Ruegeria conchae (DSM 29317, JCM 17315, KACC 15115)

Name: Ruegeria conchae (DSM 29317, JCM 17315, KACC 15115)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 24504

Type strain

Strain Designation TW15

Culture col. no. DSM 29317 JCM 17315 KACC 15115 TW15

NCBI tax ID(s) 981384

Special Collections DSMZ JCM Literature strains

History <- JCM 17315 <- J.-W. Bae; TW15 J.-W. Bae; Dept. of Biol., Kyung Hee Univ., South Korea; TW15.

Links

Ruegeria conchae TW15 is an aerobe, Gram-negative, rod-shaped bacterium that was isolated from ark clam .

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

Name and taxonomic classification

SI-ID 407032

JCM 17315,DSM 29317

@ref 20215

Last LPSN update 2026-02-09 11:23:59

Domain Bacteria

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Rhodobacterales

Family Roseobacteraceae

Genus Ruegeria

Species Ruegeria conchae

Full scientific name Ruegeria conchae Lee et al. 2012

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Motility	Confidence
30492	negative	0.75 µm	0.4 µm	rod-shaped
125438	negative					98.333

Colony morphology

20792

Incubation period1-2 days

Pigmentation

30492

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
20792	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

Culture temp

@ref	Growth	Type	Temperature (°C)
20792	positive	growth	30
30492	positive	growth	10-37
30492	positive	optimum	27.5
67770	positive	growth	30

Culture pH

@ref	Ability	Type	PH	PH range
30492	positive	optimum	8
30492	positive	growth	07-10	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
30492	aerobe
125439	obligate aerobe	96.6

Spore formation

@ref	Spore formation	Confidence
125438		91.245
125439		93.7

Halophily

@ref	Salt	Growth	Tested relation	Concentration
30492	NaCl	positive	growth	01-05 %
30492	NaCl	positive	optimum	2 %

Observation

67770

Observationquinones: Q-10

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68369	29016 ChEBI	arginine	-	hydrolysis	from API 20NE
68369	17634 ChEBI	D-glucose	+	assimilation	from API 20NE
68369	17634 ChEBI	D-glucose	-	fermentation	from API 20NE
68369	16899 ChEBI	D-mannitol	+	assimilation	from API 20NE
68369	16024 ChEBI	D-mannose	+	assimilation	from API 20NE
68369	27689 ChEBI	decanoate	-	assimilation	from API 20NE
68369	4853 ChEBI	esculin	-	hydrolysis	from API 20NE
68369	5291 ChEBI	gelatin	-	hydrolysis	from API 20NE
30492	24265 ChEBI	gluconate	+	carbon source
30492	17234 ChEBI	glucose	+	carbon source
30492	17754 ChEBI	glycerol	+	carbon source
30492	18403 ChEBI	L-arabitol	+	carbon source
68369	25115 ChEBI	malate	+	assimilation	from API 20NE
30492	17306 ChEBI	maltose	+	carbon source
68369	17306 ChEBI	maltose	+	assimilation	from API 20NE
30492	37684 ChEBI	mannose	+	carbon source
68369	59640 ChEBI	N-acetylglucosamine	+	assimilation	from API 20NE
68369	17632 ChEBI	nitrate	-	reduction	from API 20NE
30492	33942 ChEBI	ribose	+	carbon source
30492	27082 ChEBI	trehalose	+	carbon source
68369	27897 ChEBI	tryptophan	-	energy source	from API 20NE
68369	16199 ChEBI	urea	-	hydrolysis	from API 20NE
30492	18222 ChEBI	xylose	+	carbon source

Metabolite production

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

Metabolite tests

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

Enzymes

@ref	Value	Activity	Ec
30492	acid phosphatase	+	3.1.3.2
30492	alkaline phosphatase	+	3.1.3.1
68369	arginine dihydrolase	-	3.5.3.6	from API 20NE
68369	beta-glucosidase	-	3.2.1.21	from API 20NE
20792	catalase	+	1.11.1.6
30492	catalase	+	1.11.1.6
30492	cytochrome oxidase	+	1.9.3.1
20792	cytochrome-c oxidase	+	1.9.3.1
68369	gelatinase	-		from API 20NE
68369	urease	-	3.5.1.5	from API 20NE

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
20792	-	-	-	-	-	-	-	+	+	+/-	+	+	+	+	+/-	-	+/-	+	+/-	+/-	not determinedn.d.

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Invertebrates (Other)	#Mollusca

Isolation

@ref	Sample type	Host species	Geographic location	Country	Country ISO 3 Code	Continent
20792	ark clam (Scapharca broughtonii)	Scapharca broughtonii	South Sea	Republic of Korea	KOR	Asia
67770	Ark clam (Scapharca broughtonii)	Scapharca broughtonii		Republic of Korea	KOR	Asia

Taxonmaps

69479

Global distribution of 16S sequence HQ171439 (>99% sequence identity) for Ruegeria from Microbeatlas

Aquatic Samples	619
Soil Samples	17
Animal Samples	82
Plant Samples	2
Total Samples	720

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
20792	1	Risk group (German classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM366420v1 assembly for Ruegeria conchae DSM 29317	contig	GCA_003664205	981384.12	2734482173	981384	74.45
67770	ASM19247v1 assembly for Ruegeria conchae TW15	contig	GCA_000192475	981384.3	2513237272	981384	73.55

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
30492	Ruegeria conchae strain TW15 16S ribosomal RNA gene, partial sequence	HQ171439	1384		981384

GC content

@ref	GC-content (mol%)	Method
20792	55.7
67770	55.7	genome sequence analysis

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Ruegeria conchae DSM 29317
NCBI: GCA_003664205

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	93.70	no
125439	motility	BacteriaNetⓘ	no	50.10	no
125439	gram_stain	BacteriaNetⓘ	negative	89.90	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	96.60	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Ruegeria conchae strain DSM 29317
PATRIC: 981384.12

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	98.33	no
125438	anaerobic	anaerobicⓘ	no	93.81	yes
125438	aerobic	aerobicⓘ	yes	86.05	yes
125438	spore-forming	spore-formingⓘ	no	91.25	no
125438	thermophilic	thermophileⓘ	no	95.92	yes
125438	flagellated	motile2+ⓘ	no	55.70	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Ruegeria conchae sp. nov., isolated from the ark clam Scapharca broughtonii.	Lee J, Whon TW, Shin NR, Roh SW, Kim J, Park SK, Kim MS, Shin KS, Lee JS, Lee KC, Kim YO, Bae JW	Int J Syst Evol Microbiol	10.1099/ijs.0.037283-0	2012
Phylogeny	Ruegeria profundi sp. nov. and Ruegeria marisrubri sp. nov., isolated from the brine-seawater interface at Erba Deep in the Red Sea.	Zhang G, Haroon MF, Zhang R, Dong X, Wang D, Liu Y, Xun W, Dong X, Stingl U	Int J Syst Evol Microbiol	10.1099/ijsem.0.002344	2017

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 )
#20792	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 29317
#26825	IJSEM 2851 2012 ( DOI 10.1099/ijs.0.037283-0 , PubMed 22228657 )
#30492	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 #26825
#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;
#68369	Automatically annotated from API 20NE .
#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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Ruegeria conchae (DSM 29317, JCM 17315, KACC 15115)

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 20NE

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_003664205

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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