Halobaculum gomorrense (DSM 9297, JCM 9908, DS2807)

Name: Halobaculum gomorrense (DSM 9297, JCM 9908, DS2807)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 5871

Type strain

Strain Designation DS2807

Culture col. no. DSM 9297 JCM 9908 DS2807 ATCC 700876 CGMCC 1.10336

NCBI tax ID(s) 43928

Special Collections DSMZ JCM

History DSMZ <- A. Oren, Hebrew Univ. Jerusalem, Israel, DS2807 JCM <-- DSM 9297 <-- A. Oren DS 2807.

Links

Halobaculum gomorrense DS2807 is an archaeon of the family Haloferacaceae.

genome sequence 16S sequence Archaea

Name and taxonomic classification

SI-ID 44189

ATCC 700876,DSM 9297,JCM 9908

@ref 20215

Last LPSN update 2026-05-29 08:26:16

Domain Archaea

Phylum Methanobacteriota

Class Halobacteria

Order Halobacteriales

Family Haloferacaceae

Genus Halobaculum

Species Halobaculum gomorrense

Full scientific name Halobaculum gomorrense Oren et al. 1995

Morphology

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
3535	HALOBACULUM GOMORRENSE MEDIUM (DSMZ Medium 823)		Medium recipe at MediaDive	Name: HALOBACULUM GOMORRENSE MEDIUM (DSMZ Medium 823) Composition: MgCl2 x 6 H2O 160.0 g/l NaCl 125.0 g/l K2SO4 5.0 g/l Starch 2.0 g/l Casamino acids 1.0 g/l Yeast extract 1.0 g/l CaCl2 x 2 H2O 0.1 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
3535	positive	growth	35
67770	positive	growth	37

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	facultative anaerobe	90.402

Spore formation

@ref	Spore formation	Confidence
125439		99.044

Pathway annotation

Computationally determined by

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

Isolation, sampling and environmental information

Isolation

@ref	Geographic location	Country	Country ISO 3 Code	Continent	Sample type
3535	Dead Sea	Israel	ISR	Asia
67770					Dead Sea

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
3535	1	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
67770	IMG-taxon 2695420988 annotated assembly for Halobaculum gomorrense DSM 9297	scaffold	GCA_900129775	43928.3	2695420988	43928	75.14

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Halobaculum gomorrense gene for 16S ribosomal RNA, partial sequence, strain: JCM 9908, rrnA	AB477982	1432	43928
20218	Halobaculum gomorrense gene for 16S ribosomal RNA, partial sequence, strain: JCM 9908, rrnB	AB477983	1432	43928
20218	Halobaculum gomorrense gene for 16S rRNA, complete sequence, strain: JCM 9908	AB663364	1472	43928
67770	Halobaculum gomorrense 16S ribosomal RNA (16S rRNA) gene	L37444	1474	43928
124043	Halobaculum gomorrense strain JCM 9908 16S ribosomal RNA gene, partial sequence.	OR467347	1432	43928

GC content

@ref	GC-content (mol%)	Method
67770	70	high performance liquid chromatography (HPLC)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: IMG-taxon 2695420988 annotated assembly for Halobaculum gomorrense DSM 9297
NCBI: GCA_900129775

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	facultative anaerobe	90.40	no
125439	gram_stain	BacteriaNetⓘ	negative	89.95	no
125439	motility	BacteriaNetⓘ	yes	59.20	no
125439	spore_formation	BacteriaNetⓘ	no	99.04	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	The Osmoprotectant Switch of Potassium to Compatible Solutes in an Extremely Halophilic Archaea Halorubrum kocurii 2020YC7.	Ding R, Yang N, Liu J.	Genes (Basel)	10.3390/genes13060939	2022
Phylogeny	Abundance, distribution, and activity of Fe(II)-oxidizing and Fe(III)-reducing microorganisms in hypersaline sediments of Lake Kasin, southern Russia.	Emmerich M, Bhansali A, Losekann-Behrens T, Schroder C, Kappler A, Behrens S.	Appl Environ Microbiol	10.1128/aem.07637-11	2012
Metabolism	Dihydroxyacetone metabolism in Haloferax volcanii.	Ouellette M, Makkay AM, Papke RT.	Front Microbiol	10.3389/fmicb.2013.00376	2013
	Growth kinetics of extremely halophilic archaea (family halobacteriaceae) as revealed by arrhenius plots.	Robinson JL, Pyzyna B, Atrasz RG, Henderson CA, Morrill KL, Burd AM, Desoucy E, Fogleman RE, Naylor JB, Steele SM, Elliott DR, Leyva KJ, Shand RF.	J Bacteriol	10.1128/jb.187.3.923-929.2005	2005
	Low-pass sequencing for microbial comparative genomics.	Goo YA, Roach J, Glusman G, Baliga NS, Deutsch K, Pan M, Kennedy S, DasSarma S, Ng WV, Hood L.	BMC Genomics	10.1186/1471-2164-5-3	2004
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 )
#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;
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#125439	Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy: deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 .
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

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Halobaculum gomorrense (DSM 9297, JCM 9908, DS2807)

Name and taxonomic classification

Morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Pathway annotation

Isolation, sampling and environmental information

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_900129775

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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