Shimia marina (DSM 26895, JCM 13038, KCCM 42117)

Name: Shimia marina (DSM 26895, JCM 13038, KCCM 42117)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 23232

Type strain

Strain Designation CL-TA03

Culture col. no. DSM 26895 JCM 13038 KCCM 42117 CL-TA03 NCIMB 14294 2 more

NCBI tax ID(s) 321267

Special Collections DSMZ JCM CIP Literature strains

History DSMZ <- JCM <- D. H. Choi; CL-TA03 JCM <-- D. H. Choi CL-TA03.

Links

Shimia marina CL-TA03 is an aerobe, Gram-negative, motile bacterium that was isolated from from biofilm in a coastal fish farm.

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

Name and taxonomic classification

SI-ID 292325

DSM 26895,JCM 13038,CIP 109331,CECT 7688,BCRC 80068

@ref 20215

Last LPSN update 2026-05-29 08:30:24

Domain Bacteria

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Rhodobacterales

Family Roseobacteraceae

Genus Shimia

Species Shimia marina

Full scientific name Shimia marina Choi and Cho 2006

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
31768	negative	0.8-3.6 µm	0.3-0.6 µm	rod-shaped
125439	negative				97.565
125438	negative				98.5

Colony morphology

19053

Incubation period1-2 days

Pigmentation

31768

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
19053	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)
19053	positive	growth	30
31768	positive	growth	15-35
31768	positive	optimum	30-35
67770	positive	growth	30

Culture pH

@ref	Ability	Type	PH	PH range
31768	positive	optimum	7
31768	positive	growth	06-10	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
31768	aerobe
125439	obligate aerobe	97.585

Spore formation

@ref	Spore formation	Confidence
31768
125439		98.894

Halophily

@ref	Salt	Growth	Tested relation	Concentration
31768	NaCl	positive	growth	03-07 %
31768	NaCl	positive	optimum	03-07 %

Observation

@ref	Observation
31768	aggregates in chains
67770	quinones: Q-10

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
31768	16947 ChEBI	citrate	+	carbon source
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
31768	16236 ChEBI	ethanol	+	carbon source
68369	5291 ChEBI	gelatin	-	hydrolysis	from API 20NE
68369	24265 ChEBI	gluconate	-	assimilation	from API 20NE
31768	15428 ChEBI	glycine	+	carbon source
31768	28087 ChEBI	glycogen	+	carbon source
68369	30849 ChEBI	L-arabinose	-	assimilation	from API 20NE
31768	25017 ChEBI	leucine	+	carbon source
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
31768	17632 ChEBI	nitrate	+	reduction
68369	17632 ChEBI	nitrate	-	reduction	from API 20NE
31768	18257 ChEBI	ornithine	+	carbon source
31768	15361 ChEBI	pyruvate	+	carbon source
31768	16634 ChEBI	raffinose	+	carbon source
31768	30031 ChEBI	succinate	+	carbon source
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
31768	alkaline phosphatase	+	3.1.3.1
68369	arginine dihydrolase	-	3.5.3.6	from API 20NE
68369	beta-glucosidase	-	3.2.1.21	from API 20NE
19053	catalase	+	1.11.1.6
31768	catalase	+	1.11.1.6
31768	cytochrome oxidase	+	1.9.3.1
19053	cytochrome-c oxidase	+	1.9.3.1
31768	gelatinase	+
68369	gelatinase	-		from API 20NE
68369	urease	-	3.5.1.5	from API 20NE

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	threonine metabolism	100	10 of 10
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	denitrification	100	2 of 2
66794	coenzyme A metabolism	100	4 of 4
66794	formaldehyde oxidation	100	3 of 3
66794	ribulose monophosphate pathway	100	2 of 2
66794	adipate degradation	100	2 of 2
66794	reductive acetyl coenzyme A pathway	100	7 of 7
66794	methylglyoxal degradation	100	5 of 5
66794	pentose phosphate pathway	100	11 of 11
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	ethanol fermentation	100	2 of 2
66794	butanoate fermentation	100	4 of 4
66794	valine metabolism	100	9 of 9
66794	CMP-KDO biosynthesis	100	4 of 4
66794	alginate biosynthesis	100	4 of 4
66794	octane oxidation	100	3 of 3
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	palmitate biosynthesis	100	22 of 22
66794	ceramide biosynthesis	100	1 of 1
66794	C4 and CAM-carbon fixation	100	8 of 8
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	Entner Doudoroff pathway	100	10 of 10
66794	folate polyglutamylation	100	1 of 1
66794	gluconeogenesis	100	8 of 8
66794	ppGpp biosynthesis	100	4 of 4
66794	suberin monomers biosynthesis	100	2 of 2
66794	phenylalanine metabolism	92.31	12 of 13
66794	leucine metabolism	92.31	12 of 13
66794	myo-inositol biosynthesis	90	9 of 10
66794	chorismate metabolism	88.89	8 of 9
66794	d-mannose degradation	88.89	8 of 9
66794	serine metabolism	88.89	8 of 9
66794	molybdenum cofactor biosynthesis	88.89	8 of 9
66794	lipid A biosynthesis	88.89	8 of 9
66794	citric acid cycle	85.71	12 of 14
66794	tetrahydrofolate metabolism	85.71	12 of 14
66794	propanol degradation	85.71	6 of 7
66794	vitamin B1 metabolism	84.62	11 of 13
66794	NAD metabolism	83.33	15 of 18
66794	degradation of aromatic, nitrogen containing compounds	83.33	10 of 12
66794	proline metabolism	81.82	9 of 11
66794	phenylacetate degradation (aerobic)	80	4 of 5
66794	ethylmalonyl-CoA pathway	80	4 of 5
66794	peptidoglycan biosynthesis	80	12 of 15
66794	vitamin B12 metabolism	79.41	27 of 34
66794	alanine metabolism	79.31	23 of 29
66794	purine metabolism	78.72	74 of 94
66794	glutamate and glutamine metabolism	78.57	22 of 28
66794	heme metabolism	78.57	11 of 14
66794	photosynthesis	78.57	11 of 14
66794	allantoin degradation	77.78	7 of 9
66794	CO2 fixation in Crenarchaeota	77.78	7 of 9
66794	lactate fermentation	75	3 of 4
66794	isoleucine metabolism	75	6 of 8
66794	acetate fermentation	75	3 of 4
66794	carnitine metabolism	75	6 of 8
66794	biotin biosynthesis	75	3 of 4
66794	pyrimidine metabolism	73.33	33 of 45
66794	methionine metabolism	73.08	19 of 26
66794	vitamin B6 metabolism	72.73	8 of 11
66794	cysteine metabolism	72.22	13 of 18
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	ubiquinone biosynthesis	71.43	5 of 7
66794	glutathione metabolism	71.43	10 of 14
66794	tyrosine metabolism	71.43	10 of 14
66794	glycolysis	70.59	12 of 17
66794	propionate fermentation	70	7 of 10
66794	tryptophan metabolism	68.42	26 of 38
66794	oxidative phosphorylation	68.13	62 of 91
66794	methane metabolism	66.67	2 of 3
66794	cyanate degradation	66.67	2 of 3
66794	glycolate and glyoxylate degradation	66.67	4 of 6
66794	flavin biosynthesis	66.67	10 of 15
66794	arginine metabolism	66.67	16 of 24
66794	lysine metabolism	66.67	28 of 42
66794	acetoin degradation	66.67	2 of 3
66794	IAA biosynthesis	66.67	2 of 3
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	aspartate and asparagine metabolism	66.67	6 of 9
66794	non-pathway related	65.79	25 of 38
66794	lipid metabolism	64.52	20 of 31
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
66794	ketogluconate metabolism	62.5	5 of 8
66794	dTDPLrhamnose biosynthesis	62.5	5 of 8
66794	factor 420 biosynthesis	60	3 of 5
66794	metabolism of amino sugars and derivatives	60	3 of 5
66794	glycine betaine biosynthesis	60	3 of 5
66794	4-hydroxyphenylacetate degradation	60	6 of 10
66794	nitrate assimilation	55.56	5 of 9
66794	histidine metabolism	55.17	16 of 29
66794	urea cycle	53.85	7 of 13
66794	sulfate reduction	53.85	7 of 13
66794	3-phenylpropionate degradation	53.33	8 of 15
66794	polyamine pathway	52.17	12 of 23
66794	sulfopterin metabolism	50	2 of 4
66794	pantothenate biosynthesis	50	3 of 6
66794	glycine metabolism	50	5 of 10
66794	coenzyme M biosynthesis	50	5 of 10
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	glycogen biosynthesis	50	2 of 4
66794	degradation of sugar alcohols	50	8 of 16
66794	toluene degradation	50	2 of 4
66794	cyclohexanol degradation	50	2 of 4
66794	quinate degradation	50	1 of 2
66794	ascorbate metabolism	50	11 of 22
66794	phenylmercury acetate degradation	50	1 of 2
66794	selenocysteine biosynthesis	50	3 of 6
66794	degradation of sugar acids	48	12 of 25
66794	bile acid biosynthesis, neutral pathway	47.06	8 of 17
66794	d-xylose degradation	45.45	5 of 11
66794	metabolism of disaccharids	45.45	5 of 11
66794	4-hydroxymandelate degradation	44.44	4 of 9
66794	aclacinomycin biosynthesis	42.86	3 of 7
66794	degradation of pentoses	42.86	12 of 28
66794	mevalonate metabolism	42.86	3 of 7
66794	vitamin K metabolism	40	2 of 5
66794	lipoate biosynthesis	40	2 of 5
66794	hydrogen production	40	2 of 5
66794	D-cycloserine biosynthesis	40	2 of 5
66794	glycogen metabolism	40	2 of 5
66794	gallate degradation	40	2 of 5
66794	arachidonate biosynthesis	40	2 of 5
66794	phenol degradation	40	8 of 20
66794	isoprenoid biosynthesis	38.46	10 of 26
66794	androgen and estrogen metabolism	37.5	6 of 16
66794	degradation of hexoses	33.33	6 of 18
66794	sulfoquinovose degradation	33.33	1 of 3
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	arachidonic acid metabolism	33.33	6 of 18
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	sphingosine metabolism	33.33	2 of 6
66794	benzoyl-CoA degradation	28.57	2 of 7

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
19053	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	not determinedn.d.

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Food production	#Aquaculture
#Environmental	#Biofilm	-
#Host	#Fishes	-

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
19053	from biofilm in a coastal fish farm	Tongyeong	Republic of Korea	KOR	Asia
67770	Biofilm in a coastal fish farm in Tongyeong		Republic of Korea	KOR	Asia

Taxonmaps

69479

Global distribution of 16S sequence AY962292 (>99% sequence identity) for Shimia marina from Microbeatlas

Aquatic Samples	1469
Soil Samples	16
Animal Samples	141
Plant Samples	4
Total Samples	1630

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
19053	1	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	IMG-taxon 2619618961 annotated assembly for Shimia marina DSM 26895	scaffold	GCA_900112745	321267.13	2619618961	321267	71.95

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
19053	Shimia marina strain CL-TA03 16S ribosomal RNA gene, partial sequence	AY962292	1382		321267
124043	Shimia marina strain DSM 26895 16S ribosomal RNA gene, partial sequence.	MW198135	601		321267

GC content

@ref	GC-content (mol%)	Method
19053	57.2	high performance liquid chromatography (HPLC)
31768	57.2

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: IMG-taxon 2619618961 annotated assembly for Shimia marina DSM 26895
NCBI: GCA_900112745

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	97.59	no
125439	gram_stain	BacteriaNetⓘ	negative	97.57	no
125439	motility	BacteriaNetⓘ	yes	59.17	no
125439	spore_formation	BacteriaNetⓘ	no	98.89	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Shimia marina DSM 26895
NCBI: GCA_900112745.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	98.50	yes
125438	anaerobic	anaerobicⓘ	no	94.42	no
125438	aerobic	aerobicⓘ	yes	82.31	no
125438	spore-forming	spore-formingⓘ	no	88.87	yes
125438	thermophilic	thermophileⓘ	no	97.00	yes
125438	flagellated	motile2+ⓘ	yes	57.39	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Metabolism	Transporter characterisation reveals aminoethylphosphonate mineralisation as a key step in the marine phosphorus redox cycle.	Murphy ARJ, Scanlan DJ, Chen Y, Adams NBP, Cadman WA, Bottrill A, Bending G, Hammond JP, Hitchcock A, Wellington EMH, Lidbury IDEA.	Nat Commun	10.1038/s41467-021-24646-z	2021
Metabolism	Genome sequence of Shimia str. SK013, a representative of the Roseobacter group isolated from marine sediment.	Kanukollu S, Voget S, Pohlner M, Vandieken V, Petersen J, Kyrpides NC, Woyke T, Shapiro N, Goker M, Klenk HP, Cypionka H, Engelen B.	Stand Genomic Sci	10.1186/s40793-016-0143-0	2016
Genetics	Draft genome sequence of Shimia marina CECT 7688(T).	Rodrigo-Torres L, Pujalte MJ, Arahal DR	Mar Genomics	10.1016/j.margen.2016.01.006	2016
	Shimia ponticola sp. nov., an aerobic anoxygenic photoheterotrophic bacterium, isolated from surface seawater in the South China Sea.	Chen Q, He B, Lin TH, Jiao N, Zheng Q.	Int J Syst Evol Microbiol	10.1099/ijsem.0.005859	2023
Phylogeny	Shimia biformata sp. nov., isolated from surface seawater, and emended description of the genus Shimia Choi and Cho 2006.	Hameed A, Shahina M, Lin SY, Lai WA, Hsu YH, Liu YC, Huang YM, Young CC	Int J Syst Evol Microbiol	10.1099/ijs.0.053553-0	2013
Phylogeny	Shimia isoporae sp. nov., isolated from the reef-building coral Isopora palifera.	Chen MH, Sheu SY, Chen CA, Wang JT, Chen WM	Int J Syst Evol Microbiol	10.1099/ijs.0.022848-0	2010
Phylogeny	Shimia marina gen. nov., sp. nov., a novel bacterium of the Roseobacter clade isolated from biofilm in a coastal fish farm.	Choi DH, Cho BC	Int J Syst Evol Microbiol	10.1099/ijs.0.64235-0	2006

References

#19053	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 26895
#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 )
#28041	IJSEM 1869 2006 ( DOI 10.1099/ijs.0.64235-0 , PubMed 16902023 )
#31768	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 #28041
#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) .
#66794	Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg: BRENDA, the ELIXIR core data resource in 2021: new developments and updates. Nucleic Acids Res. 49: D498 - D508 2020 ( DOI 10.1093/nar/gkaa1025 , PubMed 33211880 )
#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 .
#125438	Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 )
#125439	Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy: deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 .
#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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Shimia marina (DSM 26895, JCM 13038, KCCM 42117)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Observation

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

Pathway annotation

API 20NE

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_900112745

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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