Lutimaribacter litoralis (DSM 29506, JCM 17792, KCTC 23660)

Name: Lutimaribacter litoralis (DSM 29506, JCM 17792, KCTC 23660)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 130638

Type strain

Strain Designation KU5D5

Culture col. no. DSM 29506 JCM 17792 KCTC 23660 KU5D5

NCBI tax ID(s) 1010611

Special Collections DSMZ JCM KCTC

History DSMZ <- KCTC <- H. Iwaki, Kansai University, Osaka, Japan; KU5D5 JCM <-- H. Iwaki KU5D5. KCTC <- H Iwaki, Kansai Univ., Japan

Links

Lutimaribacter litoralis KU5D5 is an aerobe, Gram-negative bacterium that was isolated from seawater.

Gram-negative aerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 405226

JCM 17792,KCTC 23660,DSM 29506

@ref 20215

Last LPSN update 2026-05-29 08:37:25

Domain Bacteria

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Rhodobacterales

Family Roseobacteraceae

Genus Lutimaribacter

Species Lutimaribacter litoralis

Full scientific name Lutimaribacter litoralis Iwaki et al. 2013

Synonyms (3)

Thalassovita litoralis
"Youngimonas litoralis"
Thalassobius litoralis

Morphology

Cell morphology

@ref	Gram stain	Confidence
67771	negative
125438	negative	98.5

Colony morphology

22066

Incubation period1-2 days

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
22066	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)
22066	positive	growth	25
67770	positive	growth	25
67771	positive	growth	25

Physiology and metabolism

Oxygen tolerance

67771

Oxygen toleranceaerobe

Spore formation

@ref	Spore formation	Confidence
125438		91.454
125439		90.422

Observation

@ref	Observation
67770	quinones: Q-10
67771	quinones: Q-10

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
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
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
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
22066	catalase	+	1.11.1.6
22066	cytochrome-c oxidase	+	1.9.3.1
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
22066	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	+	-	-	not determinedn.d.

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Marine

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
22066	seawater	coastal region of Goto Islands	Japan	JPN	Asia
67770	Seawater obtained from the coastal region of the Goto Islands		Japan	JPN	Asia
67771	From seawater	Goto Islands	Japan	JPN	Asia

Taxonmaps

69479

Global distribution of 16S sequence AB627076 (>99% sequence identity) for Lutimaribacter litoralis subclade from Microbeatlas

Aquatic Samples	302
Soil Samples	7
Animal Samples	54
Plant Samples	17
Total Samples	380

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
22066	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 2724679730 annotated assembly for Thalassovita litoralis DSM 29506	contig	GCA_900182725	1010611.6	2724679730	1010611	63.62

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
22066	Lutimaribacter litoralis gene for 16S rRNA, partial sequence	AB627076	1425		1010611

GC content

@ref	GC-content (mol%)	Method
67771	58.9
67770	58.9	high performance liquid chromatography (HPLC)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: IMG-taxon 2724679730 annotated assembly for Thalassovita litoralis DSM 29506
NCBI: GCA_900182725

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	86.27	no
125439	motility	BacteriaNetⓘ	no	62.58	no
125439	gram_stain	BacteriaNetⓘ	negative	61.58	no
125439	spore_formation	BacteriaNetⓘ	no	90.42	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Lutimaribacter litoralis strain DSM 29506
PATRIC: 1010611.6

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	98.50	yes
125438	anaerobic	anaerobicⓘ	no	92.28	yes
125438	spore-forming	spore-formingⓘ	no	91.45	no
125438	aerobic	aerobicⓘ	yes	79.41	no
125438	thermophilic	thermophileⓘ	no	96.95	yes
125438	flagellated	motile2+ⓘ	no	73.79	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of Alphaproteobacteria.	Hordt A, Lopez MG, Meier-Kolthoff JP, Schleuning M, Weinhold LM, Tindall BJ, Gronow S, Kyrpides NC, Woyke T, Goker M.	Front Microbiol	10.3389/fmicb.2020.00468	2020
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	Isolation and characterization of a marine cyclohexylacetate-degrading bacterium Lutimaribacter litoralis sp. nov., and reclassification of Oceanicola pacificus as Lutimaribacter pacificus comb. nov.	Iwaki H, Yasukawa N, Fujioka M, Takada K, Hasegawa Y	Curr Microbiol	10.1007/s00284-013-0321-x	2013

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 )
#22066	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 29506
#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) .
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#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 .
#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 litoralis (DSM 29506, JCM 17792, KCTC 23660)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

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_900182725

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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