Name: Halobaculum gomorrense DS2807
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 5871

Type strain:

Species: Halobaculum gomorrense

Strain Designation: DS2807

Culture col. no.: DSM 9297, JCM 9908, ATCC 700876, CGMCC 1.10336

Strain history: DSM 9297 <-- A. Oren DS 2807.

NCBI tax ID(s): 43928 (species)

SI-ID 44189

ATCC 700876, DSM 9297, JCM 9908

Section

Halobaculum gomorrense DS2807 is a mesophilic, Gram-negative archaeon of the family Halorubraceae.

Gram-negative
mesophilic
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	*Methanobacteriota*
	Class	*Halobacteria*
	Order	*Haloferacales*
	Family	*Halorubraceae*
	Genus	*Halobaculum*
	Species	**Halobaculum gomorrense**
	Full Scientific Name (LPSN)	Halobaculum gomorrense Oren et al. 1995

Information on morphological and physiological properties Morphology

[Ref.: #69480]	Gram stain	negative Confidence in %99.921

Information on culture and growth conditions Culture and growth conditions

[Ref.: #3535]

Culture medium

HALOBACULUM GOMORRENSE MEDIUM (DSMZ Medium 823)

[Ref.: #3535]

Culture medium growth

[Ref.: #3535]

Culture medium link

Medium recipe at MediaDive

[Ref.: #3535]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #3535]			growth	35 °C
[Ref.: #67770]			growth	37 °C

[Ref.: #3535]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.995

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	reductive acetyl coenzyme A pathway	100	7 of 7
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	L-lactaldehyde degradation	100	3 of 3
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	denitrification	100	2 of 2
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	acetate fermentation	100	4 of 4
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	aerobactin biosynthesis	100	1 of 1
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	factor 420 biosynthesis	100	5 of 5
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	vitamin K metabolism	100	5 of 5
[Ref.: #66794]	phenylacetate degradation (aerobic)	100	5 of 5
[Ref.: #66794]	starch degradation	90	9 of 10
[Ref.: #66794]	molybdenum cofactor biosynthesis	88.89	8 of 9
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	aspartate and asparagine metabolism	88.89	8 of 9
[Ref.: #66794]	glycolate and glyoxylate degradation	83.33	5 of 6
[Ref.: #66794]	pantothenate biosynthesis	83.33	5 of 6
[Ref.: #66794]	ethylmalonyl-CoA pathway	80	4 of 5
[Ref.: #66794]	threonine metabolism	80	8 of 10
[Ref.: #66794]	Entner Doudoroff pathway	80	8 of 10
[Ref.: #66794]	glycogen metabolism	80	4 of 5
[Ref.: #66794]	glutamate and glutamine metabolism	78.57	22 of 28
[Ref.: #66794]	CO2 fixation in Crenarchaeota	77.78	7 of 9
[Ref.: #66794]	valine metabolism	77.78	7 of 9
[Ref.: #66794]	vitamin B1 metabolism	76.92	10 of 13
[Ref.: #66794]	phenylalanine metabolism	76.92	10 of 13
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	toluene degradation	75	3 of 4
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
[Ref.: #66794]	isoleucine metabolism	75	6 of 8
[Ref.: #66794]	C4 and CAM-carbon fixation	75	6 of 8
[Ref.: #66794]	gluconeogenesis	75	6 of 8
[Ref.: #66794]	lipid metabolism	74.19	23 of 31
[Ref.: #66794]	vitamin B12 metabolism	73.53	25 of 34
[Ref.: #66794]	purine metabolism	73.4	69 of 94
[Ref.: #66794]	flavin biosynthesis	73.33	11 of 15
[Ref.: #66794]	citric acid cycle	71.43	10 of 14
[Ref.: #66794]	glycolysis	70.59	12 of 17
[Ref.: #66794]	propionate fermentation	70	7 of 10
[Ref.: #66794]	leucine metabolism	69.23	9 of 13
[Ref.: #66794]	tryptophan metabolism	68.42	26 of 38
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	66.67	8 of 12
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	arginine metabolism	66.67	16 of 24
[Ref.: #66794]	IAA biosynthesis	66.67	2 of 3
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	cyanate degradation	66.67	2 of 3
[Ref.: #66794]	serine metabolism	66.67	6 of 9
[Ref.: #66794]	non-pathway related	65.79	25 of 38
[Ref.: #66794]	methionine metabolism	65.38	17 of 26
[Ref.: #66794]	phenol degradation	65	13 of 20
[Ref.: #66794]	pyrimidine metabolism	64.44	29 of 45
[Ref.: #66794]	photosynthesis	64.29	9 of 14
[Ref.: #66794]	tetrahydrofolate metabolism	64.29	9 of 14
[Ref.: #66794]	ketogluconate metabolism	62.5	5 of 8
[Ref.: #66794]	dTDPLrhamnose biosynthesis	62.5	5 of 8
[Ref.: #66794]	alanine metabolism	62.07	18 of 29
[Ref.: #66794]	NAD metabolism	61.11	11 of 18
[Ref.: #66794]	3-chlorocatechol degradation	60	3 of 5
[Ref.: #66794]	glycine betaine biosynthesis	60	3 of 5
[Ref.: #66794]	cellulose degradation	60	3 of 5
[Ref.: #66794]	gallate degradation	60	3 of 5
[Ref.: #66794]	oxidative phosphorylation	59.34	54 of 91
[Ref.: #66794]	carotenoid biosynthesis	59.09	13 of 22
[Ref.: #66794]	lysine metabolism	57.14	24 of 42
[Ref.: #66794]	glutathione metabolism	57.14	8 of 14
[Ref.: #66794]	heme metabolism	57.14	8 of 14
[Ref.: #66794]	ubiquinone biosynthesis	57.14	4 of 7
[Ref.: #66794]	propanol degradation	57.14	4 of 7
[Ref.: #66794]	nitrate assimilation	55.56	5 of 9
[Ref.: #66794]	d-mannose degradation	55.56	5 of 9
[Ref.: #66794]	histidine metabolism	55.17	16 of 29
[Ref.: #66794]	proline metabolism	54.55	6 of 11
[Ref.: #66794]	pentose phosphate pathway	54.55	6 of 11
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	myo-inositol biosynthesis	50	5 of 10
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	4-hydroxyphenylacetate degradation	50	5 of 10
[Ref.: #66794]	lactate fermentation	50	2 of 4
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	resorcinol degradation	50	1 of 2
[Ref.: #66794]	mannosylglycerate biosynthesis	50	1 of 2
[Ref.: #66794]	selenocysteine biosynthesis	50	3 of 6
[Ref.: #66794]	vitamin E metabolism	50	2 of 4
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	degradation of sugar alcohols	50	8 of 16
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	50	1 of 2
[Ref.: #66794]	dolichol and dolichyl phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	kanosamine biosynthesis II	50	1 of 2
[Ref.: #66794]	cysteine metabolism	50	9 of 18
[Ref.: #66794]	degradation of pentoses	46.43	13 of 28
[Ref.: #66794]	urea cycle	46.15	6 of 13
[Ref.: #66794]	metabolism of disaccharids	45.45	5 of 11
[Ref.: #66794]	degradation of sugar acids	44	11 of 25
[Ref.: #66794]	androgen and estrogen metabolism	43.75	7 of 16
[Ref.: #66794]	cardiolipin biosynthesis	42.86	3 of 7
[Ref.: #66794]	aclacinomycin biosynthesis	42.86	3 of 7
[Ref.: #66794]	benzoyl-CoA degradation	42.86	3 of 7
[Ref.: #66794]	tyrosine metabolism	42.86	6 of 14
[Ref.: #66794]	3-phenylpropionate degradation	40	6 of 15
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	coenzyme M biosynthesis	40	4 of 10
[Ref.: #66794]	creatinine degradation	40	2 of 5
[Ref.: #66794]	bacilysin biosynthesis	40	2 of 5
[Ref.: #66794]	arachidonic acid metabolism	38.89	7 of 18
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	38.46	5 of 13
[Ref.: #66794]	isoprenoid biosynthesis	38.46	10 of 26
[Ref.: #66794]	carnitine metabolism	37.5	3 of 8
[Ref.: #66794]	cholesterol biosynthesis	36.36	4 of 11
[Ref.: #66794]	ascorbate metabolism	36.36	8 of 22
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	enterobactin biosynthesis	33.33	1 of 3
[Ref.: #66794]	lipid A biosynthesis	33.33	3 of 9
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	allantoin degradation	33.33	3 of 9
[Ref.: #66794]	degradation of hexoses	33.33	6 of 18
[Ref.: #66794]	sulfate reduction	30.77	4 of 13
[Ref.: #66794]	bile acid biosynthesis, neutral pathway	29.41	5 of 17
[Ref.: #66794]	mevalonate metabolism	28.57	2 of 7
[Ref.: #66794]	d-xylose degradation	27.27	3 of 11
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
[Ref.: #66794]	vitamin B6 metabolism	27.27	3 of 11
[Ref.: #66794]	polyamine pathway	26.09	6 of 23
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	butanoate fermentation	25	1 of 4
[Ref.: #66794]	catecholamine biosynthesis	25	1 of 4
[Ref.: #66794]	ppGpp biosynthesis	25	1 of 4
[Ref.: #66794]	methanogenesis from CO2	25	3 of 12
[Ref.: #66794]	phenylpropanoid biosynthesis	23.08	3 of 13
[Ref.: #66794]	4-hydroxymandelate degradation	22.22	2 of 9
		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	Dead Sea

[Ref.: #3535]	Geographic location (country and/or sea, region)	Dead Sea
[Ref.: #3535]	Country	Israel
[Ref.: #3535]	Country ISO 3 Code	ISR
[Ref.: #3535]	Continent	Asia
* marker position based on {}

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

[Ref.: #3535]

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:

Only first 5 entries are displayed. Click here to see all.

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Halobaculum gomorrense 16S ribosomal RNA (16S rRNA) gene	L37444	1474	ENA	43928 tax ID
[Ref.: #20218]	Halobaculum gomorrense strain JCM 9908 clone A 16S ribosomal RNA gene, partial sequence	HM159610	1472	ENA	43928 tax ID	*
[Ref.: #20218]	Halobaculum gomorrense strain JCM 9908 clone B 16S ribosomal RNA gene, partial sequence	HM159611	1472	ENA	43928 tax ID	*
[Ref.: #20218]	Halobaculum gomorrense gene for 16S ribosomal RNA, partial sequence, strain: JCM 9908, rrnA	AB477982	1432	ENA	43928 tax ID	*
[Ref.: #20218]	Halobaculum gomorrense gene for 16S rRNA, complete sequence, strain: JCM 9908	AB663364	1472	ENA	43928 tax ID	*
[Ref.: #20218]	Halobaculum gomorrense gene for 16S ribosomal RNA, partial sequence, strain: JCM 9908, rrnB	AB477983	1432	ENA	43928 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Halobaculum gomorrense DSM 9297	GCA_900129775	scaffold	GenBank	43928 tax ID
[Ref.: #66792]	Halobaculum gomorrense DSM 9297	2695420988	draft	JGI IMG/M	43928 tax ID	*
[Ref.: #66792]	Halobaculum gomorrense strain DSM 9297	43928.3	wgs	PATRIC	43928 tax ID	*

[Ref.: #67770]

GC-content

70 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: Halobaculum gomorrense DSM 9297 NCBI: GCA_900129775.1
[Ref.: #69481]	spore-forming	no	100	no

Availability in culture collections External links

[Ref.: #3535]

Culture collection no.

DSM 9297, JCM 9908, ATCC 700876, CGMCC 1.10336

[Ref.: #75351]

SI-ID 44189

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Halobaculum rubrum sp. nov., an extremely halophilic archaeon isolated from a salt lake.	Dilmurat M, Hu XY, Dilbar T, Cui HL	Int J Syst Evol Microbiol	10.1099/ijsem.0.005242	2022	*
Phylogeny	Halobaculum roseum sp. nov., isolated from underground salt deposits.	Chen S, Xu Y, Liu HC, Yang AN, Ke LX	Int J Syst Evol Microbiol	10.1099/ijsem.0.001663	2017	*
Phylogeny	Halobaculum magnesiiphilum sp. nov., a magnesium-dependent haloarchaeon isolated from commercial salt.	Shimoshige H, Yamada T, Minegishi H, Echigo A, Shimane Y, Kamekura M, Itoh T, Usami R	Int J Syst Evol Microbiol	10.1099/ijs.0.037432-0	2012	*
Phylogeny	Halolamina pelagica gen. nov., sp. nov., a new member of the family Halobacteriaceae.	Cui HL, Gao X, Yang X, Xu XW	Int J Syst Evol Microbiol	10.1099/ijs.0.026799-0	2010	*
Phylogeny	Halobaculum gomorrense gen. nov., sp. nov., a novel extremely halophilic archaeon from the Dead Sea.	Oren A, Gurevich P, Gemmell RT, Teske A	Int J Syst Bacteriol	10.1099/00207713-45-4-747	1995	*

References

#3535

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 9297

#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 )

#75351

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-ID44189.1 )

* These data were automatically processed and therefore are not curated

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Halobaculum gomorrense DSM 9297

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