Name: Ruegeria conchae TW15
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 24504

Type strain:

Species: Ruegeria conchae

Strain Designation: TW15

Culture col. no.: DSM 29317, JCM 17315, KACC 15115

Strain history: J.-W. Bae; Dept. of Biol., Kyung Hee Univ., South Korea; TW15.

NCBI tax ID(s): 981384 (species)

SI-ID 407032

DSM 29317

Section

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

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

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Pseudomonadota*
	Class	*Alphaproteobacteria*
	Order	*Rhodobacterales*
	Family	*Roseobacteraceae*
	Genus	*Ruegeria*
	Species	**Ruegeria conchae**
	Full Scientific Name (LPSN)	Ruegeria conchae Lee et al. 2012

Information on morphological and physiological properties Morphology

[Ref.: #30492]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.994

[Ref.: #30492]	Cell length	0.75 µm

[Ref.: #30492]	Cell width	0.4 µm

[Ref.: #30492]	Cell shape	rod-shaped

[Ref.: #30492]	Motility	no

[Ref.: #20792]

Incubation period

1-2 days

[Ref.: #30492]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #20792]

Culture medium

BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)

[Ref.: #20792]

Culture medium growth

[Ref.: #20792]

Culture medium link

Medium recipe at MediaDive

[Ref.: #20792]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #20792]	growth	30 °C
[Ref.: #30492]	growth	10-37 °C
[Ref.: #30492]	optimum	27.5 °C
[Ref.: #67770]	growth	30 °C

[Ref.: #20792]	Temperature range	mesophilic
[Ref.: #30492]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #30492]			optimum	8
[Ref.: #30492]			growth	07-10

Information on physiology and metabolism Physiology and metabolism

[Ref.: #30492]

Oxygen tolerance

aerobe

[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.998

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #30492]		NaCl		growth	01-05	%
[Ref.: #30492]		NaCl		optimum	2	%

[Ref.: #67770]

Observation

quinones: Q-10

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #68369]	arginine ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #68369]	D-glucose ChEBI	+	assimilation	* from API 20NE
[Ref.: #68369]	D-glucose ChEBI	-	fermentation	* from API 20NE
[Ref.: #68369]	D-mannitol ChEBI	+	assimilation	* from API 20NE
[Ref.: #68369]	D-mannose ChEBI	+	assimilation	* from API 20NE
[Ref.: #68369]	decanoate ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	esculin ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #68369]	gelatin ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #30492]	gluconate ChEBI	+	carbon source
[Ref.: #30492]	glucose ChEBI	+	carbon source
[Ref.: #30492]	glycerol ChEBI	+	carbon source
[Ref.: #30492]	L-arabitol ChEBI	+	carbon source
[Ref.: #68369]	malate ChEBI	+	assimilation	* from API 20NE
[Ref.: #30492]	maltose ChEBI	+	carbon source
[Ref.: #68369]	maltose ChEBI	+	assimilation	* from API 20NE
[Ref.: #30492]	mannose ChEBI	+	carbon source
[Ref.: #68369]	N-acetylglucosamine ChEBI	+	assimilation	* from API 20NE
[Ref.: #68369]	nitrate ChEBI	-	reduction	* from API 20NE
[Ref.: #30492]	ribose ChEBI	+	carbon source
[Ref.: #30492]	trehalose ChEBI	+	carbon source
[Ref.: #68369]	tryptophan ChEBI	-	energy source	* from API 20NE
[Ref.: #68369]	urea ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #30492]	xylose ChEBI	+	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #68369]		indole ChEBI	no	* from API 20NE

	Physiological tests	Metabolite	Indole test
[Ref.: #68369]		indole ChEBI	-	* from API 20NE

	Enzyme	Enzyme activity	EC number
[Ref.: #30492]	acid phosphatase	+	3.1.3.2
[Ref.: #30492]	alkaline phosphatase	+	3.1.3.1
[Ref.: #68369]	arginine dihydrolase	-	3.5.3.6	* from API 20NE
[Ref.: #68369]	beta-glucosidase	-	3.2.1.21	* from API 20NE
[Ref.: #20792]	catalase	+	1.11.1.6
[Ref.: #30492]	catalase	+	1.11.1.6
[Ref.: #30492]	cytochrome oxidase	+	1.9.3.1
[Ref.: #20792]	cytochrome-c oxidase	+	1.9.3.1
[Ref.: #68369]	gelatinase	-		* from API 20NE
[Ref.: #68369]	urease	-	3.5.1.5	* from API 20NE

API® 20NE:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	Reduction of nitratesNO3	Indole productionTRP	Fermentation of D-glucoseGLU_ Ferm	Arginine dihydrolaseADH (Arg)	Urease/urea hydrolysisURE	Esculin hydrolysis/beta-GlucosidaseESC	Gelatinase/gelatin hydrolysisGEL	beta-GalactosidasePNPG	Assimilation of D-glucoseGLU_ Assim	Assimilation of L-arabinoseARA	Assimilation of D-mannoseMNE	Assimilation of D-mannitolMAN	Assimilation of N-acetyl-glucosamineNAG	Assimilation of maltoseMAL	Assimilation of gluconateGNT	Assimilation of capric acidCAP	Assimilation adipic acidADI	Assimilation of malic acidMLT	Assimilation of citric acidCIT	Assimilation of phenyl-acetic acidPAC	Cytochrome oxidaseOX
[Ref.: #20792]	24036	-	-	-	-	-	-	-	+	+	+/-	+	+	+	+	+/-	-	+/-	+	+/-	+/-	not determinedn.d.

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #20792]	Sample type/isolated from	ark clam (Scapharca broughtonii)
[Ref.: #20792]	Host species	Scapharca broughtonii
[Ref.: #20792]	Geographic location (country and/or sea, region)	South Sea
[Ref.: #20792]	Country	Republic of Korea
[Ref.: #20792]	Country ISO 3 Code	KOR
[Ref.: #20792]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Ark clam (Scapharca broughtonii)
[Ref.: #67770]	Host species	Scapharca broughtonii
[Ref.: #67770]	Country	Republic of Korea
[Ref.: #67770]	Country ISO 3 Code	KOR
[Ref.: #67770]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Host

#Invertebrates (Other)

#Mollusca

What are isolation sources categories?

[Ref.: #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

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #20792]

Biosafety level

Risk group (German classification)
According to TRBA 466

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #30492]	Ruegeria conchae strain TW15 16S ribosomal RNA gene, partial sequence	HQ171439	1384	GenBank	981384 tax ID
[Ref.: #20792]		HQ17143		ENA

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Ruegeria conchae TW15	GCA_000192475	contig	GenBank	981384 tax ID
[Ref.: #66792]	Ruegeria conchae DSM 29317	GCA_003664205	contig	GenBank	981384 tax ID	*
[Ref.: #66792]	Ruegeria conchae strain DSM 29317	981384.12	wgs	PATRIC	981384 tax ID	*
[Ref.: #66792]	Ruegeria conchae TW15	2513237272	draft	JGI IMG/M	981384 tax ID	*
[Ref.: #66792]	Ruegeria conchae DSM 29317	2734482173	draft	JGI IMG/M	981384 tax ID	*

[Ref.: #20792]	GC-content	55.7 mol%
[Ref.: #67770]	GC-content	55.7 mol%	genome sequence analysis

Data predicted using genome information as a basis Genome-based predictions

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Ruegeria conchae strain DSM 29317 PATRIC: 981384.3
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Ruegeria conchae strain DSM 29317 PATRIC: 981384.12
[Ref.: #69480]	motile	no	64.242	yes
[Ref.: #69480]	flagellated	no	74.246	yes
[Ref.: #69480]	gram-positive	no	98.169	no
[Ref.: #69480]	anaerobic	no	98.732	yes
[Ref.: #69480]	halophile	yes	79.673	no
[Ref.: #69480]	spore-forming	no	95.055	no
[Ref.: #69480]	thermophile	no	95.811	yes
[Ref.: #69480]	glucose-util	yes	68.878	yes
[Ref.: #69480]	aerobic	yes	87.224	yes
[Ref.: #69480]	glucose-ferment	no	91.204	no

Availability in culture collections External links

[Ref.: #20792]

Culture collection no.

DSM 29317, JCM 17315, KACC 15115

[Ref.: #88362]

SI-ID 407032

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

#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 (see below)

#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 .

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

#88362

Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.: StrainInfo: A central database for resolving microbial strain identifiers . ( DOI 10.60712/SI-ID407032.1 )

#26825

IJSEM 2851 2012 ( DOI 10.1099/ijs.0.037283-0 , PubMed 22228657 )

* These data were automatically processed and therefore are not curated

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Ruegeria conchae strain DSM 29317

Ruegeria conchae strain DSM 29317

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