Name: Natronomonas pharaonis Gabara
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 5896

Type strain:

Species: Natronomonas pharaonis

Strain Designation: Gabara

Culture col. no.: DSM 2160, ATCC 35678, JCM 8858, CCM 3872, CIP 103997, IFO 14720, NBRC 14720, NCIMB 2260, VKM B-1749

Strain history: CIP <- 1994, IFO <- 1988, DSMZ, Halobacterium pharaonis <- H.G. Trüper: strain Gabara <- G.S.H. Soliman

NCBI tax ID(s): 348780 (strain), 2257 (species)

SI-ID 41222

ATCC 35678, DSM 2160, ATCC 43656, CIP 103997, IFO 14720, JCM 8858, CCM 3872, NCIMB 2260, VKM B-1749, NBRC 14720, CECT 4578, CGMCC 1.1965

Other strains from Natronomonas pharaonis

N. pharaonis SP1, DSM 3395, ATCC 43100, CCM ...

Section

Natronomonas pharaonis Gabara is a mesophilic, Gram-negative archaeon that was isolated from water sample.

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	*Halobacteriales*
	Family	*Halobacteriaceae*
	Genus	*Natronomonas*
	Species	**Natronomonas pharaonis**
	Full Scientific Name (LPSN)	Natronomonas pharaonis (Soliman and Trüper 1983) Kamekura et al. 1997

	Synonym	Natronobacterium pharaonis
	Synonym	Halobacterium pharaonis

Information on morphological and physiological properties Morphology

[Ref.: #121792]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.989

[Ref.: #121792]	Cell shape	rod-shaped

[Ref.: #121792]	Motility	yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #985]

Culture medium

NATRONOBACTERIA MEDIUM (DSMZ Medium 371)

[Ref.: #985]

Culture medium growth

[Ref.: #985]

Culture medium link

Medium recipe at MediaDive

[Ref.: #985]

Culture medium composition

expand / minimize

[Ref.: #985]

Culture medium

NATRONOBACTERIUM MEDIUM (DSMZ Medium 205)

[Ref.: #985]

Culture medium growth

[Ref.: #985]

Culture medium link

Medium recipe at MediaDive

[Ref.: #985]

Culture medium composition

expand / minimize

[Ref.: #40918]

Culture medium

MEDIUM 47 - for Natronomonas pharaonis

[Ref.: #40918]

Culture medium growth

[Ref.: #40918]

Culture medium composition

expand / minimize

[Ref.: #121792]

Culture medium

CIP Medium 47

[Ref.: #121792]

Culture medium growth

[Ref.: #121792]

Culture medium link

Medium recipe provided by DSMZ

		Temperature
[Ref.: #985]	growth	37 °C
[Ref.: #40918]	growth	37 °C
[Ref.: #67770]	growth	37 °C
[Ref.: #121792]	growth	30-37 °C

[Ref.: #985]	Temperature range	mesophilic
[Ref.: #40918]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic
[Ref.: #121792]	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 %99.979

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #121792]		NaCl		growth	0-6	%
[Ref.: #121792]		NaCl	no	growth	8	%

	Metabolite utilization	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #121792]		nitrate ChEBI	-	reduction
[Ref.: #121792]		nitrite ChEBI	-	reduction

	Metabolite production	Metabolite	Production
[Ref.: #121792]		indole ChEBI	no

	Enzyme	Enzyme activity	EC number
[Ref.: #121792]	alcohol dehydrogenase	-	1.1.1.1
[Ref.: #121792]	beta-galactosidase	+	3.2.1.23
[Ref.: #121792]	catalase	+	1.11.1.6
[Ref.: #121792]	gelatinase	+
[Ref.: #121792]	lysine decarboxylase	-	4.1.1.18
[Ref.: #121792]	ornithine decarboxylase	-	4.1.1.17
[Ref.: #121792]	urease	-	3.5.1.5

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	denitrification	100	2 of 2
[Ref.: #66794]	factor 420 biosynthesis	100	5 of 5
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	ethanol fermentation	100	2 of 2
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	propionate fermentation	90	9 of 10
[Ref.: #66794]	CO2 fixation in Crenarchaeota	88.89	8 of 9
[Ref.: #66794]	molybdenum cofactor biosynthesis	88.89	8 of 9
[Ref.: #66794]	aspartate and asparagine metabolism	88.89	8 of 9
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	isoleucine metabolism	87.5	7 of 8
[Ref.: #66794]	palmitate biosynthesis	86.36	19 of 22
[Ref.: #66794]	propanol degradation	85.71	6 of 7
[Ref.: #66794]	citric acid cycle	85.71	12 of 14
[Ref.: #66794]	ubiquinone biosynthesis	85.71	6 of 7
[Ref.: #66794]	vitamin B1 metabolism	84.62	11 of 13
[Ref.: #66794]	phenylalanine metabolism	84.62	11 of 13
[Ref.: #66794]	pantothenate biosynthesis	83.33	5 of 6
[Ref.: #66794]	glutamate and glutamine metabolism	82.14	23 of 28
[Ref.: #66794]	ethylmalonyl-CoA pathway	80	4 of 5
[Ref.: #66794]	flavin biosynthesis	80	12 of 15
[Ref.: #66794]	phenylacetate degradation (aerobic)	80	4 of 5
[Ref.: #66794]	vitamin K metabolism	80	4 of 5
[Ref.: #66794]	lipoate biosynthesis	80	4 of 5
[Ref.: #66794]	valine metabolism	77.78	7 of 9
[Ref.: #66794]	leucine metabolism	76.92	10 of 13
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	biotin biosynthesis	75	3 of 4
[Ref.: #66794]	ppGpp biosynthesis	75	3 of 4
[Ref.: #66794]	sulfopterin metabolism	75	3 of 4
[Ref.: #66794]	lipid metabolism	74.19	23 of 31
[Ref.: #66794]	vitamin B12 metabolism	73.53	25 of 34
[Ref.: #66794]	alanine metabolism	72.41	21 of 29
[Ref.: #66794]	NAD metabolism	72.22	13 of 18
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	reductive acetyl coenzyme A pathway	71.43	5 of 7
[Ref.: #66794]	arginine metabolism	70.83	17 of 24
[Ref.: #66794]	threonine metabolism	70	7 of 10
[Ref.: #66794]	pyrimidine metabolism	68.89	31 of 45
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	formaldehyde oxidation	66.67	2 of 3
[Ref.: #66794]	cyanate degradation	66.67	2 of 3
[Ref.: #66794]	nitrate assimilation	66.67	6 of 9
[Ref.: #66794]	glycolate and glyoxylate degradation	66.67	4 of 6
[Ref.: #66794]	enterobactin biosynthesis	66.67	2 of 3
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	purine metabolism	65.96	62 of 94
[Ref.: #66794]	glycolysis	64.71	11 of 17
[Ref.: #66794]	tetrahydrofolate metabolism	64.29	9 of 14
[Ref.: #66794]	photosynthesis	64.29	9 of 14
[Ref.: #66794]	carotenoid biosynthesis	63.64	14 of 22
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
[Ref.: #66794]	C4 and CAM-carbon fixation	62.5	5 of 8
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	61.54	8 of 13
[Ref.: #66794]	methionine metabolism	61.54	16 of 26
[Ref.: #66794]	Entner Doudoroff pathway	60	6 of 10
[Ref.: #66794]	3-chlorocatechol degradation	60	3 of 5
[Ref.: #66794]	creatinine degradation	60	3 of 5
[Ref.: #66794]	histidine metabolism	58.62	17 of 29
[Ref.: #66794]	non-pathway related	57.89	22 of 38
[Ref.: #66794]	tryptophan metabolism	57.89	22 of 38
[Ref.: #66794]	glutathione metabolism	57.14	8 of 14
[Ref.: #66794]	heme metabolism	57.14	8 of 14
[Ref.: #66794]	lipid A biosynthesis	55.56	5 of 9
[Ref.: #66794]	d-mannose degradation	55.56	5 of 9
[Ref.: #66794]	serine metabolism	55.56	5 of 9
[Ref.: #66794]	cysteine metabolism	55.56	10 of 18
[Ref.: #66794]	proline metabolism	54.55	6 of 11
[Ref.: #66794]	pentose phosphate pathway	54.55	6 of 11
[Ref.: #66794]	oxidative phosphorylation	53.85	49 of 91
[Ref.: #66794]	sulfate reduction	53.85	7 of 13
[Ref.: #66794]	lysine metabolism	52.38	22 of 42
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	cis-vaccenate biosynthesis	50	1 of 2
[Ref.: #66794]	selenocysteine biosynthesis	50	3 of 6
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	50	6 of 12
[Ref.: #66794]	quinate degradation	50	1 of 2
[Ref.: #66794]	ketogluconate metabolism	50	4 of 8
[Ref.: #66794]	dolichol and dolichyl phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	gluconeogenesis	50	4 of 8
[Ref.: #66794]	butanoate fermentation	50	2 of 4
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	50	1 of 2
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	tyrosine metabolism	50	7 of 14
[Ref.: #66794]	urea cycle	46.15	6 of 13
[Ref.: #66794]	isoprenoid biosynthesis	46.15	12 of 26
[Ref.: #66794]	4-hydroxymandelate degradation	44.44	4 of 9
[Ref.: #66794]	arachidonic acid metabolism	44.44	8 of 18
[Ref.: #66794]	mevalonate metabolism	42.86	3 of 7
[Ref.: #66794]	methanogenesis from CO2	41.67	5 of 12
[Ref.: #66794]	D-cycloserine biosynthesis	40	2 of 5
[Ref.: #66794]	4-hydroxyphenylacetate degradation	40	4 of 10
[Ref.: #66794]	glycine betaine biosynthesis	40	2 of 5
[Ref.: #66794]	coenzyme M biosynthesis	40	4 of 10
[Ref.: #66794]	degradation of sugar acids	40	10 of 25
[Ref.: #66794]	gallate degradation	40	2 of 5
[Ref.: #66794]	polyamine pathway	39.13	9 of 23
[Ref.: #66794]	chlorophyll metabolism	33.33	6 of 18
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	degradation of pentoses	32.14	9 of 28
[Ref.: #66794]	androgen and estrogen metabolism	31.25	5 of 16
[Ref.: #66794]	myo-inositol biosynthesis	30	3 of 10
[Ref.: #66794]	benzoyl-CoA degradation	28.57	2 of 7
[Ref.: #66794]	degradation of hexoses	27.78	5 of 18
[Ref.: #66794]	vitamin B6 metabolism	27.27	3 of 11
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
[Ref.: #66794]	alginate biosynthesis	25	1 of 4
[Ref.: #66794]	carnitine metabolism	25	2 of 8
[Ref.: #66794]	vitamin E metabolism	25	1 of 4
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	catecholamine biosynthesis	25	1 of 4
[Ref.: #66794]	dTDPLrhamnose biosynthesis	25	2 of 8
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	bile acid biosynthesis, neutral pathway	23.53	4 of 17
[Ref.: #66794]	phenylpropanoid biosynthesis	23.08	3 of 13
		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.: #985]	Sample type/isolated from	water sample
[Ref.: #985]	Geographic location (country and/or sea, region)	Wadi Natrun
[Ref.: #985]	Country	Egypt
[Ref.: #985]	Country ISO 3 Code	EGY
[Ref.: #985]	Continent	Africa

[Ref.: #67770]	Sample type/isolated from	Alkaline brines of eutrophic desert lakes of Wadi Natrun
[Ref.: #67770]	Country	Egypt
[Ref.: #67770]	Country ISO 3 Code	EGY
[Ref.: #67770]	Continent	Africa

[Ref.: #121792]	Sample type/isolated from	Environment, Alkaline brine in lakes of Wadi Natrum
[Ref.: #121792]	Country	Egypt
[Ref.: #121792]	Country ISO 3 Code	EGY
[Ref.: #121792]	Continent	Africa
* marker position based on {}

Isolation sources categories

#Environmental

#Aquatic

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence NR_074179 (>99% sequence identity) for Natronomonas pharaonis subclade from Microbeatlas

Aquatic Samples	25
Soil Samples	8
Animal Samples
Plant Samples
Total Samples	33

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

[Ref.: #985]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #121792]	Biosafety level	1	Risk group (French classification)

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.: #67770]	Natronobacterium pharaonis DNA for 16S rRNA	D87971	1465	ENA	348780 tax ID
[Ref.: #985]	Natronomonas pharaonis strain Gabara 16S ribosomal RNA, complete sequence	NR_074179	1466	GenBank	2257 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Natronomonas pharaonis DSM 2160 Gabara	GCA_000026045	complete	GenBank	348780 tax ID	*
[Ref.: #66792]	Natronomonas pharaonis Gabara, DSM 2160	637000187	complete	JGI IMG/M	348780 tax ID	*
[Ref.: #66792]	Natronomonas pharaonis DSM 2160 strain Gabara	348780.21	plasmid	PATRIC	348780 tax ID	*
[Ref.: #66792]	Natronomonas pharaonis DSM 2160 strain Gabara	348780.20	plasmid	PATRIC	348780 tax ID	*
[Ref.: #66792]	Natronomonas pharaonis DSM 2160	348780.14	complete	PATRIC	348780 tax ID	*

[Ref.: #67770]	GC-content	62.6 mol%	thermal denaturation, midpoint method (Tm)
[Ref.: #67770]	GC-content	64.3 mol%	thermal denaturation, midpoint method (Tm)

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: Natronomonas pharaonis DSM 2160 Gabara NCBI: GCA_000026045.1
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Natronomonas pharaonis DSM 2160 Gabara NCBI: GCA_000026045.1
[Ref.: #69480]	motile	no	78.641	no
[Ref.: #69480]	flagellated	no	97.366	no
[Ref.: #69480]	gram-positive	no	98.137	no
[Ref.: #69480]	anaerobic	no	95.261	no
[Ref.: #69480]	aerobic	yes	76.959	no
[Ref.: #69480]	halophile	yes	91.508	no
[Ref.: #69480]	spore-forming	no	94.587	no
[Ref.: #69480]	thermophile	no	79.047	no
[Ref.: #69480]	glucose-util	yes	83.877	no
[Ref.: #69480]	glucose-ferment	no	80.639	no

Availability in culture collections External links

[Ref.: #985]

Culture collection no.

DSM 2160, ATCC 35678, JCM 8858, CCM 3872, CIP 103997, IFO 14720, NBRC 14720, NCIMB 2260, VKM B-1749

[Ref.: #75376]

SI-ID 41222

Literature:

Only first 10 entries are displayed. Click here to see all.

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Natronomonas gomsonensis sp. nov., isolated from a solar saltern.	Kim TY, Kim SJ, Park SJ, Kim JG, Cha IT, Jung MY, Lee SA, Roh SW, Yim KJ, Itoh T, Rhee SK	Antonie Van Leeuwenhoek	10.1007/s10482-013-9970-9	2013	*
Phylogeny	Halomarina oriensis gen. nov., sp. nov., a halophilic archaeon isolated from a seawater aquarium.	Inoue K, Itoh T, Ohkuma M, Kogure K	Int J Syst Evol Microbiol	10.1099/ijs.0.020677-0	2010	*
Phylogeny	Natronomonas moolapensis sp. nov., non-alkaliphilic isolates recovered from a solar saltern crystallizer pond, and emended description of the genus Natronomonas.	Burns DG, Janssen PH, Itoh T, Minegishi H, Usami R, Kamekura M, Dyall-Smith ML	Int J Syst Evol Microbiol	10.1099/ijs.0.010132-0	2009	*
Metabolism	A halorhodopsin-overproducing mutant isolated from an extremely haloalkaliphilic archaeon Natronomonas pharaonis.	Ihara K, Narusawa A, Maruyama K, Takeguchi M, Kouyama T	FEBS Lett	10.1016/j.febslet.2008.07.030	2008	*
Phylogeny	Radiation sensitivity of N. pharaonis in comparison with E. coli K12 strains.	Quint RM, Solar S, Stan-Lotter H	Radiat Environ Biophys	10.1007/s00411-002-0146-7	2002	*
	An evidence of laccases in archaea.	Sharma KK, Kuhad RC	Indian J Microbiol	10.1007/s12088-009-0039-4	2009	*

References

#985	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 2160

#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 )

#40918 ; Curators of the CIP;

#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) .

#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 )

#75376

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-ID41222.1 )

#121792 Collection of Institut Pasteur ; Curators of the CIP; CIP 103997
* These data were automatically processed and therefore are not curated

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Natronomonas pharaonis DSM 2160 Gabara

Natronomonas pharaonis DSM 2160 Gabara

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