Name: Halocynthiibacter namhaensis RA2-3
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 130648

Type strain:

Species: Halocynthiibacter namhaensis

Strain Designation: RA2-3, RA2-3(T)

Culture col. no.: DSM 100421, KCTC 32362, NBRC 109999

Strain history: <- JH Yoon, Sungkyunkwan Univ.

NCBI tax ID(s): 1290553 (species)

SI-ID 396584

DSM 100421, DSM 108278

Section

Halocynthiibacter namhaensis RA2-3 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from sea squirt Halocynthia roretzi.

Gram-negative
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	*Halocynthiibacter*
	Species	**Halocynthiibacter namhaensis**
	Full Scientific Name (LPSN)	Halocynthiibacter namhaensis Kim et al. 2014

Information on morphological and physiological properties Morphology

[Ref.: #67771]	Gram stain	negative

[Ref.: #22120]

Incubation period

3-7 days

Information on culture and growth conditions Culture and growth conditions

[Ref.: #22120]

Culture medium

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

[Ref.: #22120]

Culture medium growth

[Ref.: #22120]

Culture medium link

Medium recipe at MediaDive

[Ref.: #22120]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #22120]			growth	25 °C
[Ref.: #67771]			growth	25 °C

[Ref.: #22120]	Temperature range	mesophilic
[Ref.: #67771]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #67771]

Oxygen tolerance

aerobe

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #68369]	adipate ChEBI	-	assimilation	* from API 20NE
[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.: #68369]	gluconate ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	L-arabinose ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	malate ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	maltose ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	N-acetylglucosamine ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	nitrate ChEBI	-	reduction	* from API 20NE
[Ref.: #68369]	tryptophan ChEBI	-	energy source	* from API 20NE
[Ref.: #68369]	urea ChEBI	-	hydrolysis	* from API 20NE
	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.: #68369]	arginine dihydrolase	-	3.5.3.6	* from API 20NE
[Ref.: #68369]	beta-glucosidase	-	3.2.1.21	* from API 20NE
[Ref.: #22120]	catalase	+	1.11.1.6
[Ref.: #22120]	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.: #22120]	24156	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	not determinedn.d.

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

[Ref.: #22120]	Sample type/isolated from	sea squirt Halocynthia roretzi
[Ref.: #22120]	Host species	Halocynthia roretzi
[Ref.: #22120]	Geographic location (country and/or sea, region)	South Sea
[Ref.: #22120]	Country	Republic of Korea
[Ref.: #22120]	Country ISO 3 Code	KOR
[Ref.: #22120]	Continent	Asia

[Ref.: #67771]	Sample type/isolated from	From sea squirt
[Ref.: #67771]	Geographic location (country and/or sea, region)	the South Sea
[Ref.: #67771]	Country	Republic of Korea
[Ref.: #67771]	Country ISO 3 Code	KOR
[Ref.: #67771]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Host

#Invertebrates (Other)

#Tunicata

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence KC416645 (>99% sequence identity) for Halocynthiibacter namhaensis subclade from Microbeatlas

Aquatic Samples	810
Soil Samples	29
Animal Samples	44
Plant Samples	1
Total Samples	884

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

[Ref.: #22120]

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.: #22120]	Halocynthiibacter namhaensis strain RA2-3 16S ribosomal RNA gene, partial sequence	KC416645	1391	ENA	1290553 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Halocynthiibacter namhaensis RA2-3	GCA_000812685	contig	GenBank	1290553 tax ID	*
[Ref.: #66792]	Halocynthiibacter namhaensis RA2-3	2636415494	draft	JGI IMG/M	1290553 tax ID	*

Availability in culture collections External links

[Ref.: #22120]

Culture collection no.

DSM 100421, KCTC 32362, NBRC 109999

[Ref.: #89159]

SI-ID 396584

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Halocynthiibacter namhaensis gen. nov., sp. nov., a novel alphaproteobacterium isolated from sea squirt Halocynthia roretzi.	Kim YO, Park S, Kim H, Park DS, Nam BH, Kim DG, Yoon JH	Antonie Van Leeuwenhoek	10.1007/s10482-014-0142-3	2014	*
Phylogeny	Halocynthiibacter arcticus sp. nov., isolated from Arctic marine sediment.	Baek K, Lee YM, Shin SC, Hwang K, Hwang CY, Hong SG, Lee HK	Int J Syst Evol Microbiol	10.1099/ijsem.0.000507	2015	*
Phylogeny	Pseudohalocynthiibacter aestuariivivens gen. nov., sp. nov., isolated from a tidal flat.	Won SM, Park S, Park JM, Kim BC, Yoon JH	Int J Syst Evol Microbiol	10.1099/ijs.0.000128	2015	*

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 )

#22120

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 100421

#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) .

#67771 Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;

#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 .

#89159

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-ID396584.1 )

* These data were automatically processed and therefore are not curated

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