Name: Gilvimarinus japonicus 12-2
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 133296

Type strain:

Species: Gilvimarinus japonicus

Strain Designation: 12-2

Culture col. no.: DSM 102813, KCTC 52141, NBRC 111987

Strain history: <- K. Fujii, Yamaguchi University, Fac. of Agriculture; 12-2

NCBI tax ID(s): 1796469 (species)

SI-ID 408101

DSM 102813

Other strains from Gilvimarinus japonicus

G. japonicus

Section

Gilvimarinus japonicus 12-2 is a Gram-negative, motile, rod-shaped bacterium that was isolated from piece of cotton rope fragment washed ashore on a beach.

Gram-negative
motile
rod-shaped
16S sequence
Bacteria

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	*Gammaproteobacteria*
	Order	*Cellvibrionales*
	Family	*Cellvibrionaceae*
	Genus	*Gilvimarinus*
	Species	**Gilvimarinus japonicus**
	Full Scientific Name (LPSN)	Gilvimarinus japonicus Kouzui et al. 2016

Information on morphological and physiological properties Morphology

[Ref.: #25070]	Gram stain	negative

[Ref.: #25070]	Cell length	1.5-2.0 µm

[Ref.: #25070]	Cell width	0.3-0.5 µm

[Ref.: #25070]	Cell shape	rod-shaped

[Ref.: #25070]	Motility	yes

[Ref.: #25070]	Flagellum arrangement	monotrichous, polar

[Ref.: #25070]	Colony color	dark ivory
[Ref.: #25070]	Cultivation medium used	marine agar 2216

Information on culture and growth conditions Culture and growth conditions

[Ref.: #25070]

Culture medium

Marine agar (MA)

[Ref.: #25070]

Culture medium growth

[Ref.: #42856]

Culture medium

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

[Ref.: #42856]

Culture medium growth

[Ref.: #42856]

Culture medium link

Medium recipe at MediaDive

[Ref.: #42856]

Culture medium composition

expand / minimize

	Kind of temperature		Temperature
[Ref.: #25070]		growth	10.0-35.0 °C
[Ref.: #25070]		growth	30 °C
[Ref.: #25070]		growth	25 °C
[Ref.: #25070]		growth	20 °C
[Ref.: #25070]		growth	15 °C
[Ref.: #25070]		growth	10 °C
[Ref.: #25070]	no	growth	37 °C
[Ref.: #25070]	no	growth	4 °C
[Ref.: #25070]		optimum	28.0-30.0 °C
[Ref.: #42856]		growth	28 °C

[Ref.: #25070]	Temperature range	mesophilic
[Ref.: #25070]	Temperature range	psychrophilic
[Ref.: #25070]	Temperature range	mesophilic
[Ref.: #25070]	Temperature range	psychrophilic
[Ref.: #25070]	Temperature range	mesophilic
[Ref.: #42856]	Temperature range	mesophilic

	Kind of pH		pH
[Ref.: #25070]		optimum	7.5-8.0
[Ref.: #25070]		growth	6.0-9.5
[Ref.: #25070]	no	growth	5
[Ref.: #25070]	no	growth	10

Information on physiology and metabolism Physiology and metabolism

	Salt	Tested relation		Salt conc.
[Ref.: #25070]	NaCl		optimum	2.0-3.0	%
[Ref.: #25070]	NaCl		growth	0.0-12.0	%(w/v)
[Ref.: #25070]	NaCl	no	growth	10	%(w/v)
[Ref.: #25070]	NaCl	no	growth	15	%(w/v)

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #25070]	2-dehydro-D-gluconate ChEBI	+	builds acid from
[Ref.: #25070]	4-nitrophenyl beta-D-galactopyranoside ChEBI	+	hydrolysis
[Ref.: #25070]	5-dehydro-D-gluconate ChEBI	-	builds acid from
[Ref.: #25070]	adipate ChEBI	-	assimilation
[Ref.: #25070]	amygdalin ChEBI	+	builds acid from
[Ref.: #25070]	arabinose ChEBI	-	assimilation
[Ref.: #25070]	arbutin ChEBI	+	builds acid from
[Ref.: #25070]	cellobiose ChEBI	+	builds acid from
[Ref.: #25070]	citrate ChEBI	-	assimilation
[Ref.: #25070]	D-arabinose ChEBI	-	builds acid from
[Ref.: #25070]	D-arabitol ChEBI	-	builds acid from
[Ref.: #25070]	D-fructose ChEBI	-	builds acid from
[Ref.: #25070]	D-fucose ChEBI	-	builds acid from
[Ref.: #25070]	D-galactose ChEBI	+	builds acid from
[Ref.: #25070]	D-gluconate ChEBI	-	builds acid from
[Ref.: #25070]	D-glucose ChEBI	-	fermentation
[Ref.: #25070]	D-glucose ChEBI	+	builds acid from
[Ref.: #25070]	D-lyxose ChEBI	-	builds acid from
[Ref.: #25070]	D-mannitol ChEBI	-	builds acid from
[Ref.: #25070]	D-mannose ChEBI	-	builds acid from
[Ref.: #25070]	D-ribose ChEBI	-	builds acid from
[Ref.: #25070]	D-sorbitol ChEBI	-	builds acid from
[Ref.: #25070]	D-tagatose ChEBI	-	builds acid from
[Ref.: #25070]	D-xylose ChEBI	+	builds acid from
[Ref.: #25070]	decanoate ChEBI	-	assimilation
[Ref.: #25070]	erythritol ChEBI	-	builds acid from
[Ref.: #25070]	esculin ChEBI	+	hydrolysis
[Ref.: #25070]	esculin ferric citrate	+	builds acid from
[Ref.: #25070]	galactitol ChEBI	-	builds acid from
[Ref.: #25070]	gelatin ChEBI	-	hydrolysis
[Ref.: #25070]	gentiobiose ChEBI	+	builds acid from
[Ref.: #25070]	gluconate ChEBI	-	assimilation
[Ref.: #25070]	glucose ChEBI	-	assimilation
[Ref.: #25070]	glycerol ChEBI	-	builds acid from
[Ref.: #25070]	glycogen ChEBI	+	builds acid from
[Ref.: #25070]	inulin ChEBI	-	builds acid from
[Ref.: #25070]	L-arabinose ChEBI	+	builds acid from
[Ref.: #25070]	L-arabitol ChEBI	-	builds acid from
[Ref.: #25070]	L-fucose ChEBI	-	builds acid from
[Ref.: #25070]	L-rhamnose ChEBI	-	builds acid from
[Ref.: #25070]	L-sorbose ChEBI	-	builds acid from
[Ref.: #25070]	L-xylose ChEBI	-	builds acid from
[Ref.: #25070]	lactose ChEBI	-	builds acid from
[Ref.: #25070]	malate ChEBI	-	assimilation
[Ref.: #25070]	maltose ChEBI	-	assimilation
[Ref.: #25070]	maltose ChEBI	+	builds acid from
[Ref.: #25070]	mannitol ChEBI	-	assimilation
[Ref.: #25070]	mannose ChEBI	+	assimilation
[Ref.: #25070]	melezitose ChEBI	-	builds acid from
[Ref.: #25070]	melibiose ChEBI	+	builds acid from
[Ref.: #25070]	methyl alpha-D-glucopyranoside ChEBI	-	builds acid from
[Ref.: #25070]	methyl alpha-D-mannoside ChEBI	-	builds acid from
[Ref.: #25070]	methyl beta-D-xylopyranoside ChEBI	+	builds acid from
[Ref.: #25070]	myo-inositol ChEBI	-	builds acid from
[Ref.: #25070]	N-acetylglucosamine ChEBI	+	assimilation
[Ref.: #25070]	N-acetylglucosamine ChEBI	+	builds acid from
[Ref.: #25070]	nitrate ChEBI	-	reduction
[Ref.: #25070]	phenylacetate ChEBI	-	assimilation
[Ref.: #25070]	raffinose ChEBI	-	builds acid from
[Ref.: #25070]	ribitol ChEBI	-	builds acid from
[Ref.: #25070]	salicin ChEBI	+	builds acid from
[Ref.: #25070]	starch ChEBI	+	builds acid from
[Ref.: #25070]	sucrose ChEBI	-	builds acid from
[Ref.: #25070]	trehalose ChEBI	-	builds acid from
[Ref.: #25070]	tryptophan ChEBI	-	energy source
[Ref.: #25070]	turanose ChEBI	-	builds acid from
[Ref.: #25070]	xylitol ChEBI	-	builds acid from
	Only first 10 entries are displayed. Click here to see all.

	Metabolite	Antibiotic sensitivity	Antibiotic resistance
[Ref.: #25070]	amikacin ChEBI		yes
[Ref.: #25070]	amoxicillin ChEBI	yes
[Ref.: #25070]	ampicillin ChEBI	yes
[Ref.: #25070]	carbenicillin ChEBI		yes
[Ref.: #25070]	chloramphenicol ChEBI	yes
[Ref.: #25070]	ciprofloxacin ChEBI	yes
[Ref.: #25070]	erythromycin ChEBI	yes
[Ref.: #25070]	gentamicin ChEBI	yes
[Ref.: #25070]	kanamycin ChEBI	yes
[Ref.: #25070]	lincomycin ChEBI		yes
[Ref.: #25070]	nalidixic acid ChEBI	yes
[Ref.: #25070]	neomycin ChEBI	yes
[Ref.: #25070]	norfloxacin ChEBI	yes
[Ref.: #25070]	novobiocin ChEBI	yes
[Ref.: #25070]	penicillin g ChEBI		yes
[Ref.: #25070]	polymyxin ChEBI	yes
[Ref.: #25070]	streptomycin ChEBI	yes
[Ref.: #25070]	sulfamethoxazole ChEBI	yes
[Ref.: #25070]	tetracycline ChEBI	yes
[Ref.: #25070]	trimethoprim ChEBI		yes
[Ref.: #25070]	vancomycin ChEBI		yes
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #25070]		indole ChEBI	no

	Physiological tests	Metabolite	Indole test
[Ref.: #25070]		indole ChEBI	-

	Enzyme	Enzyme activity	EC number
[Ref.: #25070]	arginine dihydrolase	-	3.5.3.6
[Ref.: #25070]	catalase	+	1.11.1.6
[Ref.: #25070]	cytochrome oxidase	+	1.9.3.1
[Ref.: #25070]	gelatinase	-
[Ref.: #25070]	tryptophan deaminase	-	4.1.99.1
[Ref.: #25070]	urease	+	3.5.1.5

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

[Ref.: #25070]	Sample type/isolated from	piece of cotton rope fragment washed ashore on a beach
[Ref.: #25070]	Geographic location (country and/or sea, region)	Yamaguchi
[Ref.: #25070]	Country	Japan
[Ref.: #25070]	Country ISO 3 Code	JPN
[Ref.: #25070]	Continent	Asia
[Ref.: #25070]	Geographic location	34.4000°/131.3830°
[Ref.: #25070]	Enrichment culture	autoclaved artificial seawater
[Ref.: #25070]	Enrichment culture composition	1.0 g of Whatman no. 7 filter paper (sole carbon source)
[Ref.: #25070]	Enrichment culture duration	14 days
[Ref.: #25070]	Enrichment culture temperature	23 ̊C
[Ref.: #25070]	Isolation/enrichment procedure	120 r.p.m

[Ref.: #42856]	Sample type/isolated from	cotten rope fragment washed ashore on a beach
[Ref.: #42856]	Geographic location (country and/or sea, region)	Yamaguchi Prefecture, Hagi city (34° 24' N 131° 23' E)
[Ref.: #42856]	Country	Japan
[Ref.: #42856]	Country ISO 3 Code	JPN
[Ref.: #42856]	Continent	Asia
[Ref.: #42856]	Geographic location	34.4000°/131.3830°
* marker position based on {}

Isolation sources categories

#Engineered	#Industrial	#Engineered product
#Environmental	#Terrestrial	#Coast

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence LC125208 (>99% sequence identity) for Gilvimarinus japonicus from Microbeatlas

Aquatic Samples	44
Soil Samples
Animal Samples	12
Plant Samples	2
Total Samples	58

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

[Ref.: #42856]

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.: #42856]	Gilvimarinus sp. KF-2016-12-2 gene for 16S ribosomal RNA, partial sequence, strain: 12-2	LC125208	1422	ENA	1796469 tax ID

[Ref.: #42856]

GC-content

52.3 mol%

high performance liquid chromatography (HPLC)

Availability in culture collections External links

[Ref.: #42856]

Culture collection no.

DSM 102813, KCTC 52141, NBRC 111987

[Ref.: #91406]

SI-ID 408101

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Gilvimarinus japonicus sp. nov., a cellulolytic and agarolytic marine bacterium isolated from coastal debris.	Kouzui H, Tokikawa K, Satomi M, Negoro T, Shimabukuro K, Fujii K	Int J Syst Evol Microbiol	10.1099/ijsem.0.001534	2016	*

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 )

#25070

H. T. Kouzui, K.,Satomi, M.,Negoro, T.,Shimabukuro, K.,Fujii, K.: Gilvimarinus japonicus sp. nov., a cellulolytic and agarolytic marine bacterium isolated from coastal debris. IJSEM 66: 5417 - 5423 2016 ( DOI 10.1099/ijsem.0.001534 , PubMed 27692037 )

#42856

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 102813

#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 .

#91406

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-ID408101.1 )

* These data were automatically processed and therefore are not curated

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