Salinibacter ruber (DSM 13855, CECT 5946, M31)

Name: Salinibacter ruber (DSM 13855, CECT 5946, M31)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 17796

Type strain

Strain Designation M31

Culture col. no. DSM 13855 CECT 5946 M31 CIP 107417

NCBI tax ID(s) 309807 146919

Special Collections DSMZ CIP

Links

Salinibacter ruber M31 is a mesophilic, Gram-negative, rod-shaped prokaryote that was isolated from solar saltern.

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

Name and taxonomic classification

SI-ID 100944

CECT 5946,ATCC BAA-605,CIP 107.417,CIP 107417,DSM 13855

@ref 20215

Last LPSN update 2025-12-16 09:51:11

Domain Pseudomonadati

Phylum Rhodothermota

Class Rhodothermia

Order Rhodothermales

Family Salinibacteraceae

Genus Salinibacter

Species Salinibacter ruber

Full scientific name Salinibacter ruber Antón et al. 2002

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Motility	Confidence
125438	negative			93.587
122278	negative	rod-shaped

Pigmentation

@ref	Production	Name
122278		flexirubin type pigments

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
5176	SALINIBACTER RUBER MEDIUM (DSMZ Medium 936)	Medium recipe at MediaDive	Name: SALINIBACTER RUBER MEDIUM (DSMZ Medium 936) Composition: NaCl 195.0 g/l MgSO4 x 7 H2O 49.5 g/l MgCl2 x 6 H2O 34.6 g/l Agar 20.0 g/l KCl 5.0 g/l CaCl2 x 2 H2O 1.25 g/l Yeast extract 1.0 g/l NaBr 0.625 g/l NaHCO3 0.25 g/l Distilled water
32764	MEDIUM 429 - for Salinibacter ruber		Sodium hydrogen carbonate (0.250 g);Distilled water make up to (1000.000 ml);Sodium chloride (195.000 g);Potassium chloride (5.000 g);Magnesium chloride hexahydrate(34.600 g);Magnesium sulphate heptahydrate (49.500 g);Calcium chloride dihydrate (1.250 g);
122278	CIP Medium 429	Medium recipe at CIP
122278	CIP Medium 72	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
5176	positive	growth	37	mesophilic
32764	positive	growth	37	mesophilic
122278	positive	growth	37-41
122278	negative	growth	5
122278	negative	growth	10
122278	negative	growth	25
122278	negative	growth	30
122278	negative	growth	45

Physiology and metabolism

Halophily

@ref	Salt	Growth	Tested relation	Concentration
122278	NaCl		growth	6 %
122278	NaCl		growth	10 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
122278	4853 ChEBI	esculin	-	hydrolysis
122278	606565 ChEBI	hippurate	-	hydrolysis
122278	17632 ChEBI	nitrate	-	reduction
122278	17632 ChEBI	nitrate	-	respiration
122278	16301 ChEBI	nitrite	-	reduction

Metabolite production

@ref	Chebi-ID	Metabolite	Production
122278	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test	Methylred-test
122278	15688 ChEBI	acetoin	-
122278	17234 ChEBI	glucose		-

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
122278	alcohol dehydrogenase	-	1.1.1.1
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
122278	amylase	+
68382	beta-galactosidase	-	3.2.1.23	from API zym
122278	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
122278	caseinase	+	3.4.21.50
122278	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
122278	gamma-glutamyltransferase	+	2.3.2.2
122278	gelatinase	+/-
122278	lecithinase	-
68382	leucine arylamidase	+	3.4.11.1	from API zym
122278	lipase	-
68382	lipase (C 14)	-		from API zym
122278	lysine decarboxylase	-	4.1.1.18
68382	N-acetyl-beta-glucosaminidase	+	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
122278	ornithine decarboxylase	-	4.1.1.17
122278	oxidase	+
122278	phenylalanine ammonia-lyase	-	4.3.1.24
122278	protease	+
68382	trypsin	+	3.4.21.4	from API zym
122278	urease	-	3.5.1.5
68382	valine arylamidase	+		from API zym

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	adipate degradation	100	2 of 2
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	ppGpp biosynthesis	100	4 of 4
66794	methylglyoxal degradation	100	5 of 5
66794	vitamin K metabolism	100	5 of 5
66794	formaldehyde oxidation	100	3 of 3
66794	coenzyme A metabolism	100	4 of 4
66794	glycogen metabolism	100	5 of 5
66794	sulfopterin metabolism	100	4 of 4
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	folate polyglutamylation	100	1 of 1
66794	suberin monomers biosynthesis	100	2 of 2
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	starch degradation	100	10 of 10
66794	cardiolipin biosynthesis	100	7 of 7
66794	palmitate biosynthesis	90.91	20 of 22
66794	chorismate metabolism	88.89	8 of 9
66794	isoleucine metabolism	87.5	7 of 8
66794	C4 and CAM-carbon fixation	87.5	7 of 8
66794	gluconeogenesis	87.5	7 of 8
66794	photosynthesis	85.71	12 of 14
66794	phenylalanine metabolism	84.62	11 of 13
66794	NAD metabolism	83.33	15 of 18
66794	pentose phosphate pathway	81.82	9 of 11
66794	vitamin B6 metabolism	81.82	9 of 11
66794	threonine metabolism	80	8 of 10
66794	lipoate biosynthesis	80	4 of 5
66794	metabolism of amino sugars and derivatives	80	4 of 5
66794	cellulose degradation	80	4 of 5
66794	serine metabolism	77.78	7 of 9
66794	valine metabolism	77.78	7 of 9
66794	CO2 fixation in Crenarchaeota	77.78	7 of 9
66794	d-mannose degradation	77.78	7 of 9
66794	leucine metabolism	76.92	10 of 13
66794	glycolysis	76.47	13 of 17
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	glutamate and glutamine metabolism	75	21 of 28
66794	acetate fermentation	75	3 of 4
66794	dTDPLrhamnose biosynthesis	75	6 of 8
66794	glycogen biosynthesis	75	3 of 4
66794	purine metabolism	74.47	70 of 94
66794	peptidoglycan biosynthesis	73.33	11 of 15
66794	pyrimidine metabolism	73.33	33 of 45
66794	methionine metabolism	73.08	19 of 26
66794	proline metabolism	72.73	8 of 11
66794	propanol degradation	71.43	5 of 7
66794	tetrahydrofolate metabolism	71.43	10 of 14
66794	isoprenoid biosynthesis	69.23	18 of 26
66794	vitamin B1 metabolism	69.23	9 of 13
66794	lysine metabolism	69.05	29 of 42
66794	alanine metabolism	68.97	20 of 29
66794	tryptophan metabolism	68.42	26 of 38
66794	octane oxidation	66.67	2 of 3
66794	aspartate and asparagine metabolism	66.67	6 of 9
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	acetyl CoA biosynthesis	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	lipid metabolism	64.52	20 of 31
66794	degradation of sugar alcohols	62.5	10 of 16
66794	ketogluconate metabolism	62.5	5 of 8
66794	non-pathway related	60.53	23 of 38
66794	flavin biosynthesis	60	9 of 15
66794	propionate fermentation	60	6 of 10
66794	Entner Doudoroff pathway	60	6 of 10
66794	histidine metabolism	58.62	17 of 29
66794	degradation of aromatic, nitrogen containing compounds	58.33	7 of 12
66794	arginine metabolism	58.33	14 of 24
66794	ubiquinone biosynthesis	57.14	4 of 7
66794	citric acid cycle	57.14	8 of 14
66794	glutathione metabolism	57.14	8 of 14
66794	tyrosine metabolism	57.14	8 of 14
66794	cysteine metabolism	55.56	10 of 18
66794	metabolism of disaccharids	54.55	6 of 11
66794	phosphatidylethanolamine bioynthesis	53.85	7 of 13
66794	oxidative phosphorylation	53.85	49 of 91
66794	glycolate and glyoxylate degradation	50	3 of 6
66794	CMP-KDO biosynthesis	50	2 of 4
66794	kanosamine biosynthesis II	50	1 of 2
66794	heme metabolism	50	7 of 14
66794	dolichol and dolichyl phosphate biosynthesis	50	1 of 2
66794	pantothenate biosynthesis	50	3 of 6
66794	coenzyme M biosynthesis	50	5 of 10
66794	phenylmercury acetate degradation	50	1 of 2
66794	ethanol fermentation	50	1 of 2
66794	biotin biosynthesis	50	2 of 4
66794	phenylpropanoid biosynthesis	46.15	6 of 13
66794	lipid A biosynthesis	44.44	4 of 9
66794	reductive acetyl coenzyme A pathway	42.86	3 of 7
66794	degradation of pentoses	42.86	12 of 28
66794	carotenoid biosynthesis	40.91	9 of 22
66794	ascorbate metabolism	40.91	9 of 22
66794	glycine metabolism	40	4 of 10
66794	gallate degradation	40	2 of 5
66794	bacilysin biosynthesis	40	2 of 5
66794	3-chlorocatechol degradation	40	2 of 5
66794	arachidonate biosynthesis	40	2 of 5
66794	urea cycle	38.46	5 of 13
66794	sulfate reduction	38.46	5 of 13
66794	d-xylose degradation	36.36	4 of 11
66794	cyanate degradation	33.33	1 of 3
66794	arachidonic acid metabolism	33.33	6 of 18
66794	selenocysteine biosynthesis	33.33	2 of 6
66794	enterobactin biosynthesis	33.33	1 of 3
66794	1,4-dihydroxy-6-naphthoate biosynthesis	33.33	2 of 6
66794	IAA biosynthesis	33.33	1 of 3
66794	degradation of hexoses	33.33	6 of 18
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	sphingosine metabolism	33.33	2 of 6
66794	androgen and estrogen metabolism	31.25	5 of 16
66794	3-phenylpropionate degradation	26.67	4 of 15
66794	cyclohexanol degradation	25	1 of 4
66794	toluene degradation	25	1 of 4
66794	carnitine metabolism	25	2 of 8
66794	butanoate fermentation	25	1 of 4
66794	catecholamine biosynthesis	25	1 of 4
66794	lactate fermentation	25	1 of 4
66794	molybdenum cofactor biosynthesis	22.22	2 of 9
66794	nitrate assimilation	22.22	2 of 9
66794	chlorophyll metabolism	22.22	4 of 18
66794	4-hydroxymandelate degradation	22.22	2 of 9

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
122278	-	+	+	-	-	+	+	-	+	-	+	+	-	-	-	+	-	+	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2
#Condition	#Saline

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Isolation date
5176	solar saltern	Mallorca	Spain	ESP	Europe
122278	Environment, Solar saltern water	Balearic Islands	Spain	ESP	Europe	1999

Taxonmaps

69479

Global distribution of 16S sequence AF323500 (>99% sequence identity) for Salinibacter ruber subclade from Microbeatlas

Aquatic Samples	176
Soil Samples	23
Animal Samples	348
Plant Samples	2
Total Samples	549

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
5176	1	Risk group (German classification) According to TRBA 466
122278	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	ASM1304v1 assembly for Salinibacter ruber DSM 13855 DSM 13855; M31	complete	GCA_000013045	309807.25	637000250	309807	96.79

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
5176	Salinibacter ruber strain M31 16S ribosomal RNA gene, partial sequence	AF323500	1482		309807

GC content

5176

GC-content (mol%)70

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Salinibacter ruber DSM 13855
PATRIC: 309807.25

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	84.40	no
125439	motility	BacteriaNetⓘ	yes	60.10	no
125439	gram_stain	BacteriaNetⓘ	negative	81.10	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate anaerobe	68.20	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Salinibacter ruber DSM 13855
NCBI: GCA_000013045.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	93.59	no
125438	anaerobic	anaerobicⓘ	no	95.25	no
125438	aerobic	aerobicⓘ	yes	68.77	no
125438	spore-forming	spore-formingⓘ	no	86.99	no
125438	thermophilic	thermophileⓘ	no	77.90	yes
125438	flagellated	motile2+ⓘ	no	58.55	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Light cues drive community-wide transcriptional shifts in the hypersaline South Bay Salt Works.	Weng MM, Klempay B, Bowman JS, Fisher L, Camplong C, Doran PT, Rundell S, Glass JB, Dutta A, Pontefract A, Bartlett DH, Schmidt B, Johnson SS.	Commun Biol	10.1038/s42003-025-07855-w	2025
	HPClas: A data-driven approach for identifying halophilic proteins based on catBoost.	Hu S, Wang X, Wang Z, Jiang M, Wang S, Wang W, Song J, Zhang G.	mLife	10.1002/mlf2.12125	2024
	Structural and bioinformatics analysis of single-domain substrate-binding protein from Rhodothermus marinus.	Nam KH.	Biochem Biophys Rep	10.1016/j.bbrep.2023.101611	2024
Phylogeny	HaloClass: Salt-Tolerant Protein Classification with Protein Language Models.	Narang K, Nath A, Hemstrom W, Chu SKS.	Protein J	10.1007/s10930-024-10236-7	2024
Proteome	Ultra-sensitive metaproteomics redefines the dark metaproteome, uncovering host-microbiome interactions and drug targets in intestinal diseases.	Xian F, Brenek M, Krisp C, Urbauer E, Ravi Kumar RK, Aguanno D, Srikumar T, Liu Q, Barry AM, Ma B, Krieger J, Haller D, Schmidt M, Gomez-Varela D.	Nat Commun	10.1038/s41467-025-61977-7	2025
	Mucosal microbiome of surgically treated terminal ileal Crohn's disease.	Loch FN, Kamphues C, Menzel P, Schwarzer R, Beyer K, Schineis C.	Front Cell Infect Microbiol	10.3389/fcimb.2023.1324668	2023
	Genome Sequence and Characterization of a Xanthorhodopsin-Containing, Aerobic Anoxygenic Phototrophic Rhodobacter Species, Isolated from Mesophilic Conditions at Yellowstone National Park.	Kyndt JA, Robertson S, Shoffstall IB, Ramaley RF, Meyer TE.	Microorganisms	10.3390/microorganisms10061169	2022
	RELMbeta sets the threshold for microbiome-dependent oral tolerance.	Stephen-Victor E, Kuziel GA, Martinez-Blanco M, Jugder BE, Benamar M, Wang Z, Chen Q, Lozano GL, Abdel-Gadir A, Cui Y, Fong J, Saint-Denis E, Chang I, Nadeau KC, Phipatanakul W, Zhang A, Farraj FA, Holder-Niles F, Zeve D, Breault DT, Schmitz-Abe K, Rachid R, Crestani E, Rakoff-Nahoum S, Chatila TA.	Nature	10.1038/s41586-024-08440-7	2025
Metabolism	Structural Flexibility of Peripheral Loops and Extended C-terminal Domain of Short Length Substrate Binding Protein from Rhodothermus marinus.	Bae JE, Kim IJ, Xu Y, Nam KH.	Protein J	10.1007/s10930-021-09970-z	2021
	Reliability of species detection in 16S microbiome analysis: Comparison of five widely used pipelines and recommendations for a more standardized approach.	Hiergeist A, Ruelle J, Emler S, Gessner A.	PLoS One	10.1371/journal.pone.0280870	2023
Phylogeny	Diversity of the Tryptophanase Gene and Its Evolutionary Implications in Living Organisms.	Boya BR, Kumar P, Lee JH, Lee J.	Microorganisms	10.3390/microorganisms9102156	2021
Enzymology	Facile synthesis of 2-hydroxyacetophenone from racemic styrene oxide catalyzed by engineered enzymes.	Soderlund I, Tjarnhage E, Hamnevik E, Widersten M.	Biotechnol Lett	10.1007/s10529-022-03271-w	2022
	The Histidine Biosynthetic Genes in the Superphylum Bacteroidota-Rhodothermota-Balneolota-Chlorobiota: Insights into the Evolution of Gene Structure and Organization.	Del Duca S, Riccardi C, Vassallo A, Fontana G, Castronovo LM, Chioccioli S, Fani R.	Microorganisms	10.3390/microorganisms9071439	2021
	Expression analysis of microbial rhodopsin-like genes in Guillardia theta.	Konno M, Yamauchi Y, Inoue K, Kandori H.	PLoS One	10.1371/journal.pone.0243387	2020
Metabolism	Biosynthetic Potential of a Novel Antarctic Actinobacterium Marisediminicola antarctica ZS314^T Revealed by Genomic Data Mining and Pigment Characterization.	Liao L, Su S, Zhao B, Fan C, Zhang J, Li H, Chen B.	Mar Drugs	10.3390/md17070388	2019
Enzymology	Deciphering Evolutionary Trajectories of Lactate Dehydrogenases Provides New Insights into Allostery.	Robin AY, Brochier-Armanet C, Bertrand Q, Barette C, Girard E, Madern D.	Mol Biol Evol	10.1093/molbev/msad223	2023
Phylogeny	From community approaches to single-cell genomics: the discovery of ubiquitous hyperhalophilic Bacteroidetes generalists.	Gomariz M, Martinez-Garcia M, Santos F, Rodriguez F, Capella-Gutierrez S, Gabaldon T, Rossello-Mora R, Meseguer I, Anton J.	ISME J	10.1038/ismej.2014.95	2015
Genetics	In silico prediction of potential indigenous microbial biomarkers in Penaeus vannamei identified through meta-analysis and genome-scale metabolic modelling.	Devika NT, Katneni VK, Jangam AK, Suganya PN, Shekhar MS, Jithendran KP.	Environ Microbiome	10.1186/s40793-022-00458-6	2023
	Structure-based insights into evolution of rhodopsins.	Zabelskii D, Dmitrieva N, Volkov O, Shevchenko V, Kovalev K, Balandin T, Soloviov D, Astashkin R, Zinovev E, Alekseev A, Round E, Polovinkin V, Chizhov I, Rogachev A, Okhrimenko I, Borshchevskiy V, Chupin V, Buldt G, Yutin N, Bamberg E, Koonin E, Gordeliy V.	Commun Biol	10.1038/s42003-021-02326-4	2021
Enzymology	Structural insights into substrate specificity and solvent tolerance in alcohol dehydrogenase ADH-'A' from Rhodococcus ruber DSM 44541.	Karabec M, Lyskowski A, Tauber KC, Steinkellner G, Kroutil W, Grogan G, Gruber K.	Chem Commun (Camb)	10.1039/c0cc00929f	2010
Genetics	Aerobic Degradation Characteristics of Decabromodiphenyl ether through Rhodococcus ruber TAW-CT127 and Its Preliminary Genome Analysis.	Xu H, Cai Q, An Q, Tang C, Wang W, Wang G, You W, Guo D, Zhao R.	Microorganisms	10.3390/microorganisms10071441	2022
	Comparative in silico analysis of ftsZ gene from different bacteria reveals the preference for core set of codons in coding sequence structuring and secondary structural elements determination.	Pal A, Saha BK, Saha J.	PLoS One	10.1371/journal.pone.0219231	2019
	Functional exploration of the glycoside hydrolase family GH113.	Couturier M, Touvrey-Loiodice M, Terrapon N, Drula E, Buon L, Chirat C, Henrissat B, Helbert W.	PLoS One	10.1371/journal.pone.0267509	2022
	Phenomics and Genomics Reveal Adaptation of Virgibacillus dokdonensis Strain 21D to Its Origin of Isolation, the Seawater-Brine Interface of the Mediterranean Sea Deep Hypersaline Anoxic Basin Discovery.	Zeaiter Z, Marasco R, Booth JM, Prosdocimi EM, Mapelli F, Callegari M, Fusi M, Michoud G, Molinari F, Daffonchio D, Borin S, Crotti E.	Front Microbiol	10.3389/fmicb.2019.01304	2019
	Chemoenzymatic Synthesis of Tenofovir.	Zdun B, Reiter T, Kroutil W, Borowiecki P.	J Org Chem	10.1021/acs.joc.3c01005	2023
	Organic-inorganic nanocrystal reductase to promote green asymmetric synthesis.	T Sriwong K, Koesoema AA, Matsuda T.	RSC Adv	10.1039/d0ra03160g	2020
Enzymology	Prokaryotic diversity in Aran-Bidgol salt lake, the largest hypersaline playa in Iran.	Makhdoumi-Kakhki A, Amoozegar MA, Kazemi B, Pasic L, Ventosa A.	Microbes Environ	10.1264/jsme2.me11267	2012
	Omega Rhodopsins: A Versatile Class of Microbial Rhodopsins.	Kwon SK, Jun SH, Kim JF.	J Microbiol Biotechnol	10.4014/jmb.1912.12010	2020
Genetics	Genomes of "Spiribacter", a streamlined, successful halophilic bacterium.	Lopez-Perez M, Ghai R, Leon MJ, Rodriguez-Olmos A, Copa-Patino JL, Soliveri J, Sanchez-Porro C, Ventosa A, Rodriguez-Valera F.	BMC Genomics	10.1186/1471-2164-14-787	2013
Metabolism	The Halophile protein database.	Sharma N, Farooqi MS, Chaturvedi KK, Lal SB, Grover M, Rai A, Pandey P.	Database (Oxford)	10.1093/database/bau114	2014
Metabolism	Identification of different alkane hydroxylase systems in Rhodococcus ruber strain SP2B, an hexane-degrading actinomycete.	Amouric A, Quemeneur M, Grossi V, Liebgott PP, Auria R, Casalot L.	J Appl Microbiol	10.1111/j.1365-2672.2009.04592.x	2010
	Spectral tuning in sensory rhodopsin I from Salinibacter ruber.	Sudo Y, Yuasa Y, Shibata J, Suzuki D, Homma M.	J Biol Chem	10.1074/jbc.m110.187948	2011
	Transmembrane Shuttling of Photosynthetically Produced Electrons to Propel Extracellular Biocatalytic Redox Reactions in a Modular Fashion.	Jurkas V, Weissensteiner F, De Santis P, Vrabl S, Sorgenfrei FA, Bierbaumer S, Kara S, Kourist R, Wangikar PP, Winkler CK, Kroutil W.	Angew Chem Int Ed Engl	10.1002/anie.202207971	2022
	Solar-panel and parasol strategies shape the proteorhodopsin distribution pattern in marine Flavobacteriia.	Kumagai Y, Yoshizawa S, Nakajima Y, Watanabe M, Fukunaga T, Ogura Y, Hayashi T, Oshima K, Hattori M, Ikeuchi M, Kogure K, DeLong EF, Iwasaki W.	ISME J	10.1038/s41396-018-0058-4	2018
Metabolism	Overcoming the thermodynamic limitation in asymmetric hydrogen transfer reactions catalyzed by whole cells.	Goldberg K, Edegger K, Kroutil W, Liese A.	Biotechnol Bioeng	10.1002/bit.21014	2006
	Biocatalytic deuterium- and hydrogen-transfer using over-expressed ADH-'A': enhanced stereoselectivity and 2H-labeled chiral alcohols.	Edegger K, Gruber CC, Poessl TM, Wallner SR, Lavandera I, Faber K, Niehaus F, Eck J, Oehrlein R, Hafner A, Kroutil W.	Chem Commun (Camb)	10.1039/b602487d	2006
	Biocatalytic approaches for the quantitative production of single stereoisomers from racemates.	Gadler P, Glueck SM, Kroutil W, Nestl BM, Larissegger-Schnell B, Ueberbacher BT, Wallner SR, Faber K.	Biochem Soc Trans	10.1042/bst20060296	2006
Phylogeny	Study of a hexane-degrading consortium in a biofilter and in liquid culture: biodiversity, kinetics and characterization of degrading strains.	Amouric A, Verhe F, Auria R, Casalot L.	FEMS Microbiol Ecol	10.1111/j.1574-6941.2005.00017.x	2006
Metabolism	Inability of Prevotella bryantii to form a functional Shine-Dalgarno interaction reflects unique evolution of ribosome binding sites in Bacteroidetes.	Accetto T, Avgustin G.	PLoS One	10.1371/journal.pone.0022914	2011
Enzymology	Primers for amplification of nitrous oxide reductase genes associated with Firmicutes and Bacteroidetes in organic-compound-rich soils.	Jung J, Choi S, Jung H, Scow KM, Park W.	Microbiology (Reading)	10.1099/mic.0.060194-0	2013
	Stereoselective Biocatalyzed Reductions of Ginger Active Components Recovered from Industrial Wastes.	Nasti R, Bassanini I, Ferrandi EE, Linguardo F, Bertuletti S, Vanoni M, Riva S, Verotta L, Monti D.	Chembiochem	10.1002/cbic.202200105	2022
Enzymology	Identification of the catalytic triad of family S46 exopeptidases, closely related to clan PA endopeptidases.	Suzuki Y, Sakamoto Y, Tanaka N, Okada H, Morikawa Y, Ogasawara W.	Sci Rep	10.1038/srep04292	2014
Enzymology	Purification and characterization of a chemotolerant alcohol dehydrogenase applicable to coupled redox reactions.	Kosjek B, Stampfer W, Pogorevc M, Goessler W, Faber K, Kroutil W.	Biotechnol Bioeng	10.1002/bit.20004	2004
Enzymology	Biocatalytic asymmetric hydrogen transfer employing Rhodococcus ruber DSM 44541.	Stampfer W, Kosjek B, Faber K, Kroutil W.	J Org Chem	10.1021/jo026216w	2003
Genetics	Osmoadaptative Strategy and Its Molecular Signature in Obligately Halophilic Heterotrophic Protists.	Harding T, Brown MW, Simpson AG, Roger AJ.	Genome Biol Evol	10.1093/gbe/evw152	2016
Enzymology	Stereoinversion via Alcohol Dehydrogenases Enables Complete Catabolism of beta-1-Type Lignin-Derived Aromatic Isomers.	Kato R, Maekawa K, Kobayashi S, Hishiyama S, Katahira R, Nambo M, Higuchi Y, Kuatsjah E, Beckham GT, Kamimura N, Masai E.	Appl Environ Microbiol	10.1128/aem.00171-23	2023
Metabolism	On the organic solvent and thermostability of the biocatalytic redox system of Rhodococcus ruber DSM 44541.	Stampfer W, Kosjek B, Kroutil W, Faber K.	Biotechnol Bioeng	10.1002/bit.10540	2003
Genetics	Salt resistance genes revealed by functional metagenomics from brines and moderate-salinity rhizosphere within a hypersaline environment.	Mirete S, Mora-Ruiz MR, Lamprecht-Grandio M, de Figueras CG, Rossello-Mora R, Gonzalez-Pastor JE.	Front Microbiol	10.3389/fmicb.2015.01121	2015
	Functions of carotenoids in xanthorhodopsin and archaerhodopsin, from action spectra of photoinhibition of cell respiration.	Boichenko VA, Wang JM, Anton J, Lanyi JK, Balashov SP.	Biochim Biophys Acta	10.1016/j.bbabio.2006.08.012	2006
Metabolism	Enantioselectivity of epoxide hydrolase catalysed oxirane ring opening: a 3D QSAR study.	Paier J, Stockner T, Steinreiber A, Faber K, Fabian WM.	J Comput Aided Mol Des	10.1023/a:1024562326498	2003
	Microbial community functional structures in wastewater treatment plants as characterized by GeoChip.	Wang X, Xia Y, Wen X, Yang Y, Zhou J.	PLoS One	10.1371/journal.pone.0093422	2014
	Global Transcriptomic Responses of Roseithermus sacchariphilus Strain RA in Media Supplemented with Beechwood Xylan.	Liew KJ, Bruce NC, Sani RK, Chong CS, Yaakop AS, Shamsir MS, Goh KM.	Microorganisms	10.3390/microorganisms8070976	2020
	Synthesis of alpha-hydroxy ketones and vicinal (R,R)-diols by Bacillus clausii DSM 8716^T butanediol dehydrogenase.	Muschallik L, Molinnus D, Jablonski M, Kipp CR, Bongaerts J, Pohl M, Wagner T, Schoning MJ, Selmer T, Siegert P.	RSC Adv	10.1039/d0ra02066d	2020
Metabolism	Salinibacter sensory rhodopsin: sensory rhodopsin I-like protein from a eubacterium.	Kitajima-Ihara T, Furutani Y, Suzuki D, Ihara K, Kandori H, Homma M, Sudo Y.	J Biol Chem	10.1074/jbc.m802990200	2008
Metabolism	Structural basis for conductance through TRIC cation channels.	Su M, Gao F, Yuan Q, Mao Y, Li DL, Guo Y, Yang C, Wang XH, Bruni R, Kloss B, Zhao H, Zeng Y, Zhang FB, Marks AR, Hendrickson WA, Chen YH.	Nat Commun	10.1038/ncomms15103	2017
Phylogeny	The genome of Salinibacter ruber: convergence and gene exchange among hyperhalophilic bacteria and archaea.	Mongodin EF, Nelson KE, Daugherty S, Deboy RT, Wister J, Khouri H, Weidman J, Walsh DA, Papke RT, Sanchez Perez G, Sharma AK, Nesbo CL, MacLeod D, Bapteste E, Doolittle WF, Charlebois RL, Legault B, Rodriguez-Valera F.	Proc Natl Acad Sci U S A	10.1073/pnas.0509073102	2005
Metabolism	From Bugs to Bioplastics: Total (+)-Dihydrocarvide Biosynthesis by Engineered Escherichia coli.	Ascue Avalos GA, Toogood HS, Tait S, Messiha HL, Scrutton NS.	Chembiochem	10.1002/cbic.201800606	2019
	Reliability and applications of statistical methods based on oligonucleotide frequencies in bacterial and archaeal genomes.	Bohlin J, Skjerve E, Ussery DW.	BMC Genomics	10.1186/1471-2164-9-104	2008
Metabolism	A reexamination of information theory-based methods for DNA-binding site identification.	Erill I, O'Neill MC.	BMC Bioinformatics	10.1186/1471-2105-10-57	2009
	Comprehensive analysis of stop codon usage in bacteria and its correlation with release factor abundance.	Korkmaz G, Holm M, Wiens T, Sanyal S.	J Biol Chem	10.1074/jbc.m114.606632	2014
	Biodegradation of Di-(2-ethylhexyl) Phthalate by Rhodococcus ruber YC-YT1 in Contaminated Water and Soil.	Yang T, Ren L, Jia Y, Fan S, Wang J, Wang J, Nahurira R, Wang H, Yan Y.	Int J Environ Res Public Health	10.3390/ijerph15050964	2018
Phylogeny	Whole-proteome phylogeny of prokaryotes by feature frequency profiles: An alignment-free method with optimal feature resolution.	Jun SR, Sims GE, Wu GA, Kim SH.	Proc Natl Acad Sci U S A	10.1073/pnas.0913033107	2010
Pathogenicity	Stimulation of expression of a silica-induced protein (Sip) in Thermus thermophilus by supersaturated silicic acid.	Doi K, Fujino Y, Inagaki F, Kawatsu R, Tahara M, Ohshima T, Okaue Y, Yokoyama T, Iwai S, Ogata S.	Appl Environ Microbiol	10.1128/aem.02387-08	2009
Genetics	Bayesian prediction of bacterial growth temperature range based on genome sequences.	Jensen DB, Vesth TC, Hallin PF, Pedersen AG, Ussery DW.	BMC Genomics	10.1186/1471-2164-13-s7-s3	2012
Genetics	Comparison of genomic data via statistical distribution.	Amiri S, Dinov ID.	J Theor Biol	10.1016/j.jtbi.2016.07.032	2016
Metabolism	Is there a common water-activity limit for the three domains of life?	Stevenson A, Cray JA, Williams JP, Santos R, Sahay R, Neuenkirchen N, McClure CD, Grant IR, Houghton JD, Quinn JP, Timson DJ, Patil SV, Singhal RS, Anton J, Dijksterhuis J, Hocking AD, Lievens B, Rangel DE, Voytek MA, Gunde-Cimerman N, Oren A, Timmis KN, McGenity TJ, Hallsworth JE.	ISME J	10.1038/ismej.2014.219	2015
Phylogeny	Phylogeny and molecular signatures (conserved proteins and indels) that are specific for the Bacteroidetes and Chlorobi species.	Gupta RS, Lorenzini E.	BMC Evol Biol	10.1186/1471-2148-7-71	2007
Genetics	Reconstructing viral genomes from the environment using fosmid clones: the case of haloviruses.	Garcia-Heredia I, Martin-Cuadrado AB, Mojica FJ, Santos F, Mira A, Anton J, Rodriguez-Valera F.	PLoS One	10.1371/journal.pone.0033802	2012
Metabolism	Nutrient-regulated transcriptional responses in the brown tide-forming alga Aureococcus anophagefferens.	Wurch LL, Haley ST, Orchard ED, Gobler CJ, Dyhrman ST.	Environ Microbiol	10.1111/j.1462-2920.2010.02351.x	2011
Metabolism	Ribonucleotide reduction - horizontal transfer of a required function spans all three domains.	Lundin D, Gribaldo S, Torrents E, Sjoberg BM, Poole AM.	BMC Evol Biol	10.1186/1471-2148-10-383	2010
Genetics	Genome evolution and the emergence of fruiting body development in Myxococcus xanthus.	Goldman B, Bhat S, Shimkets LJ.	PLoS One	10.1371/journal.pone.0001329	2007
	Planting increases the abundance and structure complexity of soil core functional genes relevant to carbon and nitrogen cycling.	Wang F, Liang Y, Jiang Y, Yang Y, Xue K, Xiong J, Zhou J, Sun B.	Sci Rep	10.1038/srep14345	2015
Metabolism	PG1058 Is a Novel Multidomain Protein Component of the Bacterial Type IX Secretion System.	Heath JE, Seers CA, Veith PD, Butler CA, Nor Muhammad NA, Chen YY, Slakeski N, Peng B, Zhang L, Dashper SG, Cross KJ, Cleal SM, Moore C, Reynolds EC.	PLoS One	10.1371/journal.pone.0164313	2016
	Molecular signature of hypersaline adaptation: insights from genome and proteome composition of halophilic prokaryotes.	Paul S, Bag SK, Das S, Harvill ET, Dutta C.	Genome Biol	10.1186/gb-2008-9-4-r70	2008
Phylogeny	Across bacterial phyla, distantly-related genomes with similar genomic GC content have similar patterns of amino acid usage.	Lightfield J, Fram NR, Ely B.	PLoS One	10.1371/journal.pone.0017677	2011
Metabolism	Genome sequence of Desulfobacterium autotrophicum HRM2, a marine sulfate reducer oxidizing organic carbon completely to carbon dioxide.	Strittmatter AW, Liesegang H, Rabus R, Decker I, Amann J, Andres S, Henne A, Fricke WF, Martinez-Arias R, Bartels D, Goesmann A, Krause L, Puhler A, Klenk HP, Richter M, Schuler M, Glockner FO, Meyerdierks A, Gottschalk G, Amann R.	Environ Microbiol	10.1111/j.1462-2920.2008.01825.x	2009
Phylogeny	Quantifying homologous replacement of loci between haloarchaeal species.	Williams D, Gogarten JP, Papke RT.	Genome Biol Evol	10.1093/gbe/evs098	2012
	Function and biotechnology of extremophilic enzymes in low water activity.	Karan R, Capes MD, Dassarma S.	Aquat Biosyst	10.1186/2046-9063-8-4	2012
Metabolism	Parallel genomic evolution and metabolic interdependence in an ancient symbiosis.	McCutcheon JP, Moran NA.	Proc Natl Acad Sci U S A	10.1073/pnas.0708855104	2007
	Phenotyping the quality of complex medium components by simple online-monitored shake flask experiments.	Diederichs S, Korona A, Staaden A, Kroutil W, Honda K, Ohtake H, Buchs J.	Microb Cell Fact	10.1186/s12934-014-0149-5	2014
Phylogeny	Genomic analysis reveals versatile organisms for quorum quenching enzymes: acyl-homoserine lactone-acylase and -lactonase.	Kalia VC, Raju SC, Purohit HJ.	Open Microbiol J	10.2174/1874285801105010001	2011
Metabolism	The elusive third subunit IIa of the bacterial B-type oxidases: the enzyme from the hyperthermophile Aquifex aeolicus.	Prunetti L, Brugna M, Lebrun R, Giudici-Orticoni MT, Guiral M.	PLoS One	10.1371/journal.pone.0021616	2011
Metabolism	Identification of prophages in bacterial genomes by dinucleotide relative abundance difference.	Srividhya KV, Alaguraj V, Poornima G, Kumar D, Singh GP, Raghavenderan L, Katta AV, Mehta P, Krishnaswamy S.	PLoS One	10.1371/journal.pone.0001193	2007
Metabolism	Rhodococcus as A Versatile Biocatalyst in Organic Synthesis.	Busch H, Hagedoorn PL, Hanefeld U.	Int J Mol Sci	10.3390/ijms20194787	2019
Metabolism	Distribution and functions of TonB-dependent transporters in marine bacteria and environments: implications for dissolved organic matter utilization.	Tang K, Jiao N, Liu K, Zhang Y, Li S.	PLoS One	10.1371/journal.pone.0041204	2012
	Annotation of Protein Domains Reveals Remarkable Conservation in the Functional Make up of Proteomes Across Superkingdoms.	Nasir A, Naeem A, Khan MJ, Nicora HD, Caetano-Anolles G.	Genes (Basel)	10.3390/genes2040869	2011
Enzymology	Purification and characterization of an inverting stereo- and enantioselective sec-alkylsulfatase from the gram-positive bacterium Rhodococcus ruber DSM 44541.	Pogorevc M, Faber K.	Appl Environ Microbiol	10.1128/aem.69.5.2810-2815.2003	2003
Metabolism	Engineering of phenylacetaldehyde reductase for efficient substrate conversion in concentrated 2-propanol.	Makino Y, Inoue K, Dairi T, Itoh N.	Appl Environ Microbiol	10.1128/aem.71.8.4713-4720.2005	2005
Genetics	Metagenomics of the deep Mediterranean, a warm bathypelagic habitat.	Martin-Cuadrado AB, Lopez-Garcia P, Alba JC, Moreira D, Monticelli L, Strittmatter A, Gottschalk G, Rodriguez-Valera F.	PLoS One	10.1371/journal.pone.0000914	2007
	Bioinformatic characterization of the trimeric intracellular cation-specific channel protein family.	Silverio AL, Saier MH.	J Membr Biol	10.1007/s00232-011-9364-8	2011
Metabolism	Cohesion group approach for evolutionary analysis of aspartokinase, an enzyme that feeds a branched network of many biochemical pathways.	Lo CC, Bonner CA, Xie G, D'Souza M, Jensen RA.	Microbiol Mol Biol Rev	10.1128/mmbr.00024-09	2009
Metabolism	Comprehensive comparative-genomic analysis of type 2 toxin-antitoxin systems and related mobile stress response systems in prokaryotes.	Makarova KS, Wolf YI, Koonin EV.	Biol Direct	10.1186/1745-6150-4-19	2009
Genetics	A genome-scale metabolic network reconstruction of extremely halophilic bacterium Salinibacter ruber.	Bagheri M, Marashi SA, Amoozegar MA	PLoS One	10.1371/journal.pone.0216336	2019
Genetics	Metagenomic islands of hyperhalophiles: the case of Salinibacter ruber.	Pasic L, Rodriguez-Mueller B, Martin-Cuadrado AB, Mira A, Rohwer F, Rodriguez-Valera F	BMC Genomics	10.1186/1471-2164-10-570	2009
Phylogeny	Salinibacter iranicus sp. nov. and Salinibacter luteus sp. nov., isolated from a salt lake, and emended descriptions of the genus Salinibacter and of Salinibacter ruber.	Makhdoumi-Kakhki A, Amoozegar MA, Ventosa A	Int J Syst Evol Microbiol	10.1099/ijs.0.031971-0	2011
Phylogeny	Salinibacter ruber gen. nov., sp. nov., a novel, extremely halophilic member of the Bacteria from saltern crystallizer ponds.	Anton J, Oren A, Benlloch S, Rodriguez-Valera F, Amann R, Rossello-Mora R	Int J Syst Evol Microbiol	10.1099/00207713-52-2-485	2002

References

#5176	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 13855
#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 )
#32764	; 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 )
#68382	Automatically annotated from API zym .
#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 .
#122278	Collection of Institut Pasteur ; Curators of the CIP; CIP 107417
#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 )

Rate our new design

Content

About us

Salinibacter ruber (DSM 13855, CECT 5946, M31)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Halophily

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

Pathway annotation

API zym

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000013045

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

Help

Social Media