Halosimplex carlsbadense (CIP 108098, JCM 11222, ATCC BAA-75)

Name: Halosimplex carlsbadense (CIP 108098, JCM 11222, ATCC BAA-75)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 135088

Type strain

Culture col. no. CIP 108098 JCM 11222 ATCC BAA-75 CGMCC 1.10340

NCBI tax ID(s) 797114 171164

Special Collections JCM CIP

Links

Halosimplex carlsbadense CIP 108098 is a mesophilic, Gram-negative, rod-shaped prokaryote of the family Haloarculaceae.

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

Name and taxonomic classification

SI-ID 111664

JCM 11222,ATCC BAA-75,CIP 108098

@ref 20215

Last LPSN update 2025-12-16 10:02:13

Domain Methanobacteriati

Phylum Methanobacteriota

Class Halobacteria

Order Halobacteriales

Family Haloarculaceae

Genus Halosimplex

Species Halosimplex carlsbadense

Full scientific name Halosimplex carlsbadense Vreeland et al. 2003

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Motility
33890	negative	rod-shaped

Colony morphology

Culture and growth conditions

Culture medium

@ref	Name	Growth	Composition	Medium link
33890	MEDIUM 497 - for Halosimplex carlsbadence		Distilled water make up to (1000.000 ml);Sodium chloride (200.000 g);Potassium chloride (4.000 g);Magnesium sulphate heptahydrate (20.000 g);Agar (20.000 g);Ammonium sulphate (1.000 g);Pyruvic acid (2.500 g);Glycerol (2.500 g);Di Potassium monohydrogenoph
33890	CIP Medium 497			Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
33890	positive	growth	37	mesophilic
33890	positive	growth	25-41
33890	negative	growth	5
33890	negative	growth	15
33890	negative	growth	45
67770	positive	growth	37	mesophilic

Physiology and metabolism

Halophily

@ref	Salt	Tested relation	Concentration
33890	NaCl	growth	0 %
33890	NaCl	growth	2 %
33890	NaCl	growth	4 %
33890	NaCl	growth	6 %
33890	NaCl	growth	8 %
33890	NaCl	growth	10 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
33890	16947 ChEBI	citrate	-	carbon source
33890	4853 ChEBI	esculin	-	hydrolysis
33890	17234 ChEBI	glucose	-	degradation
33890	606565 ChEBI	hippurate	-	hydrolysis
33890	15792 ChEBI	malonate	-	assimilation
33890	17632 ChEBI	nitrate	-	builds gas from
33890	17632 ChEBI	nitrate	-	reduction
33890	16301 ChEBI	nitrite	-	builds gas from
33890	16301 ChEBI	nitrite	-	reduction

Metabolite production

@ref	Chebi-ID	Metabolite	Production
33890	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test	Methylred-test
33890	15688 ChEBI	acetoin	-
33890	17234 ChEBI	glucose		-

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	-	3.1.3.2	from API zym
33890	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
68382	beta-galactosidase	-	3.2.1.23	from API zym
33890	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
33890	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
33890	gamma-glutamyltransferase	-	2.3.2.2
33890	gelatinase	-
68382	leucine arylamidase	+	3.4.11.1	from API zym
68382	lipase (C 14)	-		from API zym
33890	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
33890	ornithine decarboxylase	-	4.1.1.17
33890	oxidase	+
33890	phenylalanine ammonia-lyase	-	4.3.1.24
68382	trypsin	-	3.4.21.4	from API zym
33890	tryptophan deaminase	-
33890	urease	-	3.5.1.5
68382	valine arylamidase	-		from API zym

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	methylglyoxal degradation	100	5 of 5
66794	dolichol and dolichyl phosphate biosynthesis	100	2 of 2
66794	formaldehyde oxidation	100	3 of 3
66794	denitrification	100	2 of 2
66794	adipate degradation	100	2 of 2
66794	coenzyme A metabolism	100	4 of 4
66794	L-lactaldehyde degradation	100	3 of 3
66794	cardiolipin biosynthesis	100	7 of 7
66794	vitamin K metabolism	100	5 of 5
66794	phenylmercury acetate degradation	100	2 of 2
66794	factor 420 biosynthesis	100	5 of 5
66794	suberin monomers biosynthesis	100	2 of 2
66794	gluconeogenesis	100	8 of 8
66794	folate polyglutamylation	100	1 of 1
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	Entner Doudoroff pathway	90	9 of 10
66794	molybdenum cofactor biosynthesis	88.89	8 of 9
66794	aspartate and asparagine metabolism	88.89	8 of 9
66794	valine metabolism	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	degradation of sugar acids	88	22 of 25
66794	C4 and CAM-carbon fixation	87.5	7 of 8
66794	flavin biosynthesis	86.67	13 of 15
66794	palmitate biosynthesis	86.36	19 of 22
66794	phenylalanine metabolism	84.62	11 of 13
66794	pantothenate biosynthesis	83.33	5 of 6
66794	threonine metabolism	80	8 of 10
66794	glycogen metabolism	80	4 of 5
66794	gallate degradation	80	4 of 5
66794	starch degradation	80	8 of 10
66794	cellulose degradation	80	4 of 5
66794	d-mannose degradation	77.78	7 of 9
66794	CO2 fixation in Crenarchaeota	77.78	7 of 9
66794	vitamin B1 metabolism	76.92	10 of 13
66794	purine metabolism	75.53	71 of 94
66794	biotin biosynthesis	75	3 of 4
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	acetate fermentation	75	3 of 4
66794	glutamate and glutamine metabolism	75	21 of 28
66794	glycogen biosynthesis	75	3 of 4
66794	isoleucine metabolism	75	6 of 8
66794	pentose phosphate pathway	72.73	8 of 11
66794	histidine metabolism	72.41	21 of 29
66794	NAD metabolism	72.22	13 of 18
66794	photosynthesis	71.43	10 of 14
66794	tetrahydrofolate metabolism	71.43	10 of 14
66794	ubiquinone biosynthesis	71.43	5 of 7
66794	non-pathway related	71.05	27 of 38
66794	lipid metabolism	70.97	22 of 31
66794	lysine metabolism	69.05	29 of 42
66794	pyrimidine metabolism	68.89	31 of 45
66794	oxidative phosphorylation	68.13	62 of 91
66794	serine metabolism	66.67	6 of 9
66794	acetoin degradation	66.67	2 of 3
66794	glycolate and glyoxylate degradation	66.67	4 of 6
66794	enterobactin biosynthesis	66.67	2 of 3
66794	octane oxidation	66.67	2 of 3
66794	cyanate degradation	66.67	2 of 3
66794	arginine metabolism	66.67	16 of 24
66794	alanine metabolism	65.52	19 of 29
66794	heme metabolism	64.29	9 of 14
66794	citric acid cycle	64.29	9 of 14
66794	carotenoid biosynthesis	63.64	14 of 22
66794	ketogluconate metabolism	62.5	5 of 8
66794	leucine metabolism	61.54	8 of 13
66794	3-chlorocatechol degradation	60	3 of 5
66794	propionate fermentation	60	6 of 10
66794	4-hydroxyphenylacetate degradation	60	6 of 10
66794	myo-inositol biosynthesis	60	6 of 10
66794	glycine betaine biosynthesis	60	3 of 5
66794	phenylacetate degradation (aerobic)	60	3 of 5
66794	glycolysis	58.82	10 of 17
66794	tryptophan metabolism	57.89	22 of 38
66794	reductive acetyl coenzyme A pathway	57.14	4 of 7
66794	propanol degradation	57.14	4 of 7
66794	lipid A biosynthesis	55.56	5 of 9
66794	nitrate assimilation	55.56	5 of 9
66794	vitamin B6 metabolism	54.55	6 of 11
66794	metabolism of disaccharids	54.55	6 of 11
66794	d-xylose degradation	54.55	6 of 11
66794	methionine metabolism	53.85	14 of 26
66794	vitamin B12 metabolism	52.94	18 of 34
66794	lactate fermentation	50	2 of 4
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	CDP-diacylglycerol biosynthesis	50	1 of 2
66794	sulfopterin metabolism	50	2 of 4
66794	dTDPLrhamnose biosynthesis	50	4 of 8
66794	ribulose monophosphate pathway	50	1 of 2
66794	kanosamine biosynthesis II	50	1 of 2
66794	ethanol fermentation	50	1 of 2
66794	quinate degradation	50	1 of 2
66794	butanoate fermentation	50	2 of 4
66794	selenocysteine biosynthesis	50	3 of 6
66794	resorcinol degradation	50	1 of 2
66794	glycine metabolism	50	5 of 10
66794	cis-vaccenate biosynthesis	50	1 of 2
66794	cysteine metabolism	50	9 of 18
66794	coenzyme M biosynthesis	50	5 of 10
66794	tyrosine metabolism	50	7 of 14
66794	vitamin E metabolism	50	2 of 4
66794	degradation of pentoses	50	14 of 28
66794	degradation of sugar alcohols	50	8 of 16
66794	urea cycle	46.15	6 of 13
66794	phosphatidylethanolamine bioynthesis	46.15	6 of 13
66794	proline metabolism	45.45	5 of 11
66794	ascorbate metabolism	45.45	10 of 22
66794	phenol degradation	45	9 of 20
66794	arachidonic acid metabolism	44.44	8 of 18
66794	mevalonate metabolism	42.86	3 of 7
66794	isoprenoid biosynthesis	42.31	11 of 26
66794	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
66794	methanogenesis from CO2	41.67	5 of 12
66794	lipoate biosynthesis	40	2 of 5
66794	3-phenylpropionate degradation	40	6 of 15
66794	creatinine degradation	40	2 of 5
66794	bacilysin biosynthesis	40	2 of 5
66794	D-cycloserine biosynthesis	40	2 of 5
66794	ethylmalonyl-CoA pathway	40	2 of 5
66794	degradation of hexoses	38.89	7 of 18
66794	sulfate reduction	38.46	5 of 13
66794	phenylpropanoid biosynthesis	38.46	5 of 13
66794	androgen and estrogen metabolism	37.5	6 of 16
66794	dolichyl-diphosphooligosaccharide biosynthesis	36.36	4 of 11
66794	cholesterol biosynthesis	36.36	4 of 11
66794	glutathione metabolism	35.71	5 of 14
66794	polyamine pathway	34.78	8 of 23
66794	IAA biosynthesis	33.33	1 of 3
66794	4-hydroxymandelate degradation	33.33	3 of 9
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	allantoin degradation	33.33	3 of 9
66794	aclacinomycin biosynthesis	28.57	2 of 7
66794	peptidoglycan biosynthesis	26.67	4 of 15
66794	toluene degradation	25	1 of 4
66794	catecholamine biosynthesis	25	1 of 4
66794	ppGpp biosynthesis	25	1 of 4
66794	cyclohexanol degradation	25	1 of 4

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
33890	-	-	+	+	-	+	-	-	-	-	-	+	-	-	-	-	-	-	-	-

Isolation, sampling and environmental information

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
33890		New Mexico	USA	USA	North America
67770	Unsterilized salt crystal from the Permian-aged Salado Formation in southeastern New Mexico		USA	USA	North America
33890	Salt, crystal	New Mexico	United States of America	USA	North America

Taxonmaps

69479

Global distribution of 16S sequence AF320478 (>99% sequence identity) for Halosimplex carlsbadense from Microbeatlas

Aquatic Samples	1
Soil Samples
Animal Samples
Plant Samples
Total Samples	1

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
33890	1	Risk group (French classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
67770	ASM33745v1 assembly for Halosimplex carlsbadense 2-9-1	contig	GCA_000337455	797114.5	2531839487	797114	67.53

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
67770	Halosimplex carlsbadense 16S small subunit ribosomal RNA A gene, partial sequence	AF320478	1471	797114
67770	Halosimplex carlsbadense 16S small subunit ribosomal RNA B gene, partial sequence	AF320479	1470	797114
67770	Halosimplex carlsbadense 16S small subunit ribosomal RNA C gene, partial sequence	AF320480	1471	797114
124043	Halosimplex carlsbadense gene for 16S rRNA, complete sequence, strain: JCM 11222.	AB663430	1473	797114

GC content

@ref	GC-content (mol%)	Method
67770	64.4	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: Halosimplex carlsbadense 2-9-1 2/9/2001
NCBI: GCA_000337455

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	85.80	no
125439	motility	BacteriaNetⓘ	yes	51.60	no
125439	gram_stain	BacteriaNetⓘ	positive	65.90	no
125439	oxygen_tolerance	BacteriaNetⓘ	aerobe	77.90	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Halosimplex carlsbadense 2-9-1 2-9-1
NCBI: GCA_000337455.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	74.81	no
125438	anaerobic	anaerobicⓘ	no	82.05	no
125438	aerobic	aerobicⓘ	yes	79.40	no
125438	spore-forming	spore-formingⓘ	no	85.03	no
125438	thermophilic	thermophileⓘ	no	82.54	yes
125438	flagellated	motile2+ⓘ	no	87.00	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Cellulose metabolism in halo(natrono)archaea: a comparative genomics study.	Elcheninov AG, Ugolkov YA, Elizarov IM, Klyukina AA, Kublanov IV, Sorokin DY.	Front Microbiol	10.3389/fmicb.2023.1112247	2023
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
Phylogeny	Halosimplex litoreum sp. nov., isolated from a marine solar saltern.	Yuan PP, Xu JQ, Xu WM, Wang Z, Yin S, Han D, Zhang WJ, Cui HL	Antonie Van Leeuwenhoek	10.1007/s10482-015-0501-8	2015
Phylogeny	Halosimplex pelagicum sp. nov. and Halosimplex rubrum sp. nov., isolated from salted brown alga Laminaria, and emended description of the genus Halosimplex.	Han D, Cui HL	Int J Syst Evol Microbiol	10.1099/ijs.0.056887-0	2013
Phylogeny	Halosimplex carlsbadense gen. nov., sp. nov., a unique halophilic archaeon, with three 16S rRNA genes, that grows only in defined medium with glycerol and acetate or pyruvate.	Vreeland RH, Straight S, Krammes J, Dougherty K, Rosenzweig WD, Kamekura M	Extremophiles	10.1007/s00792-002-0278-3	2002

References

#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 )
#33890	Collection of Institut Pasteur ; Curators of the CIP; CIP 108098
#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;
#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 .
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#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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Halosimplex carlsbadense (CIP 108098, JCM 11222, ATCC BAA-75)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

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

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000337455

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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