Halomonas halophila (DSM 4770, CCM 3662, F 5-7)

Name: Halomonas halophila (DSM 4770, CCM 3662, F 5-7)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 6016

Type strain

Strain Designation F 5-7, F5-7

Culture col. no. DSM 4770 CCM 3662 F 5-7 NCIMB 12996 NBRC 102604 7 more

NCBI tax ID(s) 29573

Special Collections DSMZ JCM CIP

History DSMZ <- CCM <- E. Queseda, F 5-7 JCM <-- IAM 13009 <-- CCM 3662 <-- E. Quesada F5-7. CIP <- 1992, A.R. Cormenzana, Granada Univ., Spain: strain F5-7

Links

Halomonas halophila F 5-7 is a facultative anaerobe, Gram-negative, motile bacterium that was isolated from hypersaline soil.

Gram-negative motile rod-shaped facultative anaerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 2164

LMG 6456,CCM 3662,DSM 4770,ATCC 49969,CIP 103512,NCIMB 12996,IAM 13009,JCM 20791,CGMCC 1.2316,NBRC 102604

@ref 20215

Last LPSN update 2026-05-29 08:26:18

Domain Bacteria

Phylum Pseudomonadota

Class Gammaproteobacteria

Order Oceanospirillales

Family Halomonadaceae

Genus Halomonas

Species Halomonas halophila

Full scientific name Halomonas halophila (Quesada et al. 1984) Dobson and Franzmann 1996

Synonyms (3)

Deleya salina
Deleya halophila
Halomonas salina

BacDive ID	Other strains from **Halomonas halophila** (2)	Type strain
164396	H. halophila JCM 32864
164398	H. halophila JCM 32866

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Confidence
119808	negative	rod-shaped
125439	negative		94.395
125438	negative		100

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
1816	MEDIUM 514 PLUS ADDITIONAL SALT (DSMZ Medium 514b)	Medium recipe at MediaDive	Name: MEDIUM 514 plus additional salt (DSMZ Medium 514b) Composition: NaCl 19.45 g/l Agar 17.5 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
38128	Marine agar (MA)		Distilled water make up to (1000.000 ml);Marine agar (55.100 g)
119808	CIP Medium 13	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
1816	positive	growth	28
38128	positive	growth	25
67770	positive	growth	30
119808	positive	growth	5-41

Physiology and metabolism

Oxygen tolerance

119808

Oxygen tolerancefacultative anaerobe

Spore formation

@ref	Spore formation	Confidence
125438		91.264
125439		99.743

Halophily

@ref	Salt	Growth	Tested relation	Concentration
119808	NaCl	positive	growth	4-10 %
119808	NaCl		growth	0 %
119808	NaCl		growth	2 %

Observation

67770

Observationquinones: Q-9

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68371	27613 ChEBI	amygdalin	-	builds acid from	from API 50CH acid
68371	18305 ChEBI	arbutin	-	builds acid from	from API 50CH acid
68371	17057 ChEBI	cellobiose	-	builds acid from	from API 50CH acid
68371	17108 ChEBI	D-arabinose	-	builds acid from	from API 50CH acid
68371	18333 ChEBI	D-arabitol	-	builds acid from	from API 50CH acid
68371	15824 ChEBI	D-fructose	-	builds acid from	from API 50CH acid
68371	28847 ChEBI	D-fucose	-	builds acid from	from API 50CH acid
68371	12936 ChEBI	D-galactose	-	builds acid from	from API 50CH acid
68371	17634 ChEBI	D-glucose	-	builds acid from	from API 50CH acid
68371	62318 ChEBI	D-lyxose	-	builds acid from	from API 50CH acid
68371	16899 ChEBI	D-mannitol	-	builds acid from	from API 50CH acid
68371	16024 ChEBI	D-mannose	-	builds acid from	from API 50CH acid
68371	16988 ChEBI	D-ribose	-	builds acid from	from API 50CH acid
68371	17924 ChEBI	D-sorbitol	-	builds acid from	from API 50CH acid
68371	16443 ChEBI	D-tagatose	-	builds acid from	from API 50CH acid
68371	65327 ChEBI	D-xylose	-	builds acid from	from API 50CH acid
68371	17113 ChEBI	erythritol	-	builds acid from	from API 50CH acid
68371	4853 ChEBI	esculin	-	builds acid from	from API 50CH acid
68371	16813 ChEBI	galactitol	-	builds acid from	from API 50CH acid
68371	28066 ChEBI	gentiobiose	-	builds acid from	from API 50CH acid
68371	24265 ChEBI	gluconate	-	builds acid from	from API 50CH acid
68371	17754 ChEBI	glycerol	-	builds acid from	from API 50CH acid
68371	28087 ChEBI	glycogen	-	builds acid from	from API 50CH acid
68371	15443 ChEBI	inulin	-	builds acid from	from API 50CH acid
68371	30849 ChEBI	L-arabinose	-	builds acid from	from API 50CH acid
68371	18403 ChEBI	L-arabitol	-	builds acid from	from API 50CH acid
68371	18287 ChEBI	L-fucose	-	builds acid from	from API 50CH acid
68371	62345 ChEBI	L-rhamnose	-	builds acid from	from API 50CH acid
68371	17266 ChEBI	L-sorbose	-	builds acid from	from API 50CH acid
68371	65328 ChEBI	L-xylose	-	builds acid from	from API 50CH acid
68371	17716 ChEBI	lactose	-	builds acid from	from API 50CH acid
68371	17306 ChEBI	maltose	-	builds acid from	from API 50CH acid
68371	6731 ChEBI	melezitose	-	builds acid from	from API 50CH acid
68371	28053 ChEBI	melibiose	-	builds acid from	from API 50CH acid
68371	320061 ChEBI	methyl alpha-D-glucopyranoside	-	builds acid from	from API 50CH acid
68371	43943 ChEBI	methyl alpha-D-mannoside	-	builds acid from	from API 50CH acid
68371	74863 ChEBI	methyl beta-D-xylopyranoside	-	builds acid from	from API 50CH acid
68371	17268 ChEBI	myo-inositol	-	builds acid from	from API 50CH acid
68371	59640 ChEBI	N-acetylglucosamine	-	builds acid from	from API 50CH acid
119808	17632 ChEBI	nitrate	+	reduction
119808	16301 ChEBI	nitrite	-	reduction
68371	0 ChEBI	Potassium 2-ketogluconate	-	builds acid from	from API 50CH acid
68371	0 ChEBI	Potassium 5-ketogluconate	-	builds acid from	from API 50CH acid
68371	16634 ChEBI	raffinose	-	builds acid from	from API 50CH acid
68371	15963 ChEBI	ribitol	-	builds acid from	from API 50CH acid
68371	17814 ChEBI	salicin	-	builds acid from	from API 50CH acid
68371	28017 ChEBI	starch	-	builds acid from	from API 50CH acid
68371	17992 ChEBI	sucrose	-	builds acid from	from API 50CH acid
68371	27082 ChEBI	trehalose	-	builds acid from	from API 50CH acid
68371	32528 ChEBI	turanose	-	builds acid from	from API 50CH acid
68371	17151 ChEBI	xylitol	-	builds acid from	from API 50CH acid

Metabolite production

@ref	Chebi-ID	Metabolite	Production
119808	35581 ChEBI	indole

Enzymes

@ref	Value	Activity	Ec
119808	catalase	+	1.11.1.6
119808	gelatinase	-
119808	oxidase	+
119808	tryptophan deaminase	-
119808	urease	-	3.5.1.5

API 50CHac

@ref	ControlQ	GLY	ERY	DARA	LARA	RIB	DXYL	LXYL	ADO	MDX	GAL	GLU	FRU	MNE	SBE	RHA	DUL	INO	MAN	SOR	MDM	MDG	NAG	AMY	ARB	ESC	SAL	CEL	MAL	LAC	MEL	SAC	TRE	INU	MLZ	RAF	AMD	GLYG	XLT	GEN	TUR	LYX	TAG	DFUC	LFUC	DARL	LARL	GNT	2KG	5KG
119808	not determinedn.d.	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-

API biotype100

@ref	ControlQ	D-glucose as carbon sourceGLU	D-fructose as carbon sourceFRU	D-galactose as carbon sourceGAL	D-trehalose as carbon sourceTRE	D-mannose as carbon sourceMNE	L-sorbose as carbon sourceSBE	D-melibiose as carbon sourceMEL	sucrose as carbon sourceSAC	D-raffinose as carbon sourceRAF	maltotriose as carbon sourceMTE	maltose as carbon sourceMAL	lactose as carbon sourceLAC	lactulose as carbon sourceLTE	1-O-methyl-beta-galactopyranoside as carbon sourceMbGa	1-O-methyl-alpha-galactopyranoside as carbon sourceMaGa	D-cellobiose as carbon sourceCEL	gentiobiose as carbon sourceGEN	1-O-methyl-beta-D-glucopyranoside as carbon sourceMbGu	esculin as carbon sourceESC	D-ribose as carbon sourceRIB	L-arabinose as carbon sourceARA	D-xylose as carbon sourceXYL	palatinose as carbon sourcePLE	L-rhamnose as carbon sourceRHA	L-fucose as carbon sourceFUC	D-melezitose as carbon sourceMLZ	D-arabitol as carbon sourceDARL	L-arabitol as carbon sourceLARL	xylitol as carbon sourceXLT	dulcitol as carbon sourceDUL	D-tagatose as carbon sourceTAG	glycerol as carbon sourceGLY	myo-inositol as carbon sourceINO	D-mannitol as carbon sourceMAN	maltitol as carbon sourceMTL	D-turanose as carbon sourceTUR	D-sorbitol as carbon sourceSOR	adonitol as carbon sourceADO	hydroxyquinoline-beta-glucuronide as carbon sourceHBG	D-lyxose as carbon sourceLYX	i-erythritol as carbon sourceERY	1-O-methyl-alpha-D-glucoside as carbon sourceMDG	3-O-methyl-D-glucose as carbon source3MDG	D-saccharate as carbon sourceSAT	mucate as carbon sourceMUC	L-tartrate as carbon sourceLTAT	D-tartrate as carbon sourceDTAT	meso-tartrate as carbon sourceMTAT	D-malate as carbon sourceDMLT	L-malate as carbon sourceLMLT	cis-aconitate as carbon sourceCATE	trans-aconitate as carbon sourceTATE	tricarballylate as carbon sourceTTE	citrate as carbon sourceCIT	D-glucuronate as carbon sourceGRT	D-galacturonate as carbon sourceGAT	2-ketogluconate as carbon source2KG	5-ketogluconate as carbon source5KG	tryptophan as carbon sourceTRY	N-acetyl-D-glucosamine as carbon sourceNAG	D-gluconate as carbon sourceGNT	phenylacetate as carbon sourcePAC	protocatechuate as carbon sourcePAT	4-hydroxybenzoate as carbon sourcepOBE	quinate as carbon sourceQAT	gentisate as carbon sourceGTE	3-hydroxybenzoate as carbon sourcemOBE	benzoate as carbon sourceBAT	3-phenylpropionate as carbon sourcePPAT	m-coumarate as carbon sourceCMT	trigonelline as carbon sourceTGE	betaine as carbon sourceBET	putrescine as carbon sourcePCE	4-aminobutyrate as carbon sourceABT	histamine as carbon sourceHIN	DL-lactate as carbon sourceLAT	caprate as carbon sourceCAP	caprylate as carbon sourceCYT	L-histidine as carbon sourceHIS	succinate as carbon sourceSUC	fumarate as carbon sourceFUM	glutarate as carbon sourceGRE	DL-glycerate as carbon sourceGYT	5-aminovalerate as carbon sourceAVT	ethanolamine as carbon sourceETN	tryptamine as carbon sourceTTN	D-glucosamine as carbon sourceGLN	itaconate as carbon sourceITA	3-hydroxybutyrate as carbon source3OBU	L-aspartate as carbon sourceAPT	L-glutamate as carbon sourceGTT	L-proline as carbon sourcePRO	D-alanine as carbon sourceDALA	L-alanine as carbon sourceLALA	L-serine as carbon sourceSER	malonate as carbon sourceMNT	propionate as carbon sourcePROP	L-tyrosine as carbon sourceTYR	2-ketoglutarate as carbon source2KT
119808	not determinedn.d.	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Soil
#Condition	#Saline	-

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Isolation date
1816	hypersaline soil
67770	Hypersaline soil near Alicante in southeast Spain
119808	Environment, Hypersaline soils	Santa Pola	Spain	ESP	Europe	1983

Taxonmaps

69479

Global distribution of 16S sequence AM941744 (>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
1816	1	Risk group (German classification) According to TRBA 466
119808	1	Risk group (French classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
124043	ASM3040666v1 assembly for Halomonas halophila CCM 3662	complete	GCA_030406665	29573.10	8046462138	29573	99.48
124043	ASM4268548v1 assembly for Halomonas halophila CCM 3662	contig	GCA_042685485			29573	69.61
66792	ASM798946v1 assembly for Halomonas halophila NBRC 102604	contig	GCA_007989465	29573.3	8069396831	29573	61.81

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Halomonas halophila partial 16S rRNA gene, strain CCM 3662	AM941744	1461	29573
20218	Halomonas halophila partial 16S rRNA gene, strain DSM 4770	FN257740	1475	29573
20218	Deleya halophila (DSM 4770) 16S ribosomal RNA (16S rRNA) gene	M93353	1478	29573
20218	Halomonas halophila gene for 16S rRNA, partial sequence, strain: NBRC 102604	AB681879	1463	29573
124043	Halomonas halophila strain CCM 3662 16S ribosomal RNA gene, partial sequence.	MT760104	1377	29573

GC content

@ref	GC-content (mol%)	Method
67770	66.7	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: ASM3040666v1 assembly for Halomonas halophila CCM 3662
NCBI: GCA_030406665

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	facultative anaerobe	89.82	no
125439	gram_stain	BacteriaNetⓘ	negative	94.40	no
125439	motility	BacteriaNetⓘ	yes	88.81	no
125439	spore_formation	BacteriaNetⓘ	no	99.74	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Halomonas halophila strain NBRC 102604
PATRIC: 29573.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	100.00	no
125438	anaerobic	anaerobicⓘ	no	97.01	yes
125438	spore-forming	spore-formingⓘ	no	91.26	no
125438	thermophilic	thermophileⓘ	no	99.36	yes
125438	aerobic	aerobicⓘ	yes	73.25	yes
125438	flagellated	motile2+ⓘ	yes	85.17	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Generation of PHB from Spent Sulfite Liquor Using Halophilic Microorganisms.	Weissgram M, Gstottner J, Lorantfy B, Tenhaken R, Herwig C, Weber HK.	Microorganisms	10.3390/microorganisms3020268	2015
	An Overview of Biorefinery Waste for Microbial Production of Green Plastic in a Circular Economy^§.	Gudapati G, Veluru S, Bora T, Tukaram Bai M, Dwarapureddy AKP, Reddi GP, Hamzah HT.	Food Technol Biotechnol	10.17113/ftb.63.02.25.8966	2025
Biotechnology	Toward Sustainable Polyhydroxyalkanoates: A Next-Gen Biotechnology Approach.	Kalia VC, Singh RV, Gong C, Lee JK.	Polymers (Basel)	10.3390/polym17070853	2025
	Draft Genome Sequence of Halomonas sp. Strain SL1, a Putative Polyhydroxyalkanoate-Producing Halophile.	Rommel T, Kurosawa K, McCully LM, Silby MW, Bucci V, Brigham CJ.	Microbiol Resour Announc	10.1128/mra.00915-18	2019
	Unlocking efficient polyhydroxyalkanoate production by Gram-positive Priestia megaterium using waste-derived feedstocks.	Bai X, Xu L, Li K, Zhang G, Zhang M, Huang Y.	Microb Cell Fact	10.1186/s12934-025-02803-z	2025
	Biotransformation of d-Xylose-Rich Rice Husk Hydrolysate by a Rice Paddy Soil Bacterium, Priestia sp. Strain JY310, to Low Molecular Weight Poly(3-hydroxybutyrate).	Lee JY, Kim MH, Kim JS, Yun BR, Kim DY, Chung CW.	Biomolecules	10.3390/biom13010131	2023
Phylogeny	Combination of Hypotonic Lysis and Application of Detergent for Isolation of Polyhydroxyalkanoates from Extremophiles.	Novackova I, Kourilova X, Mrazova K, Sedlacek P, Kalina M, Krzyzanek V, Koller M, Obruca S.	Polymers (Basel)	10.3390/polym14091761	2022
	Polyhydroxyalkanoate Production from Eucalyptus Bark's Enzymatic Hydrolysate.	Rodrigues T, Torres CAV, Marques S, Girio F, Freitas F, Reis MAM.	Materials (Basel)	10.3390/ma17081773	2024
	Influence of zinc on the calcium carbonate biomineralization of Halomonas halophila.	Rothenstein D, Baier J, Schreiber TD, Barucha V, Bill J.	Aquat Biosyst	10.1186/2046-9063-8-31	2012
	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
	Isolation of a potentially arsenic-resistant Halomonas elongata strain (ml10562) from hypersaline systems in the Peruvian Andes, Cusco.	Pila-Lacuta S, Pauccar D, Rojas-Vargas J, Rodriguez-Cruz UE, Sierra JL, Castelan-Sanchez HG, Quispe-Ricalde MA.	PLoS One	10.1371/journal.pone.0320639	2025
Phylogeny	Structural elucidation of a novel phosphoglycolipid isolated from six species of Halomonas.	Giordano A, Vella FM, Romano I, Gambacorta A	J Lipid Res	10.1194/jlr.M700152-JLR200	2007
Cultivation	Growth rate and some physiological features of Deleya halophila CCM 3662 at different salt concentrations.	Ferrer MR, del Moral A, Quesada E, Ramos-Cormenzana A	Ann Inst Pasteur Microbiol	10.1016/0769-2609(87)90053-6	1987
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

#1816	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 4770
#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 )
#38128	; Curators of the CIP;
#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) .
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#68371	Automatically annotated from API 50CH acid .
#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 .
#119808	Collection of Institut Pasteur ; Curators of the CIP; CIP 103512
#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 )

Content

About us

Halomonas halophila (DSM 4770, CCM 3662, F 5-7)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Observation

Metabolite utilization

Metabolite production

Enzymes

API 50CHac

API biotype100

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_030406665

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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