Sphingomonas astaxanthinifaciens (DSM 22298, CCUG 53608, NBRC 102146)

Name: Sphingomonas astaxanthinifaciens (DSM 22298, CCUG 53608, NBRC 102146)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 14258

Type strain

Strain Designation TDMA-17

Culture col. no. DSM 22298 CCUG 53608 NBRC 102146 TDMA-17

NCBI tax ID(s) 1123267 407019

Special Collections DSMZ CCUG

Links

Sphingomonas astaxanthinifaciens TDMA-17 is an aerobe, mesophilic prokaryote that was isolated from fresh water.

aerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 407095

NBRC 102146,DSM 22298,CCUG 53608

@ref 20215

Last LPSN update 2025-12-16 09:50:18

Domain Pseudomonadati

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Sphingomonadales

Family Sphingomonadaceae

Genus Sphingomonas

Species Sphingomonas astaxanthinifaciens

Full scientific name Sphingomonas astaxanthinifaciens Asker et al. 2008

Synonyms (1)

Pseudosphingomonas astaxanthinifaciens

Morphology

Cell morphology

@ref	Gram stain	Confidence
125438	negative	94.476

Colony morphology

59943

Incubation period2 days

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
16261	R2A MEDIUM (DSMZ Medium 830)		Medium recipe at MediaDive	Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
16261	positive	growth	37	mesophilic
59943	positive	growth	30	mesophilic

Physiology and metabolism

Oxygen tolerance

59943

Oxygen toleranceaerobe

Spore formation

@ref	Spore formation	Confidence
125439		92.7

Compound production

16261

Compoundastaxanthin

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68369	17128 ChEBI	adipate	-	assimilation	from API 20NE
68369	29016 ChEBI	arginine	-	hydrolysis	from API 20NE
68369	17634 ChEBI	D-glucose	+	assimilation	from API 20NE
68369	17634 ChEBI	D-glucose	-	fermentation	from API 20NE
68369	16899 ChEBI	D-mannitol	-	assimilation	from API 20NE
68369	16024 ChEBI	D-mannose	-	assimilation	from API 20NE
68369	27689 ChEBI	decanoate	-	assimilation	from API 20NE
68369	4853 ChEBI	esculin	-	hydrolysis	from API 20NE
68369	5291 ChEBI	gelatin	+	hydrolysis	from API 20NE
68369	24265 ChEBI	gluconate	-	assimilation	from API 20NE
68369	30849 ChEBI	L-arabinose	-	assimilation	from API 20NE
68369	25115 ChEBI	malate	-	assimilation	from API 20NE
68369	17306 ChEBI	maltose	+	assimilation	from API 20NE
68369	59640 ChEBI	N-acetylglucosamine	-	assimilation	from API 20NE
68369	17632 ChEBI	nitrate	-	reduction	from API 20NE
68369	27897 ChEBI	tryptophan	-	energy source	from API 20NE
68369	16199 ChEBI	urea	-	hydrolysis	from API 20NE

Metabolite production

@ref	Chebi-ID	Metabolite	Production
68369	35581 ChEBI	indole		from API 20NE

Metabolite tests

@ref	Chebi-ID	Metabolite	Indole test
68369	35581 ChEBI	indole	-	from API 20NE

Enzymes

@ref	Value	Activity	Ec
68369	arginine dihydrolase	-	3.5.3.6	from API 20NE
68369	beta-glucosidase	-	3.2.1.21	from API 20NE
68369	cytochrome oxidase	-	1.9.3.1	from API 20NE
68369	gelatinase	+		from API 20NE
68369	urease	-	3.5.1.5	from API 20NE

API 20NE

@ref	Reduction of nitratesNO3	TRP	GLU_ Ferm	ADH (Arg)	URE	ESC	GEL	PNPG	GLU_ Assim	ARA	MNE	MAN	NAG	MAL	GNT	CAP	ADI	MLT	CIT	PAC	OX
16261	-	-	-	-	-	-	+	-	+	-	-	-	-	+	-	-	-	-	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Freshwater

Isolation

@ref	Sample type	Sampling date	Geographic location	Country	Country ISO 3 Code	Continent
16261	fresh water		Tottori, Misasa	Japan	JPN	Asia
59943	Water,fresh	2000	Tottori,Misasa	Japan	JPN	Asia

Taxonmaps

69479

Global distribution of 16S sequence AB681719 (>99% sequence identity) for Sphingomonas from Microbeatlas

Aquatic Samples	998
Soil Samples	1316
Animal Samples	348
Plant Samples	126
Total Samples	2788

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
16261	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
66792	ASM71171v1 assembly for Sphingomonas astaxanthinifaciens DSM 22298	contig	GCA_000711715	1123267.3	2565957137	1123267	76.82
124043	ASM3016055v1 assembly for Sphingomonas astaxanthinifaciens DSM 22298 NBRC 102146	scaffold	GCA_030160555	1123267.16	8119407321	1123267	61.77

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
20218	Sphingomonas astaxanthinifaciens gene for 16S rRNA, partial sequence, strain: NBRC 102146	AB681719	1412		1123267
16261	Sphingomonas astaxanthinifaciens gene for 16S ribosomal RNA, partial sequence	AB277583	1396		1123267

GC content

16261

GC-content (mol%)67.7

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Sphingomonas astaxanthinifaciens DSM 22298
NCBI: GCA_000711715

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	aerobe	89.90	no
125439	gram_stain	BacteriaNetⓘ	negative	85.30	no
125439	motility	BacteriaNetⓘ	yes	51.40	no
125439	spore_formation	BacteriaNetⓘ	no	92.70	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Sphingomonas astaxanthinifaciens DSM 22298
PATRIC: 1123267.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	94.48	no
125438	anaerobic	anaerobicⓘ	no	94.18	no
125438	spore-forming	spore-formingⓘ	no	87.60	no
125438	aerobic	aerobicⓘ	yes	88.73	yes
125438	thermophilic	thermophileⓘ	no	92.87	no
125438	flagellated	motile2+ⓘ	no	59.98	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Metabolism	Genomewide characterisation of the genetic diversity of carotenogenesis in bacteria of the order Sphingomonadales.	Siddaramappa S, Viswanathan V, Thiyagarajan S, Narjala A.	Microb Genom	10.1099/mgen.0.000172	2018
Metabolism	Production of the Marine Carotenoid Astaxanthin by Metabolically Engineered Corynebacterium glutamicum.	Henke NA, Heider SA, Peters-Wendisch P, Wendisch VF.	Mar Drugs	10.3390/md14070124	2016
Phylogeny	Purification and Identification of Astaxanthin and Its Novel Derivative Produced by Radio-tolerant Sphingomonas astaxanthinifaciens.	Asker D, Awad TS, Beppu T, Ueda K	Methods Mol Biol	10.1007/978-1-4939-8742-9_10	2018
Phylogeny	Sphingomonas rhizophila sp. nov., isolated from rhizosphere of Hibiscus syriacus.	Yan ZF, Lin P, Won KH, Li CT, Park G, Chin B, Kook M, Wang QJ, Yi TH	Int J Syst Evol Microbiol	10.1099/ijsem.0.002566	2018
Phylogeny	Sphingomonas lacus sp. nov., an astaxanthin-dideoxyglycoside-producing species isolated from soil near a pond.	Kim JH, Kim SH, Kim KH, Lee PC	Int J Syst Evol Microbiol	10.1099/ijs.0.000337	2015
Phylogeny	Parablastomonas arctica gen. nov., sp. nov., isolated from high Arctic glacial till.	Ren L, Chang X, Jiang F, Kan W, Qu Z, Qiu X, Fang C, Peng F	Int J Syst Evol Microbiol	10.1099/ijs.0.067231-0	2014
Phylogeny	Sphingomonas ginsengisoli sp. nov. and Sphingomonas sediminicola sp. nov.	An DS, Liu QM, Lee HG, Jung MS, Kim SC, Lee ST, Im WT	Int J Syst Evol Microbiol	10.1099/ijs.0.039578-0	2012
Phylogeny	Sphingomonas rosea sp. nov. and Sphingomonas swuensis sp. nov., rosy colored beta-glucosidase-producing bacteria isolated from soil.	Srinivasan S, Lee JJ, Kim MK	J Microbiol	10.1007/s12275-011-1017-1	2011
Phylogeny	Sphingomonas humi sp. nov., isolated from soil.	Yi TH, Han CK, Srinivasan S, Lee KJ, Kim MK	J Microbiol	10.1007/s12275-010-0011-3	2010
Phylogeny	Sphingomonas astaxanthinifaciens sp. nov., a novel astaxanthin-producing bacterium of the family Sphingomonadaceae isolated from Misasa, Tottori, Japan.	Asker D, Beppu T, Ueda K	FEMS Microbiol Lett	10.1111/j.1574-6968.2007.00760.x	2007

References

#16261	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 22298
#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 )
#20218	Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 )
#59943	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 53608
#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) .
#68369	Automatically annotated from API 20NE .
#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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Sphingomonas astaxanthinifaciens (DSM 22298, CCUG 53608, NBRC 102146)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Compound production

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

API 20NE

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000711715

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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