Halomonas smyrnensis (DSM 21644, JCM 15723, AAD6)

Name: Halomonas smyrnensis (DSM 21644, JCM 15723, AAD6)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 23064

Type strain

Strain Designation AAD6

Culture col. no. DSM 21644 JCM 15723 AAD6

NCBI tax ID(s) 720605

Special Collections DSMZ JCM Literature strains

History DSMZ <- D. Kazan, Marmara Univ., Istanbul, Turkey; AAD 6 <- A. A. Denizci JCM <-- D. Kazan AAD6.

Links

Halomonas smyrnensis AAD6 is a facultative aerobe, Gram-negative, rod-shaped bacterium that was isolated from soil from salt production ponds.

Gram-negative rod-shaped facultative aerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 405309

JCM 15723,DSM 21644

@ref 20215

Last LPSN update 2026-05-29 08:30:22

Domain Bacteria

Phylum Pseudomonadota

Class Gammaproteobacteria

Order Oceanospirillales

Family Halomonadaceae

Genus Halomonas

Species Halomonas smyrnensis

Full scientific name Halomonas smyrnensis Poli et al. 2013

BacDive ID	Other strains from **Halomonas smyrnensis** (4)	Type strain
164393	H. smyrnensis JCM 32860
164395	H. smyrnensis JCM 32863
164397	H. smyrnensis JCM 32865
164399	H. smyrnensis JCM 32867

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
30480	negative	1.6 µm	1 µm	rod-shaped
125438	negative				99.5
125439	negative				95.882

Pigmentation

30480

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
19201	HALOMONAS SYMIRNIENSIS MEDIUM (DSMZ Medium 1158)		Medium recipe at MediaDive	Name: HALOMONAS SYMIRNIENSIS MEDIUM (DSMZ Medium 1158) Composition: NaCl 100.0 g/l Agar 15.0 g/l Yeast extract 5.0 g/l Trisodium citrate 3.0 g/l MgSO4 x 7 H2O 3.0 g/l KCl 2.0 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
19201	positive	growth	37
30480	positive	growth	05-40
30480	positive	optimum	37
67770	positive	growth	37

Culture pH

@ref	Ability	Type	PH	PH range
30480	positive	optimum	7
30480	positive	growth	5.5-8.5	alkaliphile

Physiology and metabolism

Oxygen tolerance

30480

Oxygen tolerancefacultative aerobe

Spore formation

@ref	Spore formation	Confidence
125439		99.831

Halophily

@ref	Salt	Growth	Tested relation	Concentration
30480	NaCl	positive	growth	3-25 %
30480	NaCl	positive	optimum	10 %

Observation

67770

Observationquinones: Q-9

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
30480	16449 ChEBI	alanine	+	carbon source
30480	4853 ChEBI	esculin	+	hydrolysis
30480	28757 ChEBI	fructose	+	carbon source
30480	28260 ChEBI	galactose	+	carbon source
30480	17234 ChEBI	glucose	+	carbon source
30480	17306 ChEBI	maltose	+	carbon source
30480	37684 ChEBI	mannose	+	carbon source
30480	17822 ChEBI	serine	+	carbon source
30480	17992 ChEBI	sucrose	+	carbon source

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Pond (small)
#Environmental	#Terrestrial	#Soil
#Condition	#Saline	-

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
19201	soil from salt production ponds	Izmir province, Aegean Region	Turkey	TUR	Asia
67770	Salty pond soil from Izmir Province, Aegean Region of Turkey

Taxonmaps

69479

Global distribution of 16S sequence DQ131909 (>99% sequence identity) for Halomonas from Microbeatlas

Aquatic Samples	667
Soil Samples	73
Animal Samples	115
Plant Samples	14
Total Samples	869

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
19201	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	HalSmy2.0 assembly for Halomonas smyrnensis AAD6	contig	GCA_000265245	339656.4	2551306539	339656	70.38

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
19201	Halomonas smyrnensis AAD6 16S ribosomal RNA gene, partial sequence	DQ131909	1445		339656

GC content

@ref	GC-content (mol%)	Method
19201	63.0	fluorimetric
30480	63
67770	63	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: HalSmy2.0 assembly for Halomonas smyrnensis AAD6
BV-BRC: 339656.4

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	66.50	no
125439	motility	BacteriaNetⓘ	yes	87.10	no
125439	gram_stain	BacteriaNetⓘ	negative	95.88	no
125439	spore_formation	BacteriaNetⓘ	no	99.83	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Halomonas smyrnensis AAD6
PATRIC: 339656.4

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	99.50	yes
125438	anaerobic	anaerobicⓘ	no	96.83	yes
125438	spore-forming	spore-formingⓘ	no	89.48	no
125438	aerobic	aerobicⓘ	yes	81.53	no
125438	thermophilic	thermophileⓘ	no	99.36	no
125438	flagellated	motile2+ⓘ	no	71.24	yes

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Genomic analysis reveals the biotechnological and industrial potential of levan producing halophilic extremophile, Halomonas smyrnensis AAD6T.	Diken E, Ozer T, Arikan M, Emrence Z, Oner ET, Ustek D, Arga KY.	Springerplus	10.1186/s40064-015-1184-3	2015
Phylogeny	Halomonas smyrnensis sp. nov., a moderately halophilic, exopolysaccharide-producing bacterium.	Poli A, Nicolaus B, Denizci AA, Yavuzturk B, Kazan D	Int J Syst Evol Microbiol	10.1099/ijs.0.037036-0	2012

References

#19201	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 21644
#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 )
#26814	IJSEM 10 2013 ( DOI 10.1099/ijs.0.037036-0 , PubMed 22328606 )
#30480	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 #26814
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#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 .
#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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Halomonas smyrnensis (DSM 21644, JCM 15723, AAD6)

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

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000265245

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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