Halobacterium salinarum (DSM 3754, ATCC 33171, JCM 8978)

Name: Halobacterium salinarum (DSM 3754, ATCC 33171, JCM 8978)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 5912

Type strain

Strain Designation 91-R6

Culture col. no. DSM 3754 ATCC 33171 JCM 8978 NCMB 764 NRC 34002 8 more

NCBI tax ID(s) 2597657 2242

Special Collections DSMZ JCM CIP

Links

Halobacterium salinarum 91-R6 is a mesophilic, Gram-negative, rod-shaped prokaryote that was isolated from salted cow hide.

Gram-negative rod-shaped mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 40375

ATCC 33171,CIP 104033,DSM 3754,NCIMB 764,NCMB 764,JCM 8978,IAM 13166,NCMB 766,VKM B-1769,CGMCC 1.1958,NBRC 102687,VTT E-103154

@ref 20215

Last LPSN update 2025-12-16 09:48:11

Domain Methanobacteriati

Phylum Methanobacteriota

Class Halobacteria

Order Halobacteriales

Family Halobacteriaceae

Genus Halobacterium

Species Halobacterium salinarum

Full scientific name Halobacterium salinarum corrig. (Harrison and Kennedy 1922) Elazari-Volcani 1957 (Approved Lists 1980)

Synonyms (9)

Halobacterium halobium
"Halobacter cutirubrum"
Halobacterium cutirubrum
"Bacterium halobium"
Halobacterium piscisalsi
Halobacterium salinarium
"Pseudomonas salinaria"
"Halobacter salinaria"
"Serratia cutirubra"

BacDive ID	Other strains from **Halobacterium salinarum** (14)	Type strain
5908	H. salinarum 1, DSM 668, ATCC 19700
5909	H. salinarum 63-R2, DSM 669, ATCC 33170, NRC 34001, JCM ...
5910	H. salinarum DSM 670, JCM 20854, ATCC 43214, IAM 13167, ...
5911	H. salinarum R1, DSM 671, CCUG 24034, JCM 9409, ATCC 29341, ...
23038	H. salinarum DS21, GRB, DSM 22414
100563	H. salinarum ST033385(HKI),
24073	H. salinarum GRB-mut326-P577, DSM 21899, MUT mut326, MUT ...
134335	H. salinarum HPC1-2, BCC 24372, JCM 14661, PCU 302
161096	H. salinarum JCM 10927
162900	H. salinarum JCM 20370, IAM 12046
165991	H. salinarum JCM 9118, CCM 2148
165992	H. salinarum JCM 9119, CCM 2088
165993	H. salinarum JCM 9120, CCM 2090
165994	H. salinarum JCM 9121, CCM 2084

Morphology

Cell morphology

@ref	Gram stain	Cell shape
122383	negative	rod-shaped
125438
125439	positive
125439

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
1340	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
1340	HALOBACTERIUM MEDIUM (DSMZ Medium 97)	Medium recipe at MediaDive	Name: HALOBACTERIUM MEDIUM (DSMZ Medium 97) Composition: NaCl 250.0 g/l Agar 20.0 g/l MgSO4 x 7 H2O 20.0 g/l Yeast extract 10.0 g/l Casamino acids 7.5 g/l Na3-citrate 3.0 g/l KCl 2.0 g/l FeSO4 x 7 H2O 0.05 g/l MnSO4 x H2O 0.0002 g/l Distilled water
122383	CIP Medium 330	Medium recipe at CIP
122383	CIP Medium 204	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
1340	positive	growth	37	mesophilic
67770	positive	growth	37	mesophilic

Physiology and metabolism

Spore formation

@ref	Spore formation	Confidence
125439		90.3

Observation

67770

Observationquinones: MK-8, MK-8(H₂)

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Mammals	#Bovinae (Cow, Cattle)
#Host Body-Site	#Organ	#Skin, Nail, Hair
#Condition	#Saline	-

Isolation

@ref	Sample type	Country	Country ISO 3 Code	Continent
1340	salted cow hide	Canada	CAN	North America
67770	Salted cowhide
122383	Salted cow hide

Taxonmaps

69479

Global distribution of 16S sequence AB663362 (>99% sequence identity) for Halobacterium salinarum from Microbeatlas

Aquatic Samples	26
Soil Samples	5
Animal Samples	2
Plant Samples
Total Samples	33

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
1340	1	Risk group (German classification) According to TRBA 466
122383	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
66792	ASM479960v1 assembly for Halobacterium salinarum 91-R6	complete	GCA_004799605	2242.21	8075887219	2242	97.64
67770	ASM812460v1 assembly for Halobacterium salinarum DSM 3754	contig	GCA_008124605	2597657.4	2597490337	2597657	70.28

Genome browser: GCA_004799605

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
20218	Halobacterium salinarum gene for 16S rRNA, complete sequence, strain: JCM 8978	AB663362	1473		2242
1340	Halobacterium salinarum 16S rRNA gene, type strain DSM 3754T	AJ496185	1473		2597657

GC content

@ref	GC-content (mol%)	Method
67770	66.4	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: Halobacterium salinarum 91-R6
NCBI: GCA_004799605

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	90.30	no
125439	motility	BacteriaNetⓘ	no	92.20	no
125439	gram_stain	BacteriaNetⓘ	positive	97.60	no
125439	oxygen_tolerance	BacteriaNetⓘ	microaerophile	86.50	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Halobacterium salinarum 91-R6
NCBI: GCA_004799605.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	77.71	no
125438	anaerobic	anaerobicⓘ	no	84.94	no
125438	aerobic	aerobicⓘ	yes	80.54	no
125438	spore-forming	spore-formingⓘ	no	87.95	no
125438	thermophilic	thermophileⓘ	no	79.07	yes
125438	flagellated	motile2+ⓘ	no	90.83	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Salty secrets of Halobacterium salinarum AD88: a new archaeal ecotype isolated from Cuatro Cienegas Basin.	Medina-Chavez NO, Rodriguez-Cruz UE, Souza V, De la Torre-Zavala S, Travisano M.	BMC Genomics	10.1186/s12864-025-11550-9	2025
Genetics	Genome comparison reveals that Halobacterium salinarum 63-R2 is the origin of the twin laboratory strains NRC-1 and R1.	Pfeiffer F, Dyall-Smith M.	Microbiologyopen	10.1002/mbo3.1365	2023
	Bioremediation of oil-based drill cuttings by a halophilic consortium isolated from oil-contaminated saline soil.	Rezaei Somee M, Shavandi M, Dastgheib SMM, Amoozegar MA.	3 Biotech	10.1007/s13205-018-1261-8	2018
	The Stain of the Original Salt: Red Heats on Chrome Tanned Leathers and Purple Spots on Ancient Parchments Are Two Sides of the Same Ecological Coin.	Perini N, Mercuri F, Thaller MC, Orlanducci S, Castiello D, Talarico V, Migliore L.	Front Microbiol	10.3389/fmicb.2019.02459	2019
Metabolism	Three ancient documents solve the jigsaw of the parchment purple spot deterioration and validate the microbial succession model.	Migliore L, Perini N, Mercuri F, Orlanducci S, Rubechini A, Thaller MC.	Sci Rep	10.1038/s41598-018-37651-y	2019
Genetics	Discovery of the Streamlined Haloarchaeon Halorutilus salinus, Comprising a New Order Widespread in Hypersaline Environments across the World.	Duran-Viseras A, Sanchez-Porro C, Viver T, Konstantinidis KT, Ventosa A.	mSystems	10.1128/msystems.01198-22	2023
	Structural conservation of chemotaxis machinery across Archaea and Bacteria.	Briegel A, Ortega DR, Huang AN, Oikonomou CM, Gunsalus RP, Jensen GJ.	Environ Microbiol Rep	10.1111/1758-2229.12265	2015
	The Integration of Metagenomics and Chemical Physical Techniques Biodecoded the Buried Traces of the Biodeteriogens of Parchment Purple Spots.	Perini N, Mercuri F, Orlanducci S, Thaller MC, Migliore L.	Front Microbiol	10.3389/fmicb.2020.598945	2020
	Analysis of Major Bacteria and Diversity of Surface Soil to Discover Biomarkers Related to Soil Health.	Kim H, Park YH, Yang JE, Kim HS, Kim SC, Oh EJ, Moon J, Cho W, Shin W, Yu C.	Toxics	10.3390/toxics10030117	2022
Metabolism	[NiFe]-hydrogenases are constitutively expressed in an enriched Methanobacterium sp. population during electromethanogenesis.	Perona-Vico E, Blasco-Gomez R, Colprim J, Puig S, Baneras L.	PLoS One	10.1371/journal.pone.0215029	2019
	Genomic Insights Into New Species of the Genus Halomicroarcula Reveals Potential for New Osmoadaptative Strategies in Halophilic Archaea.	Duran-Viseras A, Sanchez-Porro C, Ventosa A.	Front Microbiol	10.3389/fmicb.2021.751746	2021
	Swimming behavior of selected species of Archaea.	Herzog B, Wirth R.	Appl Environ Microbiol	10.1128/aem.06723-11	2012
	Pathology of experimentally induced mouthrot caused by Tenacibaculum maritimum in Atlantic salmon smolts.	Frisch K, Smage SB, Johansen R, Duesund H, Brevik OJ, Nylund A.	PLoS One	10.1371/journal.pone.0206951	2018
	Raman spectroscopy as a potentialmethod for the detection of extremely halophilic archaea embedded in halite in terrestrial and possibly extraterrestrial samples.	Fendrihan S, Musso M, Stan-Lotter H.	J Raman Spectrosc	10.1002/jrs.2357	2009
	Concurrent jellyfish blooms and tenacibaculosis outbreaks in Northern Norwegian Atlantic salmon (Salmo salar) farms.	Smage SB, Brevik OJ, Frisch K, Watanabe K, Duesund H, Nylund A.	PLoS One	10.1371/journal.pone.0187476	2017
	Structure, mineralogy, and microbial diversity of geothermal spring microbialites associated with a deep oil drilling in Romania.	Coman C, Chiriac CM, Robeson MS, Ionescu C, Dragos N, Barbu-Tudoran L, Andrei AS, Banciu HL, Sicora C, Podar M.	Front Microbiol	10.3389/fmicb.2015.00253	2015
Metabolism	No influence of oxygen levels on pathogenesis and virus shedding in Salmonid alphavirus (SAV)-challenged Atlantic salmon (Salmo salar L.).	Andersen L, Hodneland K, Nylund A.	Virol J	10.1186/1743-422x-7-198	2010
	Novel pili-like surface structures of Halobacterium salinarum strain R1 are crucial for surface adhesion.	Losensky G, Vidakovic L, Klingl A, Pfeifer F, Frols S.	Front Microbiol	10.3389/fmicb.2014.00755	2014
Phylogeny	A 'universal' type II chaperonin PCR detection system for the investigation of Archaea in complex microbial communities.	Chaban B, Hill JE.	ISME J	10.1038/ismej.2011.96	2012
	Methanogenic Archaea and human periodontal disease.	Lepp PW, Brinig MM, Ouverney CC, Palm K, Armitage GC, Relman DA.	Proc Natl Acad Sci U S A	10.1073/pnas.0308766101	2004
Genetics	Bacterial community structure and bacterial isolates having antimicrobial potential in shrimp pond aquaculture.	Ali S, Xie J, Zada S, Hu Z, Zhang Y, Cai R, Wang H.	AMB Express	10.1186/s13568-022-01423-9	2022
Metabolism	Trehalose/2-sulfotrehalose biosynthesis and glycine-betaine uptake are widely spread mechanisms for osmoadaptation in the Halobacteriales.	Youssef NH, Savage-Ashlock KN, McCully AL, Luedtke B, Shaw EI, Hoff WD, Elshahed MS.	ISME J	10.1038/ismej.2013.165	2014
Genetics	Whole-genome comparison between the type strain of Halobacterium salinarum (DSM 3754(T) ) and the laboratory strains R1 and NRC-1.	Pfeiffer F, Losensky G, Marchfelder A, Habermann B, Dyall-Smith M	Microbiologyopen	10.1002/mbo3.974	2019
Genetics	The Genome Sequence of the Halobacterium salinarum Type Strain Is Closely Related to That of Laboratory Strains NRC-1 and R1.	Pfeiffer F, Marchfelder A, Habermann B, Dyall-Smith ML	Microbiol Resour Announc	10.1128/MRA.00429-19	2019
	Biofilm formation by haloarchaea.	Frols S, Dyall-Smith M, Pfeifer F	Environ Microbiol	10.1111/j.1462-2920.2012.02895.x	2012
Phylogeny	Halobacterium piscisalsi Yachai et al. 2008 is a later heterotypic synonym of Halobacterium salinarum Elazari-Volcani 1957.	Minegishi H, Echigo A, Shimane Y, Kamekura M, Tanasupawat S, Visessanguan W, Usami R	Int J Syst Evol Microbiol	10.1099/ijs.0.036905-0	2011
Metabolism	Genomic-based phylogenetic and metabolic analyses of the genus Natronomonas, and description of Natronomonas aquatica sp. nov.	Garcia-Roldan A, Duran-Viseras A, de la Haba RR, Corral P, Sanchez-Porro C, Ventosa A.	Front Microbiol	10.3389/fmicb.2023.1109549	2023
	Natronomonas salsuginis sp. nov., a New Inhabitant of a Marine Solar Saltern.	Duran-Viseras A, Sanchez-Porro C, Ventosa A.	Microorganisms	10.3390/microorganisms8040605	2020
	Haloglomus irregulare gen. nov., sp. nov., a New Halophilic Archaeon Isolated from a Marine Saltern.	Duran-Viseras A, Sanchez-Porro C, Ventosa A.	Microorganisms	10.3390/microorganisms8020206	2020
Phylogeny	Halobacterium litoreum sp. nov., isolated from a marine solar saltern.	Lu ZZ, Li Y, Zhou Y, Cui HL, Li ZR	Int J Syst Evol Microbiol	10.1099/ijsem.0.002259	2017
Phylogeny	Haloferax chudinovii sp. nov., a halophilic archaeon from Permian potassium salt deposits.	Saralov AI, Baslerov RV, Kuznetsov BB	Extremophiles	10.1007/s00792-013-0534-8	2013
Phylogeny	Halobacterium piscisalsi sp. nov., from fermented fish (pla-ra) in Thailand.	Yachai M, Tanasupawat S, Itoh T, Benjakul S, Visessanguan W, Valyasevi R	Int J Syst Evol Microbiol	10.1099/ijs.0.65592-0	2008
Phylogeny	Halobacterium jilantaiense sp. nov., a halophilic archaeon isolated from a saline lake in Inner Mongolia, China.	Yang Y, Cui HL, Zhou PJ, Liu SJ	Int J Syst Evol Microbiol	10.1099/ijs.0.64437-0	2006

References

#1340	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 3754
#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) .
#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 .
#122383	Collection of Institut Pasteur ; Curators of the CIP; CIP 104033
#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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Halobacterium salinarum (DSM 3754, ATCC 33171, JCM 8978)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Spore formation

Observation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_004799605

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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