Shimia haliotis (DSM 28453, JCM 18870, KACC 17212)

Name: Shimia haliotis (DSM 28453, JCM 18870, KACC 17212)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 24508

Type strain

Strain Designation WM35

Culture col. no. DSM 28453 JCM 18870 KACC 17212 WM35

NCBI tax ID(s) 1280847

Special Collections DSMZ JCM Literature strains

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Shimia haliotis WM35 is an aerobe, mesophilic, Gram-negative prokaryote that was isolated from intestinal tract of an abalone Haliotis discus hannai.

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

Name and taxonomic classification

SI-ID 400689

JCM 18870,DSM 28453

@ref 20215

Last LPSN update 2025-12-16 09:52:51

Domain Pseudomonadati

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Rhodobacterales

Family Roseobacteraceae

Genus Shimia

Species Shimia haliotis

Full scientific name Shimia haliotis Hyun et al. 2013

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
31134	negative	2 µm	0.8 µm	rod-shaped
125438	negative				97.833
125439	negative				97.6

Colony morphology

21101

Incubation period2-3 days

Pigmentation

31134

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
21101	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
21101	positive	growth	30	mesophilic
31134	positive	growth	15-37
31134	positive	optimum	30	mesophilic
67770	positive	growth	30	mesophilic

Culture pH

@ref	Ability	Type	PH	PH range
31134	positive	optimum	7
31134	positive	growth	06-09	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
31134	aerobe
125439	obligate aerobe	99.5

Halophily

@ref	Salt	Growth	Tested relation	Concentration
31134	NaCl	positive	growth	0-5 %
31134	NaCl	positive	optimum	3 %

Observation

@ref	Observation
31134	aggregates in clumps
67770	quinones: Q-10

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
31134	30089 ChEBI	acetate	+	carbon source
68369	17128 ChEBI	adipate	-	assimilation	from API 20NE
31134	16449 ChEBI	alanine	+	carbon source
68369	29016 ChEBI	arginine	-	hydrolysis	from API 20NE
31134	22653 ChEBI	asparagine	+	carbon source
31134	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
68369	5291 ChEBI	gelatin	+	hydrolysis	from API 20NE
68369	24265 ChEBI	gluconate	-	assimilation	from API 20NE
31134	17234 ChEBI	glucose	+	carbon source
31134	29987 ChEBI	glutamate	+	carbon source
31134	21217 ChEBI	L-alaninamide	+	carbon source
68369	30849 ChEBI	L-arabinose	-	assimilation	from API 20NE
31134	24996 ChEBI	lactate	+	carbon source
68369	25115 ChEBI	malate	-	assimilation	from API 20NE
68369	17306 ChEBI	maltose	-	assimilation	from API 20NE
31134	28053 ChEBI	melibiose	+	carbon source
31134	51850 ChEBI	methyl pyruvate	+	carbon source
68369	59640 ChEBI	N-acetylglucosamine	-	assimilation	from API 20NE
31134	17632 ChEBI	nitrate	+	reduction
68369	17632 ChEBI	nitrate	-	reduction	from API 20NE
31134	18257 ChEBI	ornithine	+	carbon source
31134	26271 ChEBI	proline	+	carbon source
31134	17272 ChEBI	propionate	+	carbon source
31134	17822 ChEBI	serine	+	carbon source
31134	30031 ChEBI	succinate	+	carbon source
31134	17748 ChEBI	thymidine	+	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
31134	acid phosphatase	+	3.1.3.2
31134	alkaline phosphatase	+	3.1.3.1
31134	alpha-galactosidase	+	3.2.1.22
68369	arginine dihydrolase	-	3.5.3.6	from API 20NE
68369	beta-glucosidase	-	3.2.1.21	from API 20NE
21101	catalase	+	1.11.1.6
31134	catalase	+	1.11.1.6
31134	cytochrome oxidase	+	1.9.3.1
21101	cytochrome-c oxidase	+	1.9.3.1
31134	gelatinase	+
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
21101	-	-	-	-	-	-	+	+	-	-	-	-	-	-	-	-	-	-	-	-	not determinedn.d.

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Invertebrates (Other)	#Mollusca
#Host Body-Site	#Gastrointestinal tract	-

Isolation

@ref	Sample type	Host species	Geographic location	Country	Country ISO 3 Code	Continent
21101	intestinal tract of an abalone Haliotis discus hannai	Haliotis discus hannai	Jeju, northern coast	Republic of Korea	KOR	Asia
67770	Intestinal tract of an abalone, Haliotis discus hannai, which was collected from the northern coast of Jeju	Haliotis discus hannai		Republic of Korea	KOR	Asia

Taxonmaps

69479

Global distribution of 16S sequence KC196071 (>99% sequence identity) for Shimia haliotis from Microbeatlas

Aquatic Samples	982
Soil Samples	4
Animal Samples	23
Plant Samples	10
Total Samples	1019

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
21101	1	Risk group (German classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
67770	IMG-taxon 2619619046 annotated assembly for Shimia haliotis DSM 28453	contig	GCA_900114415	1280847.3	2619619046	1280847	74.91

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
21101	Shimia haliotis strain WM35 16S ribosomal RNA gene, partial sequence	KC196071	1386		1280847
124043	Shimia haliotis strain DSM 28453 16S ribosomal RNA gene, partial sequence.	MW198115	601		1280847

GC content

@ref	GC-content (mol%)	Method
21101	53.8
67770	53.8	thermal denaturation, midpoint method (Tm)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Shimia haliotis DSM 28453
NCBI: GCA_900114415

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	99.50	no
125439	gram_stain	BacteriaNetⓘ	negative	97.60	no
125439	motility	BacteriaNetⓘ	no	52.30	no
125439	spore_formation	BacteriaNetⓘ	no	88.40	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Shimia haliotis strain DSM 28453
PATRIC: 1280847.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	97.83	yes
125438	anaerobic	anaerobicⓘ	no	95.04	yes
125438	spore-forming	spore-formingⓘ	no	88.76	no
125438	aerobic	aerobicⓘ	yes	85.74	yes
125438	thermophilic	thermophileⓘ	no	97.25	yes
125438	flagellated	motile2+ⓘ	yes	56.97	no

Literature

Topic	Title	Authors	Journal	DOI	Year
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
Phylogeny	Shimia haliotis sp. nov., a bacterium isolated from the gut of an abalone, Haliotis discus hannai.	Hyun DW, Kim MS, Shin NR, Kim JY, Kim PS, Whon TW, Yun JH, Bae JW	Int J Syst Evol Microbiol	10.1099/ijs.0.053140-0	2013
Phylogeny	Ruegeria lutea sp. nov., isolated from marine sediment, Masan Bay, South Korea.	Kim J, Kim DY, Yang KH, Kim S, Lee SS	Int J Syst Evol Microbiol	10.1099/ijsem.0.003568	2019

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 )
#21101	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 28453
#31134	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 #27462 (see below)
#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 haliotis (DSM 28453, JCM 18870, KACC 17212)

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

Halophily

Observation

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_900114415

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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