Halomonas cupida (DSM 4740, ATCC 27124, CCUG 16075)

Name: Halomonas cupida (DSM 4740, ATCC 27124, CCUG 16075)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 6015

Type strain

Culture col. no. DSM 4740 ATCC 27124 CCUG 16075 LMG 3448 CIP 74.06 7 more

NCBI tax ID(s) 44933

Special Collections DSMZ CCUG JCM CIP

Links

Halomonas cupida DSM 4740 is a mesophilic, Gram-negative, rod-shaped prokaryote that was isolated from seawater.

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

Name and taxonomic classification

SI-ID 2161

LMG 3448,ATCC 27124,DSM 4740,NCMB 1978,CCUG 16075,CIP 103199,NCIMB 1978,IAM12552,CIP 74.06,CECT 5001,NCIB 1978,KCTC 12173,NBRC 102219,JCM 20632,CGMCC 1.2312

@ref 20215

Last LPSN update 2025-12-16 09:48:12

Domain Pseudomonadati

Phylum Pseudomonadota

Class Gammaproteobacteria

Order Oceanospirillales

Family Halomonadaceae

Genus Halomonas

Species Halomonas cupida

Full scientific name Halomonas cupida (Baumann et al. 1972) Dobson and Franzmann 1996

Synonyms (2)

Deleya cupida
Alcaligenes cupidus

BacDive ID	Other strains from **Halomonas cupida** (1)	Type strain
138948	H. cupida CIP 74.6

Morphology

Cell morphology

@ref	Gram stain	Cell shape
118818	negative	rod-shaped
125438	negative
125439	negative
125439

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
1746	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
1746	MARINE AGAR (DSMZ Medium 123)	Medium recipe at MediaDive	Name: MARINE AGAR (DSMZ Medium 123) Composition: NaCl 24.0 g/l Agar 15.0 g/l MgCl2 x 6 H2O 11.0 g/l Bacto peptone 5.0 g/l Na2SO4 4.0 g/l CaCl2 x 6 H2O 2.0 g/l Yeast extract 1.0 g/l KCl 0.7 g/l KBr 0.1 g/l SrCl2 x 6 H2O 0.04 g/l H3BO3 0.03 g/l NaSiO3 x 9 H2O 0.005 g/l NaF 0.003 g/l NH4NO3 0.002 g/l Fe(III)PO4 x 4 H2O 0.001 g/l Distilled water
34123	Marine agar (MA)		Distilled water make up to (1000.000 ml);Marine agar (55.100 g)
118818	CIP Medium 72	Medium recipe at CIP
118818	CIP Medium 13	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
1746	positive	growth	25	mesophilic
1746	positive	growth	26	mesophilic
34123	positive	growth	30	mesophilic
46437	positive	growth	26	mesophilic
67770	positive	growth	25	mesophilic
118818	positive	growth	5-41
118818	negative	growth	45

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	obligate aerobe	90.3

Spore formation

@ref	Spore formation	Confidence
125438		91.549
125439		99.5

Halophily

@ref	Salt	Growth	Tested relation	Concentration
118818	NaCl	positive	growth	0-10 %

Observation

67770

Observationquinones: Q-9

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
118818	16947 ChEBI	citrate	+	carbon source
118818	4853 ChEBI	esculin	-	hydrolysis
118818	606565 ChEBI	hippurate	+	hydrolysis
118818	15792 ChEBI	malonate	+	assimilation
118818	17632 ChEBI	nitrate	+	reduction
118818	17632 ChEBI	nitrate	-	respiration
118818	16301 ChEBI	nitrite	-	reduction

Metabolite production

@ref	Chebi-ID	Metabolite	Production
118818	35581 ChEBI	indole

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
118818	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
118818	amylase	-
68382	beta-galactosidase	-	3.2.1.23	from API zym
118818	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
118818	caseinase	-	3.4.21.50
118818	catalase	+	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
118818	DNase	+
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
118818	gamma-glutamyltransferase	+	2.3.2.2
118818	gelatinase	+/-
118818	lecithinase	-
68382	leucine arylamidase	+	3.4.11.1	from API zym
118818	lipase	-
68382	lipase (C 14)	-		from API zym
118818	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
118818	ornithine decarboxylase	-	4.1.1.17
118818	oxidase	+
118818	phenylalanine ammonia-lyase	-	4.3.1.24
118818	protease	-
68382	trypsin	-	3.4.21.4	from API zym
118818	tryptophan deaminase	-
118818	tween esterase	+
118818	urease	-	3.5.1.5
68382	valine arylamidase	+		from API zym

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
118818	-	+	+	+	-	+	+	-	-	-	+	+	-	-	-	+	+	-	-	-

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
118818	not determinedn.d.	+	+	+	+	+	-	+	+	+	+	+	+	+	-	-	+	+	+	+	+	+	+	+	-	-	-	+	+	+	-	-	+	+	+	+	+	+	+	-	+	+	+	+	+	+	-	+	+	+	+	+	-	-	+	+	+	+	-	-	+	+	-	+	+	-	-	-	-	-	-	-	+	+	+	-	+	+	-	+	+	+	+	+	+	-	-	+	-	+	+	+	+	+	+	+	+	+	+	+

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Marine

Isolation

@ref	Sample type
1746	seawater
46437	Seawater enrichment with allantoin
118818	Environment, Seawater

Taxonmaps

69479

Global distribution of 16S sequence AB681733 (>99% sequence identity) for Halomonas cupida from Microbeatlas

Aquatic Samples	157
Soil Samples	42
Animal Samples	145
Plant Samples	32
Total Samples	376

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
1746	1	Risk group (German classification) According to TRBA 466
118818	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
67770	IMG-taxon 2599185207 annotated assembly for Halomonas cupida DSM 4740	scaffold	GCA_900142755	44933.4	2599185207	44933	70.58
67770	ASM799115v1 assembly for Halomonas cupida NBRC 102219	contig	GCA_007991155	44933.8		44933	32.36

Genome browser: GCA_900142755

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Halomonas cupida partial 16S rRNA gene, strain DSM 4740	FN257742	1464	44933
20218	Halomonas cupida gene for 16S rRNA, partial sequence, strain: NBRC 102219	AB681733	1465	44933
1746	Halomonas cupida strain DSM 4740 16S ribosomal RNA gene, partial sequence	L42615	1471	44933

GC content

@ref	GC-content (mol%)	Method
67770	60	thermal denaturation, midpoint method (Tm)
67770	60.7	Buoyant density centrifugation (BD)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Halomonas cupida DSM 4740
NCBI: GCA_900142755

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	99.50	no
125439	motility	BacteriaNetⓘ	yes	92.70	no
125439	gram_stain	BacteriaNetⓘ	negative	99.60	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	90.30	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Halomonas cupida strain DSM 4740
PATRIC: 44933.4

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	100.00	no
125438	anaerobic	anaerobicⓘ	no	98.46	no
125438	spore-forming	spore-formingⓘ	no	91.55	no
125438	aerobic	aerobicⓘ	yes	83.57	no
125438	thermophilic	thermophileⓘ	no	99.00	yes
125438	flagellated	motile2+ⓘ	yes	80.67	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Extremozymes and compatible solute production potential of halophilic and halotolerant bacteria isolated from crop rhizospheric soils of Southwest Saurashtra Gujarat.	Reang L, Bhatt S, Tomar RS, Joshi K, Padhiyar S, Bhalani H, Kheni J, Vyas UM, Parakhia MV.	Sci Rep	10.1038/s41598-024-63581-z	2024
	Halomonas binhaiensis sp. nov., isolated from saline-alkali soil.	Li X, Lu H, Wang Q, Yang H, Yang H, Wu J, Huang H.	Int J Syst Evol Microbiol	10.1099/ijsem.0.005652	2022
Phylogeny	Halomonas sediminicola sp. nov., a moderately halophilic bacterium isolated from a solar saltern sediment.	Lee JC, Kim SJ, Whang KS	Int J Syst Evol Microbiol	10.1099/ijsem.0.001278	2016
Phylogeny	Halomonas huangheensis sp. nov., a moderately halophilic bacterium isolated from a saline-alkali soil.	Miao C, Jia F, Wan Y, Zhang W, Lin M, Jin W	Int J Syst Evol Microbiol	10.1099/ijs.0.056556-0	2013

References

#1746	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 4740
#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 )
#34123	; Curators of the CIP;
#46437	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 16075
#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 .
#118818	Collection of Institut Pasteur ; Curators of the CIP; CIP 103199
#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 cupida (DSM 4740, ATCC 27124, CCUG 16075)

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 zym

API biotype100

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_900142755

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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