Name: Coraliomargarita akajimensis 04OKA010-24
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 17651

Type strain:

Species: Coraliomargarita akajimensis

Strain Designation: 04OKA010-24, 04OKA10-24

Culture col. no.: DSM 45221, IAM 15411, JCM 23193, KCTC 12865, MBIC 06463

Strain history: <- JW Yoon, Tokyo Univ. <- M Yasumoto-Hirose, MBI

NCBI tax ID(s): 583355 (strain), 395922 (species)

SI-ID 308606

IAM 15411, KCTC 12865, JCM 23193, NBRC 103620, DSM 45221

Section

Coraliomargarita akajimensis 04OKA010-24 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from seawater surrounding the hard coral x Galaxea fascicularis.

coccus-shaped
Gram-negative
aerobe
mesophilic
16S sequence
Bacteria
genome sequence

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Verrucomicrobiota*
	Class	*Opitutia*
	Order	*Puniceicoccales*
	Family	*Puniceicoccaceae*
	Genus	*Coraliomargarita*
	Species	**Coraliomargarita akajimensis**
	Full Scientific Name (LPSN)	Coraliomargarita akajimensis Yoon et al. 2007

Information on morphological and physiological properties Morphology

[Ref.: #31982]	Gram stain	negative
[Ref.: #67771]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.985

[Ref.: #31982]	Cell length	1.2 µm

[Ref.: #31982]	Cell width	0.5 µm

[Ref.: #31982]	Cell shape	coccus-shaped
[Ref.: #67771]	Cell shape	coccus-shaped

[Ref.: #31982]	Motility	no
[Ref.: #67771]	Motility	no

[Ref.: #31982]

Pigment production

Multimedia content

[Ref.: #15802]

Caption:

Medium 514 25°C

[Ref.: #15802]

Intellectual property rights:

Information on culture and growth conditions Culture and growth conditions

[Ref.: #15802]

Culture medium

BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)

[Ref.: #15802]

Culture medium growth

[Ref.: #15802]

Culture medium link

Medium recipe at MediaDive

[Ref.: #15802]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #15802]	growth	25 °C
[Ref.: #31982]	growth	20-30 °C
[Ref.: #31982]	optimum	25 °C
[Ref.: #67770]	growth	25 °C
[Ref.: #67771]	growth	20-30 °C

[Ref.: #15802]	Temperature range	mesophilic
[Ref.: #31982]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #31982]			optimum	8
[Ref.: #31982]			growth	07-09

Information on physiology and metabolism Physiology and metabolism

[Ref.: #31982]	Oxygen tolerance	aerobe
[Ref.: #67771]	Oxygen tolerance	aerobe

[Ref.: #31982]	Ability of spore formation	no
[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.985

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #31982]		NaCl		growth	0.1-5	%
[Ref.: #31982]		NaCl		optimum	2.5	%

[Ref.: #67770]	Observation	quinones: MK-7
[Ref.: #67771]	Observation	quinones: MK-7

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #31982]	2-dehydro-D-gluconate ChEBI	+	carbon source
[Ref.: #31982]	5-dehydro-D-gluconate ChEBI	+	carbon source
[Ref.: #31982]	arabinose ChEBI	+	carbon source
[Ref.: #31982]	cellobiose ChEBI	+	carbon source
[Ref.: #31982]	fructose ChEBI	+	carbon source
[Ref.: #31982]	fucose ChEBI	+	carbon source
[Ref.: #31982]	galactose ChEBI	+	carbon source
[Ref.: #31982]	gluconate ChEBI	+	carbon source
[Ref.: #31982]	glucose ChEBI	+	carbon source
[Ref.: #31982]	glycogen ChEBI	+	carbon source
[Ref.: #31982]	L-arabitol ChEBI	+	carbon source
[Ref.: #31982]	lactose ChEBI	+	carbon source
[Ref.: #31982]	maltose ChEBI	+	carbon source
[Ref.: #31982]	mannitol ChEBI	+	carbon source
[Ref.: #31982]	mannose ChEBI	+	carbon source
[Ref.: #31982]	melibiose ChEBI	+	carbon source
[Ref.: #31982]	N-acetylglucosamine ChEBI	+	carbon source
[Ref.: #31982]	raffinose ChEBI	+	carbon source
[Ref.: #31982]	rhamnose ChEBI	+	carbon source
[Ref.: #31982]	ribitol ChEBI	+	carbon source
[Ref.: #31982]	ribose ChEBI	+	carbon source
[Ref.: #31982]	salicin ChEBI	+	carbon source
[Ref.: #31982]	sorbitol ChEBI	+	carbon source
[Ref.: #31982]	sucrose ChEBI	+	carbon source
[Ref.: #31982]	trehalose ChEBI	+	carbon source
[Ref.: #31982]	urea ChEBI	+	carbon source
[Ref.: #31982]	xylitol ChEBI	+	carbon source
[Ref.: #31982]	xylose ChEBI	+	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Enzymes	Enzyme	Enzyme activity	EC number
[Ref.: #31982]		cytochrome oxidase	+	1.9.3.1
[Ref.: #31982]		urease	+	3.5.1.5

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	vitamin K metabolism	100	5 of 5
[Ref.: #66794]	kanosamine biosynthesis II	100	2 of 2
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	CMP-KDO biosynthesis	100	4 of 4
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	sulfopterin metabolism	100	4 of 4
[Ref.: #66794]	tetrahydrofolate metabolism	92.86	13 of 14
[Ref.: #66794]	pentose phosphate pathway	90.91	10 of 11
[Ref.: #66794]	Entner Doudoroff pathway	90	9 of 10
[Ref.: #66794]	lipid A biosynthesis	88.89	8 of 9
[Ref.: #66794]	valine metabolism	88.89	8 of 9
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	gluconeogenesis	87.5	7 of 8
[Ref.: #66794]	isoleucine metabolism	87.5	7 of 8
[Ref.: #66794]	C4 and CAM-carbon fixation	87.5	7 of 8
[Ref.: #66794]	reductive acetyl coenzyme A pathway	85.71	6 of 7
[Ref.: #66794]	photosynthesis	85.71	12 of 14
[Ref.: #66794]	glycolate and glyoxylate degradation	83.33	5 of 6
[Ref.: #66794]	NAD metabolism	83.33	15 of 18
[Ref.: #66794]	propionate fermentation	80	8 of 10
[Ref.: #66794]	threonine metabolism	80	8 of 10
[Ref.: #66794]	heme metabolism	78.57	11 of 14
[Ref.: #66794]	citric acid cycle	78.57	11 of 14
[Ref.: #66794]	molybdenum cofactor biosynthesis	77.78	7 of 9
[Ref.: #66794]	d-mannose degradation	77.78	7 of 9
[Ref.: #66794]	vitamin B1 metabolism	76.92	10 of 13
[Ref.: #66794]	phenylalanine metabolism	76.92	10 of 13
[Ref.: #66794]	glycolysis	76.47	13 of 17
[Ref.: #66794]	degradation of sugar acids	76	19 of 25
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
[Ref.: #66794]	purine metabolism	74.47	70 of 94
[Ref.: #66794]	peptidoglycan biosynthesis	73.33	11 of 15
[Ref.: #66794]	flavin biosynthesis	73.33	11 of 15
[Ref.: #66794]	d-xylose degradation	72.73	8 of 11
[Ref.: #66794]	propanol degradation	71.43	5 of 7
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	pyrimidine metabolism	71.11	32 of 45
[Ref.: #66794]	starch degradation	70	7 of 10
[Ref.: #66794]	serine metabolism	66.67	6 of 9
[Ref.: #66794]	acetyl CoA biosynthesis	66.67	2 of 3
[Ref.: #66794]	nitrate assimilation	66.67	6 of 9
[Ref.: #66794]	enterobactin biosynthesis	66.67	2 of 3
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	aspartate and asparagine metabolism	66.67	6 of 9
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	alanine metabolism	65.52	19 of 29
[Ref.: #66794]	glutamate and glutamine metabolism	64.29	18 of 28
[Ref.: #66794]	vitamin B6 metabolism	63.64	7 of 11
[Ref.: #66794]	degradation of sugar alcohols	62.5	10 of 16
[Ref.: #66794]	dTDPLrhamnose biosynthesis	62.5	5 of 8
[Ref.: #66794]	leucine metabolism	61.54	8 of 13
[Ref.: #66794]	isoprenoid biosynthesis	61.54	16 of 26
[Ref.: #66794]	non-pathway related	60.53	23 of 38
[Ref.: #66794]	phenylacetate degradation (aerobic)	60	3 of 5
[Ref.: #66794]	cellulose degradation	60	3 of 5
[Ref.: #66794]	lipoate biosynthesis	60	3 of 5
[Ref.: #66794]	gallate degradation	60	3 of 5
[Ref.: #66794]	glycogen metabolism	60	3 of 5
[Ref.: #66794]	ubiquinone biosynthesis	57.14	4 of 7
[Ref.: #66794]	polyamine pathway	56.52	13 of 23
[Ref.: #66794]	CO2 fixation in Crenarchaeota	55.56	5 of 9
[Ref.: #66794]	proline metabolism	54.55	6 of 11
[Ref.: #66794]	methionine metabolism	53.85	14 of 26
[Ref.: #66794]	sulfate reduction	53.85	7 of 13
[Ref.: #66794]	urea cycle	53.85	7 of 13
[Ref.: #66794]	degradation of pentoses	53.57	15 of 28
[Ref.: #66794]	tryptophan metabolism	52.63	20 of 38
[Ref.: #66794]	histidine metabolism	51.72	15 of 29
[Ref.: #66794]	oxidative phosphorylation	50.55	46 of 91
[Ref.: #66794]	lactate fermentation	50	2 of 4
[Ref.: #66794]	adipate degradation	50	1 of 2
[Ref.: #66794]	ribulose monophosphate pathway	50	1 of 2
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	lysine metabolism	50	21 of 42
[Ref.: #66794]	ascorbate metabolism	50	11 of 22
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	ketogluconate metabolism	50	4 of 8
[Ref.: #66794]	ppGpp biosynthesis	50	2 of 4
[Ref.: #66794]	butanoate fermentation	50	2 of 4
[Ref.: #66794]	glutathione metabolism	50	7 of 14
[Ref.: #66794]	cysteine metabolism	50	9 of 18
[Ref.: #66794]	quinate degradation	50	1 of 2
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	lipid metabolism	48.39	15 of 31
[Ref.: #66794]	arginine metabolism	45.83	11 of 24
[Ref.: #66794]	degradation of hexoses	44.44	8 of 18
[Ref.: #66794]	tyrosine metabolism	42.86	6 of 14
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
[Ref.: #66794]	glycine betaine biosynthesis	40	2 of 5
[Ref.: #66794]	glycine metabolism	40	4 of 10
[Ref.: #66794]	3-phenylpropionate degradation	40	6 of 15
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	phenol degradation	40	8 of 20
[Ref.: #66794]	myo-inositol biosynthesis	40	4 of 10
[Ref.: #66794]	ethylmalonyl-CoA pathway	40	2 of 5
[Ref.: #66794]	metabolism of disaccharids	36.36	4 of 11
[Ref.: #66794]	cyanate degradation	33.33	1 of 3
[Ref.: #66794]	selenocysteine biosynthesis	33.33	2 of 6
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	coenzyme M biosynthesis	30	3 of 10
[Ref.: #66794]	4-hydroxyphenylacetate degradation	30	3 of 10
[Ref.: #66794]	cholesterol biosynthesis	27.27	3 of 11
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
[Ref.: #66794]	vitamin B12 metabolism	26.47	9 of 34
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	androgen and estrogen metabolism	25	4 of 16
[Ref.: #66794]	alginate biosynthesis	25	1 of 4
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	23.08	3 of 13
[Ref.: #66794]	carotenoid biosynthesis	22.73	5 of 22
		Only first 10 entries are displayed. Click here to see all.

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #15802]	Sample type/isolated from	seawater surrounding the hard coral x Galaxea fascicularis
[Ref.: #15802]	Host species	Galaxea fascicularis
[Ref.: #15802]	Geographic location (country and/or sea, region)	Majanohama, Akajima
[Ref.: #15802]	Country	Japan
[Ref.: #15802]	Country ISO 3 Code	JPN
[Ref.: #15802]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Seawater surrounding the hard coral Galaxea facicularis L.
[Ref.: #67770]	Host species	Galaxea facicularis
[Ref.: #67770]	Geographic location (country and/or sea, region)	Majanohama, Akajima
[Ref.: #67770]	Country	Japan
[Ref.: #67770]	Country ISO 3 Code	JPN
[Ref.: #67770]	Continent	Asia

[Ref.: #67771]	Sample type/isolated from	From seawater
[Ref.: #67771]	Geographic location (country and/or sea, region)	Okinawa
[Ref.: #67771]	Country	Japan
[Ref.: #67771]	Country ISO 3 Code	JPN
[Ref.: #67771]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Marine
#Host	#Invertebrates (Other)	#Cnidaria (Corals)

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AB266750 (>99% sequence identity) for Coraliomargarita akajimensis subclade from Microbeatlas

Aquatic Samples	4409
Soil Samples	570
Animal Samples	119
Plant Samples	49
Total Samples	5147

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #15802]

Biosafety level

Risk group (German classification)
According to TRBA 466

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #15802]	Coraliomargarita akajimensis gene for 16S rRNA, partial sequence	AB266750	1457	ENA	583355 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Coraliomargarita akajimensis DSM 45221	GCA_000025905	complete	GenBank	583355 tax ID	*
[Ref.: #66792]	Coraliomargarita akajimensis DSM 45221	583355.3	complete	PATRIC	583355 tax ID	*
[Ref.: #66792]	Coraliomargarita akajimensis DSM 45221	646564524	complete	JGI IMG/M	583355 tax ID	*

[Ref.: #15802]	GC-content	53.9 mol%
[Ref.: #67770]	GC-content	53.9 mol%	high performance liquid chromatography (HPLC)

Data predicted using genome information as a basis Genome-based predictions

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Coraliomargarita akajimensis DSM 45221 DSM 45221 NCBI: GCA_000025905.1
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Coraliomargarita akajimensis DSM 45221 DSM 45221 NCBI: GCA_000025905.1
[Ref.: #69480]	motile	no	92.76	no
[Ref.: #69480]	flagellated	no	96.963	yes
[Ref.: #69480]	gram-positive	no	98.201	yes
[Ref.: #69480]	anaerobic	no	96.735	yes
[Ref.: #69480]	aerobic	yes	71.779	no
[Ref.: #69480]	halophile	no	68.779	no
[Ref.: #69480]	spore-forming	no	97.49	yes
[Ref.: #69480]	thermophile	no	96.602	yes
[Ref.: #69480]	glucose-util	yes	85.361	no
[Ref.: #69480]	glucose-ferment	no	76.057	no

Availability in culture collections External links

[Ref.: #15802]

Culture collection no.

DSM 45221, IAM 15411, JCM 23193, KCTC 12865, MBIC 06463

[Ref.: #86642]

SI-ID 308606

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Oceanipulchritudo coccoides gen. nov., sp. nov., isolated from marine sediment within the family Puniceicoccaceae.	Feng X, Zou QH, Zhang XY, Ye MQ, Du ZJ	Int J Syst Evol Microbiol	10.1099/ijsem.0.004458	2020	*
Phylogeny	Coraliomargarita sinensis sp. nov., isolated from a marine solar saltern.	Zhou LY, Wang NN, Mu DS, Liu Y, Du ZJ	Int J Syst Evol Microbiol	10.1099/ijsem.0.003205	2019	*
Genetics	Complete genome sequence of Coraliomargarita akajimensis type strain (04OKA010-24).	Mavromatis K, Abt B, Brambilla E, Lapidus A, Copeland A, Deshpande S, Nolan M, Lucas S, Tice H, Cheng JF, Han C, Detter JC, Woyke T, Goodwin L, Pitluck S, Held B, Brettin T, Tapia R, Ivanova N, Mikhailova N, Pati A, Liolios K, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Rohde M, Goker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Klenk HP, Kyrpides NC	Stand Genomic Sci	10.4056/sigs.952166	2010	*
Phylogeny	Coraliomargarita akajimensis gen. nov., sp. nov., a novel member of the phylum 'Verrucomicrobia' isolated from seawater in Japan.	Yoon J, Yasumoto-Hirose M, Katsuta A, Sekiguchi H, Matsuda S, Kasai H, Yokota A	Int J Syst Evol Microbiol	10.1099/ijs.0.64755-0	2007	*

References

#15802

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 45221

#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 )

#31982

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 #28236 (see below)

#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;
#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 .

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

#86642

Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.: StrainInfo: A central database for resolving microbial strain identifiers . ( DOI 10.60712/SI-ID308606.1 )

#28236

IJSEM 959 2007 ( DOI 10.1099/ijs.0.64755-0 , PubMed 17473241 )

* These data were automatically processed and therefore are not curated

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Coraliomargarita akajimensis DSM 45221 DSM 45221

Coraliomargarita akajimensis DSM 45221 DSM 45221

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