Shewanella japonica (DSM 15915, CIP 106860, KMM 3299)

Name: Shewanella japonica (DSM 15915, CIP 106860, KMM 3299)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 14071

Type strain

Culture col. no. DSM 15915 CIP 106860 KMM 3299 LMG 19691 NBRC 103171 4 more

NCBI tax ID(s) 93973

Special Collections DSMZ JCM CIP

History DSMZ <- E. P. Ivanova CIP <- 2001, E. Ivanova, Russian Academy Sci., Vladivostok, Russia: strain KMM 3299 JCM <-- IAM 14956 <-- E. P. Ivanova KMM 3299. CIP <- 2001, E. Ivanova, Russian Academy Sci., Vladivostok, Russia: strain KMM 3299

Links

Shewanella japonica DSM 15915 is a Gram-negative, motile, rod-shaped bacterium that was isolated from seawater.

Gram-negative motile rod-shaped 16S sequence Bacteria

Name and taxonomic classification

SI-ID 13461

LMG 19691,CIP 106860,KCTC 12923,NCIMB 13823,ATCC BAA-316,IAM 14956,DSM 15915,JCM 21433,NBRC 103171

@ref 20215

Last LPSN update 2026-05-29 08:28:12

Domain Bacteria

Phylum Pseudomonadota

Class Gammaproteobacteria

Order Alteromonadales

Family Shewanellaceae

Genus Shewanella

Species Shewanella japonica

Full scientific name Shewanella japonica Ivanova et al. 2001

Synonyms (1)

Shewanella pacifica

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Motility
120315	negative	rod-shaped

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
6181	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
39595	Marine agar (MA)		Distilled water make up to (1000.000 ml);Marine agar (55.100 g)
120315	CIP Medium 13	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
6181	positive	growth	25
39595	positive	growth	30
67770	positive	growth	25
120315	positive	growth	25-30
120315	negative	growth	5
120315	negative	growth	10
120315	negative	growth	37
120315	negative	growth	41

Physiology and metabolism

Halophily

@ref	Salt	Growth	Tested relation	Concentration
120315	NaCl	positive	growth	4-10 %
120315	NaCl		growth	0 %
120315	NaCl		growth	2 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
120315	16947 ChEBI	citrate	-	carbon source
120315	4853 ChEBI	esculin	+	hydrolysis
120315	17632 ChEBI	nitrate	+	reduction
120315	16301 ChEBI	nitrite	-	reduction
120315	132112 ChEBI	sodium thiosulfate	-	builds gas from

Metabolite production

@ref	Chebi-ID	Metabolite	Production
120315	35581 ChEBI	indole

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
120315	alcohol dehydrogenase	-	1.1.1.1
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
120315	amylase	+
68382	beta-galactosidase	-	3.2.1.23	from API zym
120315	beta-galactosidase	-	3.2.1.23
68382	beta-glucosidase	-	3.2.1.21	from API zym
68382	beta-glucuronidase	-	3.2.1.31	from API zym
120315	caseinase	+	3.4.21.50
120315	catalase	+	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
120315	gelatinase	+/-
120315	lecithinase	+
68382	leucine arylamidase	+	3.4.11.1	from API zym
120315	lipase	+
68382	lipase (C 14)	-		from API zym
120315	lysine decarboxylase	-	4.1.1.18
68382	N-acetyl-beta-glucosaminidase	+	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
120315	ornithine decarboxylase	-	4.1.1.17
120315	oxidase	+
120315	protease	+
68382	trypsin	-	3.4.21.4	from API zym
120315	tryptophan deaminase	-
120315	tween esterase	+
120315	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
120315	-	+	+	+	-	+	-	-	-	+	+	+	-	-	-	-	-	+	-	-

API biotype100

@ref	ControlQ	D-glucose as carbon sourceGLU	D-fructose as carbon sourceFRU	D-galactose as carbon sourceGAL	D-trehalose as carbon sourceTRE	D-mannose as carbon sourceMNE	L-sorbose as carbon sourceSBE	D-melibiose as carbon sourceMEL	sucrose as carbon sourceSAC	D-raffinose as carbon sourceRAF	maltotriose as carbon sourceMTE	maltose as carbon sourceMAL	lactose as carbon sourceLAC	lactulose as carbon sourceLTE	1-O-methyl-beta-galactopyranoside as carbon sourceMbGa	1-O-methyl-alpha-galactopyranoside as carbon sourceMaGa	D-cellobiose as carbon sourceCEL	gentiobiose as carbon sourceGEN	1-O-methyl-beta-D-glucopyranoside as carbon sourceMbGu	esculin as carbon sourceESC	D-ribose as carbon sourceRIB	L-arabinose as carbon sourceARA	D-xylose as carbon sourceXYL	palatinose as carbon sourcePLE	L-rhamnose as carbon sourceRHA	L-fucose as carbon sourceFUC	D-melezitose as carbon sourceMLZ	D-arabitol as carbon sourceDARL	L-arabitol as carbon sourceLARL	xylitol as carbon sourceXLT	dulcitol as carbon sourceDUL	D-tagatose as carbon sourceTAG	glycerol as carbon sourceGLY	myo-inositol as carbon sourceINO	D-mannitol as carbon sourceMAN	maltitol as carbon sourceMTL	D-turanose as carbon sourceTUR	D-sorbitol as carbon sourceSOR	adonitol as carbon sourceADO	hydroxyquinoline-beta-glucuronide as carbon sourceHBG	D-lyxose as carbon sourceLYX	i-erythritol as carbon sourceERY	1-O-methyl-alpha-D-glucoside as carbon sourceMDG	3-O-methyl-D-glucose as carbon source3MDG	D-saccharate as carbon sourceSAT	mucate as carbon sourceMUC	L-tartrate as carbon sourceLTAT	D-tartrate as carbon sourceDTAT	meso-tartrate as carbon sourceMTAT	D-malate as carbon sourceDMLT	L-malate as carbon sourceLMLT	cis-aconitate as carbon sourceCATE	trans-aconitate as carbon sourceTATE	tricarballylate as carbon sourceTTE	citrate as carbon sourceCIT	D-glucuronate as carbon sourceGRT	D-galacturonate as carbon sourceGAT	2-ketogluconate as carbon source2KG	5-ketogluconate as carbon source5KG	tryptophan as carbon sourceTRY	N-acetyl-D-glucosamine as carbon sourceNAG	D-gluconate as carbon sourceGNT	phenylacetate as carbon sourcePAC	protocatechuate as carbon sourcePAT	4-hydroxybenzoate as carbon sourcepOBE	quinate as carbon sourceQAT	gentisate as carbon sourceGTE	3-hydroxybenzoate as carbon sourcemOBE	benzoate as carbon sourceBAT	3-phenylpropionate as carbon sourcePPAT	m-coumarate as carbon sourceCMT	trigonelline as carbon sourceTGE	betaine as carbon sourceBET	putrescine as carbon sourcePCE	4-aminobutyrate as carbon sourceABT	histamine as carbon sourceHIN	DL-lactate as carbon sourceLAT	caprate as carbon sourceCAP	caprylate as carbon sourceCYT	L-histidine as carbon sourceHIS	succinate as carbon sourceSUC	fumarate as carbon sourceFUM	glutarate as carbon sourceGRE	DL-glycerate as carbon sourceGYT	5-aminovalerate as carbon sourceAVT	ethanolamine as carbon sourceETN	tryptamine as carbon sourceTTN	D-glucosamine as carbon sourceGLN	itaconate as carbon sourceITA	3-hydroxybutyrate as carbon source3OBU	L-aspartate as carbon sourceAPT	L-glutamate as carbon sourceGTT	L-proline as carbon sourcePRO	D-alanine as carbon sourceDALA	L-alanine as carbon sourceLALA	L-serine as carbon sourceSER	malonate as carbon sourceMNT	propionate as carbon sourcePROP	L-tyrosine as carbon sourceTYR	2-ketoglutarate as carbon source2KT
120315	not determinedn.d.	-	+	-	-	-	-	-	-	-	-	+	-	-	-	-	+	-	-	+	-	-	+	-	-	-	-	-	-	-	-	-	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	+	-	-	-	-	-	-	+	-	-	-	-	-	-	-	+	+	-	-	+	+	+	-	-	-	+	-	+	-	-	-	+	+	-	-	-	+	-	+	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Marine

Isolation

@ref	Sample type	Country	Country ISO 3 Code	Continent	Geographic location	Isolation date
6181	seawater	Japan	JPN	Asia
67770	Seawater				Sea of Japan
120315	Environment, Sea water	Sea of Japan				1994

Taxonmaps

69479

Global distribution of 16S sequence AF145921 (>99% sequence identity) for Shewanella japonica from Microbeatlas

Aquatic Samples	2532
Soil Samples	182
Animal Samples	2105
Plant Samples	39
Total Samples	4858

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
6181	1	Risk group (German classification) According to TRBA 466
120315	1	Risk group (French classification) According to TRBA 466

Sequence information

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
20218	Shewanella sp. KMM3299 16S ribosomal RNA gene, partial sequence	AF145921	1462		93973
20218	Shewanella japonica gene for 16S rRNA, partial sequence, strain: NBRC 103171	AB681978	1406		93973

GC content

@ref	GC-content (mol%)	Method
6181	43-44
67770	43-43.8	thermal denaturation, midpoint method (Tm)

Genome-based predictions

Literature

Topic	Title	Authors	Journal	DOI	Year
	Total Synthesis of the Conjugation-Ready Tetrasaccharide Repeating Unit of Shewanella japonica Type Strain KMM 3299^T.	Ghotekar BK, Kulkarni SS.	Org Lett	10.1021/acs.orglett.4c01354	2024
	The Cultivable Surface Microbiota of the Brown Alga Ascophyllum nodosum is Enriched in Macroalgal-Polysaccharide-Degrading Bacteria.	Martin M, Barbeyron T, Martin R, Portetelle D, Michel G, Vandenbol M.	Front Microbiol	10.3389/fmicb.2015.01487	2015
	Iron cycling at corroding carbon steel surfaces.	Lee JS, McBeth JM, Ray RI, Little BJ, Emerson D.	Biofouling	10.1080/08927014.2013.836184	2013
Genetics	Structure of the O-specific polysaccharide from Shewanella japonica type strain KMM 3299T containing the rare amino sugar Fuc4NAc.	Kilcoyne M, Shashkov AS, Perepelov AV, Nazarenko EL, Gorshkova RP, Ivanova EP, Widmalm G, Savage AV	Carbohydr Res	10.1016/j.carres.2005.01.040	2005
Phylogeny	Shewanella intestini sp. nov., isolated from the intestine of abalone, Haliotis diversicolor.	Gai Y, Huang Z, Lai Q, Shao Z	Int J Syst Evol Microbiol	10.1099/ijsem.0.001878	2017
Phylogeny	Shewanella pacifica sp. nov., a polyunsaturated fatty acid-producing bacterium isolated from sea water.	Ivanova EP, Gorshkova NM, Bowman JP, Lysenko AM, Zhukova NV, Sergeev AF, Mikhailov VV, Nicolau DV	Int J Syst Evol Microbiol	10.1099/ijs.0.02993-0	2004
Phylogeny	Shewanella japonica sp. nov.	Ivanova EP, Sawabe T, Gorshkova NM, Svetashev VI, Mikhailov VV, Nicolau DV, Christen R	Int J Syst Evol Microbiol	10.1099/00207713-51-3-1027	2001

References

#6181	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 15915
#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 )
#20218	Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 )
#39595	; Curators of the CIP;
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#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 .
#120315	Collection of Institut Pasteur ; Curators of the CIP; CIP 106860
#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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Shewanella japonica (DSM 15915, CIP 106860, KMM 3299)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Halophily

Metabolite utilization

Metabolite production

Enzymes

API zym

API biotype100

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

16S sequences

GC content

Genome-based predictions

Literature

Literature

References

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