Sphingosinicella microcystinivorans (DSM 19791, JCM 13185, KCTC 12019)

Name: Sphingosinicella microcystinivorans (DSM 19791, JCM 13185, KCTC 12019)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 14293

Type strain

Strain Designation Y2

Culture col. no. DSM 19791 JCM 13185 KCTC 12019 Y2 NCIMB 14270 1 more

NCBI tax ID(s) 335406

Special Collections DSMZ JCM KCTC CIP Literature strains

Links

Sphingosinicella microcystinivorans Y2 is an aerobe, mesophilic, Gram-negative prokaryote that was isolated from eutrophic lake.

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

Name and taxonomic classification

SI-ID 289871

JCM 13185,KCTC 12019,CIP 109169,DSM 19791

@ref 20215

Last LPSN update 2025-12-16 09:50:19

Domain Pseudomonadati

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Sphingomonadales

Family Sphingosinicellaceae

Genus Sphingosinicella

Species Sphingosinicella microcystinivorans

Full scientific name Sphingosinicella microcystinivorans Maruyama et al. 2006

Morphology

Cell morphology

@ref	Gram stain	Cell width	Cell shape
31549	negative	0.3-0.7 µm	rod-shaped
67771	negative
120947	negative		oval-shaped
125439	negative
125438	negative

Colony morphology

Pigmentation

31549

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
8320	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
37472	MEDIUM 328- for nutrient agar		Distilled water make up to (1000.000 ml);Agar (15.000 g);Peptone (5.000g);Beef extract (3.000 g)
120947	CIP Medium 328	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
8320	positive	growth	28	mesophilic
31549	positive	growth	10-37
31549	positive	optimum	30	mesophilic
37472	positive	growth	30	mesophilic
67770	positive	growth	30	mesophilic
67771	positive	growth	30	mesophilic

Culture pH

@ref	Ability	Type	PH
31549	positive	optimum	7
31549	positive	growth	07-09

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance
31549	aerobe
67771	aerobe
120947	obligate aerobe
125439	aerobe

Spore formation

@ref	Spore formation
31549
125439
125438

Observation

@ref	Observation
31549	aggregates in chains
67771	quinones: Q-10

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
120947	17632 ChEBI	nitrate	-	reduction
120947	16301 ChEBI	nitrite	-	reduction

Metabolite production

@ref	Chebi-ID	Metabolite	Production
120947	35581 ChEBI	indole

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
120947	alcohol dehydrogenase	-	1.1.1.1
68382	alkaline phosphatase	+	3.1.3.1	from API zym
68382	alpha-chymotrypsin	-	3.4.21.1	from API zym
68382	alpha-fucosidase	-	3.2.1.51	from API zym
68382	alpha-galactosidase	-	3.2.1.22	from API zym
68382	alpha-glucosidase	-	3.2.1.20	from API zym
68382	alpha-mannosidase	-	3.2.1.24	from API zym
68382	beta-galactosidase	-	3.2.1.23	from API zym
68382	beta-glucosidase	-	3.2.1.21	from API zym
68382	beta-glucuronidase	-	3.2.1.31	from API zym
31549	catalase	+	1.11.1.6
120947	catalase	+	1.11.1.6
68382	cystine arylamidase	+	3.4.11.3	from API zym
31549	cytochrome oxidase	+	1.9.3.1
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
68382	leucine arylamidase	+	3.4.11.1	from API zym
68382	lipase (C 14)	-		from API zym
120947	lysine decarboxylase	-	4.1.1.18
68382	N-acetyl-beta-glucosaminidase	+	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
120947	ornithine decarboxylase	-	4.1.1.17
120947	oxidase	+
68382	trypsin	+	3.4.21.4	from API zym
120947	urease	-	3.5.1.5
68382	valine arylamidase	+		from API zym

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	methylglyoxal degradation	100	5 of 5
66794	formaldehyde oxidation	100	3 of 3
66794	phenylacetate degradation (aerobic)	100	5 of 5
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	adipate degradation	100	2 of 2
66794	valine metabolism	100	9 of 9
66794	ethanol fermentation	100	2 of 2
66794	aspartate and asparagine metabolism	100	9 of 9
66794	L-lactaldehyde degradation	100	3 of 3
66794	biotin biosynthesis	100	4 of 4
66794	palmitate biosynthesis	100	22 of 22
66794	ppGpp biosynthesis	100	4 of 4
66794	C4 and CAM-carbon fixation	100	8 of 8
66794	gluconeogenesis	100	8 of 8
66794	suberin monomers biosynthesis	100	2 of 2
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	coenzyme A metabolism	100	4 of 4
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	leucine metabolism	92.31	12 of 13
66794	phenylalanine metabolism	92.31	12 of 13
66794	threonine metabolism	90	9 of 10
66794	propionate fermentation	90	9 of 10
66794	serine metabolism	88.89	8 of 9
66794	CO2 fixation in Crenarchaeota	88.89	8 of 9
66794	photosynthesis	85.71	12 of 14
66794	methionine metabolism	80.77	21 of 26
66794	peptidoglycan biosynthesis	80	12 of 15
66794	Entner Doudoroff pathway	80	8 of 10
66794	glycogen metabolism	80	4 of 5
66794	ethylmalonyl-CoA pathway	80	4 of 5
66794	purine metabolism	78.72	74 of 94
66794	tetrahydrofolate metabolism	78.57	11 of 14
66794	citric acid cycle	78.57	11 of 14
66794	glutamate and glutamine metabolism	78.57	22 of 28
66794	NAD metabolism	77.78	14 of 18
66794	molybdenum cofactor biosynthesis	77.78	7 of 9
66794	chorismate metabolism	77.78	7 of 9
66794	histidine metabolism	75.86	22 of 29
66794	butanoate fermentation	75	3 of 4
66794	cyclohexanol degradation	75	3 of 4
66794	isoleucine metabolism	75	6 of 8
66794	sulfopterin metabolism	75	3 of 4
66794	acetate fermentation	75	3 of 4
66794	proline metabolism	72.73	8 of 11
66794	pentose phosphate pathway	72.73	8 of 11
66794	alanine metabolism	72.41	21 of 29
66794	reductive acetyl coenzyme A pathway	71.43	5 of 7
66794	propanol degradation	71.43	5 of 7
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	ubiquinone biosynthesis	71.43	5 of 7
66794	heme metabolism	71.43	10 of 14
66794	glycolysis	70.59	12 of 17
66794	vitamin B1 metabolism	69.23	9 of 13
66794	tryptophan metabolism	68.42	26 of 38
66794	cyanate degradation	66.67	2 of 3
66794	octane oxidation	66.67	2 of 3
66794	methane metabolism	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	tyrosine metabolism	64.29	9 of 14
66794	glutathione metabolism	64.29	9 of 14
66794	vitamin B6 metabolism	63.64	7 of 11
66794	arginine metabolism	62.5	15 of 24
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
66794	pyrimidine metabolism	62.22	28 of 45
66794	urea cycle	61.54	8 of 13
66794	phosphatidylethanolamine bioynthesis	61.54	8 of 13
66794	lipid metabolism	61.29	19 of 31
66794	cysteine metabolism	61.11	11 of 18
66794	metabolism of amino sugars and derivatives	60	3 of 5
66794	vitamin K metabolism	60	3 of 5
66794	myo-inositol biosynthesis	60	6 of 10
66794	3-phenylpropionate degradation	60	9 of 15
66794	lipoate biosynthesis	60	3 of 5
66794	degradation of aromatic, nitrogen containing compounds	58.33	7 of 12
66794	isoprenoid biosynthesis	57.69	15 of 26
66794	androgen and estrogen metabolism	56.25	9 of 16
66794	d-mannose degradation	55.56	5 of 9
66794	non-pathway related	55.26	21 of 38
66794	lysine metabolism	52.38	22 of 42
66794	oxidative phosphorylation	50.55	46 of 91
66794	CMP-KDO biosynthesis	50	2 of 4
66794	toluene degradation	50	2 of 4
66794	resorcinol degradation	50	1 of 2
66794	degradation of sugar alcohols	50	8 of 16
66794	glycogen biosynthesis	50	2 of 4
66794	lactate fermentation	50	2 of 4
66794	ribulose monophosphate pathway	50	1 of 2
66794	quinate degradation	50	1 of 2
66794	polyamine pathway	47.83	11 of 23
66794	bile acid biosynthesis, neutral pathway	47.06	8 of 17
66794	sulfate reduction	46.15	6 of 13
66794	metabolism of disaccharids	45.45	5 of 11
66794	degradation of hexoses	44.44	8 of 18
66794	carotenoid biosynthesis	40.91	9 of 22
66794	factor 420 biosynthesis	40	2 of 5
66794	4-hydroxyphenylacetate degradation	40	4 of 10
66794	D-cycloserine biosynthesis	40	2 of 5
66794	arachidonate biosynthesis	40	2 of 5
66794	glycine betaine biosynthesis	40	2 of 5
66794	creatinine degradation	40	2 of 5
66794	glycine metabolism	40	4 of 10
66794	gallate degradation	40	2 of 5
66794	hydrogen production	40	2 of 5
66794	flavin biosynthesis	40	6 of 15
66794	arachidonic acid metabolism	38.89	7 of 18
66794	ketogluconate metabolism	37.5	3 of 8
66794	d-xylose degradation	36.36	4 of 11
66794	degradation of pentoses	35.71	10 of 28
66794	phenol degradation	35	7 of 20
66794	enterobactin biosynthesis	33.33	1 of 3
66794	nitrate assimilation	33.33	3 of 9
66794	IAA biosynthesis	33.33	1 of 3
66794	4-hydroxymandelate degradation	33.33	3 of 9
66794	sphingosine metabolism	33.33	2 of 6
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	lipid A biosynthesis	33.33	3 of 9
66794	pantothenate biosynthesis	33.33	2 of 6
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	selenocysteine biosynthesis	33.33	2 of 6
66794	glycolate and glyoxylate degradation	33.33	2 of 6
66794	ascorbate metabolism	31.82	7 of 22
66794	coenzyme M biosynthesis	30	3 of 10
66794	benzoyl-CoA degradation	28.57	2 of 7
66794	dTDPLrhamnose biosynthesis	25	2 of 8
66794	carnitine metabolism	25	2 of 8
66794	degradation of sugar acids	24	6 of 25

API zym

@ref	Control	Alkaline phosphatase	Esterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	Lipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	Trypsin	alpha- Chymotrypsin	Acid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	alpha- Galactosidase	beta- Galactosidase	beta- Glucuronidase	alpha- Glucosidase	beta- Glucosidase	N-acetyl-beta- glucosaminidase	alpha- Mannosidase	alpha- Fucosidase
120947	-	+	+	+	-	+	+	+	+	-	+	+	-	-	-	-	-	+	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Lake (large)

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
8320	eutrophic lake	Lake Suwa	Japan	JPN	Asia
67770	Toxic Microcystis blooming lake	Lake Suwa	Japan	JPN	Asia
67771	From a toxic Microcystis blooming lake	Lake Suwa	Japan	JPN	Asia
120947	Environment, Blooming lake	Suwa lake	Japan	JPN	Asia

Taxonmaps

69479

Global distribution of 16S sequence AB084247 (>99% sequence identity) for Sphingosinicella from Microbeatlas

Aquatic Samples	7685
Soil Samples	5974
Animal Samples	2606
Plant Samples	1345
Total Samples	17610

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
8320	1	Risk group (German classification) According to TRBA 466
120947	1	Risk group (French classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
67770	ASM363421v1 assembly for Sphingosinicella microcystinivorans DSM 19791	scaffold	GCA_003634215	335406.3	2770939615	335406	75.59

Genome browser: GCA_003634215

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
8320	Sphingosinicella microcystinivorans gene for 16S rRNA, partial sequence, strain:Y2	AB084247	1449		335406

GC content

@ref	GC-content (mol%)
31549	63.6
67770	63.6-63.7

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Sphingosinicella microcystinivorans DSM 19791
NCBI: GCA_003634215

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	97.00	no
125439	motility	BacteriaNetⓘ	yes	63.80	no
125439	gram_stain	BacteriaNetⓘ	negative	97.60	no
125439	oxygen_tolerance	BacteriaNetⓘ	aerobe	98.10	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Sphingosinicella microcystinivorans strain DSM 19791
PATRIC: 335406.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	95.99	yes
125438	anaerobic	anaerobicⓘ	no	95.58	yes
125438	spore-forming	spore-formingⓘ	no	90.10	yes
125438	aerobic	aerobicⓘ	yes	88.24	no
125438	thermophilic	thermophileⓘ	no	94.01	no
125438	flagellated	motile2+ⓘ	yes	62.21	no

Literature

Title	Authors	Journal	DOI	Year
New Multidrug Efflux Systems in a Microcystin-Degrading Bacterium Blastomonas fulva and Its Genomic Feature.	Jin L, Cui C, Zhang C, Ko SR, Li T, Jin FJ, Ahn CY, Oh HM, Lee HG.	Int J Mol Sci	10.3390/ijms231810856	2022
Sphingosinicella cucumeris sp. nov., isolated from soil of a cucumber garden.	Akter S, Du J, Won K, Yin CS, Kook M, Yi TH	Antonie Van Leeuwenhoek	10.1007/s10482-015-0572-6	2015
Sphingosinicella microcystinivorans gen. nov., sp. nov., a microcystin-degrading bacterium.	Maruyama T, Park HD, Ozawa K, Tanaka Y, Sumino T, Hamana K, Hiraishi A, Kato K	Int J Syst Evol Microbiol	10.1099/ijs.0.63789-0	2006

References

#8320	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 19791
#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 )
#31549	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 #27840 (see below)
#37472	; Curators of the CIP;
#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;
#67771	Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;
#68382	Automatically annotated from API zym .
#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 .
#120947	Collection of Institut Pasteur ; Curators of the CIP; CIP 109169
#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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Sphingosinicella microcystinivorans (DSM 19791, JCM 13185, KCTC 12019)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Observation

Metabolite utilization

Metabolite production

Enzymes

Pathway annotation

API zym

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_003634215

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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