Aquimarina spongiae (DSM 22623, KCTC 22663, A6)

Name: Aquimarina spongiae (DSM 22623, KCTC 22663, A6)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 5595

Type strain

Strain Designation A6

Culture col. no. DSM 22623 KCTC 22663 A6

NCBI tax ID(s) 570521

Special Collections DSMZ KCTC Literature strains

History <- B.-J. Yoon, Jeju National Univ., Rep. of Korea; A6 <- BJ Yoon, Jeju Natl. Univ

Links

Aquimarina spongiae A6 is an aerobe, Gram-negative, rod-shaped bacterium that was isolated from marine sponge, Halichondria oshoro.

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

Name and taxonomic classification

SI-ID 404718

KCTC 22663,DSM 22623

@ref 20215

Last LPSN update 2026-02-09 11:19:00

Domain Bacteria

Phylum Bacteroidota

Class Flavobacteriia

Order Flavobacteriales

Family Flavobacteriaceae

Genus Aquimarina

Species Aquimarina spongiae

Full scientific name Aquimarina spongiae Yoon et al. 2011

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
29832	negative	4.75 µm	0.3 µm	rod-shaped
67771				rod-shaped
67771	negative
125439	negative				99.3
125438					94
125438	negative				98.432

Pigmentation

29832

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
16433	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)
16433	positive	growth	28
29832	positive	growth	10-35
29832	positive	optimum	32.5
67771	positive	growth	30

Culture pH

@ref	Ability	Type	PH	PH range
29832	positive	optimum	7.5
29832	positive	growth	06-11	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
29832	aerobe
67771	aerobe
125439	obligate aerobe	92.6

Spore formation

@ref	Spore formation	Confidence
125439		96.3

Halophily

@ref	Salt	Growth	Tested relation	Concentration
29832	NaCl	positive	growth	01-05 %
29832	NaCl	positive	optimum	3 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
29832	4853 ChEBI	esculin	+	hydrolysis
29832	17234 ChEBI	glucose	+	carbon source

Enzymes

@ref	Value	Activity	Ec
29832	acid phosphatase	+	3.1.3.2
29832	alkaline phosphatase	+	3.1.3.1
29832	catalase	+	1.11.1.6
29832	cytochrome oxidase	+	1.9.3.1
29832	gelatinase	+

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	cellulose degradation	100	5 of 5
66794	reductive acetyl coenzyme A pathway	100	7 of 7
66794	kanosamine biosynthesis II	100	2 of 2
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	CMP-KDO biosynthesis	100	4 of 4
66794	threonine metabolism	100	10 of 10
66794	octane oxidation	100	3 of 3
66794	acetate fermentation	100	4 of 4
66794	palmitate biosynthesis	100	22 of 22
66794	ppGpp biosynthesis	100	4 of 4
66794	methylglyoxal degradation	100	5 of 5
66794	adipate degradation	100	2 of 2
66794	starch degradation	100	10 of 10
66794	biotin biosynthesis	100	4 of 4
66794	gluconeogenesis	100	8 of 8
66794	molybdenum cofactor biosynthesis	100	9 of 9
66794	aerobactin biosynthesis	100	1 of 1
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	suberin monomers biosynthesis	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	sulfopterin metabolism	100	4 of 4
66794	coenzyme A metabolism	100	4 of 4
66794	formaldehyde oxidation	100	3 of 3
66794	vitamin K metabolism	100	5 of 5
66794	phenylacetate degradation (aerobic)	100	5 of 5
66794	folate polyglutamylation	100	1 of 1
66794	tetrahydrofolate metabolism	92.86	13 of 14
66794	phenylalanine metabolism	92.31	12 of 13
66794	serine metabolism	88.89	8 of 9
66794	lipid A biosynthesis	88.89	8 of 9
66794	NAD metabolism	88.89	16 of 18
66794	chorismate metabolism	88.89	8 of 9
66794	C4 and CAM-carbon fixation	87.5	7 of 8
66794	photosynthesis	85.71	12 of 14
66794	leucine metabolism	84.62	11 of 13
66794	tryptophan metabolism	81.58	31 of 38
66794	Entner Doudoroff pathway	80	8 of 10
66794	peptidoglycan biosynthesis	80	12 of 15
66794	glycine betaine biosynthesis	80	4 of 5
66794	purine metabolism	79.79	75 of 94
66794	heme metabolism	78.57	11 of 14
66794	glutamate and glutamine metabolism	78.57	22 of 28
66794	aspartate and asparagine metabolism	77.78	7 of 9
66794	valine metabolism	77.78	7 of 9
66794	vitamin B1 metabolism	76.92	10 of 13
66794	pyrimidine metabolism	75.56	34 of 45
66794	isoleucine metabolism	75	6 of 8
66794	glycogen biosynthesis	75	3 of 4
66794	ketogluconate metabolism	75	6 of 8
66794	butanoate fermentation	75	3 of 4
66794	dTDPLrhamnose biosynthesis	75	6 of 8
66794	lipid metabolism	74.19	23 of 31
66794	lysine metabolism	73.81	31 of 42
66794	proline metabolism	72.73	8 of 11
66794	pentose phosphate pathway	72.73	8 of 11
66794	citric acid cycle	71.43	10 of 14
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	glycolysis	70.59	12 of 17
66794	propionate fermentation	70	7 of 10
66794	urea cycle	69.23	9 of 13
66794	arginine metabolism	66.67	16 of 24
66794	cysteine metabolism	66.67	12 of 18
66794	enterobactin biosynthesis	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	d-mannose degradation	66.67	6 of 9
66794	CO2 fixation in Crenarchaeota	66.67	6 of 9
66794	acetyl CoA biosynthesis	66.67	2 of 3
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	flavin biosynthesis	66.67	10 of 15
66794	cyanate degradation	66.67	2 of 3
66794	alanine metabolism	65.52	19 of 29
66794	histidine metabolism	65.52	19 of 29
66794	tyrosine metabolism	64.29	9 of 14
66794	vitamin B6 metabolism	63.64	7 of 11
66794	carotenoid biosynthesis	63.64	14 of 22
66794	d-xylose degradation	63.64	7 of 11
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
66794	methionine metabolism	61.54	16 of 26
66794	non-pathway related	60.53	23 of 38
66794	3-chlorocatechol degradation	60	3 of 5
66794	glycogen metabolism	60	3 of 5
66794	arachidonate biosynthesis	60	3 of 5
66794	propanol degradation	57.14	4 of 7
66794	ubiquinone biosynthesis	57.14	4 of 7
66794	nitrate assimilation	55.56	5 of 9
66794	isoprenoid biosynthesis	53.85	14 of 26
66794	degradation of pentoses	53.57	15 of 28
66794	oxidative phosphorylation	52.75	48 of 91
66794	glycine metabolism	50	5 of 10
66794	degradation of aromatic, nitrogen containing compounds	50	6 of 12
66794	pantothenate biosynthesis	50	3 of 6
66794	glycolate and glyoxylate degradation	50	3 of 6
66794	quinate degradation	50	1 of 2
66794	ethanol fermentation	50	1 of 2
66794	cyclohexanol degradation	50	2 of 4
66794	degradation of hexoses	50	9 of 18
66794	glutathione metabolism	50	7 of 14
66794	sulfate reduction	46.15	6 of 13
66794	ascorbate metabolism	45.45	10 of 22
66794	degradation of sugar acids	44	11 of 25
66794	metabolism of amino sugars and derivatives	40	2 of 5
66794	gallate degradation	40	2 of 5
66794	bacilysin biosynthesis	40	2 of 5
66794	myo-inositol biosynthesis	40	4 of 10
66794	lipoate biosynthesis	40	2 of 5
66794	degradation of sugar alcohols	37.5	6 of 16
66794	carnitine metabolism	37.5	3 of 8
66794	androgen and estrogen metabolism	37.5	6 of 16
66794	phenol degradation	35	7 of 20
66794	IAA biosynthesis	33.33	1 of 3
66794	3-phenylpropionate degradation	33.33	5 of 15
66794	sphingosine metabolism	33.33	2 of 6
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	selenocysteine biosynthesis	33.33	2 of 6
66794	chlorophyll metabolism	33.33	6 of 18
66794	sulfoquinovose degradation	33.33	1 of 3
66794	phosphatidylethanolamine bioynthesis	30.77	4 of 13
66794	polyamine pathway	30.43	7 of 23
66794	coenzyme M biosynthesis	30	3 of 10
66794	mevalonate metabolism	28.57	2 of 7
66794	arachidonic acid metabolism	27.78	5 of 18
66794	metabolism of disaccharids	27.27	3 of 11
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	lactate fermentation	25	1 of 4
66794	vitamin E metabolism	25	1 of 4
66794	toluene degradation	25	1 of 4
66794	vitamin B12 metabolism	23.53	8 of 34
66794	4-hydroxymandelate degradation	22.22	2 of 9

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Marine
#Host	#Invertebrates (Other)	#Porifera (Sponges)

Isolation

@ref	Sample type	Host species	Geographic location	Country	Country ISO 3 Code	Continent
16433	marine sponge, Halichondria oshoro	Halichondria oshoro	Jeju, coastal area	Republic of Korea	KOR	Asia
67771	From marine sponge, `Halichondria oshoro`		the coast of Jeju Island	Republic of Korea	KOR	Asia

Taxonmaps

69479

Global distribution of 16S sequence FJ348470 (>99% sequence identity) for Aquimarina spongiae subclade from Microbeatlas

Aquatic Samples	587
Soil Samples	30
Animal Samples	101
Plant Samples	7
Total Samples	725

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
16433	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 2622736502 annotated assembly for Aquimarina spongiae DSM 22623	scaffold	GCA_900141785	570521.3	2622736502	570521	68.46

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
16433	Aquimarina spongiae strain A6 16S ribosomal RNA gene, partial sequence	FJ348470	1420		570521

GC content

@ref	GC-content (mol%)	Method
16433	36.0	thermal denaturation, midpoint method (Tm)
29832	36
67771	36.0

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Aquimarina spongiae DSM 22623
NCBI: GCA_900141785

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	96.30	no
125439	motility	BacteriaNetⓘ	no	69.20	no
125439	gram_stain	BacteriaNetⓘ	negative	99.30	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	92.60	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Aquimarina spongiae DSM 22623
NCBI: GCA_900141785.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	98.43	no
125438	anaerobic	anaerobicⓘ	no	97.76	yes
125438	aerobic	aerobicⓘ	yes	87.99	yes
125438	spore-forming	spore-formingⓘ	no	86.25	no
125438	thermophilic	thermophileⓘ	no	97.96	yes
125438	flagellated	motile2+ⓘ	no	94.00	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Insights into the Antimicrobial Activities and Metabolomes of Aquimarina (Flavobacteriaceae, Bacteroidetes) Species from the Rare Marine Biosphere.	Silva SG, Paula P, da Silva JP, Mil-Homens D, Teixeira MC, Fialho AM, Costa R, Keller-Costa T.	Mar Drugs	10.3390/md20070423	2022
Genetics	Marine Sponge and Octocoral-Associated Bacteria Show Versatile Secondary Metabolite Biosynthesis Potential and Antimicrobial Activities against Human Pathogens.	Almeida JF, Marques M, Oliveira V, Egas C, Mil-Homens D, Viana R, Cleary DFR, Huang YM, Fialho AM, Teixeira MC, Gomes NCM, Costa R, Keller-Costa T.	Mar Drugs	10.3390/md21010034	2022
	Crystal structure and catalytic mechanism of drimenol synthase, an unusual bifunctional terpene cyclase-phosphatase.	Osika KR, Gaynes MN, Christianson DW.	Proc Natl Acad Sci U S A	10.1073/pnas.2506584122	2025
	Structural insights into a bacterial terpene cyclase fused with haloacid Dehalogenase-like phosphatase.	Fujiyama K, Takagi H, Vo NNQ, Morita N, Nogawa T, Takahashi S.	Chem Sci	10.1039/d5sc04719f	2025
	Unified enantiospecific synthesis of drimane meroterpenoids enabled by enzyme catalysis and transition metal catalysis.	You Y, Zhang XJ, Xiao W, Kunthic T, Xiang Z, Xu C.	Chem Sci	10.1039/d4sc06060a	2024
	The Evolutionary History and Modern Diversity of Triterpenoid Cyclases.	McShea HS, Viens RA, Olagunju BO, Giner JL, Welander PV.	Mol Biol Evol	10.1093/molbev/msaf203	2025
	Identification and Characterization of Bifunctional Drimenol Synthases of Marine Bacterial Origin.	Vo NNQ, Nomura Y, Kinugasa K, Takagi H, Takahashi S.	ACS Chem Biol	10.1021/acschembio.2c00163	2022
	Discovery, Structure, and Mechanism of a Class II Sesquiterpene Cyclase.	Pan X, Du W, Zhang X, Lin X, Li FR, Yang Q, Wang H, Rudolf JD, Zhang B, Dong LB.	J Am Chem Soc	10.1021/jacs.2c09412	2022
Pathogenicity	Novel L-amino acid oxidase with algicidal activity against toxic cyanobacterium Microcystis aeruginosa synthesized by a bacterium Aquimarina sp.	Chen WM, Sheu FS, Sheu SY.	Enzyme Microb Technol	10.1016/j.enzmictec.2011.06.016	2011
Phylogeny	Aquimarina gracilis sp. nov., isolated from the gut microflora of a mussel, Mytilus coruscus, and emended description of Aquimarina spongiae.	Park SC, Choe HN, Baik KS, Seong CN.	Int J Syst Evol Microbiol	10.1099/ijs.0.044289-0	2013
Phylogeny	Aquimarina spongiae sp. nov., isolated from marine sponge Halichondria oshoro.	Yoon BJ, You HS, Lee DH, Oh DC	Int J Syst Evol Microbiol	10.1099/ijs.0.022046-0	2010
Phylogeny	Aquimarina acroporae sp. nov., isolated from seawater surrounding scleractinian coral Acropora digitifera.	Sun H, Rao C, Yang X, Xie Z, Chen B, Zheng H, Liao B, Xiao B	Int J Syst Evol Microbiol	10.1099/ijsem.0.005607	2022

References

#16433	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 22623
#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 )
#26208	IJSEM 417 2011 ( DOI 10.1099/ijs.0.022046-0 , PubMed 20348323 )
#29832	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 #26208
#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 )
#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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Aquimarina spongiae (DSM 22623, KCTC 22663, A6)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Metabolite utilization

Enzymes

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_900141785

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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