Shimia aestuarii (DSM 15283, KCTC 12049, JC2049)

Name: Shimia aestuarii (DSM 15283, KCTC 12049, JC2049)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 13803

Type strain

Strain Designation JC2049

Culture col. no. DSM 15283 KCTC 12049 JC2049 IMSNU 14011 JCM 14332

NCBI tax ID(s) 254406

Special Collections DSMZ JCM KCTC

Links

Shimia aestuarii JC2049 is an aerobe, mesophilic, Gram-negative prokaryote that was isolated from sediment sample of getbol.

Gram-negative aerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 127389

DSM 15283,KCTC12049,JCM 14332,CECT 8650

@ref 20215

Last LPSN update 2025-12-16 09:50:11

Domain Pseudomonadati

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Rhodobacterales

Family Roseobacteraceae

Genus Shimia

Species Shimia aestuarii

Full scientific name Shimia aestuarii (Yi and Chun 2007) Wirth and Whitman 2018

Synonyms (2)

Thalassovita aestuarii
Thalassobius aestuarii

Morphology

Cell morphology

@ref	Gram stain	Confidence
67771	negative
125438	negative	97.333
125439	negative	93.2

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
5792	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)	Range
5792	positive	growth	35	mesophilic
67770	positive	growth	30	mesophilic
67771	positive	growth	28	mesophilic

Physiology and metabolism

Oxygen tolerance

67771

Oxygen toleranceaerobe

Spore formation

@ref	Spore formation	Confidence
125438		94.645

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	valine metabolism	100	9 of 9
66794	phenylacetate degradation (aerobic)	100	5 of 5
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	ethylmalonyl-CoA pathway	100	5 of 5
66794	gallate degradation	100	5 of 5
66794	adipate degradation	100	2 of 2
66794	CMP-KDO biosynthesis	100	4 of 4
66794	threonine metabolism	100	10 of 10
66794	ethanol fermentation	100	2 of 2
66794	octane oxidation	100	3 of 3
66794	molybdenum cofactor biosynthesis	100	9 of 9
66794	ppGpp biosynthesis	100	4 of 4
66794	palmitate biosynthesis	100	22 of 22
66794	butanoate fermentation	100	4 of 4
66794	reductive acetyl coenzyme A pathway	100	7 of 7
66794	ribulose monophosphate pathway	100	2 of 2
66794	C4 and CAM-carbon fixation	100	8 of 8
66794	denitrification	100	2 of 2
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	methylglyoxal degradation	100	5 of 5
66794	suberin monomers biosynthesis	100	2 of 2
66794	ceramide biosynthesis	100	1 of 1
66794	folate polyglutamylation	100	1 of 1
66794	taurine degradation	100	1 of 1
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	formaldehyde oxidation	100	3 of 3
66794	coenzyme A metabolism	100	4 of 4
66794	gluconeogenesis	100	8 of 8
66794	citric acid cycle	92.86	13 of 14
66794	degradation of aromatic, nitrogen containing compounds	91.67	11 of 12
66794	propionate fermentation	90	9 of 10
66794	serine metabolism	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	CO2 fixation in Crenarchaeota	88.89	8 of 9
66794	allantoin degradation	88.89	8 of 9
66794	leucine metabolism	84.62	11 of 13
66794	phenylalanine metabolism	84.62	11 of 13
66794	NAD metabolism	83.33	15 of 18
66794	vitamin B12 metabolism	82.35	28 of 34
66794	glutamate and glutamine metabolism	82.14	23 of 28
66794	pentose phosphate pathway	81.82	9 of 11
66794	proline metabolism	81.82	9 of 11
66794	peptidoglycan biosynthesis	80	12 of 15
66794	Entner Doudoroff pathway	80	8 of 10
66794	hydrogen production	80	4 of 5
66794	alanine metabolism	79.31	23 of 29
66794	tyrosine metabolism	78.57	11 of 14
66794	heme metabolism	78.57	11 of 14
66794	photosynthesis	78.57	11 of 14
66794	aspartate and asparagine metabolism	77.78	7 of 9
66794	lipid A biosynthesis	77.78	7 of 9
66794	purine metabolism	77.66	73 of 94
66794	tryptophan metabolism	76.32	29 of 38
66794	dTDPLrhamnose biosynthesis	75	6 of 8
66794	isoleucine metabolism	75	6 of 8
66794	biotin biosynthesis	75	3 of 4
66794	acetate fermentation	75	3 of 4
66794	arginine metabolism	75	18 of 24
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	phenol degradation	75	15 of 20
66794	glycogen biosynthesis	75	3 of 4
66794	carnitine metabolism	75	6 of 8
66794	sulfopterin metabolism	75	3 of 4
66794	3-phenylpropionate degradation	73.33	11 of 15
66794	propanol degradation	71.43	5 of 7
66794	glutathione metabolism	71.43	10 of 14
66794	ubiquinone biosynthesis	71.43	5 of 7
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	glycolysis	70.59	12 of 17
66794	4-hydroxyphenylacetate degradation	70	7 of 10
66794	lysine metabolism	69.05	29 of 42
66794	pyrimidine metabolism	68.89	31 of 45
66794	non-pathway related	68.42	26 of 38
66794	lipid metabolism	67.74	21 of 31
66794	flavin biosynthesis	66.67	10 of 15
66794	d-mannose degradation	66.67	6 of 9
66794	4-hydroxymandelate degradation	66.67	6 of 9
66794	cyanate degradation	66.67	2 of 3
66794	IAA biosynthesis	66.67	2 of 3
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	glycolate and glyoxylate degradation	66.67	4 of 6
66794	(5R)-carbapenem carboxylate biosynthesis	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	methane metabolism	66.67	2 of 3
66794	histidine metabolism	65.52	19 of 29
66794	methionine metabolism	65.38	17 of 26
66794	tetrahydrofolate metabolism	64.29	9 of 14
66794	ketogluconate metabolism	62.5	5 of 8
66794	vitamin B1 metabolism	61.54	8 of 13
66794	cysteine metabolism	61.11	11 of 18
66794	factor 420 biosynthesis	60	3 of 5
66794	coenzyme M biosynthesis	60	6 of 10
66794	myo-inositol biosynthesis	60	6 of 10
66794	lipoate biosynthesis	60	3 of 5
66794	3-chlorocatechol degradation	60	3 of 5
66794	oxidative phosphorylation	59.34	54 of 91
66794	isoprenoid biosynthesis	57.69	15 of 26
66794	nitrate assimilation	55.56	5 of 9
66794	vitamin B6 metabolism	54.55	6 of 11
66794	urea cycle	53.85	7 of 13
66794	sulfate reduction	53.85	7 of 13
66794	degradation of pentoses	53.57	15 of 28
66794	bile acid biosynthesis, neutral pathway	52.94	9 of 17
66794	polyamine pathway	52.17	12 of 23
66794	quinate degradation	50	1 of 2
66794	cyclohexanol degradation	50	2 of 4
66794	selenocysteine biosynthesis	50	3 of 6
66794	pantothenate biosynthesis	50	3 of 6
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	starch degradation	50	5 of 10
66794	glycine metabolism	50	5 of 10
66794	arachidonic acid metabolism	50	9 of 18
66794	phenylmercury acetate degradation	50	1 of 2
66794	degradation of sugar alcohols	43.75	7 of 16
66794	androgen and estrogen metabolism	43.75	7 of 16
66794	benzoyl-CoA degradation	42.86	3 of 7
66794	metabolism of amino sugars and derivatives	40	2 of 5
66794	glycogen metabolism	40	2 of 5
66794	creatinine degradation	40	2 of 5
66794	glycine betaine biosynthesis	40	2 of 5
66794	D-cycloserine biosynthesis	40	2 of 5
66794	vitamin K metabolism	40	2 of 5
66794	arachidonate biosynthesis	40	2 of 5
66794	degradation of sugar acids	40	10 of 25
66794	degradation of hexoses	38.89	7 of 18
66794	d-xylose degradation	36.36	4 of 11
66794	metabolism of disaccharids	36.36	4 of 11
66794	sphingosine metabolism	33.33	2 of 6
66794	enterobactin biosynthesis	33.33	1 of 3
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	sulfoquinovose degradation	33.33	1 of 3
66794	phosphatidylethanolamine bioynthesis	30.77	4 of 13
66794	aclacinomycin biosynthesis	28.57	2 of 7
66794	ascorbate metabolism	27.27	6 of 22
66794	catecholamine biosynthesis	25	1 of 4
66794	alginate biosynthesis	25	1 of 4
66794	lactate fermentation	25	1 of 4
66794	toluene degradation	25	1 of 4
66794	chlorophyll metabolism	22.22	4 of 18

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Sediment
#Environmental	#Terrestrial	#Tidal flat

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
5792	sediment sample of getbol	Korea, Ganghwa island	Republic of Korea	KOR	Asia
67770	Sediment sample of tidal flat	Ganghwa Island	Republic of Korea	KOR	Asia
67771	From a tidal flat sediment sample		Republic of Korea	KOR	Asia

Taxonmaps

69479

Global distribution of 16S sequence AY442178 (>99% sequence identity) for Shimia from Microbeatlas

Aquatic Samples	348
Soil Samples	22
Animal Samples	17
Plant Samples	2
Total Samples	389

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
5792	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
67770	IMG-taxon 2616644822 annotated assembly for Shimia aestuarii DSM 15283	contig	GCA_900114635	254406.10	2616644822	254406	74.33

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
20218	Thalassobius aestuarii strain JC2049 16S ribosomal RNA gene, partial sequence	AY442178	1386		254406

GC content

@ref	GC-content (mol%)	Method
67770	61	high performance liquid chromatography (HPLC)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Shimia aestuarii DSM 15283
NCBI: GCA_900114635

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	83.70	no
125439	motility	BacteriaNetⓘ	yes	67.00	no
125439	gram_stain	BacteriaNetⓘ	negative	93.20	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	87.40	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Shimia aestuarii strain DSM 15283
PATRIC: 254406.10

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	97.33	yes
125438	anaerobic	anaerobicⓘ	no	91.92	yes
125438	spore-forming	spore-formingⓘ	no	94.65	no
125438	aerobic	aerobicⓘ	yes	77.13	no
125438	thermophilic	thermophileⓘ	no	96.29	no
125438	flagellated	motile2+ⓘ	no	59.82	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	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	Thiosulfatihalobacter marinus gen. nov. sp. nov., a novel member of the family Roseobacteraceae, isolated from the West Pacific Ocean.	Wu Y, Ren WT, Zhong YW, Guo LL, Zhou P, Xu XW	Int J Syst Evol Microbiol	10.1099/ijsem.0.005286	2022
Phylogeny	Shimia sediminis sp. nov., a bacterium isolated from marine sediment in the East China Sea.	Zhu S, Chen C, Cheng Y, Guo C, Peng N, Zhang W, He S	Int J Syst Evol Microbiol	10.1099/ijsem.0.004782	2021
Phylogeny	Thalassobius abyssi sp. nov., a marine bacterium isolated from cold-seep sediment.	Nogi Y, Mori K, Makita H, Hatada Y	Int J Syst Evol Microbiol	10.1099/ijsem.0.000758	2015
Phylogeny	Epibacterium ulvae gen. nov., sp. nov., epibiotic bacteria isolated from the surface of a marine alga.	Penesyan A, Breider S, Schumann P, Tindall BJ, Egan S, Brinkhoff T	Int J Syst Evol Microbiol	10.1099/ijs.0.042838-0	2012
Phylogeny	Tropicibacter naphthalenivorans gen. nov., sp. nov., a polycyclic aromatic hydrocarbon-degrading bacterium isolated from Semarang Port in Indonesia.	Harwati TU, Kasai Y, Kodama Y, Susilaningsih D, Watanabe K	Int J Syst Evol Microbiol	10.1099/ijs.0.65821-0	2009
Phylogeny	Thalassobius aestuarii sp. nov., isolated from tidal flat sediment.	Yi H, Chun J	J Microbiol	2368	2006

References

#5792	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 15283
#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 )
#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;
#67771	Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;
#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 .
#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 aestuarii (DSM 15283, KCTC 12049, JC2049)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_900114635

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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