Name: Marinicella litoralis DSM 25488
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 17915

Type strain:

Species: Marinicella litoralis

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

Strain history: N. Tanaka <-- L. A. Romanenko SW2-10 (=KMM 3900).

NCBI tax ID(s): 644220 (species)

SI-ID 401159

DSM 25488

Section

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

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

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Pseudomonadota*
	Class	*Gammaproteobacteria*
	Order	*Lysobacterales*
	Family	"Marinicellaceae"
	Genus	*Marinicella*
	Species	**Marinicella litoralis**
	Full Scientific Name (LPSN)	Marinicella litoralis Romanenko et al. 2010

Information on morphological and physiological properties Morphology

[Ref.: #29574]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.994

[Ref.: #29574]	Cell length	1.8-4.5 µm

[Ref.: #29574]	Cell width	0.4-0.6 µm

[Ref.: #29574]	Cell shape	rod-shaped

[Ref.: #29574]	Motility	no

[Ref.: #29574]

Pigment production

yes

Multimedia content

[Ref.: #18044]

Intellectual property rights:

Information on culture and growth conditions Culture and growth conditions

[Ref.: #18044]

Culture medium

REACTIVATION WITH LIQUID MEDIUM 514 (DSMZ Medium 514c)

[Ref.: #18044]

Culture medium growth

[Ref.: #18044]

Culture medium link

Medium recipe at MediaDive

[Ref.: #18044]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #18044]	growth	28 °C
[Ref.: #29574]	growth	05-35 °C
[Ref.: #29574]	optimum	25-28 °C
[Ref.: #67770]	growth	25 °C

[Ref.: #18044]	Temperature range	mesophilic
[Ref.: #29574]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #29574]			optimum	8.5-9.5
[Ref.: #29574]			growth	06-11

Information on physiology and metabolism Physiology and metabolism

[Ref.: #29574]

Oxygen tolerance

aerobe

[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.997

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #29574]		NaCl		growth	01-05	%
[Ref.: #29574]		NaCl		optimum	02-03	%

[Ref.: #29574]	Observation	aggregates in chains
[Ref.: #67770]	Observation	quinones: Q-8

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #29574]	adipate ChEBI	+	carbon source
[Ref.: #29574]	arabinose ChEBI	+	carbon source
[Ref.: #29574]	citrate ChEBI	+	carbon source
[Ref.: #29574]	gluconate ChEBI	+	carbon source
[Ref.: #29574]	glucose ChEBI	+	carbon source
[Ref.: #29574]	malate ChEBI	+	carbon source
[Ref.: #29574]	maltose ChEBI	+	carbon source
[Ref.: #29574]	mannitol ChEBI	+	carbon source
[Ref.: #29574]	mannose ChEBI	+	carbon source
[Ref.: #29574]	tween 20 ChEBI	+	carbon source
[Ref.: #29574]	tween 40 ChEBI	+	carbon source
[Ref.: #29574]	tween 80 ChEBI	+	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Enzymes	Enzyme	Enzyme activity	EC number
[Ref.: #29574]		catalase	+	1.11.1.6
[Ref.: #29574]		cytochrome oxidase	+	1.9.3.1

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	denitrification	100	2 of 2
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	sulfopterin metabolism	100	4 of 4
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	phenylacetate degradation (aerobic)	100	5 of 5
[Ref.: #66794]	molybdenum cofactor biosynthesis	100	9 of 9
[Ref.: #66794]	cardiolipin biosynthesis	100	7 of 7
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	valine metabolism	100	9 of 9
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	photosynthesis	92.86	13 of 14
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	serine metabolism	88.89	8 of 9
[Ref.: #66794]	CO2 fixation in Crenarchaeota	88.89	8 of 9
[Ref.: #66794]	tetrahydrofolate metabolism	85.71	12 of 14
[Ref.: #66794]	alanine metabolism	82.76	24 of 29
[Ref.: #66794]	tryptophan metabolism	81.58	31 of 38
[Ref.: #66794]	cellulose degradation	80	4 of 5
[Ref.: #66794]	threonine metabolism	80	8 of 10
[Ref.: #66794]	glycine betaine biosynthesis	80	4 of 5
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	purine metabolism	78.72	74 of 94
[Ref.: #66794]	heme metabolism	78.57	11 of 14
[Ref.: #66794]	aspartate and asparagine metabolism	77.78	7 of 9
[Ref.: #66794]	lipid A biosynthesis	77.78	7 of 9
[Ref.: #66794]	leucine metabolism	76.92	10 of 13
[Ref.: #66794]	phenylalanine metabolism	76.92	10 of 13
[Ref.: #66794]	pyrimidine metabolism	75.56	34 of 45
[Ref.: #66794]	CMP-KDO biosynthesis	75	3 of 4
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	gluconeogenesis	75	6 of 8
[Ref.: #66794]	C4 and CAM-carbon fixation	75	6 of 8
[Ref.: #66794]	isoleucine metabolism	75	6 of 8
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	glutamate and glutamine metabolism	75	21 of 28
[Ref.: #66794]	methionine metabolism	73.08	19 of 26
[Ref.: #66794]	NAD metabolism	72.22	13 of 18
[Ref.: #66794]	ubiquinone biosynthesis	71.43	5 of 7
[Ref.: #66794]	lysine metabolism	71.43	30 of 42
[Ref.: #66794]	lipid metabolism	70.97	22 of 31
[Ref.: #66794]	propionate fermentation	70	7 of 10
[Ref.: #66794]	methane metabolism	66.67	2 of 3
[Ref.: #66794]	IAA biosynthesis	66.67	2 of 3
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	glycolysis	64.71	11 of 17
[Ref.: #66794]	citric acid cycle	64.29	9 of 14
[Ref.: #66794]	glutathione metabolism	64.29	9 of 14
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
[Ref.: #66794]	histidine metabolism	62.07	18 of 29
[Ref.: #66794]	lipoate biosynthesis	60	3 of 5
[Ref.: #66794]	flavin biosynthesis	60	9 of 15
[Ref.: #66794]	D-cycloserine biosynthesis	60	3 of 5
[Ref.: #66794]	gallate degradation	60	3 of 5
[Ref.: #66794]	tyrosine metabolism	57.14	8 of 14
[Ref.: #66794]	allantoin degradation	55.56	5 of 9
[Ref.: #66794]	cysteine metabolism	55.56	10 of 18
[Ref.: #66794]	d-mannose degradation	55.56	5 of 9
[Ref.: #66794]	proline metabolism	54.55	6 of 11
[Ref.: #66794]	vitamin B6 metabolism	54.55	6 of 11
[Ref.: #66794]	isoprenoid biosynthesis	53.85	14 of 26
[Ref.: #66794]	non-pathway related	52.63	20 of 38
[Ref.: #66794]	phenol degradation	50	10 of 20
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	arachidonic acid metabolism	50	9 of 18
[Ref.: #66794]	resorcinol degradation	50	1 of 2
[Ref.: #66794]	toluene degradation	50	2 of 4
[Ref.: #66794]	Entner Doudoroff pathway	50	5 of 10
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	50	6 of 12
[Ref.: #66794]	ketogluconate metabolism	50	4 of 8
[Ref.: #66794]	dTDPLrhamnose biosynthesis	50	4 of 8
[Ref.: #66794]	urea cycle	46.15	6 of 13
[Ref.: #66794]	pentose phosphate pathway	45.45	5 of 11
[Ref.: #66794]	propanol degradation	42.86	3 of 7
[Ref.: #66794]	reductive acetyl coenzyme A pathway	42.86	3 of 7
[Ref.: #66794]	arginine metabolism	41.67	10 of 24
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	starch degradation	40	4 of 10
[Ref.: #66794]	4-hydroxyphenylacetate degradation	40	4 of 10
[Ref.: #66794]	3-chlorocatechol degradation	40	2 of 5
[Ref.: #66794]	sulfate reduction	38.46	5 of 13
[Ref.: #66794]	carnitine metabolism	37.5	3 of 8
[Ref.: #66794]	enterobactin biosynthesis	33.33	1 of 3
[Ref.: #66794]	glycolate and glyoxylate degradation	33.33	2 of 6
[Ref.: #66794]	3-phenylpropionate degradation	33.33	5 of 15
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	pantothenate biosynthesis	33.33	2 of 6
[Ref.: #66794]	nitrate assimilation	33.33	3 of 9
[Ref.: #66794]	selenocysteine biosynthesis	33.33	2 of 6
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	cyanate degradation	33.33	1 of 3
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	ascorbate metabolism	31.82	7 of 22
[Ref.: #66794]	androgen and estrogen metabolism	31.25	5 of 16
[Ref.: #66794]	vitamin B1 metabolism	30.77	4 of 13
[Ref.: #66794]	aclacinomycin biosynthesis	28.57	2 of 7
[Ref.: #66794]	degradation of hexoses	27.78	5 of 18
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
[Ref.: #66794]	cholesterol biosynthesis	27.27	3 of 11
[Ref.: #66794]	metabolism of disaccharids	27.27	3 of 11
[Ref.: #66794]	oxidative phosphorylation	26.37	24 of 91
[Ref.: #66794]	polyamine pathway	26.09	6 of 23
[Ref.: #66794]	butanoate fermentation	25	1 of 4
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	catecholamine biosynthesis	25	1 of 4
[Ref.: #66794]	vitamin E metabolism	25	1 of 4
[Ref.: #66794]	4-hydroxymandelate degradation	22.22	2 of 9
[Ref.: #66794]	degradation of pentoses	21.43	6 of 28
		Only first 10 entries are displayed. Click here to see all.

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #18044]	Sample type/isolated from	coastal seawater
[Ref.: #18044]	Geographic location (country and/or sea, region)	Sea of Japan
[Ref.: #18044]	Country	Russia
[Ref.: #18044]	Country ISO 3 Code	RUS
[Ref.: #18044]	Continent	Asia
[Ref.: #18044]	Geographic location	42.8300°/133.3690°

[Ref.: #67770]	Sample type/isolated from	Coastal seawater sample collected from the Sea of Japan
[Ref.: #67770]	Country	Russia
[Ref.: #67770]	Country ISO 3 Code	RUS
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Marine
#Environmental	#Terrestrial	#Coast

What are isolation sources categories?

[Ref.: #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

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #18044]

Biosafety level

Risk group (German classification)
According to TRBA 466

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #18044]	Marinicella litoralis gene for 16S ribosomal RNA, partial sequence	AB500095	1519	ENA	644220 tax ID

Genome sequence information:

Only first 5 entries are displayed. Click here to see all.

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Marinicella litoralis KMM 3900	GCA_002591915	scaffold	GenBank	644220 tax ID
[Ref.: #67770]	Marinicella litoralis DSM 25488	GCA_004363335	scaffold	GenBank	644220 tax ID
[Ref.: #66792]	Marinicella litoralis strain DSM 25488	644220.5	wgs	PATRIC	644220 tax ID	*
[Ref.: #66792]	Marinicella litoralis strain KMM 3900	644220.3	wgs	PATRIC	644220 tax ID	*
[Ref.: #66792]	Marinicella litoralis KMM 3900	2833851722	draft	JGI IMG/M	644220 tax ID	*
[Ref.: #66792]	Marinicella litoralis DSM 25488	2757320364	draft	JGI IMG/M	644220 tax ID	*

[Ref.: #18044]	GC-content	43.8 mol%
[Ref.: #67770]	GC-content	43.8 mol%	high performance liquid chromatography (HPLC)

Data predicted using genome information as a basis Genome-based predictions

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Marinicella litoralis DSM 25488 NCBI: GCA_004363335.1
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Marinicella litoralis strain DSM 25488 PATRIC: 644220.5
[Ref.: #69480]	gram-positive	no	98.722	yes
[Ref.: #69480]	anaerobic	no	99.268	yes
[Ref.: #69480]	halophile	no	57.355	no
[Ref.: #69480]	spore-forming	no	98.276	no
[Ref.: #69480]	glucose-util	yes	71.891	no
[Ref.: #69480]	thermophile	no	99.101	yes
[Ref.: #69480]	flagellated	no	96.509	yes
[Ref.: #69480]	aerobic	yes	89.66	no
[Ref.: #69480]	motile	no	89.601	yes
[Ref.: #69480]	glucose-ferment	no	89.703	no

Availability in culture collections External links

[Ref.: #18044]

Culture collection no.

DSM 25488, JCM 16154, KMM 3900, NRIC 0758

[Ref.: #86904]

SI-ID 401159

Literature:

Topic	Title	Authors	Journal	DOI	Year
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	*
	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	*

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 )

#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 (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 )

#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 .

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

#86904

Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.: StrainInfo: A central database for resolving microbial strain identifiers . ( DOI 10.60712/SI-ID401159.1 )

#25967

IJSEM 1613 2010 ( DOI 10.1099/ijs.0.016147-0 , PubMed 19700452 )

* These data were automatically processed and therefore are not curated

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Marinicella litoralis DSM 25488

Marinicella litoralis strain DSM 25488

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