Sphingomicrobium marinum (JCM 18554, BCRC 80466, CC-AMZ-30M)

Name: Sphingomicrobium marinum (JCM 18554, BCRC 80466, CC-AMZ-30M)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 134043

Type strain

Strain Designation CC-AMZ-30M

Culture col. no. JCM 18554 BCRC 80466 CC-AMZ-30M

NCBI tax ID(s) 1227950

Special Collections JCM Literature strains

History JCM <-- C.-C. Young CC-AMZ-30M.

Links

Sphingomicrobium marinum CC-AMZ-30M is an aerobe, Gram-negative, rod-shaped bacterium that was isolated from seawater.

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

Name and taxonomic classification

SI-ID 27124

BCRC 80466,JCM 18554

@ref 20215

Last LPSN update 2026-05-29 08:38:14

Domain Bacteria

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Sphingomonadales

Family Sphingomonadaceae

Genus Sphingomicrobium

Species Sphingomicrobium marinum

Full scientific name Sphingomicrobium marinum Shahina et al. 2013

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
31126	negative	1.6 µm	0.55 µm	rod-shaped
125438	negative				97.5

Pigmentation

31126

Productionyes

Culture and growth conditions

Culture temp

@ref	Growth	Type	Temperature (°C)
31126	positive	growth	20-45
31126	positive	optimum	33.5
67770	positive	growth	30

Culture pH

@ref	Ability	Type	PH	PH range
31126	positive	optimum	7.5
31126	positive	growth	6.5-10.5	alkaliphile

Physiology and metabolism

Oxygen tolerance

31126

Oxygen toleranceaerobe

Spore formation

@ref	Spore formation	Confidence
31126
125438		93.85

Halophily

@ref	Salt	Growth	Tested relation	Concentration
31126	NaCl	positive	growth	01-03 %
31126	NaCl	positive	optimum	1 %

Observation

@ref	Observation
31126	aggregates in clumps
67770	quinones: Q-10

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
31126	62064 ChEBI	2,3-butanediol	+	carbon source
31126	16449 ChEBI	alanine	+	carbon source
31126	40585 ChEBI	alpha-cyclodextrin	+	carbon source
31126	22653 ChEBI	asparagine	+	carbon source
31126	17057 ChEBI	cellobiose	+	carbon source
31126	16947 ChEBI	citrate	+	carbon source
31126	17126 ChEBI	DL-carnitine	+	carbon source
31126	4853 ChEBI	esculin	+	hydrolysis
31126	15740 ChEBI	formate	+	carbon source
31126	28757 ChEBI	fructose	+	carbon source
31126	33984 ChEBI	fucose	+	carbon source
31126	28260 ChEBI	galactose	+	carbon source
31126	24175 ChEBI	galacturonate	+	carbon source
31126	24265 ChEBI	gluconate	+	carbon source
31126	5417 ChEBI	glucosamine	+	carbon source
31126	17234 ChEBI	glucose	+	carbon source
31126	32323 ChEBI	glucuronamide	+	carbon source
31126	28087 ChEBI	glycogen	+	carbon source
31126	27570 ChEBI	histidine	+	carbon source
31126	21217 ChEBI	L-alaninamide	+	carbon source
31126	18403 ChEBI	L-arabitol	+	carbon source
31126	17716 ChEBI	lactose	+	carbon source
31126	25017 ChEBI	leucine	+	carbon source
31126	17306 ChEBI	maltose	+	carbon source
31126	28053 ChEBI	melibiose	+	carbon source
31126	37657 ChEBI	methyl D-glucoside	+	carbon source
31126	17268 ChEBI	myo-inositol	+	carbon source
31126	506227 ChEBI	N-acetylglucosamine	+	carbon source
31126	18257 ChEBI	ornithine	+	carbon source
31126	28044 ChEBI	phenylalanine	+	carbon source
31126	26271 ChEBI	proline	+	carbon source
31126	17272 ChEBI	propionate	+	carbon source
31126	26490 ChEBI	quinate	+	carbon source
31126	16634 ChEBI	raffinose	+	carbon source
31126	26546 ChEBI	rhamnose	+	carbon source
31126	15963 ChEBI	ribitol	+	carbon source
31126	17822 ChEBI	serine	+	carbon source
31126	30911 ChEBI	sorbitol	+	carbon source
31126	30031 ChEBI	succinate	+	carbon source
31126	17992 ChEBI	sucrose	+	carbon source
31126	26986 ChEBI	threonine	+	carbon source
31126	27082 ChEBI	trehalose	+	carbon source
31126	16704 ChEBI	uridine	+	carbon source
31126	17151 ChEBI	xylitol	+	carbon source

Enzymes

@ref	Value	Activity	Ec
31126	acid phosphatase	+	3.1.3.2
31126	alkaline phosphatase	+	3.1.3.1
31126	catalase	+	1.11.1.6
31126	cytochrome oxidase	+	1.9.3.1

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Marine

Isolation

@ref	Sample type	Country	Country ISO 3 Code	Continent
31126	seawater
67770	Surface seawater (10 cm in depth) collected near Taichung harbour	Taiwan, Province of China	TWN	Asia

Taxonmaps

69479

Global distribution of 16S sequence JX235672 (>99% sequence identity) for Sphingomicrobium marinum subclade from Microbeatlas

Aquatic Samples	650
Soil Samples	20
Animal Samples	34
Plant Samples	1
Total Samples	705

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM2615710v1 assembly for Sphingomicrobium marinum JCM 18554	contig	GCA_026157105	1227950.4	8048681786	1227950	78.81

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
31126	Sphingomicrobium marinum strain CC-AMZ-30M 16S ribosomal RNA gene, partial sequence	JX235672	1443		1227950

GC content

@ref	GC-content (mol%)	Method
31126	64.2
67770	64.2	high performance liquid chromatography (HPLC)

Genome-based predictions

Predictions

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Sphingomicrobium marinum JCM 18554
NCBI: GCA_026157105.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	97.50	yes
125438	anaerobic	anaerobicⓘ	no	95.40	yes
125438	aerobic	aerobicⓘ	yes	84.24	yes
125438	spore-forming	spore-formingⓘ	no	93.85	yes
125438	thermophilic	thermophileⓘ	no	94.13	yes
125438	flagellated	motile2+ⓘ	no	66.65	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Sphingomicrobium marinum sp. nov. and Sphingomicrobium flavum sp. nov., isolated from surface seawater, and emended description of the genus Sphingomicrobium.	Shahina M, Hameed A, Lin SY, Hsu YH, Liu YC, Huang YM, Lin JC, Young CC	Int J Syst Evol Microbiol	10.1099/ijs.0.052837-0	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 )
#27455	IJSEM 4469 2013 ( DOI 10.1099/ijs.0.052837-0 , PubMed 23859943 )
#31126	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 #27455
#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 .
#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 )
#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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Sphingomicrobium marinum (JCM 18554, BCRC 80466, CC-AMZ-30M)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

Culture and growth conditions

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Observation

Metabolite utilization

Enzymes

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Sequence information

Genome sequences

Genome browser: GCA_026157105

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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