Halomonas alimentaria (DSM 15356, JCM 10888, KCCM 41042)

Name: Halomonas alimentaria (DSM 15356, JCM 10888, KCCM 41042)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 6034

Type strain

Strain Designation YKJ-16

Culture col. no. DSM 15356 JCM 10888 KCCM 41042 KCTC 12950 YKJ-16 2 more

NCBI tax ID(s) 147248

Special Collections DSMZ JCM KCTC CIP

History <- JCM <- Y.-H. Park; YKJ-16 Y.-H. Park YKJ-16. <- JCM <- Y-H Park YKJ-16 CIP <- 2002, JCM <- 2000, Y. H. Park: strain YKJ-16

Links

Halomonas alimentaria YKJ-16 is an aerobe, mesophilic, Gram-negative prokaryote that was isolated from seafood jeotgal.

Gram-negative aerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 100675

JCM 10888,DSM 15356,KCTC 12950,CIP 107381

@ref 20215

Last LPSN update 2025-12-16 09:48:13

Domain Pseudomonadati

Phylum Pseudomonadota

Class Gammaproteobacteria

Order Oceanospirillales

Family Halomonadaceae

Genus Halomonas

Species Halomonas alimentaria

Full scientific name Halomonas alimentaria Yoon et al. 2002

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Confidence
67771	negative
116234	negative	rod-shaped
125439	negative		99
125438	negative		99.5

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
5871	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
33783	Marine agar (MA)		Distilled water make up to (1000.000 ml);Marine agar (55.100 g)
116234	CIP Medium 13	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
5871	positive	growth	30	mesophilic
33783	positive	growth	30	mesophilic
67770	positive	growth	30	mesophilic
67771	positive	growth	30	mesophilic
116234	positive	growth	5-45

Physiology and metabolism

Oxygen tolerance

67771

Oxygen toleranceaerobe

Spore formation

@ref	Spore formation	Confidence
125439		99.7
125438		90.607

Halophily

@ref	Salt	Growth	Tested relation	Concentration
116234	NaCl	positive	growth	4-10 %
116234	NaCl		growth	0 %
116234	NaCl		growth	2 %

Observation

@ref	Observation
67770	quinones: Q-9
67771	quinones: Q-9

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
116234	16947 ChEBI	citrate	-	carbon source
116234	4853 ChEBI	esculin	-	hydrolysis
116234	606565 ChEBI	hippurate	+	hydrolysis
116234	15792 ChEBI	malonate	-	assimilation
116234	17632 ChEBI	nitrate	+	reduction
116234	17632 ChEBI	nitrate	+	respiration
116234	16301 ChEBI	nitrite	-	reduction

Metabolite production

@ref	Chebi-ID	Metabolite	Production
116234	35581 ChEBI	indole

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	-	3.1.3.2	from API zym
116234	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
116234	amylase	-
68382	beta-galactosidase	-	3.2.1.23	from API zym
116234	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
116234	caseinase	-	3.4.21.50
116234	catalase	+	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
68382	esterase (C 4)	-		from API zym
68382	esterase lipase (C 8)	-		from API zym
116234	gamma-glutamyltransferase	+	2.3.2.2
116234	gelatinase	-
116234	lecithinase	-
68382	leucine arylamidase	+	3.4.11.1	from API zym
116234	lipase	-
68382	lipase (C 14)	-		from API zym
116234	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
116234	ornithine decarboxylase	-	4.1.1.17
116234	oxidase	+
116234	phenylalanine ammonia-lyase	-	4.3.1.24
68382	trypsin	-	3.4.21.4	from API zym
116234	tryptophan deaminase	-
116234	tween esterase	-
116234	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
116234	-	+	-	-	-	+	-	-	-	-	-	+	-	-	-	-	-	-	-	-

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
116234	not determinedn.d.	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Food production	#Seafood
#Engineered	#Food production	#Fermented

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Isolation date
5871	seafood jeotgal	Korea	Republic of Korea	KOR	Asia
67770	Jeotgal, Korean traditional fermented seafood		Republic of Korea	KOR	Asia
67771	From jeotgal (Korean traditional fermented seafood)		Republic of Korea	KOR	Asia
116234	Food, Jeotgal, korean traditinal fermented seafood		Republic of Korea	KOR	Asia	1999

Taxonmaps

69479

Global distribution of 16S sequence AF211860 (>99% sequence identity) for Halomonas from Microbeatlas

Aquatic Samples	297
Soil Samples	49
Animal Samples	54
Plant Samples	6
Total Samples	406

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
5871	1	Risk group (German classification) According to TRBA 466
116234	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
66792	ASM990200v1 assembly for Halomonas alimentaria DSM 15356	scaffold	GCA_009902005	147248.4	8069420432	147248	73.37

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
5871	Halomonas alimentaria 16S ribosomal RNA gene, partial sequence	AF211860	1493		147248

GC content

@ref	GC-content (mol%)	Method
5871	63	high performance liquid chromatography (HPLC)
67771	63.0	high performance liquid chromatography (HPLC)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Halomonas alimentaria DSM 15356
NCBI: GCA_009902005

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	99.70	no
125439	motility	BacteriaNetⓘ	yes	86.10	no
125439	gram_stain	BacteriaNetⓘ	negative	99.00	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate anaerobe	71.60	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Halomonas alimentaria DSM 15356
NCBI: GCA_009902005.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	99.50	no
125438	anaerobic	anaerobicⓘ	no	96.02	yes
125438	aerobic	aerobicⓘ	yes	80.60	yes
125438	spore-forming	spore-formingⓘ	no	90.61	no
125438	thermophilic	thermophileⓘ	no	96.48	no
125438	flagellated	motile2+ⓘ	no	66.31	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Draft genome sequence of Halomonas sp. SSL-5, a halophilic Mn(II)-oxidizing, perchlorate-tolerant bacterium.	Lee CJ, Greene AC.	Microbiol Resour Announc	10.1128/mra.01028-23	2024
Phylogeny	Halomonas icarae sp. nov., a moderately halophilic bacterium isolated from beach soil in India.	Pandiyan K, Kushwaha P, Bagul SY, Chakdar H, Madhaiyan M, Krishnamurthi S, Kumar P, Karthikeyan N, Singh A, Kumar M, Singh UB, Saxena AK	Int J Syst Evol Microbiol	10.1099/ijsem.0.004611	2020
Phylogeny	Halomonas marinisediminis sp. nov., A Moderately Halophilic Bacterium Isolated from the Bohai Gulf.	Zhao H, Wang C, Tian Y, Zhang Y, Wu Y, Zhang Y, Du Z, Li B, Ji X	Curr Microbiol	10.1007/s00284-020-02147-4	2020
Phylogeny	Halomonas alkalicola sp. nov., isolated from a household product plant.	Tang X, Zhai L, Lin Y, Yao S, Wang L, Ge Y, Liu Y, Zhang X, Zhang T, Zhang L, Liu J, Cheng C	Int J Syst Evol Microbiol	10.1099/ijsem.0.001757	2017
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 korlensis sp. nov., a moderately halophilic, denitrifying bacterium isolated from saline and alkaline soil.	Li HB, Zhang LP, Chen SF	Int J Syst Evol Microbiol	10.1099/ijs.0.65711-0	2008
Phylogeny	Halomonas nitroreducens sp. nov., a novel nitrate- and nitrite-reducing species.	Gonzalez-Domenech CM, Bejar V, Martinez-Checa F, Quesada E	Int J Syst Evol Microbiol	10.1099/ijs.0.65415-0	2008
Phylogeny	Halomonas shengliensis sp. nov., a moderately halophilic, denitrifying, crude-oil-utilizing bacterium.	Wang YN, Cai H, Chi CQ, Lu AH, Lin XG, Jiang ZF, Wu XL	Int J Syst Evol Microbiol	10.1099/ijs.0.64973-0	2007
Phylogeny	Halomonas alimentaria sp. nov., isolated from jeotgal, a traditional Korean fermented seafood.	Yoon JH, Lee KC, Kho YH, Kang KH, Kim CJ, Park YH	Int J Syst Evol Microbiol	10.1099/00207713-52-1-123	2002

References

#5871	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 15356
#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 )
#33783	; 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;
#67771	Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;
#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 .
#116234	Collection of Institut Pasteur ; Curators of the CIP; CIP 107381
#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 alimentaria (DSM 15356, JCM 10888, KCCM 41042)

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_009902005

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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