Nesterenkonia halobia (DSM 20541, ATCC 21727, CCM 2591)

Name: Nesterenkonia halobia (DSM 20541, ATCC 21727, CCM 2591)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 7762

Type strain

Strain Designation 28-3

Culture col. no. DSM 20541 ATCC 21727 CCM 2591 CCUG 38889 28-3 19 more

NCBI tax ID(s) 37922

Special Collections DSMZ CCUG JCM KCTC CIP Wink compendium JMRC

History DSMZ <- CCM <- H. Onishi, 28-3 JCM <-- CIP 81.68 <-- CCM 2591 <-- H. Onishi 28-3. CIP <- 1981, CCM, Micrococcus halobius <- H. Onishi: strain 28-3

Links

Nesterenkonia halobia 28-3 is an aerobe, Gram-positive, coccus-shaped bacterium that was isolated from unrefined solar salt.

Gram-positive coccus-shaped aerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 9303

LMG 14214,ATCC 21727,CCM 2591,CCRC 11656,DSM 20541,IAM 13001,IFO 15353,NCIMB 2204,MTCC 701,CCUG 38889,VKM B-1317,VKM B-1421,CIP 81.68,LMG 21452,CECT 5018,IMET 11383,JCM 11483,KCTC 3518,NBRC 15353,BCRC 11656,VKM Ac-2256,CGMCC 1.2323

@ref 20215

Last LPSN update 2026-05-29 08:26:43

Domain Bacteria

Phylum Actinomycetota

Class Actinomycetes

Order Micrococcales

Family Micrococcaceae

Genus Nesterenkonia

Species Nesterenkonia halobia

Full scientific name Nesterenkonia halobia (Onishi and Kamekura 1972) Stackebrandt et al. 1995

Synonyms (1)

Micrococcus halobius

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Motility
119799	positive	coccus-shaped

Colony morphology

@ref	Colony color	Incubation period	Medium used
18756	Cream	10-14 days	5006
18756	Cream	10-14 days	5428
18756	Cream	10-14 days	5428+6% NaCl
18756	Cream	10-14 days	5530
18756	Beige	10-14 days	ISP 2

Multicellular morphology

@ref	Forms multicellular complex	Medium name
18756		ISP 2
18756		5006
18756		5428+6% NaCl
18756		5428
18756		5530

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
8770	BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)	Medium recipe at MediaDive	Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water
18756	ISP 2		Name: ISP 2 / Yeast Malt Agar (5265); 5265 Composition Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l Agar 15.0 g/l Preparation: Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.0 Usage: Maintenance and Taxonomy Organisms: All Actinomycetes
18756	5006		Medium: 5006 Name: Composition (g/l) Sucrose 3,0 Dextrin 15,0 Meat extract 1,0 Yeast extract 2,0 Tryptone soy broth (Oxoid) 5,0 NaCl 0,5 K2HPO4 0,5 MgSO4 x 7 H2O 0,5 FeSO4 x 7 H2O 0,01 Agar 20,0 Preparation: Sterilisation: 20 minutes at 121°C pH before sterilisation: 7,3 Usage: Maintenance Organisms: All Actinomycetes
18756	5428+6% NaCl
18756	5428
18756	5530
37624	Marine agar (MA)		Distilled water make up to (1000.000 ml);Marine agar (55.100 g)
119799	CIP Medium 13	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
8770	positive	growth	28
18756	positive	optimum	28
37624	positive	growth	30
54531	positive	growth	30-37
67770	positive	growth	28

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
54531	aerobe
119799	obligate aerobe
125439	obligate aerobe	98.574

Spore formation

@ref	Spore formation	Confidence
119799
125439		97.475

Compound production

@ref	Compound
8770	amylase, halophilic
20216	Amylase (halophilic)
67770	Halophilic amylase

Halophily

@ref	Salt	Growth	Tested relation	Concentration
54531	NaCl	positive	growth	>6 %

Murein

@ref	Murein short key	Type
8770	A11.56	A4alpha L-Lys-Gly-L-Glu

Observation

67770

Observationquinones: MK-8

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68368	29016 ChEBI	arginine	-	hydrolysis	from API 20E
68368	16947 ChEBI	citrate	-	assimilation	from API 20E
68379	17634 ChEBI	D-glucose	-	fermentation	from API Coryne
68379	16899 ChEBI	D-mannitol	-	fermentation	from API Coryne
68379	16988 ChEBI	D-ribose	-	fermentation	from API Coryne
68379	65327 ChEBI	D-xylose	-	fermentation	from API Coryne
68379	4853 ChEBI	esculin	+	hydrolysis	from API Coryne
68379	5291 ChEBI	gelatin	-	hydrolysis	from API Coryne
68368	5291 ChEBI	gelatin	-	hydrolysis	from API 20E
68379	28087 ChEBI	glycogen	-	fermentation	from API Coryne
68379	17716 ChEBI	lactose	-	fermentation	from API Coryne
68368	25094 ChEBI	lysine	-	degradation	from API 20E
68379	17306 ChEBI	maltose	-	fermentation	from API Coryne
68379	17632 ChEBI	nitrate	-	reduction	from API Coryne
119799	17632 ChEBI	nitrate	-	reduction
119799	16301 ChEBI	nitrite	-	reduction
68368	18257 ChEBI	ornithine	-	degradation	from API 20E
68379	17992 ChEBI	sucrose	-	fermentation	from API Coryne
68368	27897 ChEBI	tryptophan	-	energy source	from API 20E
68379	16199 ChEBI	urea	-	hydrolysis	from API Coryne
68368	16199 ChEBI	urea	-	hydrolysis	from API 20E

Metabolite production

@ref	Chebi-ID	Metabolite
68368	15688 ChEBI	acetoin	from API 20E
68368	16136 ChEBI	hydrogen sulfide	from API 20E
119799	35581 ChEBI	indole
68368	35581 ChEBI	indole	from API 20E

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test	Indole test
68368	15688 ChEBI	acetoin	+		from API 20E
68368	35581 ChEBI	indole		-	from API 20E

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	-	3.1.3.2	from API zym
68379	alkaline phosphatase	-	3.1.3.1	from API Coryne
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
68379	alpha-glucosidase	+	3.2.1.20	from API Coryne
68382	alpha-mannosidase	-	3.2.1.24	from API zym
68368	arginine dihydrolase	-	3.5.3.6	from API 20E
68379	beta-galactosidase	+	3.2.1.23	from API Coryne
68368	beta-galactosidase	-	3.2.1.23	from API 20E
68382	beta-glucosidase	+	3.2.1.21	from API zym
68379	beta-glucosidase	+	3.2.1.21	from API Coryne
68382	beta-glucuronidase	-	3.2.1.31	from API zym
68379	beta-glucuronidase	-	3.2.1.31	from API Coryne
119799	catalase	+	1.11.1.6
68379	gelatinase	-		from API Coryne
68368	gelatinase	-		from API 20E
68382	leucine arylamidase	+	3.4.11.1	from API zym
68368	lysine decarboxylase	-	4.1.1.18	from API 20E
68382	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API zym
68379	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API Coryne
68368	ornithine decarboxylase	-	4.1.1.17	from API 20E
119799	oxidase	+
68379	pyrazinamidase	-	3.5.1.B15	from API Coryne
68379	pyrrolidonyl arylamidase	-	3.4.19.3	from API Coryne
68382	trypsin	-	3.4.21.4	from API zym
68368	tryptophan deaminase	-	4.1.99.1	from API 20E
119799	urease	-	3.5.1.5
68379	urease	-	3.5.1.5	from API Coryne
68368	urease	-	3.5.1.5	from API 20E
68382	valine arylamidase	+		from API zym

API 20E

@ref	ONPG	ADH (Arg)	LDC (Lys)	ODC	CIT	H2S productionH2S	URE	TDA (Trp)	IND	Acetoin production (Voges Proskauer test)VP	GEL	GLU	MAN	INO	Sor	RHA	SAC	MEL	AMY	ARA	OX	Nitrite productionNO2	Reduction to N2N2	MotilityMOB	Growth on MacConkey mediumMAC	OF-O	OF-F
18756	-	-	-	-	-	-	-	-	-	+	-	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.

API coryne

@ref	Reduction of nitrateNIT	PYZ	PYRA	PAL	beta GUR	beta GAL	alpha GLU	beta NAG	ESC	URE	GEL	Control fermentationControl	GLU	RIB	XYL	MAN	MAL	LAC	SAC	GLYG	CAT
18756	-	-	-	-	-	+	+	-	+	-	-	not determinedn.d.	-	-	-	-	-	-	-	-	not determinedn.d.

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
18756	not determinedn.d.	-	-	-	-	+	+	-	-	-	-	-	-	-	-	+	+	-	-	-
119799	-	+	+	+	+	+	+	+	-	+	-	+	-	+	-	+	+	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2
#Condition	#Saline

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
8770	unrefined solar salt
54531	Unrefined solar salt
67770	Unrefined solar salt	Noda, Chiba Pref.	Japan	JPN	Asia
119799	Unrefined solar salt

Taxonmaps

69479

Global distribution of 16S sequence X80747 (>99% sequence identity) for Nesterenkonia from Microbeatlas

Aquatic Samples	234
Soil Samples	126
Animal Samples	1996
Plant Samples	70
Total Samples	2426

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
8770	1	Risk group (German classification) According to TRBA 466
18756	1	Risk group (German classification) According to TRBA 466
119799	1	Risk group (French classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	NCBI tax ID	Score
124043	ASM3953600v1 assembly for Nesterenkonia halobia JCM 11483	scaffold	GCA_039536005	37922	63.3

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
20218	M.halobius 16S rDNA	X80747	1451		37922
124043	Nesterenkonia halobia strain CCM 2591 16S ribosomal RNA gene, partial sequence.	MT760092	763		37922

GC content

@ref	GC-content (mol%)	Method
8770	71.5
67770	70	fluorimetric
67770	71.5	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: ASM3953600v1 assembly for Nesterenkonia halobia JCM 11483
NCBI: GCA_039536005

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	98.57	no
125439	gram_stain	BacteriaNetⓘ	positive	77.48	no
125439	motility	BacteriaNetⓘ	yes	52.71	no
125439	spore_formation	BacteriaNetⓘ	no	97.48	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Biology of moderately halophilic aerobic bacteria.	Ventosa A, Nieto JJ, Oren A.	Microbiol Mol Biol Rev	10.1128/mmbr.62.2.504-544.1998	1998
	Organic compatible solutes of halotolerant and halophilic microorganisms.	Roberts MF.	Saline Syst	10.1186/1746-1448-1-5	2005
	Nesteretal A, A Novel Class of Cage-Like Polyketide from Marine-Derived Actinomycete Nesterenkonia halobia.	Xie CL, Chen R, Yang S, Xia JM, Zhang GY, Chen CH, Zhang Y, Yang XW.	Org Lett	10.1021/acs.orglett.9b02634	2019
Phylogeny	Biochemical and Molecular Characterization of a Native Haloalkalophilic Tolerant Strain from the Texcoco Lake.	Soto-Padilla MY, Gortares-Moroyoqui P, Cira-Chavez LA, Estrada-Alvarado MI.	Pol J Microbiol	10.21307/pjm-2018-047	2018
Phylogeny	Cultivation-dependent assessment, diversity, and ecology of haloalkaliphilic bacteria in arid saline systems of southern Tunisia.	El Hidri D, Guesmi A, Najjari A, Cherif H, Ettoumi B, Hamdi C, Boudabous A, Cherif A.	Biomed Res Int	10.1155/2013/648141	2013
	Precipitation of carbonates by Nesterenkonia halobia in liquid media.	Rivadeneyra MA, Delgado G, Soriano M, Ramos-Cormenzana A, Delgado R.	Chemosphere	10.1016/s0045-6535(99)00496-8	2000
	Diversity of alkaliphilic and alkalitolerant bacteria cultivated from decomposing reed rhizomes in a Hungarian soda lake.	Borsodi AK, Micsinai A, Rusznyak A, Vladar P, Kovacs G, Toth EM, Marialigeti K.	Microb Ecol	10.1007/s00248-004-0063-1	2005
Phylogeny	[Occurrence of bacteria in the mouth from genera of Micrococcus, Kocuria, Nesterenkonia, Kytococcus and Dermacoccus].	Szczerba I, Krzeminski Z.	Med Dosw Mikrobiol		2002
Metabolism	Starch-hydrolyzing bacteria from Ethiopian soda lakes.	Martins RF, Davids W, Abu Al-Soud W, Abu Al-Soud W, Levander F, Radstrom P, Hatti-Kaul R.	Extremophiles	10.1007/s007920100183	2001
Phylogeny	Taxonomic dissection of the genus Micrococcus: Kocuria gen. nov., Nesterenkonia gen. nov., Kytococcus gen. nov., Dermacoccus gen. nov., and Micrococcus Cohn 1872 gen. emend.	Stackebrandt E, Koch C, Gvozdiak O, Schumann P.	Int J Syst Bacteriol	10.1099/00207713-45-4-682	1995
Enzymology	Halophilic bacteria are colonizing the exhibition areas of the Capuchin Catacombs in Palermo, Italy.	Pinar G, Krakova L, Pangallo D, Piombino-Mascali D, Maixner F, Zink A, Sterflinger K.	Extremophiles	10.1007/s00792-014-0649-6	2014
Phylogeny	Moderately halophilic gram-positive bacterial diversity in hypersaline environments.	Ventosa A, Marquez MC, Garabito MJ, Arahal DR.	Extremophiles	10.1007/s007920050072	1998
Enzymology	Potential for plant growth promotion of rhizobacteria associated with Salicornia growing in Tunisian hypersaline soils.	Mapelli F, Marasco R, Rolli E, Barbato M, Cherif H, Guesmi A, Ouzari I, Daffonchio D, Borin S.	Biomed Res Int	10.1155/2013/248078	2013
Metabolism	Carbonate crystals precipitated by freshwater bacteria and their use as a limestone consolidant.	Zamarreno DV, Inkpen R, May E.	Appl Environ Microbiol	10.1128/aem.02079-08	2009
Metabolism	Cloning and characterization of the gene cluster for biosynthesis of ectoine from Nesterenkonia halobia DSM 20541.	Zhang B, Bao X, Wang L, Yang SS	J Microbiol	10.1007/s12275-008-0001-x	2008
Phylogeny	[Study on isolation and systematic taxonomy of strains of genus Nesterenkonia].	Chen HH, Li WJ, Zhang YQ, Wang D, Tang SK	Wei Sheng Wu Xue Bao		2004
Phylogeny	Polyphasic taxonomy of Nesterenkonia halobia.	Mota RR, Marquez MC, Arahal DR, Mellado E, Ventosa A	Int J Syst Bacteriol	10.1099/00207713-47-4-1231	1997
Enzymology	Purification and Some Properties of an Extracellular Amylase from a Moderate Halophile, Micrococcus halobius.	Onishi H, Sonoda K	Appl Environ Microbiol	10.1128/aem.38.4.616-620.1979	1979
Phylogeny	Nesterenkonia suensis sp. nov., a haloalkaliphilic actinobacterium isolated from a salt pan.	Govender L, Naidoo L, Setati ME.	Int J Syst Evol Microbiol	10.1099/ijs.0.035006-0	2013
Phylogeny	Nesterenkonia aethiopica sp. nov., an alkaliphilic, moderate halophile isolated from an Ethiopian soda lake.	Delgado O, Quillaguaman J, Bakhtiar S, Mattiasson B, Gessesse A, Hatti-Kaul R.	Int J Syst Evol Microbiol	10.1099/ijs.0.63633-0	2006
Phylogeny	Nesterenkonia lacusekhoensis sp. nov., isolated from hypersaline Ekho Lake, East Antarctica, and emended description of the genus Nesterenkonia.	Collins MD, Lawson PA, Labrenz M, Tindall BJ, Weiss N, Hirsch P.	Int J Syst Evol Microbiol	10.1099/00207713-52-4-1145	2002
Phylogeny	Nesterenkonia halophila sp. nov., a moderately halophilic, alkalitolerant actinobacterium isolated from a saline soil.	Li WJ, Zhang YQ, Schumann P, Liu HY, Yu LY, Zhang YQ, Stackebrandt E, Xu LH, Jiang CL	Int J Syst Evol Microbiol	10.1099/ijs.0.64226-0	2008

References

#8770	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 20541
#18756	Wink, J.: Compendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig .
#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 )
#20216	Curators of the JMRC: Jena Microbial Resource Collection (JMRC):
#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 )
#37624	; Curators of the CIP;
#54531	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 38889
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#68368	Automatically annotated from API 20E .
#68379	Automatically annotated from API Coryne .
#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 .
#119799	Collection of Institut Pasteur ; Curators of the CIP; CIP 81.68
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#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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Nesterenkonia halobia (DSM 20541, ATCC 21727, CCM 2591)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Multicellular morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Compound production

Halophily

Murein

Observation

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

API 20E

API coryne

API zym

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_039536005

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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