Aquimarina brevivitae (DSM 17196, KCTC 12390, SMK-19)

Name: Aquimarina brevivitae (DSM 17196, KCTC 12390, SMK-19)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 5592

Type strain

Strain Designation SMK-19

Culture col. no. DSM 17196 KCTC 12390 SMK-19

NCBI tax ID(s) 1121005 323412

Special Collections DSMZ KCTC Literature strains

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Aquimarina brevivitae SMK-19 is an aerobe, mesophilic, Gram-negative prokaryote that was isolated from tidal flat sediment.

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

Name and taxonomic classification

SI-ID 289860

DSM 17196,KCTC 12390

@ref 20215

Last LPSN update 2025-12-16 09:48:06

Domain Pseudomonadati

Phylum Bacteroidota

Class Flavobacteriia

Order Flavobacteriales

Family Flavobacteriaceae

Genus Aquimarina

Species Aquimarina brevivitae

Full scientific name Aquimarina brevivitae (Yoon et al. 2006) Nedashkovskaya et al. 2006

Synonyms (1)

Gaetbulimicrobium brevivitae

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Flagellum arrangement	Confidence
31551	negative	01-15 µm	0.2-0.3 µm	rod-shaped	gliding
67771				rod-shaped
67771	negative
125439	negative					96.9
125438						93.1
125438	negative					97.981

Pigmentation

31551

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
6722	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
6722	positive	growth	37	mesophilic
31551	positive	growth	10-41
31551	positive	optimum	37	mesophilic
67771	positive	growth	37	mesophilic

Culture pH

@ref	Ability	Type	PH
31551	positive	optimum	07-08
31551	positive	growth	5.5-8

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
31551	aerobe
67771	aerobe
125439	obligate aerobe	92.6

Spore formation

@ref	Spore formation	Confidence
31551
67771
125439		96.5
125438		92.5

Halophily

@ref	Salt	Growth	Tested relation	Concentration
31551	NaCl	positive	growth	02-03 %
31551	NaCl	positive	optimum	02-03 %

Observation

@ref	Observation
31551	aggregates in chains
67771	quinones: MK-6

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
31551	4853 ChEBI	esculin	+	hydrolysis
31551	17306 ChEBI	maltose	+	carbon source
31551	15361 ChEBI	pyruvate	+	carbon source

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	reductive acetyl coenzyme A pathway	100	7 of 7
66794	octane oxidation	100	3 of 3
66794	CMP-KDO biosynthesis	100	4 of 4
66794	ppGpp biosynthesis	100	4 of 4
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	sulfopterin metabolism	100	4 of 4
66794	acetoin degradation	100	3 of 3
66794	biotin biosynthesis	100	4 of 4
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	phenylacetate degradation (aerobic)	100	5 of 5
66794	methylglyoxal degradation	100	5 of 5
66794	vitamin K metabolism	100	5 of 5
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	adipate degradation	100	2 of 2
66794	suberin monomers biosynthesis	100	2 of 2
66794	palmitate biosynthesis	100	22 of 22
66794	coenzyme A metabolism	100	4 of 4
66794	threonine metabolism	90	9 of 10
66794	chorismate metabolism	88.89	8 of 9
66794	serine metabolism	88.89	8 of 9
66794	C4 and CAM-carbon fixation	87.5	7 of 8
66794	gluconeogenesis	87.5	7 of 8
66794	photosynthesis	85.71	12 of 14
66794	heme metabolism	85.71	12 of 14
66794	phenylalanine metabolism	84.62	11 of 13
66794	NAD metabolism	83.33	15 of 18
66794	peptidoglycan biosynthesis	80	12 of 15
66794	glycine betaine biosynthesis	80	4 of 5
66794	starch degradation	80	8 of 10
66794	cellulose degradation	80	4 of 5
66794	glutamate and glutamine metabolism	78.57	22 of 28
66794	tetrahydrofolate metabolism	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	valine metabolism	77.78	7 of 9
66794	leucine metabolism	76.92	10 of 13
66794	butanoate fermentation	75	3 of 4
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	acetate fermentation	75	3 of 4
66794	isoleucine metabolism	75	6 of 8
66794	glycogen biosynthesis	75	3 of 4
66794	purine metabolism	74.47	70 of 94
66794	tryptophan metabolism	73.68	28 of 38
66794	flavin biosynthesis	73.33	11 of 15
66794	proline metabolism	72.73	8 of 11
66794	citric acid cycle	71.43	10 of 14
66794	tyrosine metabolism	71.43	10 of 14
66794	propanol degradation	71.43	5 of 7
66794	propionate fermentation	70	7 of 10
66794	vitamin B1 metabolism	69.23	9 of 13
66794	histidine metabolism	68.97	20 of 29
66794	pyrimidine metabolism	68.89	31 of 45
66794	lipid metabolism	67.74	21 of 31
66794	cysteine metabolism	66.67	12 of 18
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	formaldehyde oxidation	66.67	2 of 3
66794	molybdenum cofactor biosynthesis	66.67	6 of 9
66794	acetyl CoA biosynthesis	66.67	2 of 3
66794	CO2 fixation in Crenarchaeota	66.67	6 of 9
66794	alanine metabolism	65.52	19 of 29
66794	glycolysis	64.71	11 of 17
66794	lysine metabolism	64.29	27 of 42
66794	vitamin B6 metabolism	63.64	7 of 11
66794	arginine metabolism	62.5	15 of 24
66794	arachidonate biosynthesis	60	3 of 5
66794	Entner Doudoroff pathway	60	6 of 10
66794	non-pathway related	57.89	22 of 38
66794	ubiquinone biosynthesis	57.14	4 of 7
66794	glutathione metabolism	57.14	8 of 14
66794	d-mannose degradation	55.56	5 of 9
66794	ascorbate metabolism	54.55	12 of 22
66794	pentose phosphate pathway	54.55	6 of 11
66794	methionine metabolism	53.85	14 of 26
66794	urea cycle	53.85	7 of 13
66794	pantothenate biosynthesis	50	3 of 6
66794	kanosamine biosynthesis II	50	1 of 2
66794	grixazone biosynthesis	50	1 of 2
66794	glycine metabolism	50	5 of 10
66794	ethanol fermentation	50	1 of 2
66794	dTDPLrhamnose biosynthesis	50	4 of 8
66794	phenylmercury acetate degradation	50	1 of 2
66794	cyclohexanol degradation	50	2 of 4
66794	isoprenoid biosynthesis	50	13 of 26
66794	degradation of sugar alcohols	50	8 of 16
66794	quinate degradation	50	1 of 2
66794	phenylpropanoid biosynthesis	46.15	6 of 13
66794	metabolism of disaccharids	45.45	5 of 11
66794	cardiolipin biosynthesis	42.86	3 of 7
66794	oxidative phosphorylation	41.76	38 of 91
66794	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
66794	carotenoid biosynthesis	40.91	9 of 22
66794	factor 420 biosynthesis	40	2 of 5
66794	lipoate biosynthesis	40	2 of 5
66794	sulfate reduction	38.46	5 of 13
66794	androgen and estrogen metabolism	37.5	6 of 16
66794	ketogluconate metabolism	37.5	3 of 8
66794	d-xylose degradation	36.36	4 of 11
66794	phenol degradation	35	7 of 20
66794	sphingosine metabolism	33.33	2 of 6
66794	cyanate degradation	33.33	1 of 3
66794	nitrate assimilation	33.33	3 of 9
66794	glycolate and glyoxylate degradation	33.33	2 of 6
66794	IAA biosynthesis	33.33	1 of 3
66794	enterobactin biosynthesis	33.33	1 of 3
66794	4-hydroxymandelate degradation	33.33	3 of 9
66794	selenocysteine biosynthesis	33.33	2 of 6
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	degradation of pentoses	32.14	9 of 28
66794	polyamine pathway	30.43	7 of 23
66794	coenzyme M biosynthesis	30	3 of 10
66794	aclacinomycin biosynthesis	28.57	2 of 7
66794	mevalonate metabolism	28.57	2 of 7
66794	degradation of hexoses	27.78	5 of 18
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	3-phenylpropionate degradation	26.67	4 of 15
66794	toluene degradation	25	1 of 4
66794	catecholamine biosynthesis	25	1 of 4
66794	lactate fermentation	25	1 of 4
66794	carnitine metabolism	25	2 of 8
66794	phosphatidylethanolamine bioynthesis	23.08	3 of 13

Isolation, sampling and environmental information

Isolation source categories

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

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
6722	tidal flat sediment	Pyunsan, Saemankum	Republic of Korea	KOR	Asia
67771	From gaetbul		Republic of Korea	KOR	Asia

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
6722	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	ASM421689v1 assembly for Aquimarina brevivitae DSM 17196	scaffold	GCA_004216895	323412.3	2799112219	323412	69.55

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
6722	Gaetbulimicrobium brevivitae strain SMK-19 16S ribosomal RNA gene, partial sequence	AY987367	1480		323412

GC content

@ref	GC-content (mol%)
6722	36.0
31551	36

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Aquimarina brevivitae DSM 17196
NCBI: GCA_004216895

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	96.50	no
125439	motility	BacteriaNetⓘ	no	63.90	no
125439	gram_stain	BacteriaNetⓘ	negative	96.90	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 brevivitae DSM 17196
NCBI: GCA_004216895.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	97.98	yes
125438	anaerobic	anaerobicⓘ	no	96.22	yes
125438	aerobic	aerobicⓘ	yes	88.23	yes
125438	spore-forming	spore-formingⓘ	no	92.50	yes
125438	thermophilic	thermophileⓘ	no	96.40	yes
125438	flagellated	motile2+ⓘ	no	93.10	yes

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Aquimarina longa sp. nov., isolated from seawater, and emended description of Aquimarina muelleri.	Yu T, Yin Q, Song X, Zhao R, Shi X, Zhang XH	Int J Syst Evol Microbiol	10.1099/ijs.0.041509-0	2012
Phylogeny	Aquimarina litoralis sp. nov., isolated from a coastal seawater.	Oh YS, Kahng HY, Lee YS, Yoon BJ, Lim SB, Jung JS, Oh DC, Lee DH	J Microbiol	10.1007/s12275-010-0088-8	2010
Phylogeny	Gaetbulimicrobium brevivitae gen. nov., sp. nov., a novel member of the family Flavobacteriaceae isolated from a tidal flat of the Yellow Sea in Korea.	Yoon JH, Kang SJ, Jung SY, Oh HW, Oh TK	Int J Syst Evol Microbiol	10.1099/ijs.0.63795-0	2006

References

#6722	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 17196
#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 )
#31551	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 #27842 (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 )
#67771	Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;
#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 brevivitae (DSM 17196, KCTC 12390, SMK-19)

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

Observation

Metabolite utilization

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_004216895

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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