Marinicella litoralis (DSM 25488, JCM 16154, KMM 3900)

Name: Marinicella litoralis (DSM 25488, JCM 16154, KMM 3900)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 17915

Type strain

Culture col. no. DSM 25488 JCM 16154 KMM 3900 NRIC 0758

NCBI tax ID(s) 644220

Special Collections DSMZ JCM Literature strains

History DSMZ <- L. A. Romanenko, Pacific Inst. Bioorg. Chem., RAS, Vladivostok, Russia; KMM 3900 JCM <-- N. Tanaka <-- L. A. Romanenko SW2-10 (=KMM 3900).

Links

Marinicella litoralis DSM 25488 is an aerobe, Gram-negative, rod-shaped bacterium that was isolated from coastal seawater.

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

Name and taxonomic classification

SI-ID 401159

JCM 16154,DSM 25488

@ref 20215

Last LPSN update 2026-05-29 08:29:07

Domain Bacteria

Phylum Pseudomonadota

Class Gammaproteobacteria

Order Lysobacterales

Family Marinicellaceae

Genus Marinicella

Species Marinicella litoralis

Full scientific name Marinicella litoralis Romanenko et al. 2010

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
29574	negative	1.8-4.5 µm	0.4-0.6 µm	rod-shaped
125438	negative				98.833
125439	negative				95.59

Pigmentation

29574

Productionyes

Multimedia

@ref:	18044
multimedia content:	DSM_25488.jpg
multimedia.multimedia content:	https://www.dsmz.de/microorganisms/photos/DSM_25488.jpg
intellectual property rights:	© Leibniz-Institut DSMZ
manual_annotation:	1

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
18044	REACTIVATION WITH LIQUID MEDIUM 514 (DSMZ Medium 514c)		Medium recipe at MediaDive	Name: REACTIVATION WITH LIQUID MEDIUM 514 (DSMZ Medium 514c) Composition: NaCl 19.45 g/l Agar 18.0 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 Na2CO3 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)
18044	positive	growth	28
29574	positive	growth	05-35
29574	positive	optimum	25-28
67770	positive	growth	25

Culture pH

@ref	Ability	Type	PH	PH range
29574	positive	optimum	8.5-9.5
29574	positive	growth	06-11	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
29574	aerobe
125439	obligate aerobe	99.3

Spore formation

@ref	Spore formation	Confidence
125439		99.278
125438		95.691

Halophily

@ref	Salt	Growth	Tested relation	Concentration
29574	NaCl	positive	growth	01-05 %
29574	NaCl	positive	optimum	02-03 %

Observation

@ref	Observation
29574	aggregates in chains
67770	quinones: Q-8

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
29574	17128 ChEBI	adipate	+	carbon source
29574	22599 ChEBI	arabinose	+	carbon source
29574	16947 ChEBI	citrate	+	carbon source
29574	24265 ChEBI	gluconate	+	carbon source
29574	17234 ChEBI	glucose	+	carbon source
29574	25115 ChEBI	malate	+	carbon source
29574	17306 ChEBI	maltose	+	carbon source
29574	29864 ChEBI	mannitol	+	carbon source
29574	37684 ChEBI	mannose	+	carbon source
29574	53424 ChEBI	tween 20	+	carbon source
29574	53423 ChEBI	tween 40	+	carbon source
29574	53426 ChEBI	tween 80	+	carbon source

Enzymes

@ref	Value	Activity	Ec
29574	catalase	+	1.11.1.6
29574	cytochrome oxidase	+	1.9.3.1

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	denitrification	100	2 of 2
66794	methylglyoxal degradation	100	5 of 5
66794	sulfopterin metabolism	100	4 of 4
66794	coenzyme A metabolism	100	4 of 4
66794	formaldehyde oxidation	100	3 of 3
66794	adipate degradation	100	2 of 2
66794	phenylacetate degradation (aerobic)	100	5 of 5
66794	molybdenum cofactor biosynthesis	100	9 of 9
66794	cardiolipin biosynthesis	100	7 of 7
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	palmitate biosynthesis	100	22 of 22
66794	biotin biosynthesis	100	4 of 4
66794	folate polyglutamylation	100	1 of 1
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	suberin monomers biosynthesis	100	2 of 2
66794	ppGpp biosynthesis	100	4 of 4
66794	valine metabolism	100	9 of 9
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	photosynthesis	92.86	13 of 14
66794	chorismate metabolism	88.89	8 of 9
66794	serine metabolism	88.89	8 of 9
66794	CO2 fixation in Crenarchaeota	88.89	8 of 9
66794	tetrahydrofolate metabolism	85.71	12 of 14
66794	alanine metabolism	82.76	24 of 29
66794	tryptophan metabolism	81.58	31 of 38
66794	cellulose degradation	80	4 of 5
66794	threonine metabolism	80	8 of 10
66794	glycine betaine biosynthesis	80	4 of 5
66794	peptidoglycan biosynthesis	80	12 of 15
66794	purine metabolism	78.72	74 of 94
66794	heme 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	leucine metabolism	76.92	10 of 13
66794	phenylalanine metabolism	76.92	10 of 13
66794	pyrimidine metabolism	75.56	34 of 45
66794	CMP-KDO biosynthesis	75	3 of 4
66794	glycogen biosynthesis	75	3 of 4
66794	gluconeogenesis	75	6 of 8
66794	C4 and CAM-carbon fixation	75	6 of 8
66794	isoleucine metabolism	75	6 of 8
66794	acetate fermentation	75	3 of 4
66794	glutamate and glutamine metabolism	75	21 of 28
66794	methionine metabolism	73.08	19 of 26
66794	NAD metabolism	72.22	13 of 18
66794	ubiquinone biosynthesis	71.43	5 of 7
66794	lysine metabolism	71.43	30 of 42
66794	lipid metabolism	70.97	22 of 31
66794	propionate fermentation	70	7 of 10
66794	methane metabolism	66.67	2 of 3
66794	IAA biosynthesis	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	octane oxidation	66.67	2 of 3
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	glycolysis	64.71	11 of 17
66794	citric acid cycle	64.29	9 of 14
66794	glutathione metabolism	64.29	9 of 14
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
66794	histidine metabolism	62.07	18 of 29
66794	lipoate biosynthesis	60	3 of 5
66794	flavin biosynthesis	60	9 of 15
66794	D-cycloserine biosynthesis	60	3 of 5
66794	gallate degradation	60	3 of 5
66794	tyrosine metabolism	57.14	8 of 14
66794	allantoin degradation	55.56	5 of 9
66794	cysteine metabolism	55.56	10 of 18
66794	d-mannose degradation	55.56	5 of 9
66794	proline metabolism	54.55	6 of 11
66794	vitamin B6 metabolism	54.55	6 of 11
66794	isoprenoid biosynthesis	53.85	14 of 26
66794	non-pathway related	52.63	20 of 38
66794	phenol degradation	50	10 of 20
66794	glycine metabolism	50	5 of 10
66794	ethanol fermentation	50	1 of 2
66794	arachidonic acid metabolism	50	9 of 18
66794	resorcinol degradation	50	1 of 2
66794	toluene degradation	50	2 of 4
66794	Entner Doudoroff pathway	50	5 of 10
66794	degradation of aromatic, nitrogen containing compounds	50	6 of 12
66794	ketogluconate metabolism	50	4 of 8
66794	dTDPLrhamnose biosynthesis	50	4 of 8
66794	urea cycle	46.15	6 of 13
66794	pentose phosphate pathway	45.45	5 of 11
66794	propanol degradation	42.86	3 of 7
66794	reductive acetyl coenzyme A pathway	42.86	3 of 7
66794	arginine metabolism	41.67	10 of 24
66794	arachidonate biosynthesis	40	2 of 5
66794	starch degradation	40	4 of 10
66794	4-hydroxyphenylacetate degradation	40	4 of 10
66794	3-chlorocatechol degradation	40	2 of 5
66794	sulfate reduction	38.46	5 of 13
66794	carnitine metabolism	37.5	3 of 8
66794	enterobactin biosynthesis	33.33	1 of 3
66794	glycolate and glyoxylate degradation	33.33	2 of 6
66794	3-phenylpropionate degradation	33.33	5 of 15
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	pantothenate biosynthesis	33.33	2 of 6
66794	nitrate assimilation	33.33	3 of 9
66794	selenocysteine biosynthesis	33.33	2 of 6
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	cyanate degradation	33.33	1 of 3
66794	sphingosine metabolism	33.33	2 of 6
66794	ascorbate metabolism	31.82	7 of 22
66794	androgen and estrogen metabolism	31.25	5 of 16
66794	vitamin B1 metabolism	30.77	4 of 13
66794	aclacinomycin biosynthesis	28.57	2 of 7
66794	degradation of hexoses	27.78	5 of 18
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	cholesterol biosynthesis	27.27	3 of 11
66794	metabolism of disaccharids	27.27	3 of 11
66794	oxidative phosphorylation	26.37	24 of 91
66794	polyamine pathway	26.09	6 of 23
66794	butanoate fermentation	25	1 of 4
66794	lactate fermentation	25	1 of 4
66794	cyclohexanol degradation	25	1 of 4
66794	catecholamine biosynthesis	25	1 of 4
66794	vitamin E metabolism	25	1 of 4
66794	4-hydroxymandelate degradation	22.22	2 of 9
66794	degradation of pentoses	21.43	6 of 28

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Marine
#Environmental	#Terrestrial	#Coast

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Latitude	Longitude
18044	coastal seawater	Sea of Japan	Russia	RUS	Asia	42.83	133.369 42.83/133.369
67770	Coastal seawater sample collected from the Sea of Japan		Russia	RUS

Taxonmaps

69479

Global distribution of 16S sequence AB500095 (>99% sequence identity) for Marinicella litoralis subclade from Microbeatlas

Aquatic Samples	1053
Soil Samples	4
Animal Samples	56
Plant Samples	7
Total Samples	1120

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
18044	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
67770	ASM436333v1 assembly for Marinicella litoralis DSM 25488	scaffold	GCA_004363335	644220.5	2757320364	644220	72.3
67770	ASM259191v1 assembly for Marinicella litoralis KMM 3900	scaffold	GCA_002591915	644220.3	2833851722	644220	70.52

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
18044	Marinicella litoralis gene for 16S ribosomal RNA, partial sequence	AB500095	1519		644220

GC content

@ref	GC-content (mol%)	Method
18044	43.8
67770	43.8	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: ASM436333v1 assembly for Marinicella litoralis DSM 25488
BV-BRC: 644220.5

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	99.30	no
125439	motility	BacteriaNetⓘ	yes	52.16	no
125439	gram_stain	BacteriaNetⓘ	negative	95.59	no
125439	spore_formation	BacteriaNetⓘ	no	99.28	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Marinicella litoralis strain DSM 25488
PATRIC: 644220.5

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	98.83	yes
125438	anaerobic	anaerobicⓘ	no	96.08	yes
125438	aerobic	aerobicⓘ	yes	78.18	no
125438	spore-forming	spore-formingⓘ	no	95.69	no
125438	thermophilic	thermophileⓘ	no	96.71	yes
125438	flagellated	motile2+ⓘ	no	70.96	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Bacterial Abundance, Diversity and Activity During Long-Term Colonization of Non-biodegradable and Biodegradable Plastics in Seawater.	Odobel C, Dussud C, Philip L, Derippe G, Lauters M, Eyheraguibel B, Burgaud G, Ter Halle A, Meistertzheim AL, Bruzaud S, Barbe V, Ghiglione JF.	Front Microbiol	10.3389/fmicb.2021.734782	2021
	Horizontal gene transfer and symbiotic microorganisms regulate the adaptive evolution of intertidal algae, Porphyra sense lato.	Wang W, Ge Q, Wen J, Zhang H, Guo Y, Li Z, Xu Y, Ji D, Chen C, Guo L, Xu M, Shi C, Fan G, Xie C.	Commun Biol	10.1038/s42003-024-06663-y	2024
	Structure of phosphorylated and sulfated polysaccharides from lipopolysaccharide of marine bacterium Marinicella litoralis KMM 3900(T).	Kokoulin MS, Lizanov IN, Romanenko LA, Chikalovets IV	Carbohydr Res	10.1016/j.carres.2020.107961	2020
Phylogeny	Marinicella meishanensis sp. nov., a novel Marinicella member isolated from coastal mudflat sediment of Meishan Islandin the East China Sea.	Liu X, Chen Y, Guo Y, He S, Zhang W, Ding L.	Int J Syst Evol Microbiol	10.1099/ijsem.0.006374	2024
Phylogeny	Marinicella rhabdoformis sp. nov., isolated from coastal sediment.	Zhong YL, Sun XK, Hui JG, Teng HL, Du ZJ	Int J Syst Evol Microbiol	10.1099/ijsem.0.004210	2020
Phylogeny	Marinicella sediminis sp. nov., isolated from marine sediment.	Wang XQ, Li CM, Dunlap CA, Rooney AP, Du ZJ	Int J Syst Evol Microbiol	10.1099/ijsem.0.002839	2018
Phylogeny	Marinicella pacifica sp. nov., isolated from seawater.	Wang Y, Liu Y, Zhang Z, Zheng Y, Zhang XH	Int J Syst Evol Microbiol	10.1099/ijsem.0.001027	2016
Phylogeny	Marinicella litoralis gen. nov., sp. nov., a gammaproteobacterium isolated from coastal seawater.	Romanenko LA, Tanaka N, Frolova GM, Mikhailov VV	Int J Syst Evol Microbiol	10.1099/ijs.0.016147-0	2009

References

#18044	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 25488
#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 )
#25967	IJSEM 1613 2010 ( DOI 10.1099/ijs.0.016147-0 , PubMed 19700452 )
#29574	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 #25967
#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;
#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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Marinicella litoralis (DSM 25488, JCM 16154, KMM 3900)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

Multimedia

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Observation

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_004363335

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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