Halorhabdus tiamatea (DSM 18392, JCM 14471, SARL4B)

Name: Halorhabdus tiamatea (DSM 18392, JCM 14471, SARL4B)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 5882

Type strain

Strain Designation SARL4B

Culture col. no. DSM 18392 JCM 14471 SARL4B

NCBI tax ID(s) 1033806 430914

Special Collections DSMZ JCM Literature strains

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Halorhabdus tiamatea SARL4B is an anaerobe, thermophilic, Gram-negative prokaryote that was isolated from brine–sediment interface of the Shaban Deep.

Gram-negative rod-shaped anaerobe thermophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 323967

DSM 18392,JCM 14471

@ref 20215

Last LPSN update 2025-12-16 09:48:10

Domain Methanobacteriati

Phylum Methanobacteriota

Class Halobacteria

Order Halobacteriales

Family Haloarculaceae

Genus Halorhabdus

Species Halorhabdus tiamatea

Full scientific name Halorhabdus tiamatea Antunes et al. 2008

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Motility
32325	negative	4.5 µm	0.75 µm	rod-shaped

Pigmentation

32325

Productionno

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
7521	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

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
7521	positive	growth	45	thermophilic
32325	positive	growth	15-55
32325	positive	optimum	45	thermophilic
67770	positive	growth	37	mesophilic

Culture pH

@ref	Ability	Type	PH	PH range
32325	positive	optimum	6.75
32325	positive	growth	5.5-8.5	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance
7521	anaerobe
32325	anaerobe

Spore formation

@ref	Spore formation	Confidence
125439		93.6

Halophily

@ref	Salt	Growth	Tested relation	Concentration
32325	NaCl	positive	growth	10-30 %
32325	NaCl	positive	optimum	27 %

Observation

67770

Observationquinones: MK-8(VIII-H₂)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
32325	4853 ChEBI	esculin	+	hydrolysis
32325	28757 ChEBI	fructose	+	carbon source
32325	28260 ChEBI	galactose	+	carbon source
32325	17234 ChEBI	glucose	+	carbon source
32325	26271 ChEBI	proline	+	carbon source

Enzymes

@ref	Value	Activity	Ec
32325	alpha-galactosidase	+	3.2.1.22
32325	catalase	+	1.11.1.6
32325	gelatinase	+

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	cyanate degradation	100	3 of 3
66794	vitamin K metabolism	100	5 of 5
66794	factor 420 biosynthesis	100	5 of 5
66794	glycogen metabolism	100	5 of 5
66794	formaldehyde oxidation	100	3 of 3
66794	coenzyme A metabolism	100	4 of 4
66794	palmitate biosynthesis	100	22 of 22
66794	ethanol fermentation	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	cis-vaccenate biosynthesis	100	2 of 2
66794	isoleucine metabolism	87.5	7 of 8
66794	flavin biosynthesis	86.67	13 of 15
66794	photosynthesis	85.71	12 of 14
66794	ubiquinone biosynthesis	85.71	6 of 7
66794	heme metabolism	85.71	12 of 14
66794	pantothenate biosynthesis	83.33	5 of 6
66794	hydrogen production	80	4 of 5
66794	threonine metabolism	80	8 of 10
66794	cellulose degradation	80	4 of 5
66794	starch degradation	80	8 of 10
66794	valine metabolism	77.78	7 of 9
66794	aspartate and asparagine metabolism	77.78	7 of 9
66794	chorismate metabolism	77.78	7 of 9
66794	vitamin B1 metabolism	76.92	10 of 13
66794	phenylalanine metabolism	76.92	10 of 13
66794	purine metabolism	75.53	71 of 94
66794	ppGpp biosynthesis	75	3 of 4
66794	glycogen biosynthesis	75	3 of 4
66794	acetate fermentation	75	3 of 4
66794	ketogluconate metabolism	75	6 of 8
66794	C4 and CAM-carbon fixation	75	6 of 8
66794	gluconeogenesis	75	6 of 8
66794	pyrimidine metabolism	73.33	33 of 45
66794	methionine metabolism	73.08	19 of 26
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	Entner Doudoroff pathway	70	7 of 10
66794	non-pathway related	68.42	26 of 38
66794	serine metabolism	66.67	6 of 9
66794	acetoin degradation	66.67	2 of 3
66794	NAD metabolism	66.67	12 of 18
66794	glycolate and glyoxylate degradation	66.67	4 of 6
66794	octane oxidation	66.67	2 of 3
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	enterobactin biosynthesis	66.67	2 of 3
66794	molybdenum cofactor biosynthesis	66.67	6 of 9
66794	glycolysis	64.71	11 of 17
66794	glutamate and glutamine metabolism	64.29	18 of 28
66794	d-xylose degradation	63.64	7 of 11
66794	pentose phosphate pathway	63.64	7 of 11
66794	oxidative phosphorylation	62.64	57 of 91
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
66794	sulfate reduction	61.54	8 of 13
66794	methylglyoxal degradation	60	3 of 5
66794	phenylacetate degradation (aerobic)	60	3 of 5
66794	3-chlorocatechol degradation	60	3 of 5
66794	degradation of sugar acids	60	15 of 25
66794	carotenoid biosynthesis	59.09	13 of 22
66794	alanine metabolism	58.62	17 of 29
66794	arginine metabolism	58.33	14 of 24
66794	propanol degradation	57.14	4 of 7
66794	tetrahydrofolate metabolism	57.14	8 of 14
66794	reductive acetyl coenzyme A pathway	57.14	4 of 7
66794	degradation of sugar alcohols	56.25	9 of 16
66794	d-mannose degradation	55.56	5 of 9
66794	cysteine metabolism	55.56	10 of 18
66794	histidine metabolism	55.17	16 of 29
66794	metabolism of disaccharids	54.55	6 of 11
66794	proline metabolism	54.55	6 of 11
66794	leucine metabolism	53.85	7 of 13
66794	degradation of pentoses	53.57	15 of 28
66794	lipid metabolism	51.61	16 of 31
66794	4-hydroxyphenylacetate degradation	50	5 of 10
66794	coenzyme M biosynthesis	50	5 of 10
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	ribulose monophosphate pathway	50	1 of 2
66794	CDP-diacylglycerol biosynthesis	50	1 of 2
66794	selenocysteine biosynthesis	50	3 of 6
66794	lactate fermentation	50	2 of 4
66794	adipate degradation	50	1 of 2
66794	glycine metabolism	50	5 of 10
66794	phenylmercury acetate degradation	50	1 of 2
66794	isoprenoid biosynthesis	50	13 of 26
66794	glutathione metabolism	50	7 of 14
66794	tryptophan metabolism	47.37	18 of 38
66794	CO2 fixation in Crenarchaeota	44.44	4 of 9
66794	nitrate assimilation	44.44	4 of 9
66794	citric acid cycle	42.86	6 of 14
66794	mevalonate metabolism	42.86	3 of 7
66794	tyrosine metabolism	42.86	6 of 14
66794	methanogenesis from CO2	41.67	5 of 12
66794	lysine metabolism	40.48	17 of 42
66794	arachidonate biosynthesis	40	2 of 5
66794	phenol degradation	40	8 of 20
66794	gallate degradation	40	2 of 5
66794	metabolism of amino sugars and derivatives	40	2 of 5
66794	arachidonic acid metabolism	38.89	7 of 18
66794	degradation of hexoses	38.89	7 of 18
66794	urea cycle	38.46	5 of 13
66794	phosphatidylethanolamine bioynthesis	38.46	5 of 13
66794	dTDPLrhamnose biosynthesis	37.5	3 of 8
66794	vitamin B6 metabolism	36.36	4 of 11
66794	cholesterol biosynthesis	36.36	4 of 11
66794	dolichyl-diphosphooligosaccharide biosynthesis	36.36	4 of 11
66794	ascorbate metabolism	36.36	8 of 22
66794	sphingosine metabolism	33.33	2 of 6
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	IAA biosynthesis	33.33	1 of 3
66794	degradation of aromatic, nitrogen containing compounds	33.33	4 of 12
66794	sulfoquinovose degradation	33.33	1 of 3
66794	4-hydroxymandelate degradation	33.33	3 of 9
66794	androgen and estrogen metabolism	31.25	5 of 16
66794	phenylpropanoid biosynthesis	30.77	4 of 13
66794	myo-inositol biosynthesis	30	3 of 10
66794	aclacinomycin biosynthesis	28.57	2 of 7
66794	polyamine pathway	26.09	6 of 23
66794	biotin biosynthesis	25	1 of 4
66794	butanoate fermentation	25	1 of 4
66794	cyclohexanol degradation	25	1 of 4
66794	toluene degradation	25	1 of 4
66794	carnitine metabolism	25	2 of 8
66794	vitamin E metabolism	25	1 of 4
66794	CMP-KDO biosynthesis	25	1 of 4
66794	catecholamine biosynthesis	25	1 of 4
66794	sulfopterin metabolism	25	1 of 4
66794	lipid A biosynthesis	22.22	2 of 9

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2
#Environmental	#Aquatic
#Condition	#Saline

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
7521	brine–sediment interface of the Shaban Deep	Red Sea	Saudi Arabia	SAU	Asia
67770	Brine-sediment interface of the Shaban Deep in the northern Red Sea

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
7521	1	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	HATI1 assembly for Halorhabdus tiamatea SARL4B type strain: SARL4B	complete	GCA_000470655	1033806.12	2654588040	1033806	98.4
67770	HLRTI_V2 assembly for Halorhabdus tiamatea SARL4B	contig	GCA_000215915	1033806.93	2562617191	1033806	60.37

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Halorhabdus tiamatea gene for 16S ribosomal RNA, partial sequence	AB576122	1472	1033806
20218	Halorhabdus tiamatea gene for 16S rRNA, complete sequence, strain: JCM 14471	AB663399	1472	1033806
7521	Halorhabdus tiamatea strain SARL4B 16S ribosomal RNA gene, partial sequence	EF127229	1362	1033806

GC content

@ref	GC-content (mol%)	Method
7521	61.7
67770	61.7	high performance liquid chromatography (HPLC)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Halorhabdus tiamatea SARL4B
PATRIC: 1033806.12

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate anaerobe	70.40	no
125439	gram_stain	BacteriaNetⓘ	negative	71.50	no
125439	motility	BacteriaNetⓘ	no	51.90	no
125439	spore_formation	BacteriaNetⓘ	no	93.60	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Halorhabdus tiamatea: proteogenomics and glycosidase activity measurements identify the first cultivated euryarchaeon from a deep-sea anoxic brine lake as potential polysaccharide degrader.	Werner J, Ferrer M, Michel G, Mann AJ, Huang S, Juarez S, Ciordia S, Albar JP, Alcaide M, La Cono V, Yakimov MM, Antunes A, Taborda M, da Costa MS, Hai T, Glockner FO, Golyshina OV, Golyshin PN, Teeling H	Environ Microbiol	10.1111/1462-2920.12393	2014
Phylogeny	Halorhabdus amylolytica sp. nov. and Halorhabdus salina sp. nov., isolated from hypersaline environments.	Wang R, Chen F, Wang J, Liu A, Ke L, Wan F, Chen S	Int J Syst Evol Microbiol	10.1099/ijsem.0.005346	2022
Phylogeny	Halorhabdus rudnickae sp. nov., a halophilic archaeon isolated from a salt mine borehole in Poland.	Albuquerque L, Kowalewicz-Kulbat M, Drzewiecka D, Staczek P, d'Auria G, Rossello-Mora R, da Costa MS	Syst Appl Microbiol	10.1016/j.syapm.2015.12.004	2015
Phylogeny	Halorhabdus tiamatea sp. nov., a non-pigmented, extremely halophilic archaeon from a deep-sea, hypersaline anoxic basin of the Red Sea, and emended description of the genus Halorhabdus.	Antunes A, Taborda M, Huber R, Moissl C, Nobre MF, da Costa MS	Int J Syst Evol Microbiol	10.1099/ijs.0.65316-0	2008

References

#7521	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 18392
#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 )
#32325	Barberan A, Caceres Velazquez H, Jones S, Fierer N.: Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information. mSphere 2: 2017 ( DOI 10.1128/mSphere.00237-17 , PubMed 28776041 ) - originally annotated from #28559 (see below)
#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;
#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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Halorhabdus tiamatea (DSM 18392, JCM 14471, SARL4B)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Observation

Metabolite utilization

Enzymes

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000470655

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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