Halorubrum sodomense (DSM 3755, ATCC 33755, NCMB 2197)

Name: Halorubrum sodomense (DSM 3755, ATCC 33755, NCMB 2197)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 5939

Type strain

Strain Designation RD 26

Culture col. no. DSM 3755 ATCC 33755 NCMB 2197 RD 26 JCM 8880 6 more

NCBI tax ID(s) 35743

Special Collections DSMZ JCM CIP

History DSMZ <- B.J. Tindall <- NCMB <- ATCC <- A. Oren, RD 26 JCM <-- IFO 14740 <-- ATCC 33755 <-- A. Oren RD-26. CIP <- 1997, JCM <- IFO <- ATCC <- A. Oren RD-26

Links

Halorubrum sodomense RD 26 is a Gram-negative, motile, oval-shaped archaeon of the family Haloferacaceae.

Gram-negative motile oval-shaped genome sequence 16S sequence Archaea

Name and taxonomic classification

SI-ID 40673

ATCC 33755,DSM 3755,IFO 14740,NCMB 2197,CIP 105330,JCM 8880,NCIMB 2197,VKM B-1771,NBRC 14740,CGMCC 1.2206

@ref 20215

Last LPSN update 2026-05-29 08:26:17

Domain Archaea

Phylum Methanobacteriota

Class Halobacteria

Order Halobacteriales

Family Haloferacaceae

Genus Halorubrum

Species Halorubrum sodomense

Full scientific name Halorubrum sodomense (Oren 1983) McGenity and Grant 1996

Synonyms (2)

Halobacterium sodomense
Halorubrobacterium sodomense

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Motility	Confidence
122649	negative	oval-shaped
125439	negative			94.349

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
1341	HALOBACTERIA MEDIUM (DSMZ Medium 372)	Medium recipe at MediaDive	Name: HALOBACTERIA MEDIUM (DSMZ Medium 372) Composition: NaCl 200.0 g/l MgSO4 x 7 H2O 20.0 g/l Agar 20.0 g/l Yeast extract 5.0 g/l Casamino acids 5.0 g/l Na3-citrate 3.0 g/l KCl 2.0 g/l Na glutamate 1.0 g/l FeCl2 x 4 H2O 0.036 g/l MnCl2 x 4 H2O 0.00036 g/l Distilled water
35812	MEDIUM 204 - for Halorubrum, Marinococcus and Natrialba		Distilled water make up to (1000.000 ml);Sodium chloride (200.000 g);Potassium chloride (2.000 g);ManganeseII chloride tetrahydrate (0.360 mg);Magnesium sulphate heptahydrate (20.000 g);Agar (20.000 g);Yeast extract (5.000 g);Ferrous chloride tetrahydrate
122649	CIP Medium 240	Medium recipe at CIP
122649	CIP Medium 204	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
1341	positive	growth	37
35812	positive	growth	37
67770	positive	growth	37
122649	positive	growth	15-37
122649	negative	growth	5
122649	negative	growth	45

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	facultative anaerobe	93.346

Spore formation

@ref	Spore formation	Confidence
125439		98.988

Compound production

@ref	Compound
1341	amyloglucosidase
1341	bacteriorhodopsin

Observation

67770

Observationquinones: MK-8, MK-8(H₂)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68371	27613 ChEBI	amygdalin	-	builds acid from	from API 50CH acid
68371	18305 ChEBI	arbutin	-	builds acid from	from API 50CH acid
68371	17057 ChEBI	cellobiose	-	builds acid from	from API 50CH acid
68371	18333 ChEBI	D-arabitol	-	builds acid from	from API 50CH acid
68371	15824 ChEBI	D-fructose	-	builds acid from	from API 50CH acid
68371	12936 ChEBI	D-galactose	-	builds acid from	from API 50CH acid
68371	17634 ChEBI	D-glucose	-	builds acid from	from API 50CH acid
68371	16899 ChEBI	D-mannitol	-	builds acid from	from API 50CH acid
68371	16024 ChEBI	D-mannose	-	builds acid from	from API 50CH acid
68371	17924 ChEBI	D-sorbitol	-	builds acid from	from API 50CH acid
68371	17113 ChEBI	erythritol	-	builds acid from	from API 50CH acid
68371	4853 ChEBI	esculin	-	builds acid from	from API 50CH acid
68371	16813 ChEBI	galactitol	-	builds acid from	from API 50CH acid
68371	28066 ChEBI	gentiobiose	-	builds acid from	from API 50CH acid
68371	24265 ChEBI	gluconate	-	builds acid from	from API 50CH acid
68371	17754 ChEBI	glycerol	-	builds acid from	from API 50CH acid
68371	28087 ChEBI	glycogen	-	builds acid from	from API 50CH acid
68371	15443 ChEBI	inulin	-	builds acid from	from API 50CH acid
68371	18403 ChEBI	L-arabitol	-	builds acid from	from API 50CH acid
68371	18287 ChEBI	L-fucose	-	builds acid from	from API 50CH acid
68371	62345 ChEBI	L-rhamnose	-	builds acid from	from API 50CH acid
68371	17266 ChEBI	L-sorbose	-	builds acid from	from API 50CH acid
68371	65328 ChEBI	L-xylose	-	builds acid from	from API 50CH acid
68371	17716 ChEBI	lactose	-	builds acid from	from API 50CH acid
68371	17306 ChEBI	maltose	-	builds acid from	from API 50CH acid
68371	6731 ChEBI	melezitose	-	builds acid from	from API 50CH acid
68371	28053 ChEBI	melibiose	-	builds acid from	from API 50CH acid
68371	320061 ChEBI	methyl alpha-D-glucopyranoside	-	builds acid from	from API 50CH acid
68371	43943 ChEBI	methyl alpha-D-mannoside	-	builds acid from	from API 50CH acid
68371	74863 ChEBI	methyl beta-D-xylopyranoside	-	builds acid from	from API 50CH acid
68371	17268 ChEBI	myo-inositol	-	builds acid from	from API 50CH acid
68371	59640 ChEBI	N-acetylglucosamine	-	builds acid from	from API 50CH acid
122649	17632 ChEBI	nitrate	+	reduction
122649	16301 ChEBI	nitrite	-	reduction
68371	0 ChEBI	Potassium 2-ketogluconate	-	builds acid from	from API 50CH acid
68371	0 ChEBI	Potassium 5-ketogluconate	+	builds acid from	from API 50CH acid
68371	16634 ChEBI	raffinose	-	builds acid from	from API 50CH acid
68371	15963 ChEBI	ribitol	-	builds acid from	from API 50CH acid
68371	17814 ChEBI	salicin	-	builds acid from	from API 50CH acid
68371	28017 ChEBI	starch	-	builds acid from	from API 50CH acid
68371	17992 ChEBI	sucrose	-	builds acid from	from API 50CH acid
68371	27082 ChEBI	trehalose	-	builds acid from	from API 50CH acid
68371	32528 ChEBI	turanose	-	builds acid from	from API 50CH acid
68371	17151 ChEBI	xylitol	-	builds acid from	from API 50CH acid

Metabolite production

@ref	Chebi-ID	Metabolite	Production
122649	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test	Methylred-test
122649	15688 ChEBI	acetoin	-
122649	17234 ChEBI	glucose		+

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	-	3.1.3.2	from API zym
68382	alkaline phosphatase	+	3.1.3.1	from API zym
68382	alpha-chymotrypsin	+	3.4.21.1	from API zym
68382	alpha-fucosidase	-	3.2.1.51	from API zym
68382	alpha-galactosidase	-	3.2.1.22	from API zym
68382	alpha-glucosidase	-	3.2.1.20	from API zym
68382	alpha-mannosidase	-	3.2.1.24	from API zym
68382	beta-galactosidase	-	3.2.1.23	from API zym
122649	beta-galactosidase	-	3.2.1.23
68382	beta-glucosidase	+	3.2.1.21	from API zym
68382	beta-glucuronidase	-	3.2.1.31	from API zym
122649	catalase	+	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
122649	gamma-glutamyltransferase	-	2.3.2.2
122649	gelatinase	-
68382	leucine arylamidase	+	3.4.11.1	from API zym
68382	lipase (C 14)	-		from API zym
68382	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
122649	oxidase	+
122649	phenylalanine ammonia-lyase	-	4.3.1.24
68382	trypsin	-	3.4.21.4	from API zym
122649	tryptophan deaminase	-
122649	urease	-	3.5.1.5
68382	valine arylamidase	-		from API zym

API zym

@ref	Control	Alkaline phosphatase	Esterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	Lipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	Trypsin	alpha- Chymotrypsin	Acid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	alpha- Galactosidase	beta- Galactosidase	beta- Glucuronidase	alpha- Glucosidase	beta- Glucosidase	N-acetyl-beta- glucosaminidase	alpha- Mannosidase	alpha- Fucosidase
122649	-	+	+	+	-	+	-	-	-	+	-	+	-	-	-	-	+	-	-	-

API 50CHac

@ref	ControlQ	GLY	ERY	DARA	LARA	RIB	DXYL	LXYL	ADO	MDX	GAL	GLU	FRU	MNE	SBE	RHA	DUL	INO	MAN	SOR	MDM	MDG	NAG	AMY	ARB	ESC	SAL	CEL	MAL	LAC	MEL	SAC	TRE	INU	MLZ	RAF	AMD	GLYG	XLT	GEN	TUR	LYX	TAG	DFUC	LFUC	DARL	LARL	GNT	2KG	5KG
122649	not determinedn.d.	-	-	+/-	+/-	+/-	+/-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+/-	+/-	+/-	-	-	-	-	-	+

Isolation, sampling and environmental information

Isolation

@ref	Geographic location	Country	Country ISO 3 Code	Continent	Sample type
1341	Dead Sea
67770					Surface water from the Dead Sea
122649	Dead Sea	Israel	ISR	Asia

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
1341	1	Risk group (German classification) According to TRBA 466
122649	1	Risk group (French 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 2617270732 annotated assembly for Halorubrum sodomense RD 26	scaffold	GCA_900111935	35743.4	2617270732	35743	75.16

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	H.sodomense 16S rRNA gene	X82169	1462	35743
20218	Halorubrum sodomense gene for 16S rRNA, complete sequence, strain: JCM 8880	AB663420	1470	35743
1341	Halorubrum sodomense gene for 16S rRNA	D13379	1469	35743

GC content

@ref	GC-content (mol%)	Method
1341	67.4
67770	68	Buoyant density centrifugation (BD)
67770	67.4	Buoyant density centrifugation (BD)
67770	66	thermal denaturation, midpoint method (Tm)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: IMG-taxon 2617270732 annotated assembly for Halorubrum sodomense RD 26
NCBI: GCA_900111935

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	facultative anaerobe	93.35	no
125439	gram_stain	BacteriaNetⓘ	negative	94.35	no
125439	motility	BacteriaNetⓘ	yes	54.91	no
125439	spore_formation	BacteriaNetⓘ	no	98.99	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Halorubrum sodomense RD 26
NCBI: GCA_900111935.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	79.69	no
125438	anaerobic	anaerobicⓘ	no	84.04	no
125438	aerobic	aerobicⓘ	yes	79.36	no
125438	spore-forming	spore-formingⓘ	no	88.40	no
125438	thermophilic	thermophileⓘ	no	82.79	yes
125438	flagellated	motile2+ⓘ	no	88.00	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Genomic insights into Halorubrum ezzemoulense strain TC23: Genetic basis for halophilic traits and biotechnological potential.	Kesbic FI.	Sci Prog	10.1177/00368504251364316	2025
Genetics	Insights into head-tailed viruses infecting extremely halophilic archaea.	Pietila MK, Laurinmaki P, Russell DA, Ko CC, Jacobs-Sera D, Butcher SJ, Bamford DH, Hendrix RW.	J Virol	10.1128/jvi.03397-12	2013
	Two states of a light-sensitive membrane protein captured at room temperature using thin-film sample mounts.	Axford D, Judge PJ, Bada Juarez JF, Kwan TOC, Birch J, Vinals J, Watts A, Moraes I.	Acta Crystallogr D Struct Biol	10.1107/s2059798321011220	2022
Metabolism	Structures of the archaerhodopsin-3 transporter reveal that disordering of internal water networks underpins receptor sensitization.	Bada Juarez JF, Judge PJ, Adam S, Axford D, Vinals J, Birch J, Kwan TOC, Hoi KK, Yen HY, Vial A, Milhiet PE, Robinson CV, Schapiro I, Moraes I, Watts A.	Nat Commun	10.1038/s41467-020-20596-0	2021
Genetics	Evidence from phylogenetic and genome fingerprinting analyses suggests rapidly changing variation in Halorubrum and Haloarcula populations.	Ram Mohan N, Fullmer MS, Makkay AM, Wheeler R, Ventosa A, Naor A, Gogarten JP, Papke RT.	Front Microbiol	10.3389/fmicb.2014.00143	2014
	Carotenoid characterization, fatty acid profiles, and antioxidant activities of haloarchaeal extracts.	Kesbic FI, Gultepe N.	J Basic Microbiol	10.1002/jobm.202300330	2024
	Effects of chaotropic salts on global proteome stability in halophilic archaea: Implications for life signatures on Mars.	Carre L, Gonzalez D, Girard E, Franzetti B.	Environ Microbiol	10.1111/1462-2920.16451	2023
Metabolism	Photocycle dynamics of the Archaerhodopsin 3 based fluorescent voltage sensor Archon2.	Penzkofer A, Silapetere A, Hegemann P.	J Photochem Photobiol B	10.1016/j.jphotobiol.2021.112331	2021
	Elucidation of Expression Patterns and Functional Properties of Archaerhodopsin Derived from Halorubrum sp. Ejinoor.	Chao L, Yang Y.	Biology (Basel)	10.3390/biology14040360	2025
	Implantable Light-Powered Human Designer Cells for Electrical Energy Generation.	Xue S, Lin Z, Maity D, Ray PG, Xie M, Fussenegger M.	Adv Mater	10.1002/adma.202502618	2025
	Detection of carotenoids of halophilic prokaryotes in solid inclusions inside laboratory-grown chloride and sulfate crystals using a portable Raman spectrometer: applications for Mars exploration.	Culka A, Kosek F, Oren A, Mana L, Jehlicka J.	FEMS Microbiol Lett	10.1093/femsle/fnz239	2019
	Proton motive force generated by microbial rhodopsin promotes extracellular electron transfer.	Ding W, Lin T, Yang Y, Li WW, Cheng S, Song H.	Synth Syst Biotechnol	10.1016/j.synbio.2025.01.001	2025
	Using a portable Raman spectrometer to detect carotenoids of halophilic prokaryotes in synthetic inclusions in NaCl, KCl, and sulfates.	Jehlicka J, Culka A, Mana L, Oren A.	Anal Bioanal Chem	10.1007/s00216-018-1098-3	2018
Pathogenicity	Effects of nicotine on the biosynthesis of carotenoids in halophilic Archaea (class Halobacteria): an HPLC and Raman spectroscopy study.	Oren A, Hirschberg J, Mann V, Jehlicka J.	Extremophiles	10.1007/s00792-018-0995-x	2018
	Carotenoids from Halophilic Archaea: A Novel Approach to Improve Egg Quality and Cecal Microbiota in Laying Hens.	Dou X, Zhang G, Tang H, Chen X, Chen B, Mei Y, Jiao H, Ren M.	Animals (Basel)	10.3390/ani14233470	2024
	Absorption and Emission Spectroscopic Investigation of the Thermal Dynamics of the Archaerhodopsin 3 Based Fluorescent Voltage Sensor Archon2.	Penzkofer A, Silapetere A, Hegemann P.	Int J Mol Sci	10.3390/ijms21186576	2020
	Photocycle Dynamics of the Archaerhodopsin 3 Based Fluorescent Voltage Sensor QuasAr1.	Penzkofer A, Silapetere A, Hegemann P.	Int J Mol Sci	10.3390/ijms21010160	2019
Metabolism	Important roles for membrane lipids in haloarchaeal bioenergetics.	Kellermann MY, Yoshinaga MY, Valentine RC, Wormer L, Valentine DL.	Biochim Biophys Acta	10.1016/j.bbamem.2016.08.010	2016
	Tools and methods for cell ablation and cell inhibition in Caenorhabditis elegans.	Rentsch D, Bergs A, Shao J, Elvers N, Ruse C, Seidenthal M, Aoki I, Gottschalk A.	Genetics	10.1093/genetics/iyae119	2025
	Comparison of Miniaturized Raman Spectrometers for Discrimination of Carotenoids of Halophilic Microorganisms.	Jehlicka J, Culka A, Mana L, Oren A.	Front Microbiol	10.3389/fmicb.2019.01155	2019
	A versatile approach to high-density microcrystals in lipidic cubic phase for room-temperature serial crystallography.	Birch J, Kwan TOC, Judge PJ, Axford D, Aller P, Butryn A, Reis RI, Bada Juarez JF, Vinals J, Owen RL, Nango E, Tanaka R, Tono K, Joti Y, Tanaka T, Owada S, Sugahara M, Iwata S, Orville AM, Watts A, Moraes I.	J Appl Crystallogr	10.1107/s1600576723006428	2023
	Absorption and Emission Spectroscopic Investigation of the Thermal Dynamics of the Archaerhodopsin 3 Based Fluorescent Voltage Sensor QuasAr1.	Penzkofer A, Silapetere A, Hegemann P.	Int J Mol Sci	10.3390/ijms20174086	2019
	Identification, Antioxidant Capacity, and Matrix Metallopeptidase 9 (MMP-9) In Silico Inhibition of Haloarchaeal Carotenoids from Natronococcus sp. and Halorubrum tebenquichense.	Delgado-Garcia M, Gomez-Secundino O, Rodriguez JA, Mateos-Diaz JC, Muller-Santos M, Aguilar CN, Camacho-Ruiz RM.	Microorganisms	10.3390/microorganisms11092344	2023
	Archaerhodopsin 3 is an ideal template for the engineering of highly fluorescent optogenetic reporters.	Herasymenko K, Walisinghe D, Konno M, Barneschi L, de Waele I, Sliwa M, Inoue K, Olivucci M, Haacke S.	Chem Sci	10.1039/d4sc05120c	2025
	Opticool: Cutting-edge transgenic optical tools.	Fenelon KD, Krause J, Koromila T.	PLoS Genet	10.1371/journal.pgen.1011208	2024
	Bacterioruberin and salinixanthin carotenoids of extremely halophilic Archaea and Bacteria: a Raman spectroscopic study.	Jehlicka J, Edwards HG, Oren A.	Spectrochim Acta A Mol Biomol Spectrosc	10.1016/j.saa.2012.12.081	2013
	A blue-shifted anion channelrhodopsin from the Colpodellida alga Vitrella brassicaformis.	Kojima K, Kawanishi S, Nishimura Y, Hasegawa M, Nakao S, Nagata Y, Yoshizawa S, Sudo Y.	Sci Rep	10.1038/s41598-023-34125-8	2023
	Rational Design of Far-Red Archaerhodopsin-3-Based Fluorescent Genetically Encoded Voltage Indicators: from Elucidation of the Fluorescence Mechanism in Archers to Novel Red-Shifted Variants.	Nikolaev DM, Mironov VN, Metelkina EM, Shtyrov AA, Mereshchenko AS, Demidov NA, Vyazmin SY, Tennikova TB, Moskalenko SE, Bondarev SA, Zhouravleva GA, Vasin AV, Panov MS, Ryazantsev MN.	ACS Phys Chem Au	10.1021/acsphyschemau.3c00073	2024
	Potential and limits of Raman spectroscopy for carotenoid detection in microorganisms: implications for astrobiology.	Jehlicka J, Edwards HG, Osterrothova K, Novotna J, Nedbalova L, Kopecky J, Nemec I, Oren A.	Philos Trans A Math Phys Eng Sci	10.1098/rsta.2014.0199	2014
Enzymology	Hydrolytic enzyme screening and carotenoid production evaluation of halophilic archaea isolated from highly heavy metal-enriched solar saltern sediments.	Baati H, Siala M, Azri C, Ammar E, Trigui M.	Braz J Microbiol	10.1007/s42770-022-00855-6	2022
	Imaging Voltage with Microbial Rhodopsins.	Zhang XM, Yokoyama T, Sakamoto M.	Front Mol Biosci	10.3389/fmolb.2021.738829	2021
	Detergent-free Lipodisq Nanoparticles Facilitate High-Resolution Mass Spectrometry of Folded Integral Membrane Proteins.	Hoi KK, Bada Juarez JF, Judge PJ, Yen HY, Wu D, Vinals J, Taylor GF, Watts A, Robinson CV.	Nano Lett	10.1021/acs.nanolett.0c04911	2021
Metabolism	Directed evolution of a far-red fluorescent rhodopsin.	McIsaac RS, Engqvist MK, Wannier T, Rosenthal AZ, Herwig L, Flytzanis NC, Imasheva ES, Lanyi JK, Balashov SP, Gradinaru V, Arnold FH.	Proc Natl Acad Sci U S A	10.1073/pnas.1413987111	2014
	Redshifted and Near-infrared Active Analog Pigments Based upon Archaerhodopsin-3.	Ganapathy S, Kratz S, Chen Q, Hellingwerf KJ, de Groot HJM, Rothschild KJ, de Grip WJ.	Photochem Photobiol	10.1111/php.13093	2019
	Modified Rhodopsins From Aureobasidium pullulans Excel With Very High Proton-Transport Rates.	Panzer S, Zhang C, Konte T, Brauer C, Diemar A, Yogendran P, Yu-Strzelczyk J, Nagel G, Gao S, Terpitz U.	Front Mol Biosci	10.3389/fmolb.2021.750528	2021
Metabolism	Functional characterization of sodium-pumping rhodopsins with different pumping properties.	Tsunoda SP, Prigge M, Abe-Yoshizumi R, Inoue K, Kozaki Y, Ishizuka T, Yawo H, Yizhar O, Kandori H.	PLoS One	10.1371/journal.pone.0179232	2017
	Genotypic and Lipid Analyses of Strains From the Archaeal Genus Halorubrum Reveal Insights Into Their Taxonomy, Divergence, and Population Structure.	de la Haba RR, Corral P, Sanchez-Porro C, Infante-Dominguez C, Makkay AM, Amoozegar MA, Ventosa A, Papke RT.	Front Microbiol	10.3389/fmicb.2018.00512	2018
	Exploring the Retinal Binding Cavity of Archaerhodopsin-3 by Replacing the Retinal Chromophore With a Dimethyl Phenylated Derivative.	Tsuneishi T, Takahashi M, Tsujimura M, Kojima K, Ishikita H, Takeuchi Y, Sudo Y.	Front Mol Biosci	10.3389/fmolb.2021.794948	2021
	A general approach to engineer positive-going eFRET voltage indicators.	Abdelfattah AS, Valenti R, Zheng J, Wong A, GENIE Project Team, Podgorski K, Koyama M, Kim DS, Schreiter ER.	Nat Commun	10.1038/s41467-020-17322-1	2020
	A high-light sensitivity optical neural silencer: development and application to optogenetic control of non-human primate cortex.	Han X, Chow BY, Zhou H, Klapoetke NC, Chuong A, Rajimehr R, Yang A, Baratta MV, Winkle J, Desimone R, Boyden ES.	Front Syst Neurosci	10.3389/fnsys.2011.00018	2011
	Archaeal viruses multiply: temporal screening in a solar saltern.	Atanasova NS, Demina TA, Buivydas A, Bamford DH, Oksanen HM.	Viruses	10.3390/v7041902	2015
	Optogenetic acidification of synaptic vesicles and lysosomes.	Rost BR, Schneider F, Grauel MK, Wozny C, Bentz C, Blessing A, Rosenmund T, Jentsch TJ, Schmitz D, Hegemann P, Rosenmund C.	Nat Neurosci	10.1038/nn.4161	2015
	Far-Red Absorbing Rhodopsins, Insights From Heterodimeric Rhodopsin-Cyclases.	Broser M.	Front Mol Biosci	10.3389/fmolb.2021.806922	2021
	Genetically encoded molecular tools for light-driven silencing of targeted neurons.	Chow BY, Han X, Boyden ES.	Prog Brain Res	10.1016/b978-0-444-59426-6.00003-3	2012
	Near-IR resonance Raman spectroscopy of archaerhodopsin 3: effects of transmembrane potential.	Saint Clair EC, Ogren JI, Mamaev S, Russano D, Kralj JM, Rothschild KJ.	J Phys Chem B	10.1021/jp309996a	2012
Phylogeny	Prefrontal Regulation of Safety Learning during Ethologically Relevant Thermal Threat.	Felix-Ortiz AC, Terrell JM, Gonzalez C, Msengi HD, Boggan MB, Ramos AR, Magalhaes G, Burgos-Robles A.	eNeuro	10.1523/eneuro.0140-23.2024	2024
Phylogeny	Diverse antimicrobial interactions of halophilic archaea and bacteria extend over geographical distances and cross the domain barrier.	Atanasova NS, Pietila MK, Oksanen HM.	Microbiologyopen	10.1002/mbo3.115	2013
	Designs and sensing mechanisms of genetically encoded fluorescent voltage indicators.	St-Pierre F, Chavarha M, Lin MZ.	Curr Opin Chem Biol	10.1016/j.cbpa.2015.05.003	2015
Metabolism	High-performance genetically targetable optical neural silencing by light-driven proton pumps.	Chow BY, Han X, Dobry AS, Qian X, Chuong AS, Li M, Henninger MA, Belfort GM, Lin Y, Monahan PE, Boyden ES.	Nature	10.1038/nature08652	2010
Metabolism	Enhancement of the long-wavelength sensitivity of optogenetic microbial rhodopsins by 3,4-dehydroretinal.	Sineshchekov OA, Govorunova EG, Wang J, Spudich JL.	Biochemistry	10.1021/bi2018859	2012
	Genetic voltage indicators.	Bando Y, Grimm C, Cornejo VH, Yuste R.	BMC Biol	10.1186/s12915-019-0682-0	2019
	Recent advances in engineering microbial rhodopsins for optogenetics.	McIsaac RS, Bedbrook CN, Arnold FH.	Curr Opin Struct Biol	10.1016/j.sbi.2015.05.001	2015
Metabolism	Fluorescence Enhancement of a Microbial Rhodopsin via Electronic Reprogramming.	Marin MDC, Agathangelou D, Orozco-Gonzalez Y, Valentini A, Kato Y, Abe-Yoshizumi R, Kandori H, Choi A, Jung KH, Haacke S, Olivucci M.	J Am Chem Soc	10.1021/jacs.8b09311	2019
	Raman spectroscopy in halophile research.	Jehlicka J, Oren A.	Front Microbiol	10.3389/fmicb.2013.00380	2013
	Analog Retinal Redshifts Visible Absorption of QuasAr Transmembrane Voltage Sensors into Near-infrared.	Mei G, Mamaeva N, Ganapathy S, Wang P, DeGrip WJ, Rothschild KJ.	Photochem Photobiol	10.1111/php.13169	2020
Metabolism	Optical recording of action potentials in mammalian neurons using a microbial rhodopsin.	Kralj JM, Douglass AD, Hochbaum DR, Maclaurin D, Cohen AE.	Nat Methods	10.1038/nmeth.1782	2011
	Conformational changes in the archaerhodopsin-3 proton pump: detection of conserved strongly hydrogen bonded water networks.	Clair EC, Ogren JI, Mamaev S, Kralj JM, Rothschild KJ.	J Biol Phys	10.1007/s10867-011-9246-4	2012
	Making Sense of Optogenetics.	Guru A, Post RJ, Ho YY, Warden MR.	Int J Neuropsychopharmacol	10.1093/ijnp/pyv079	2015
Phylogeny	Diversity, taxonomy, and evolution of archaeal viruses of the class Caudoviricetes.	Liu Y, Demina TA, Roux S, Aiewsakun P, Kazlauskas D, Simmonds P, Prangishvili D, Oksanen HM, Krupovic M.	PLoS Biol	10.1371/journal.pbio.3001442	2021
	Sialic Acid-Like Sugars in Archaea: Legionaminic Acid Biosynthesis in the Halophile Halorubrum sp. PV6.	Zaretsky M, Roine E, Eichler J.	Front Microbiol	10.3389/fmicb.2018.02133	2018
Genetics	Open Issues for Protein Function Assignment in Haloferax volcanii and Other Halophilic Archaea.	Pfeiffer F, Dyall-Smith M.	Genes (Basel)	10.3390/genes12070963	2021
Metabolism	New approaches for the study of orexin function.	Yamanaka A, Tsunematsu T.	J Neuroendocrinol	10.1111/j.1365-2826.2010.02015.x	2010
	Directed Evolution of a Bright Near-Infrared Fluorescent Rhodopsin Using a Synthetic Chromophore.	Herwig L, Rice AJ, Bedbrook CN, Zhang RK, Lignell A, Cahn JKB, Renata H, Dodani SC, Cho I, Cai L, Gradinaru V, Arnold FH.	Cell Chem Biol	10.1016/j.chembiol.2017.02.008	2017
Enzymology	Seasonal fluctuations in ionic concentrations drive microbial succession in a hypersaline lake community.	Podell S, Emerson JB, Jones CM, Ugalde JA, Welch S, Heidelberg KB, Banfield JF, Allen EE.	ISME J	10.1038/ismej.2013.221	2014
Metabolism	A Chimera Na+-Pump Rhodopsin as an Effective Optogenetic Silencer.	Hoque MR, Ishizuka T, Inoue K, Abe-Yoshizumi R, Igarashi H, Mishima T, Kandori H, Yawo H.	PLoS One	10.1371/journal.pone.0166820	2016
Metabolism	Structural and Functional Studies of a Newly Grouped Haloquadratum walsbyi Bacteriorhodopsin Reveal the Acid-resistant Light-driven Proton Pumping Activity.	Hsu MF, Fu HY, Cai CJ, Yi HP, Yang CS, Wang AH.	J Biol Chem	10.1074/jbc.m115.685065	2015
	Simultaneous mapping of membrane voltage and calcium in zebrafish heart in vivo reveals chamber-specific developmental transitions in ionic currents.	Hou JH, Kralj JM, Douglass AD, Engert F, Cohen AE.	Front Physiol	10.3389/fphys.2014.00344	2014
	Microbial Diversity of the Hypersaline Sidi Ameur and Himalatt Salt Lakes of the Algerian Sahara.	Boutaiba S, Hacene H, Bidle KA, Maupin-Furlow JA.	J Arid Environ	10.1016/j.jaridenv.2011.04.010	2011
	Seizing Control: From Current Treatments to Optogenetic Interventions in Epilepsy.	Bui AD, Alexander A, Soltesz I.	Neuroscientist	10.1177/1073858415619600	2017
Metabolism	Optogenetic tools for modulating and probing the epileptic network.	Zhao M, Alleva R, Ma H, Daniel AG, Schwartz TH.	Epilepsy Res	10.1016/j.eplepsyres.2015.06.010	2015
Stress	X-ray Crystallographic Structure of Thermophilic Rhodopsin: IMPLICATIONS FOR HIGH THERMAL STABILITY AND OPTOGENETIC FUNCTION.	Tsukamoto T, Mizutani K, Hasegawa T, Takahashi M, Honda N, Hashimoto N, Shimono K, Yamashita K, Yamamoto M, Miyauchi S, Takagi S, Hayashi S, Murata T, Sudo Y.	J Biol Chem	10.1074/jbc.m116.719815	2016
	Fast silencing reveals a lost role for reciprocal inhibition in locomotion.	Moult PR, Cottrell GA, Li WC.	Neuron	10.1016/j.neuron.2012.10.040	2013
	Microbial light-activatable proton pumps as neuronal inhibitors to functionally dissect neuronal networks in C. elegans.	Husson SJ, Liewald JF, Schultheis C, Stirman JN, Lu H, Gottschalk A.	PLoS One	10.1371/journal.pone.0040937	2012
Metabolism	Thermal and spectroscopic characterization of a proton pumping rhodopsin from an extreme thermophile.	Tsukamoto T, Inoue K, Kandori H, Sudo Y.	J Biol Chem	10.1074/jbc.m113.479394	2013
Metabolism	A blue-shifted light-driven proton pump for neural silencing.	Sudo Y, Okazaki A, Ono H, Yagasaki J, Sugo S, Kamiya M, Reissig L, Inoue K, Ihara K, Kandori H, Takagi S, Hayashi S.	J Biol Chem	10.1074/jbc.m113.475533	2013
	Differences in lateral gene transfer in hypersaline versus thermal environments.	Rhodes ME, Spear JR, Oren A, House CH.	BMC Evol Biol	10.1186/1471-2148-11-199	2011
	Illuminating neural circuits and behaviour in Caenorhabditis elegans with optogenetics.	Fang-Yen C, Alkema MJ, Samuel AD.	Philos Trans R Soc Lond B Biol Sci	10.1098/rstb.2014.0212	2015
Phylogeny	Archaeal diversity at the great salt plains of Oklahoma described by cultivation and molecular analyses.	Caton TM, Caton IR, Witte LR, Schneegurt MA.	Microb Ecol	10.1007/s00248-009-9507-y	2009
	Combined use of cultivation-dependent and cultivation-independent methods indicates that members of most haloarchaeal groups in an Australian crystallizer pond are cultivable.	Burns DG, Camakaris HM, Janssen PH, Dyall-Smith ML.	Appl Environ Microbiol	10.1128/aem.70.9.5258-5265.2004	2004
	Amygdala inputs to prefrontal cortex guide behavior amid conflicting cues of reward and punishment.	Burgos-Robles A, Kimchi EY, Izadmehr EM, Porzenheim MJ, Ramos-Guasp WA, Nieh EH, Felix-Ortiz AC, Namburi P, Leppla CA, Presbrey KN, Anandalingam KK, Pagan-Rivera PA, Anahtar M, Beyeler A, Tye KM.	Nat Neurosci	10.1038/nn.4553	2017
Metabolism	Targeting light-gated chloride channels to neuronal somatodendritic domain reduces their excitatory effect in the axon.	Messier JE, Chen H, Cai ZL, Xue M.	Elife	10.7554/elife.38506	2018
	Prediction of consensus structural motifs in a family of coregulated RNA sequences.	Hu YJ.	Nucleic Acids Res	10.1093/nar/gkf485	2002
	Diminishing fear: Optogenetic approach toward understanding neural circuits of fear control.	Luchkina NV, Bolshakov VY.	Pharmacol Biochem Behav	10.1016/j.pbb.2017.05.005	2018
	Optical silencing of C. elegans cells with arch proton pump.	Okazaki A, Sudo Y, Takagi S.	PLoS One	10.1371/journal.pone.0035370	2012
Metabolism	Box C/D RNA guides for the ribose methylation of archaeal tRNAs. The tRNATrp intron guides the formation of two ribose-methylated nucleosides in the mature tRNATrp.	Clouet d'Orval B, Bortolin ML, Gaspin C, Bachellerie JP.	Nucleic Acids Res	10.1093/nar/29.22.4518	2001
	Virion architecture unifies globally distributed pleolipoviruses infecting halophilic archaea.	Pietila MK, Atanasova NS, Manole V, Liljeroos L, Butcher SJ, Oksanen HM, Bamford DH.	J Virol	10.1128/jvi.06915-11	2012
	Evolution of rhodopsin ion pumps in haloarchaea.	Sharma AK, Walsh DA, Bapteste E, Rodriguez-Valera F, Ford Doolittle W, Papke RT.	BMC Evol Biol	10.1186/1471-2148-7-79	2007
Metabolism	pH dependence of light-driven proton pumping by an archaerhodopsin from Tibet: comparison with bacteriorhodopsin.	Ming M, Lu M, Balashov SP, Ebrey TG, Li Q, Ding J.	Biophys J	10.1529/biophysj.105.076547	2006
	Nanotechnology for Neuroscience: Promising Approaches for Diagnostics, Therapeutics and Brain Activity Mapping.	Kumar A, Tan A, Wong J, Spagnoli JC, Lam J, Blevins BD, G N, Thorne L, Ashkan K, Xie J, Liu H.	Adv Funct Mater	10.1002/adfm.201700489	2017
	Next-generation transgenic mice for optogenetic analysis of neural circuits.	Asrican B, Augustine GJ, Berglund K, Chen S, Chow N, Deisseroth K, Feng G, Gloss B, Hira R, Hoffmann C, Kasai H, Katarya M, Kim J, Kudolo J, Lee LM, Lo SQ, Mancuso J, Matsuzaki M, Nakajima R, Qiu L, Tan G, Tang Y, Ting JT, Tsuda S, Wen L, Zhang X, Zhao S.	Front Neural Circuits	10.3389/fncir.2013.00160	2013
	Optical neural interfaces.	Warden MR, Cardin JA, Deisseroth K.	Annu Rev Biomed Eng	10.1146/annurev-bioeng-071813-104733	2014
Metabolism	Principles for applying optogenetic tools derived from direct comparative analysis of microbial opsins.	Mattis J, Tye KM, Ferenczi EA, Ramakrishnan C, O'Shea DJ, Prakash R, Gunaydin LA, Hyun M, Fenno LE, Gradinaru V, Yizhar O, Deisseroth K.	Nat Methods	10.1038/nmeth.1808	2011
	Specificity, Versatility, and Continual Development: The Power of Optogenetics for Epilepsy Research.	Christenson Wick Z, Krook-Magnuson E.	Front Cell Neurosci	10.3389/fncel.2018.00151	2018
	Solar salt lake as natural environmental source for extraction halophilic pigments.	Khanafari A, Khavarinejad D, Mashinchian A	Iran J Microbiol		2010
Phylogeny	Halorubrum ejinorense sp. nov., isolated from Lake Ejinor, Inner Mongolia, China.	Castillo AM, Gutierrez MC, Kamekura M, Xue Y, Ma Y, Cowan DA, Jones BE, Grant WD, Ventosa A.	Int J Syst Evol Microbiol	10.1099/ijs.0.65241-0	2007
Phylogeny	Halorubrum xinjiangense sp. nov., a novel halophile isolated from saline lakes in China.	Feng J, Zhou PJ, Liu SJ.	Int J Syst Evol Microbiol	10.1099/ijs.0.63209-0	2004
Phylogeny	Halorubrum tibetense sp. nov., a novel haloalkaliphilic archaeon from Lake Zabuye in Tibet, China.	Fan H, Xue Y, Ma Y, Ventosa A, Grant WD.	Int J Syst Evol Microbiol	10.1099/ijs.0.03032-0	2004
	Characterization of Halorubrum sfaxense sp. nov., a New Halophilic Archaeon Isolated from the Solar Saltern of Sfax in Tunisia.	Trigui H, Masmoudi S, Brochier-Armanet C, Maalej S, Dukan S.	Int J Microbiol	10.1155/2011/240191	2011
Phylogeny	Halorubrum salinarum sp. nov., an extremely halophilic archaeon isolated from a saturated brine pond of a saltern.	Han HL, Danganan RE, Li Z, Shin NR, Bennett RM, Dedeles GR, Kim SG	Int J Syst Evol Microbiol	10.1099/ijsem.0.005231	2022
Phylogeny	Halorubrum californiense sp. nov., an extreme archaeal halophile isolated from a crystallizer pond at a solar salt plant in California, USA.	Pesenti PT, Sikaroodi M, Gillevet PM, Sanchez-Porro C, Ventosa A, Litchfield CD	Int J Syst Evol Microbiol	10.1099/ijs.0.2008/002410-0	2008

References

#1341	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 3755
#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 )
#35812	; Curators of the CIP;
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#68371	Automatically annotated from API 50CH acid .
#68382	Automatically annotated from API zym .
#122649	Collection of Institut Pasteur ; Curators of the CIP; CIP 105330
#125438	Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 )
#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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Halorubrum sodomense (DSM 3755, ATCC 33755, NCMB 2197)

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