Marinicella pacifica (DSM 25600, CGMCC 1.12181, JCM 18208)

Name: Marinicella pacifica (DSM 25600, CGMCC 1.12181, JCM 18208)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 132977

Type strain

Strain Designation sw153

Culture col. no. DSM 25600 CGMCC 1.12181 JCM 18208 sw153

NCBI tax ID(s) 1171543

Special Collections DSMZ JCM Literature strains

History <- X.-H. Zhang, Ocean Univ. China, Qingdao, P. R. China; sw153 X.-H. Zhang sw153.

Links

Marinicella pacifica sw153 is an aerobe, Gram-negative, rod-shaped bacterium that forms circular colonies and was isolated from surface seawater.

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

Name and taxonomic classification

SI-ID 405704

JCM 18208,DSM 25600

@ref 20215

Last LPSN update 2026-02-09 11:31:50

Domain Bacteria

Phylum Pseudomonadota

Class Gammaproteobacteria

Order Lysobacterales

Family Marinicellaceae

Genus Marinicella

Species Marinicella pacifica

Full scientific name Marinicella pacifica Wang et al. 2016

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
43959	negative	1.8-2.2 µm	0.5 µm	rod-shaped
125438	negative				96.833
125439	negative				95

Colony morphology

@ref	Colony size	Colony color	Colony shape	Incubation period	Medium used
43959	0.4-0.5 mm	transparent	circular	2 days	Marine agar 2216

Multimedia

@ref:	24765
multimedia content:	DSM_25600.jpg
multimedia.multimedia content:	https://www.dsmz.de/microorganisms/photos/DSM_25600.jpg
intellectual property rights:	© Leibniz-Institut DSMZ
manual_annotation:	1

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
43959	Marine agar (MA)
24765	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)
24765	positive	growth	28
43959	positive	growth	10-42
43959	positive	optimum	28
67770	positive	growth	28

Culture pH

@ref	Ability	Type	PH	PH range
43959	positive	optimum	7.5-8.5
43959	positive	growth	6.0-10.0	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
43959	aerobe
125439	obligate aerobe	94.8

Spore formation

@ref	Spore formation	Confidence
125438		91.983
125439		98.8

Halophily

@ref	Salt	Growth	Tested relation	Concentration
43959	NaCl	positive	growth	1-8 %(w/v)
43959	NaCl	positive	optimum	2 %(w/v)

Observation

@ref	Observation
43959	quinone Q-8
67770	quinones: Q-8

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
43959	27613 ChEBI	amygdalin	-	builds acid from
43959	22599 ChEBI	arabinose	-	builds acid from
43959	85146 ChEBI	carboxymethylcellulose	+	hydrolysis
43959		casein	+	hydrolysis
43959	17057 ChEBI	cellobiose	-	carbon source
43959	17029 ChEBI	chitin	+	hydrolysis
43959	16947 ChEBI	citrate	-	carbon source
43959	16947 ChEBI	citrate	+	carbon source
43959	15824 ChEBI	D-fructose	+	carbon source
43959	12936 ChEBI	D-galactose	+	carbon source
43959	17784 ChEBI	D-glucosaminic acid	-	carbon source
43959	14314 ChEBI	D-glucose 6-phosphate	-	carbon source
43959	16899 ChEBI	D-mannitol	-	carbon source
43959	16024 ChEBI	D-mannose	-	builds acid from
43959	27605 ChEBI	D-psicose	+	carbon source
43959	16551 ChEBI	D-trehalose	-	carbon source
43959	16991 ChEBI	dna	+	hydrolysis
43959	5291 ChEBI	gelatin	+	hydrolysis
43959	5417 ChEBI	glucosamine	-	builds acid from
43959	17234 ChEBI	glucose	-	fermentation
43959	29042 ChEBI	glucose 1-phosphate	-	carbon source
43959	14336 ChEBI	glycerol 1-phosphate	-	carbon source
43959	17716 ChEBI	lactose	-	builds acid from
43959	6359 ChEBI	lactulose	-	carbon source
43959	17306 ChEBI	maltose	-	carbon source
43959	29864 ChEBI	mannitol	-	builds acid from
43959	28053 ChEBI	melibiose	-	builds acid from
43959	17268 ChEBI	myo-inositol	-	builds acid from
43959	17632 ChEBI	nitrate	-	reduction
43959	16634 ChEBI	raffinose	-	builds acid from
43959	16634 ChEBI	raffinose	+	carbon source
43959	26546 ChEBI	rhamnose	-	builds acid from
43959	17814 ChEBI	salicin	-	builds acid from
43959	28017 ChEBI	starch	+	hydrolysis
43959	17992 ChEBI	sucrose	-	builds acid from
43959	32528 ChEBI	turanose	-	carbon source
43959	53424 ChEBI	tween 20	+	hydrolysis
43959	53423 ChEBI	tween 40	+	hydrolysis
43959	53426 ChEBI	tween 80	+	hydrolysis

Metabolite production

@ref	Chebi-ID	Metabolite
43959	15688 ChEBI	acetoin
43959	16136 ChEBI	hydrogen sulfide
43959	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test	Methylred-test
43959	15688 ChEBI	acetoin	-
43959	17234 ChEBI	glucose		-

Enzymes

@ref	Value	Activity	Ec
43959	catalase	+	1.11.1.6
43959	cytochrome oxidase	+	1.9.3.1

Fatty acid profile

Metadata FA analysis

@ref

43959

Fatty acid	Percentage
C15:0 iso	46.3
C16:1ω6c / C16:1ω7c	19.1
C11:0 iso 3OH	7.1
C11:0 iso	5.6
C16:0	4.9
C16:0 N alcohol	4.1
C15:0 anteiso	3.1
C17:0 iso	1.5
C16:1ω7c alcohol	1.4

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Marine
#Environmental	#Aquatic	#Surface water

Isolation

@ref	Sample type	Geographic location	Latitude	Longitude	Enrichment culture	Enrichment culture duration	Enrichment culture temperature
24765	surface seawater	Pacific Ocean, South Pacific Gyre	-39.3167	-139.8 -39.3167/-139.8
43959	surface seawater of the South Pacific Gyre	South Pacific Gyre	-39.3167	-139.8 -39.3167/-139.8	Marine agar 2216	7 days	28
67770	Surface seawater of the South Pacific Gyre (39° 19' S 139° 48' W)		-39.3167	-139.8 -39.3167/-139.8

Taxonmaps

69479

Global distribution of 16S sequence JQ082140 (>99% sequence identity) for Marinicella pacifica subclade from Microbeatlas

Aquatic Samples	11
Soil Samples
Animal Samples	2
Plant Samples	1
Total Samples	14

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
24765	1	Risk group (German classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
124043	ASM3954316v1 assembly for Marinicella pacifica JCM 18208	contig	GCA_039543165			1171543	64.49
66792	ASM1463663v1 assembly for Marinicella pacifica CGMCC 1.12181	scaffold	GCA_014636635	1171543.3	2989183890	1171543	62.02

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
24765	Marinicella pacifica strain sw153 16S ribosomal RNA gene, partial sequence	JQ082140	1506		1171543

GC content

@ref	GC-content (mol%)	Method
24765	44.5	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: Marinicella pacifica CGMCC 1.12181
NCBI: GCA_014636635

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	94.80	no
125439	gram_stain	BacteriaNetⓘ	negative	95.00	no
125439	motility	BacteriaNetⓘ	yes	57.50	no
125439	spore_formation	BacteriaNetⓘ	no	98.80	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Marinicella pacifica CGMCC 1.12181
NCBI: GCA_014636635.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	96.83	yes
125438	anaerobic	anaerobicⓘ	no	94.14	yes
125438	aerobic	aerobicⓘ	yes	78.02	yes
125438	spore-forming	spore-formingⓘ	no	91.98	no
125438	thermophilic	thermophileⓘ	no	93.73	no
125438	flagellated	motile2+ⓘ	no	71.33	yes

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

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 )
#24765	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 25600
#43959	Yanan Wang, Yan Liu, Zenghu Zhang, Yanfen Zheng, Xiao-Hua Zhang: Marinicella pacifica sp. nov., isolated from seawater. IJSEM 66: 2313 - 2318 2016 ( DOI 10.1099/ijsem.0.001027 , PubMed 26978647 )
#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;
#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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Marinicella pacifica (DSM 25600, CGMCC 1.12181, JCM 18208)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Multimedia

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Observation

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

Fatty acid profile

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_039543165

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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