Haladaptatus cibarius (DSM 19505, JCM 15962, KCTC 4055)

Name: Haladaptatus cibarius (DSM 19505, JCM 15962, KCTC 4055)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 5972

Type strain

Strain Designation D43

Culture col. no. DSM 19505 JCM 15962 KCTC 4055 D43

NCBI tax ID(s) 1455608 453847

Special Collections DSMZ JCM KCTC Literature strains

History DSMZ <- S. W. Roh, Korea Res. Inst. Biosci. & Biotechnol. (KRIBB), Taejon, South Korea; D43 JCM <-- J.-W. Bae D43.

Links

Haladaptatus cibarius D43 is an aerobe, Gram-negative, motile archaeon that was isolated from salt-fermented seafood.

Gram-negative motile coccus-shaped aerobe genome sequence 16S sequence Archaea

Name and taxonomic classification

SI-ID 399544

JCM 15962,DSM 19505

@ref 20215

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

Domain Archaea

Phylum Methanobacteriota

Class Halobacteria

Order Halobacteriales

Family Halobacteriaceae

Genus Haladaptatus

Species Haladaptatus cibarius

Full scientific name Haladaptatus cibarius Roh et al. 2010

Morphology

Cell morphology

@ref	Gram stain	Cell width	Cell shape	Motility
29432	negative	1 µm	coccus-shaped

Pigmentation

29432

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
8136	MEDIUM FOR H. DOMBROWSKII (DSMZ Medium 954)		Medium recipe at MediaDive	Name: MEDIUM FOR H. DOMBROWSKII (DSMZ Medium 954) Composition: NaCl 200.0 g/l MgCl2 x 6 H2O 20.0 g/l Agar 20.0 g/l Tris 12.1 g/l Yeast extract 5.0 g/l Casamino acids 5.0 g/l KCl 2.0 g/l CaCl2 x 2 H2O 0.2 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
8136	positive	growth	37
29432	positive	growth	15-50
29432	positive	optimum	37
67770	positive	growth	37

Culture pH

@ref	Ability	Type	PH
29432	positive	optimum	7
29432	positive	growth	06-08

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
29432	aerobe
125439	facultative anaerobe	91.344

Spore formation

@ref	Spore formation	Confidence
125439		94.292

Halophily

@ref	Salt	Growth	Tested relation	Concentration
29432	NaCl	positive	growth	10-30 %
29432	NaCl	positive	optimum	15 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
29432	30089 ChEBI	acetate	+	carbon source
29432	15740 ChEBI	formate	+	carbon source
29432	28757 ChEBI	fructose	+	carbon source
29432	17234 ChEBI	glucose	+	carbon source
29432	17716 ChEBI	lactose	+	carbon source
29432	17992 ChEBI	sucrose	+	carbon source

Metabolite production

@ref	Chebi-ID	Metabolite	Production
29432	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Indole test
29432	35581 ChEBI	indole	+

Enzymes

@ref	Value	Activity	Ec
29432	catalase	+	1.11.1.6
29432	cytochrome oxidase	+	1.9.3.1
29432	gelatinase	+

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Food production	#Seafood
#Condition	#Saline	-
#Engineered	#Food production	#Fermented

Isolation

@ref	Sample type	Country	Country ISO 3 Code	Continent
8136	salt-fermented seafood	Republic of Korea	KOR	Asia
67770	Jeotgal, traditional Korean fermented seafood	Republic of Korea	KOR	Asia

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
8136	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
67770	HAPD43.1 assembly for Haladaptatus cibarius D43	contig	GCA_000710615	1455608.3	2582580505	1455608	76.88

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
20218	Haladaptatus cibarius gene for 16S rRNA, complete sequence, strain: JCM 15962	AB663345	1471		1455608
8136	Haladaptatus cibarius D43 16S ribosomal RNA gene, partial sequence	EF660747	1405		1455608

GC content

@ref	GC-content (mol%)	Method
8136	56.5	fluorimetric
29432	56.5
67770	56.5	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: HAPD43.1 assembly for Haladaptatus cibarius D43
NCBI: GCA_000710615

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	facultative anaerobe	91.34	no
125439	gram_stain	BacteriaNetⓘ	negative	71.26	no
125439	motility	BacteriaNetⓘ	no	74.65	no
125439	spore_formation	BacteriaNetⓘ	no	94.29	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Decoding the Chemical Language of Ribosomally Synthesized and Post-Translationally Modified Peptides from the Untapped Archaea Domain.	Song ZM, Cai C, Gao Y, Lin X, Yang Q, Zhang D, Wu G, Liang H, Zhuo Q, Zhang J, Cai P, Jiang H, Liu W, Li YX.	Angew Chem Int Ed Engl	10.1002/anie.202501074	2025
Genetics	Draft genome sequence of the extremely halophilic archaeon Haladaptatus cibarius type strain D43(T) isolated from fermented seafood.	Lee HW, Kim DW, Lee MH, Kim BY, Cho YJ, Yim KJ, Song HS, Rhee JK, Seo MJ, Choi HJ, Choi JS, Lee DG, Yoon C, Nam YD, Roh SW.	Stand Genomic Sci	10.1186/s40793-015-0051-8	2015
Phylogeny	Haladaptatus pallidirubidus sp. nov., a halophilic archaeon isolated from saline soil samples in Yunnan and Xinjiang, China.	Liu BB, Zhao WY, Chu X, Hozzein WN, Prabhu DM, Wadaan MA, Tang SK, Zhang LL, Li WJ	Antonie Van Leeuwenhoek	10.1007/s10482-014-0259-4	2014
Phylogeny	Haladaptatus cibarius sp. nov., an extremely halophilic archaeon from seafood, and emended description of the genus Haladaptatus.	Roh SW, Lee ML, Bae JW	Int J Syst Evol Microbiol	10.1099/ijs.0.013037-0	2009

References

#8136	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 19505
#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 )
#25838	IJSEM 1187 2010 ( DOI 10.1099/ijs.0.013037-0 , PubMed 19667394 )
#29432	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 #25838
#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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Haladaptatus cibarius (DSM 19505, JCM 15962, KCTC 4055)

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

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000710615

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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