Simiduia litorea (DSM 29670, JCM 19759, KMM 9504)

Name: Simiduia litorea (DSM 29670, JCM 19759, KMM 9504)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 130812

Type strain

Culture col. no. DSM 29670 JCM 19759 KMM 9504 NRIC 0917

NCBI tax ID(s) 1435348

Special Collections DSMZ JCM

History <- N. Tanaka, NODAI Culture Collection Centre, Tokyo University of Agriculture <- L. A. Romanenko, G.B. Eliakov Pacific Institute of Bioorganic Chemistry, Vladivostoc NRIC 0917 <-- L. A. Romanenko KMM 9504.

Links

Simiduia litorea DSM 29670 is a bacterium that was isolated from seashore sediment, water depth 0.5 m.

genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 407029

JCM 19759,DSM 29670

@ref 20215

Last LPSN update 2026-02-09 11:31:19

Domain Bacteria

Phylum Pseudomonadota

Class Gammaproteobacteria

Order Cellvibrionales

Family Cellvibrionaceae

Genus Simiduia

Species Simiduia litorea

Full scientific name Simiduia litorea Tanaka et al. 2014

Morphology

Multimedia

@ref:	22064
multimedia content:	DSM_29670.jpg
multimedia.multimedia content:	https://www.dsmz.de/microorganisms/photos/DSM_29670.jpg
intellectual property rights:	© Leibniz-Institut DSMZ
manual_annotation:	1

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
22064	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)
22064	positive	growth	28
67770	positive	growth	28

Physiology and metabolism

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68369	17128 ChEBI	adipate	-	assimilation	from API 20NE
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
68369	24265 ChEBI	gluconate	-	assimilation	from API 20NE
68369	30849 ChEBI	L-arabinose	+	assimilation	from API 20NE
68369	25115 ChEBI	malate	-	assimilation	from API 20NE
68369	17306 ChEBI	maltose	+	assimilation	from API 20NE
68369	59640 ChEBI	N-acetylglucosamine	+	assimilation	from API 20NE
68369	17632 ChEBI	nitrate	-	reduction	from API 20NE
68369	27897 ChEBI	tryptophan	-	energy source	from API 20NE
68369	16199 ChEBI	urea	-	hydrolysis	from API 20NE

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
68369	arginine dihydrolase	-	3.5.3.6	from API 20NE
68369	beta-glucosidase	+	3.2.1.21	from API 20NE
68369	cytochrome oxidase	+	1.9.3.1	from API 20NE
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
22064	-	-	-	-	-	+	-	-	+	+	-	+	+	+	-	-	-	-	-	-	+

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	-
#Environmental	#Terrestrial	#Coast
#Environmental	#Terrestrial	#Sediment

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
22064	seashore sediment, water depth 0.5 m	Sea of Japan	Russia	RUS	Asia
67770	Sediment from the seashore of the Sea of Japan, at a water depth of 0.5 m		Russia	RUS

Taxonmaps

69479

Global distribution of 16S sequence AB894237 (>99% sequence identity) for Simiduia from Microbeatlas

Aquatic Samples	1602
Soil Samples	40
Animal Samples	45
Plant Samples	6
Total Samples	1693

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
22064	1	Risk group (German classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	NCBI tax ID	Score
124043	ASM4285346v1 assembly for Simiduia litorea KMM 9504	complete	GCA_042853465	1435348	99.61

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
22064	Simiduia litorea gene for 16S ribosomal RNA, partial sequence	AB894237	1506		1435348

Genome-based predictions

Literature

Topic	Title	Authors	Journal	DOI	Year
	Complete genome sequencing of four marine bacteria, Gilvimarinus japonicus NBRC 111987^T, Halioxenophilus aromaticivorans JCM 19134^T, Maricurvus nonylphenolicus JCM 17778^T, and Simiduia litorea JCM 19759^T belonging to the family Cellvibrionaceae.	Miura T, Miyakawa T, Kusuya Y, Kamino K.	Microbiol Resour Announc	10.1128/mra.00873-24	2024
	Structure of 3,6-dideoxy-3-[(R)-2-hydroxypropanoylamino]-D-galactose-containing O-polysaccharide from marine bacterium Simiduia litorea KMM 9504(T).	Kokoulin MS, Romanenko LA, Mikhailov VV	Carbohydr Res	10.1016/j.carres.2018.03.010	2018
Phylogeny	Simiduia curdlanivorans sp. nov., a curdlan-degrading bacterium isolated from the junction between the ocean and a freshwater spring, and emended description of the genus Simiduia.	Park S, Kim SI, Jung YT, Yoon JH	Int J Syst Evol Microbiol	10.1099/ijs.0.065334-0	2014
Phylogeny	Simiduia litorea sp. nov., isolated from seashore sediments of the Sea of Japan.	Tanaka N, Romanenko LA, Svetashev VI, Mikhailov VV	Int J Syst Evol Microbiol	10.1099/ijs.0.061846-0	2014

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 )
#22064	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 29670
#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 .
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#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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Simiduia litorea (DSM 29670, JCM 19759, KMM 9504)

Name and taxonomic classification

Morphology

Multimedia

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

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_042853465

16S sequences

Genome-based predictions

Literature

Literature

References

BacDive

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