmitate biosynthesis	95.45	21 of 22
[Ref.: #66794]	valine metabolism	88.89	8 of 9
[Ref.: #66794]	isoleucine metabolism	87.5	7 of 8
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	hydrogen production	80	4 of 5
[Ref.: #66794]	threonine metabolism	80	8 of 10
[Ref.: #66794]	photosynthesis	78.57	11 of 14
[Ref.: #66794]	tetrahydrofolate metabolism	78.57	11 of 14
[Ref.: #66794]	molybdenum cofactor biosynthesis	77.78	7 of 9
[Ref.: #66794]	lipid A biosynthesis	77.78	7 of 9
[Ref.: #66794]	NAD metabolism	77.78	14 of 18
[Ref.: #66794]	CMP-KDO biosynthesis	75	3 of 4
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	starch degradation	70	7 of 10
[Ref.: #66794]	vitamin B1 metabolism	69.23	9 of 13
[Ref.: #66794]	phenylalanine metabolism	69.23	9 of 13
[Ref.: #66794]	formaldehyde oxidation	66.67	2 of 3
[Ref.: #66794]	flavin biosynthesis	66.67	10 of 15
[Ref.: #66794]	L-lactaldehyde degradation	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]	cyanate degradation	66.67	2 of 3
[Ref.: #66794]	alanine metabolism	65.52	19 of 29
[Ref.: #66794]	heme metabolism	64.29	9 of 14
[Ref.: #66794]	glutamate and glutamine metabolism	64.29	18 of 28
[Ref.: #66794]	purine metabolism	63.83	60 of 94
[Ref.: #66794]	C4 and CAM-carbon fixation	62.5	5 of 8
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
[Ref.: #66794]	glycogen metabolism	60	3 of 5
[Ref.: #66794]	cellulose degradation	60	3 of 5
[Ref.: #66794]	glycolysis	58.82	10 of 17
[Ref.: #66794]	citric acid cycle	57.14	8 of 14
[Ref.: #66794]	ubiquinone biosynthesis	57.14	4 of 7
[Ref.: #66794]	serine metabolism	55.56	5 of 9
[Ref.: #66794]	aspartate and asparagine metabolism	55.56	5 of 9
[Ref.: #66794]	pyrimidine metabolism	55.56	25 of 45
[Ref.: #66794]	vitamin B6 metabolism	54.55	6 of 11
[Ref.: #66794]	urea cycle	53.85	7 of 13
[Ref.: #66794]	methionine metabolism	53.85	14 of 26
[Ref.: #66794]	isoprenoid biosynthesis	53.85	14 of 26
[Ref.: #66794]	propionate fermentation	50	5 of 10
[Ref.: #66794]	cis-vaccenate biosynthesis	50	1 of 2
[Ref.: #66794]	gluconeogenesis	50	4 of 8
[Ref.: #66794]	dTDPLrhamnose biosynthesis	50	4 of 8
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	adipate degradation	50	1 of 2
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	degradation of hexoses	50	9 of 18
[Ref.: #66794]	mannosylglycerate biosynthesis	50	1 of 2
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	1,4-dihydroxy-6-naphthoate biosynthesis	50	3 of 6
[Ref.: #66794]	myo-inositol biosynthesis	50	5 of 10
[Ref.: #66794]	leucine metabolism	46.15	6 of 13
[Ref.: #66794]	proline metabolism	45.45	5 of 11
[Ref.: #66794]	histidine metabolism	44.83	13 of 29
[Ref.: #66794]	non-pathway related	44.74	17 of 38
[Ref.: #66794]	CO2 fixation in Crenarchaeota	44.44	4 of 9
[Ref.: #66794]	reductive acetyl coenzyme A pathway	42.86	3 of 7
[Ref.: #66794]	propanol degradation	42.86	3 of 7
[Ref.: #66794]	tyrosine metabolism	42.86	6 of 14
[Ref.: #66794]	cardiolipin biosynthesis	42.86	3 of 7
[Ref.: #66794]	arginine metabolism	41.67	10 of 24
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
[Ref.: #66794]	lysine metabolism	40.48	17 of 42
[Ref.: #66794]	lipoate biosynthesis	40	2 of 5
[Ref.: #66794]	O-antigen biosynthesis	40	2 of 5
[Ref.: #66794]	tryptophan metabolism	39.47	15 of 38
[Ref.: #66794]	ketogluconate metabolism	37.5	3 of 8
[Ref.: #66794]	metabolism of disaccharids	36.36	4 of 11
[Ref.: #66794]	pentose phosphate pathway	36.36	4 of 11
[Ref.: #66794]	oxidative phosphorylation	35.16	32 of 91
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	cysteine metabolism	33.33	6 of 18
[Ref.: #66794]	octane oxidation	33.33	1 of 3
[Ref.: #66794]	selenocysteine biosynthesis	33.33	2 of 6
[Ref.: #66794]	polyamine pathway	30.43	7 of 23
[Ref.: #66794]	coenzyme M biosynthesis	30	3 of 10
[Ref.: #66794]	aclacinomycin biosynthesis	28.57	2 of 7
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	butanoate fermentation	25	1 of 4
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	sulfate reduction	23.08	3 of 13
[Ref.: #66794]	lipid metabolism	22.58	7 of 31
[Ref.: #66794]	chlorophyll metabolism	22.22	4 of 18
[Ref.: #66794]	nitrate assimilation	22.22	2 of 9
[Ref.: #66794]	degradation of pentoses	21.43	6 of 28
[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.: #67770]	Sample type/isolated from	Marine hydrothermal area of Vulcano Island
[Ref.: #67770]	Country	Italy
[Ref.: #67770]	Country ISO 3 Code	ITA
[Ref.: #67770]	Continent	Europe

[Ref.: #4588]	Geographic location (country and/or sea, region)	Vulcano, Porto di Levante
[Ref.: #4588]	Country	Italy
[Ref.: #4588]	Country ISO 3 Code	ITA
[Ref.: #4588]	Continent	Europe
* marker position based on {}

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

[Ref.: #4588]

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.: #4588]	Hydrogenothermus marinus partial 16S rRNA gene	AJ292525	1433	ENA	133270 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Hydrogenothermus marinus VM1	GCA_003688665	scaffold	GenBank	133270 tax ID
[Ref.: #66792]	Hydrogenothermus marinus strain VM1	133270.3	wgs	PATRIC	133270 tax ID	*
[Ref.: #66792]	Hydrogenothermus marinus DSM 12046	2734482257	draft	JGI IMG/M	133270 tax ID	*

[Ref.: #67770]

GC-content

43 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: Hydrogenothermus marinus VM1 NCBI: GCA_003688665.1
[Ref.: #69481]	spore-forming	no	51	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Hydrogenothermus marinus strain VM1 PATRIC: 133270.3
[Ref.: #69480]	motile	yes	85.008	no
[Ref.: #69480]	gram-positive	no	99.481	no
[Ref.: #69480]	anaerobic	yes	70.898	no
[Ref.: #69480]	halophile	no	83.69	no
[Ref.: #69480]	spore-forming	no	97.077	no
[Ref.: #69480]	thermophile	yes	100	no
[Ref.: #69480]	glucose-util	yes	55.043	no
[Ref.: #69480]	aerobic	no	98.067	no
[Ref.: #69480]	flagellated	no	85.519	no
[Ref.: #69480]	glucose-ferment	no	87.225	no

Availability in culture collections External links

[Ref.: #4588]

Culture collection no.

DSM 12046, JCM 10974, ATCC BAA-483

[Ref.: #70193]

SI-ID 49229

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Hydrogenothermus marinus gen. nov., sp. nov., a novel thermophilic hydrogen-oxidizing bacterium, recognition of Calderobacterium hydrogenophilum as a member of the genus Hydrogenobacter and proposal of the reclassification of Hydrogenobacter acidophilus as Hydrogenobaculum acidophilum gen. nov., comb. nov., in the phylum 'Hydrogenobacter/Aquifex'.	Stohr R, Waberski A, Volker H, Tindall BJ, Thomm M	Int J Syst Evol Microbiol	10.1099/00207713-51-5-1853	2001	*

References

#4588

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 12046

#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 )

#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 )

#70193

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-ID49229.1 )

* 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 Hydrogenothermus marinus in external resources:
SILVA
BRENDA
PANGAEA
StrainInfo
GBIF

Hydrogenothermus marinus VM1

Hydrogenothermus marinus strain VM1

Change proposal

Change proposal