Donghicola eburneus (DSM 29127, JCM 13604, KCTC 12735)

Name: Donghicola eburneus (DSM 29127, JCM 13604, KCTC 12735)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 24510

Type strain

Strain Designation SW-277

Culture col. no. DSM 29127 JCM 13604 KCTC 12735 SW-277 CIP 109518

NCBI tax ID(s) 393278

Special Collections DSMZ JCM KCTC CIP Literature strains

Links

Donghicola eburneus SW-277 is an aerobe, mesophilic, Gram-negative prokaryote that was isolated from seawater sample.

Gram-negative coccus-shaped aerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 297173

JCM 13604,KCTC 12735,CIP 109518,DSM 29127

@ref 20215

Last LPSN update 2025-12-16 09:52:51

Domain Pseudomonadati

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Rhodobacterales

Family Roseobacteraceae

Genus Donghicola

Species Donghicola eburneus

Full scientific name Donghicola eburneus Yoon et al. 2007

BacDive ID	Other strains from **Donghicola eburneus** (1)	Type strain
175254	D. eburneus KarMa, DSM 110933

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
31875	negative	1.3 µm	0.7 µm	coccus-shaped
67771	negative
125438	negative				99
125439	negative				95.8
118991	negative			rod-shaped

Colony morphology

21156

Incubation period1-2 days

Pigmentation

31875

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
21156	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
37752	Marine agar (MA)		Distilled water make up to (1000.000 ml);Marine agar (55.100 g)
118991	CIP Medium 13	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
21156	positive	growth	30	mesophilic
31875	positive	growth	10-42
31875	positive	optimum	26	mesophilic
37752	positive	growth	37	mesophilic
67770	positive	growth	37	mesophilic
67771	positive	growth	37	mesophilic

Culture pH

@ref	Ability	Type	PH
31875	positive	optimum	7.5
31875	positive	growth	07-08

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
31875	aerobe
67771	aerobe
125439	obligate aerobe	90

Spore formation

@ref	Spore formation	Confidence
31875
125438		94.122
125439		97.4

Halophily

@ref	Salt	Growth	Tested relation	Concentration
31875	NaCl	positive	growth	01-12 %
31875	NaCl	positive	optimum	2 %

Observation

@ref	Observation
31875	aggregates in chains
67770	quinones: Q-10

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
31875	30089 ChEBI	acetate	+	carbon source
68369	17128 ChEBI	adipate	-	assimilation	from API 20NE
68371	27613 ChEBI	amygdalin	-	builds acid from	from API 50CH acid
31875	22599 ChEBI	arabinose	+	carbon source
68371	18305 ChEBI	arbutin	-	builds acid from	from API 50CH acid
68369	29016 ChEBI	arginine	-	hydrolysis	from API 20NE
31875	17057 ChEBI	cellobiose	+	carbon source
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
68369	17634 ChEBI	D-glucose	+	assimilation	from API 20NE
68369	17634 ChEBI	D-glucose	-	fermentation	from API 20NE
68371	62318 ChEBI	D-lyxose	-	builds acid from	from API 50CH acid
68371	16899 ChEBI	D-mannitol	-	builds acid from	from API 50CH acid
68369	16899 ChEBI	D-mannitol	+	assimilation	from API 20NE
68371	16024 ChEBI	D-mannose	-	builds acid from	from API 50CH acid
68369	16024 ChEBI	D-mannose	+	assimilation	from API 20NE
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
68369	27689 ChEBI	decanoate	-	assimilation	from API 20NE
68371	17113 ChEBI	erythritol	-	builds acid from	from API 50CH acid
68369	4853 ChEBI	esculin	+	hydrolysis	from API 20NE
31875	28757 ChEBI	fructose	+	carbon source
68371	16813 ChEBI	galactitol	-	builds acid from	from API 50CH acid
31875	28260 ChEBI	galactose	+	carbon source
68369	5291 ChEBI	gelatin	-	hydrolysis	from API 20NE
68371	28066 ChEBI	gentiobiose	-	builds acid from	from API 50CH acid
68371	24265 ChEBI	gluconate	-	builds acid from	from API 50CH acid
68369	24265 ChEBI	gluconate	+	assimilation	from API 20NE
31875	17234 ChEBI	glucose	+	carbon source
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
68369	30849 ChEBI	L-arabinose	+	assimilation	from API 20NE
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
31875	17716 ChEBI	lactose	+	carbon source
68371	17716 ChEBI	lactose	-	builds acid from	from API 50CH acid
31875	25115 ChEBI	malate	+	carbon source
68369	25115 ChEBI	malate	+	assimilation	from API 20NE
31875	17306 ChEBI	maltose	+	carbon source
68371	17306 ChEBI	maltose	-	builds acid from	from API 50CH acid
68369	17306 ChEBI	maltose	+	assimilation	from API 20NE
31875	29864 ChEBI	mannitol	+	carbon source
31875	37684 ChEBI	mannose	+	carbon source
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
68369	59640 ChEBI	N-acetylglucosamine	-	assimilation	from API 20NE
31875	17632 ChEBI	nitrate	+	reduction
118991	17632 ChEBI	nitrate	-	reduction
68369	17632 ChEBI	nitrate	+	reduction	from API 20NE
118991	16301 ChEBI	nitrite	-	reduction
68371		Potassium 2-ketogluconate	-	builds acid from	from API 50CH acid
31875	15361 ChEBI	pyruvate	+	carbon source
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
31875	30911 ChEBI	sorbitol	+	carbon source
68371	28017 ChEBI	starch	-	builds acid from	from API 50CH acid
31875	30031 ChEBI	succinate	+	carbon source
31875	17992 ChEBI	sucrose	+	carbon source
68371	17992 ChEBI	sucrose	-	builds acid from	from API 50CH acid
68371	27082 ChEBI	trehalose	-	builds acid from	from API 50CH acid
68369	27897 ChEBI	tryptophan	-	energy source	from API 20NE
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
68369	35581 ChEBI	indole		from API 20NE
118991	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Indole test
68369	35581 ChEBI	indole	-	from API 20NE

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	-	3.1.3.2	from API zym
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
68369	arginine dihydrolase	-	3.5.3.6	from API 20NE
68382	beta-galactosidase	-	3.2.1.23	from API zym
68382	beta-glucosidase	-	3.2.1.21	from API zym
68369	beta-glucosidase	+	3.2.1.21	from API 20NE
68382	beta-glucuronidase	-	3.2.1.31	from API zym
21156	catalase	+	1.11.1.6
31875	catalase	+	1.11.1.6
118991	catalase	+	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
31875	cytochrome oxidase	+	1.9.3.1
21156	cytochrome-c oxidase	+	1.9.3.1
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
68369	gelatinase	-		from API 20NE
68382	leucine arylamidase	-	3.4.11.1	from API zym
68382	lipase (C 14)	-		from API zym
68382	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	-		from API zym
118991	oxidase	+
68382	trypsin	-	3.4.21.4	from API zym
118991	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
118991	-	+	+	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-

API 20NE

@ref	Reduction of nitratesNO3	TRP	GLU_ Ferm	ADH (Arg)	URE	ESC	GEL	PNPG	GLU_ Assim	ARA	MNE	MAN	NAG	MAL	GNT	CAP	ADI	MLT	CIT	PAC	OX
21156	+	-	-	-	+/-	+	-	-	+	+	+	+	-	+	+	-	-	+	+	-	not determinedn.d.

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
118991	not determinedn.d.	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+/-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+/-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Marine

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
21156	seawater sample	East Sea, Jongdongjin	Republic of Korea	KOR	Asia
67770	Seawater
67771	From seawater		Republic of Korea	KOR	Asia
118991	Environment, Sea water	East Sea, Jongdongjin	Republic of Korea	KOR	Asia

Taxonmaps

69479

Global distribution of 16S sequence DQ667965 (>99% sequence identity) for Donghicola eburneus subclade from Microbeatlas

Aquatic Samples	1273
Soil Samples	13
Animal Samples	44
Plant Samples	1
Total Samples	1331

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
21156	1	Risk group (German classification)
118991	1	Risk group (French classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
67770	IMG-taxon 2684622851 annotated assembly for Donghicola eburneus DSM 29127	contig	GCA_900115865	393278.4	2684622851	393278	67.68

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
21156	Donghicola eburneus strain SW-277 16S ribosomal RNA gene, partial sequence	DQ667965	1416		393278

GC content

@ref	GC-content (mol%)	Method
31875	59.7
21156	59.7	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: Donghicola eburneus DSM 29127
NCBI: GCA_900115865

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	97.40	no
125439	motility	BacteriaNetⓘ	yes	69.20	no
125439	gram_stain	BacteriaNetⓘ	negative	95.80	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	90.00	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Donghicola eburneus strain DSM 29127
PATRIC: 393278.4

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	99.00	no
125438	anaerobic	anaerobicⓘ	no	94.75	yes
125438	spore-forming	spore-formingⓘ	no	94.12	no
125438	aerobic	aerobicⓘ	yes	78.46	yes
125438	thermophilic	thermophileⓘ	no	99.00	yes
125438	flagellated	motile2+ⓘ	yes	66.85	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Monaibacterium marinum, gen. nov, sp. nov, a new member of the Alphaproteobacteria isolated from seawater of Menai Straits, Wales, UK.	Chernikova TN, Dallimore J, Lunsdorf H, Heipieper HJ, Golyshin PN	Int J Syst Evol Microbiol	10.1099/ijsem.0.002111	2017
Phylogeny	Arenibacterium halophilum gen. nov., sp. nov., a halotolerant bacterium in the family Rhodobacteraceae isolated from a coastal sand dune.	Baek J, Kim JH, Yoon JH, Lee JS, Sukhoom A, Kim W	Int J Syst Evol Microbiol	10.1099/ijsem.0.004534	2020
Phylogeny	Aquicoccus porphyridii gen. nov., sp. nov., isolated from a small marine red alga, Porphyridium marinum.	Feng T, Kim KH, Jeong SE, Kim W, Jeon CO	Int J Syst Evol Microbiol	10.1099/ijsem.0.002498	2017
Phylogeny	Youngimonas vesicularis gen. nov., sp. nov., of the family Rhodobacteraceae, isolated from surface seawater, reclassification of Donghicola xiamenensis Tan et al. 2009 as Pseudodonghicola xiamenensis gen. nov., comb. nov. and emended description of the genus Donghicola Yoon et al. 2007.	Hameed A, Shahina M, Lin SY, Nakayan P, Liu YC, Lai WA, Hsu YH	Int J Syst Evol Microbiol	10.1099/ijs.0.060962-0	2014
Phylogeny	Pontibaca methylaminivorans gen. nov., sp. nov., a member of the family Rhodobacteraceae.	Kim KK, Lee JS, Lee KC, Oh HM, Kim SG	Int J Syst Evol Microbiol	10.1099/ijs.0.020172-0	2009
Phylogeny	Donghicola xiamenensis sp. nov., a marine bacterium isolated from seawater of the Taiwan Strait in China.	Tan T, Wang B, Shao Z	Int J Syst Evol Microbiol	10.1099/ijs.0.000901-0	2009
Phylogeny	Donghicola mangrovi sp. nov., a member of the family Rhodobacteraceae isolated from mangrove forest in Thailand.	Charoenyingcharoen P, Kim JS, Theeragool G, Lee KC, Yukphan P, Lee JS	Int J Syst Evol Microbiol	10.1099/ijsem.0.004570	2020
Phylogeny	Donghicola tyrosinivorans sp. nov., a tyrosine-degrading bacterium isolated from seawater.	Sung HR, Lee JM, Kim M, Yun BR, Shin KS	Int J Syst Evol Microbiol	10.1099/ijsem.0.000543	2015
Phylogeny	Donghicola eburneus gen. nov., sp. nov., isolated from seawater of the East Sea in Korea.	Yoon JH, Kang SJ, Oh TK	Int J Syst Evol Microbiol	10.1099/ijs.0.64577-0	2007

References

#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 )
#21156	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 29127
#28135	IJSEM 73 2007 ( DOI 10.1099/ijs.0.64577-0 , PubMed 17220445 )
#31875	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 #28135
#37752	; Curators of the CIP;
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#67771	Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;
#68369	Automatically annotated from API 20NE .
#68371	Automatically annotated from API 50CH acid .
#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 .
#118991	Collection of Institut Pasteur ; Curators of the CIP; CIP 109518
#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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Donghicola eburneus (DSM 29127, JCM 13604, KCTC 12735)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Observation

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

API zym

API 20NE

API 50CHac

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_900115865

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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