Sphingomicrobium astaxanthinifaciens (JCM 18551, BCRC 80465, CC-AMO-30B)

Name: Sphingomicrobium astaxanthinifaciens (JCM 18551, BCRC 80465, CC-AMO-30B)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 133944

Type strain

Strain Designation CC-AMO-30B

Culture col. no. JCM 18551 BCRC 80465 CC-AMO-30B

NCBI tax ID(s) 1227949

Special Collections JCM Literature strains

Links

Sphingomicrobium astaxanthinifaciens CC-AMO-30B is an aerobe, Gram-negative, rod-shaped prokaryote that was isolated from seawater.

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

Name and taxonomic classification

SI-ID 129386

BCRC 80465,JCM 18551

@ref 20215

Last LPSN update 2025-12-16 10:01:55

Domain Pseudomonadati

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Sphingomonadales

Family Sphingomonadaceae

Genus Sphingomicrobium

Species Sphingomicrobium astaxanthinifaciens

Full scientific name Sphingomicrobium astaxanthinifaciens Shahina et al. 2013

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
30926	negative	1.95 µm	0.6 µm	rod-shaped
125439	negative				98.7
125438	negative				96.969

Pigmentation

30926

Productionyes

Culture and growth conditions

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
30926	positive	growth	20-45
30926	positive	optimum	33.5	mesophilic
67770	positive	growth	30	mesophilic

Culture pH

@ref	Ability	Type	PH	PH range
30926	positive	optimum	7
30926	positive	growth	6.5-10.5	alkaliphile

Physiology and metabolism

Oxygen tolerance

30926

Oxygen toleranceaerobe

Spore formation

@ref	Spore formation	Confidence
30926
125439		97.1
125438		93.844

Halophily

@ref	Salt	Growth	Tested relation	Concentration
30926	NaCl	positive	growth	01-04 %
30926	NaCl	positive	optimum	3 %

Observation

@ref	Observation
30926	aggregates in clumps
67770	quinones: Q-10, Q-9

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
30926	62064 ChEBI	2,3-butanediol	+	carbon source
30926	16449 ChEBI	alanine	+	carbon source
30926	40585 ChEBI	alpha-cyclodextrin	+	carbon source
30926	35391 ChEBI	aspartate	+	carbon source
30926	16947 ChEBI	citrate	+	carbon source
30926	4853 ChEBI	esculin	+	hydrolysis
30926	28757 ChEBI	fructose	+	carbon source
30926	33984 ChEBI	fucose	+	carbon source
30926	28260 ChEBI	galactose	+	carbon source
30926	24175 ChEBI	galacturonate	+	carbon source
30926	24265 ChEBI	gluconate	+	carbon source
30926	17234 ChEBI	glucose	+	carbon source
30926	32323 ChEBI	glucuronamide	+	carbon source
30926	29987 ChEBI	glutamate	+	carbon source
30926	15428 ChEBI	glycine	+	carbon source
30926	27570 ChEBI	histidine	+	carbon source
30926	21217 ChEBI	L-alaninamide	+	carbon source
30926	18403 ChEBI	L-arabitol	+	carbon source
30926	24996 ChEBI	lactate	+	carbon source
30926	17716 ChEBI	lactose	+	carbon source
30926	25017 ChEBI	leucine	+	carbon source
30926	15792 ChEBI	malonate	+	carbon source
30926	17306 ChEBI	maltose	+	carbon source
30926	29864 ChEBI	mannitol	+	carbon source
30926	37657 ChEBI	methyl D-glucoside	+	carbon source
30926	506227 ChEBI	N-acetylglucosamine	+	carbon source
30926	18257 ChEBI	ornithine	+	carbon source
30926	28044 ChEBI	phenylalanine	+	carbon source
30926	26271 ChEBI	proline	+	carbon source
30926	16634 ChEBI	raffinose	+	carbon source
30926	26546 ChEBI	rhamnose	+	carbon source
30926	15963 ChEBI	ribitol	+	carbon source
30926	17822 ChEBI	serine	+	carbon source
30926	30911 ChEBI	sorbitol	+	carbon source
30926	30031 ChEBI	succinate	+	carbon source
30926	26986 ChEBI	threonine	+	carbon source
30926	17748 ChEBI	thymidine	+	carbon source
30926	27082 ChEBI	trehalose	+	carbon source
30926	17151 ChEBI	xylitol	+	carbon source

Enzymes

@ref	Value	Activity	Ec
30926	acid phosphatase	+	3.1.3.2
30926	alkaline phosphatase	+	3.1.3.1
30926	catalase	+	1.11.1.6
30926	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
30926	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 JX235675 (>99% sequence identity) for Sphingomicrobium from Microbeatlas

Aquatic Samples	99
Soil Samples	113
Animal Samples	30
Plant Samples	28
Total Samples	270

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM2286510v1 assembly for Sphingomicrobium astaxanthinifaciens JCM 18551	contig	GCA_022865105	1227949.4	8118781336	1227949	73.07
66792	ASM2615715v1 assembly for Sphingomicrobium astaxanthinifaciens JCM 18551	scaffold	GCA_026157155	1227949.5	8048684090	1227949	72.47

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
30926	Sphingomicrobium astaxanthinifaciens strain CC-AMO-30B 16S ribosomal RNA gene, partial sequence	JX235675	1443		1227949

GC content

@ref	GC-content (mol%)	Method
30926	70.6
67770	70.6	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: Sphingomicrobium astaxanthinifaciens JCM 18551
NCBI: GCA_022865105

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	97.10	no
125439	motility	BacteriaNetⓘ	yes	72.20	no
125439	gram_stain	BacteriaNetⓘ	negative	98.70	no
125439	oxygen_tolerance	BacteriaNetⓘ	facultative aerobe	68.70	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Sphingomicrobium astaxanthinifaciens JCM 18551
NCBI: GCA_026157155.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	96.97	yes
125438	anaerobic	anaerobicⓘ	no	95.38	yes
125438	aerobic	aerobicⓘ	yes	83.88	yes
125438	spore-forming	spore-formingⓘ	no	93.84	yes
125438	thermophilic	thermophileⓘ	no	93.23	yes
125438	flagellated	motile2+ⓘ	yes	52.92	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Sphingomicrobium clamense sp. nov., Isolated from Sediment of Clam Island Beach in China.	Li X, Mu L, Zhang Y, Zhu Z, Xiao Y, Fang Z.	Curr Microbiol	10.1007/s00284-024-03639-3	2024
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
Phylogeny	Sphingomicrobium astaxanthinifaciens sp. nov., an astaxanthin-producing glycolipid-rich bacterium isolated from surface seawater and emended description of the genus Sphingomicrobium.	Shahina M, Hameed A, Lin SY, Hsu YH, Liu YC, Cheng IC, Lee MR, Lai WA, Lee RJ, Young CC	Int J Syst Evol Microbiol	10.1099/ijs.0.047704-0	2013
Phylogeny	Sphingomicrobium arenosum sp. nov., isolated from marine sediment.	Zhang Q, Kanjanasuntree R, Kim JH, Yoon JH, Sukhoom A, Kantachote D, Kim W	Int J Syst Evol Microbiol	10.1099/ijsem.0.002875	2018
Phylogeny	Sphingomicrobium aestuariivivum sp. nov., isolated from a tidal flat.	Park S, Park JM, Sun Joo E, Won SM, Kyum Kim M, Yoon JH	Int J Syst Evol Microbiol	10.1099/ijs.0.000320	2015

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 )
#30926	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 #27256 (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) .
#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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Sphingomicrobium astaxanthinifaciens (JCM 18551, BCRC 80465, CC-AMO-30B)

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_022865105

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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