Lutimaribacter saemankumensis (DSM 28010, CCUG 55760, KCTC 22244)

Name: Lutimaribacter saemankumensis (DSM 28010, CCUG 55760, KCTC 22244)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 24514

Type strain

Strain Designation SMK-117

Culture col. no. DSM 28010 CCUG 55760 KCTC 22244 SMK-117

NCBI tax ID(s) 490829

Special Collections DSMZ CCUG KCTC Literature strains

History <- KCTC <- J. H. Yoon, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, South Korea; SMK-117 <- JH Yoon, KRIBB

Links

Lutimaribacter saemankumensis SMK-117 is a facultative anaerobe, mesophilic, Gram-negative prokaryote that was isolated from sediment from tidal flat.

Gram-negative rod-shaped facultative anaerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 398622

KCTC 22244,DSM 28010,CCUG 55760

@ref 20215

Last LPSN update 2026-02-09 11:23:59

Domain Bacteria

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Rhodobacterales

Family Roseobacteraceae

Genus Lutimaribacter

Species Lutimaribacter saemankumensis

Full scientific name Lutimaribacter saemankumensis Yoon et al. 2009

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
28875	negative	5.5 µm	0.6 µm	rod-shaped
67771	negative
125438	negative				99
125439	negative				98.9

Colony morphology

@ref	Incubation period
21193	2-3 days
60719	2 days

Pigmentation

28875

Productionno

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
21193	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
21193	positive	growth	30	mesophilic
28875	positive	growth	10-45
28875	positive	optimum	30	mesophilic
60719	positive	growth	30	mesophilic
67771	positive	growth	30	mesophilic

Culture pH

@ref	Ability	Type	PH
28875	positive	optimum	7.5
28875	positive	growth	5.5-8.0

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance
28875	facultative anaerobe
60719	aerobe
67771	aerobe

Spore formation

@ref	Spore formation	Confidence
125438		92.296
125439		98.6

Halophily

@ref	Salt	Growth	Tested relation	Concentration
28875	NaCl	positive	growth	>12 %
28875	NaCl	positive	optimum	2 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68369	17128 ChEBI	adipate	-	assimilation	from API 20NE
68369	29016 ChEBI	arginine	-	hydrolysis	from API 20NE
28875	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
68369	30849 ChEBI	L-arabinose	-	assimilation	from API 20NE
68369	25115 ChEBI	malate	+	assimilation	from API 20NE
68369	17306 ChEBI	maltose	-	assimilation	from API 20NE
28875	37684 ChEBI	mannose	+	carbon source
68369	59640 ChEBI	N-acetylglucosamine	-	assimilation	from API 20NE
68369	17632 ChEBI	nitrate	-	reduction	from API 20NE
68369	27897 ChEBI	tryptophan	-	energy source	from API 20NE
28875	53424 ChEBI	tween 20	+	carbon source
28875	53423 ChEBI	tween 40	+	carbon source
28875	53425 ChEBI	tween 60	+	carbon source
28875	53426 ChEBI	tween 80	+	carbon source
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
68369	arginine dihydrolase	-	3.5.3.6	from API 20NE
68369	beta-glucosidase	-	3.2.1.21	from API 20NE
21193	catalase	+	1.11.1.6
28875	catalase	+	1.11.1.6
28875	cytochrome oxidase	+	1.9.3.1
21193	cytochrome-c oxidase	+	1.9.3.1
68369	gelatinase	-		from API 20NE
68369	urease	-	3.5.1.5	from API 20NE

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	phenylacetate degradation (aerobic)	100	5 of 5
66794	gluconeogenesis	100	8 of 8
66794	C4 and CAM-carbon fixation	100	8 of 8
66794	methylglyoxal degradation	100	5 of 5
66794	ppGpp biosynthesis	100	4 of 4
66794	palmitate biosynthesis	100	22 of 22
66794	threonine metabolism	100	10 of 10
66794	ethylmalonyl-CoA pathway	100	5 of 5
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	octane oxidation	100	3 of 3
66794	glycolate and glyoxylate degradation	100	6 of 6
66794	butanoate fermentation	100	4 of 4
66794	cyanate degradation	100	3 of 3
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	ceramide biosynthesis	100	1 of 1
66794	folate polyglutamylation	100	1 of 1
66794	suberin monomers biosynthesis	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	CMP-KDO biosynthesis	100	4 of 4
66794	denitrification	100	2 of 2
66794	valine metabolism	100	9 of 9
66794	coenzyme A metabolism	100	4 of 4
66794	formaldehyde oxidation	100	3 of 3
66794	adipate degradation	100	2 of 2
66794	citric acid cycle	92.86	13 of 14
66794	phenylalanine metabolism	92.31	12 of 13
66794	propionate fermentation	90	9 of 10
66794	Entner Doudoroff pathway	90	9 of 10
66794	CO2 fixation in Crenarchaeota	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	molybdenum cofactor biosynthesis	88.89	8 of 9
66794	serine metabolism	88.89	8 of 9
66794	heme metabolism	85.71	12 of 14
66794	degradation of aromatic, nitrogen containing compounds	83.33	10 of 12
66794	NAD metabolism	83.33	15 of 18
66794	glutamate and glutamine metabolism	82.14	23 of 28
66794	purine metabolism	81.91	77 of 94
66794	proline metabolism	81.82	9 of 11
66794	tryptophan metabolism	81.58	31 of 38
66794	peptidoglycan biosynthesis	80	12 of 15
66794	tyrosine metabolism	78.57	11 of 14
66794	photosynthesis	78.57	11 of 14
66794	allantoin degradation	77.78	7 of 9
66794	lipid A biosynthesis	77.78	7 of 9
66794	4-hydroxymandelate degradation	77.78	7 of 9
66794	vitamin B1 metabolism	76.92	10 of 13
66794	leucine metabolism	76.92	10 of 13
66794	alanine metabolism	75.86	22 of 29
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	isoleucine metabolism	75	6 of 8
66794	acetate fermentation	75	3 of 4
66794	phenol degradation	75	15 of 20
66794	3-phenylpropionate degradation	73.33	11 of 15
66794	flavin biosynthesis	73.33	11 of 15
66794	methionine metabolism	73.08	19 of 26
66794	chlorophyll metabolism	72.22	13 of 18
66794	ubiquinone biosynthesis	71.43	5 of 7
66794	glutathione metabolism	71.43	10 of 14
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	reductive acetyl coenzyme A pathway	71.43	5 of 7
66794	propanol degradation	71.43	5 of 7
66794	pyrimidine metabolism	71.11	32 of 45
66794	lipid metabolism	70.97	22 of 31
66794	arginine metabolism	70.83	17 of 24
66794	acetyl CoA biosynthesis	66.67	2 of 3
66794	d-mannose degradation	66.67	6 of 9
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	methane metabolism	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	IAA biosynthesis	66.67	2 of 3
66794	glycolysis	64.71	11 of 17
66794	vitamin B6 metabolism	63.64	7 of 11
66794	pentose phosphate pathway	63.64	7 of 11
66794	degradation of sugar alcohols	62.5	10 of 16
66794	isoprenoid biosynthesis	61.54	16 of 26
66794	urea cycle	61.54	8 of 13
66794	sulfate reduction	61.54	8 of 13
66794	non-pathway related	60.53	23 of 38
66794	oxidative phosphorylation	60.44	55 of 91
66794	gallate degradation	60	3 of 5
66794	4-hydroxyphenylacetate degradation	60	6 of 10
66794	hydrogen production	60	3 of 5
66794	lipoate biosynthesis	60	3 of 5
66794	lysine metabolism	59.52	25 of 42
66794	histidine metabolism	58.62	17 of 29
66794	tetrahydrofolate metabolism	57.14	8 of 14
66794	androgen and estrogen metabolism	56.25	9 of 16
66794	nitrate assimilation	55.56	5 of 9
66794	aspartate and asparagine metabolism	55.56	5 of 9
66794	cysteine metabolism	55.56	10 of 18
66794	coenzyme M biosynthesis	50	5 of 10
66794	selenocysteine biosynthesis	50	3 of 6
66794	ketogluconate metabolism	50	4 of 8
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	glycine metabolism	50	5 of 10
66794	phenylmercury acetate degradation	50	1 of 2
66794	dTDPLrhamnose biosynthesis	50	4 of 8
66794	sulfopterin metabolism	50	2 of 4
66794	biotin biosynthesis	50	2 of 4
66794	ethanol fermentation	50	1 of 2
66794	mannosylglycerate biosynthesis	50	1 of 2
66794	glycogen biosynthesis	50	2 of 4
66794	quinate degradation	50	1 of 2
66794	bile acid biosynthesis, neutral pathway	47.06	8 of 17
66794	arachidonic acid metabolism	44.44	8 of 18
66794	benzoyl-CoA degradation	42.86	3 of 7
66794	creatinine degradation	40	2 of 5
66794	3-chlorocatechol degradation	40	2 of 5
66794	arachidonate biosynthesis	40	2 of 5
66794	glycine betaine biosynthesis	40	2 of 5
66794	glycogen metabolism	40	2 of 5
66794	elloramycin biosynthesis	40	2 of 5
66794	vitamin K metabolism	40	2 of 5
66794	factor 420 biosynthesis	40	2 of 5
66794	D-cycloserine biosynthesis	40	2 of 5
66794	polyamine pathway	39.13	9 of 23
66794	degradation of hexoses	38.89	7 of 18
66794	carnitine metabolism	37.5	3 of 8
66794	vitamin B12 metabolism	35.29	12 of 34
66794	enterobactin biosynthesis	33.33	1 of 3
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	sphingosine metabolism	33.33	2 of 6
66794	degradation of pentoses	32.14	9 of 28
66794	ascorbate metabolism	31.82	7 of 22
66794	phosphatidylethanolamine bioynthesis	30.77	4 of 13
66794	myo-inositol biosynthesis	30	3 of 10
66794	metabolism of disaccharids	27.27	3 of 11
66794	catecholamine biosynthesis	25	1 of 4
66794	lactate fermentation	25	1 of 4
66794	cyclohexanol degradation	25	1 of 4
66794	toluene degradation	25	1 of 4
66794	methanogenesis from CO2	25	3 of 12
66794	alginate biosynthesis	25	1 of 4
66794	degradation of sugar acids	24	6 of 25
66794	carotenoid biosynthesis	22.73	5 of 22

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
21193	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	not determinedn.d.

Isolation, sampling and environmental information

Isolation source categories

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

Isolation

@ref	Sample type	Sampling date	Geographic location	Country	Country ISO 3 Code	Continent
21193	sediment from tidal flat		Saemankum, Yellow Sea	Republic of Korea	KOR	Asia
60719	Tidal flat sediment	2006	Saemankum,Yellow Sea	Republic of Korea	KOR	Asia
67771	From tideland		Saemankum	Republic of Korea	KOR	Asia

Taxonmaps

69479

Global distribution of 16S sequence EU336981 (>99% sequence identity) for Lutimaribacter saemankumensis subclade from Microbeatlas

Aquatic Samples	210
Soil Samples	17
Animal Samples	1
Plant Samples
Total Samples	228

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
21193	1	Risk group (German classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	IMG-taxon 2675903213 annotated assembly for Lutimaribacter saemankumensis DSM 28010	contig	GCA_900100005	490829.3	2675903213	490829	69.77

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
28875	Lutimaribacter saemankumensis strain SMK-117 16S ribosomal RNA gene, partial sequence	EU336981	1420		490829
124043	Lutimaribacter saemankumensis strain DSM 28010 16S ribosomal RNA gene, partial sequence.	MZ276313	1366		490829

GC content

@ref	GC-content (mol%)	Method
21193	63.5	high performance liquid chromatography (HPLC)
28875	63.5

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Lutimaribacter saemankumensis DSM 28010
NCBI: GCA_900100005

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	98.60	no
125439	motility	BacteriaNetⓘ	yes	75.20	no
125439	gram_stain	BacteriaNetⓘ	negative	98.90	no
125439	oxygen_tolerance	BacteriaNetⓘ	facultative aerobe	76.90	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Lutimaribacter saemankumensis strain DSM 28010
PATRIC: 490829.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	99.00	yes
125438	anaerobic	anaerobicⓘ	no	92.81	no
125438	spore-forming	spore-formingⓘ	no	92.30	no
125438	aerobic	aerobicⓘ	yes	86.93	no
125438	thermophilic	thermophileⓘ	no	97.44	yes
125438	flagellated	motile2+ⓘ	no	81.68	yes

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Lutimaribacter marinistellae sp. nov., isolated from a starfish.	Zhang Y, Tang P, Xu Y, Fang W, Wang X, Fang Z, Xiao Y	Int J Syst Evol Microbiol	10.1099/ijsem.0.001251	2016
Phylogeny	Lutimaribacter saemankumensis gen. nov., sp. nov., isolated from a tidal flat of the Yellow Sea.	Yoon JH, Kang SJ, Lee JS, Oh TK	Int J Syst Evol Microbiol	10.1099/ijs.0.000109-0	2009

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 )
#21193	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 28010
#25315	IJSEM 48 2009 ( DOI 10.1099/ijs.0.000109-0 , PubMed 19126722 )
#28875	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 #25315
#60719	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 55760
#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;
#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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Lutimaribacter saemankumensis (DSM 28010, CCUG 55760, KCTC 22244)

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

Spore formation

Halophily

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

Pathway annotation

API 20NE

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_900100005

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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