Sphingobium amiense (DSM 16289, CIP 107839, IAM 15006)

Name: Sphingobium amiense (DSM 16289, CIP 107839, IAM 15006)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 14182

Type strain

Strain Designation YT

Culture col. no. DSM 16289 CIP 107839 IAM 15006 JCM 11777 YT

NCBI tax ID(s) 135719

Special Collections DSMZ JCM CIP

History <- H. Ohta, University Ami-machi, Japan; YT CIP <- 2003, H. Ohta, Ibaraki Univ., Ibaraki, Japan: strain YT <- Y. Takahara

Links

Sphingobium amiense YT is an obligate aerobe, Gram-negative bacterium that was isolated from river sediment.

Gram-negative obligate aerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 128017

CIP 107839,IAM 15006,JCM 11777,DSM 16289,NBRC 102518

@ref 20215

Last LPSN update 2026-02-09 11:21:21

Domain Bacteria

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Sphingomonadales

Family Sphingomonadaceae

Genus Sphingobium

Species Sphingobium amiense

Full scientific name Sphingobium amiense Ushiba et al. 2003

Morphology

Cell morphology

@ref	Gram stain	Confidence
116330	negative
125439	negative	98.2
125438	negative	96.569

Pigmentation

@ref	Production	Name
116330		Pyocyanin

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
6275	CASO AGAR (MERCK 105458) (DSMZ Medium 220)	Medium recipe at MediaDive	Name: CASO AGAR (Merck 105458) (DSMZ Medium 220) Composition: Agar 15.0 g/l Casein peptone 15.0 g/l NaCl 5.0 g/l Soy peptone 5.0 g/l Distilled water
6275	TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)	Medium recipe at MediaDive	Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water
40728	MEDIUM 72- for trypto casein soja agar		Distilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
116330	CIP Medium 72	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
6275	positive	growth	28
40728	positive	growth	30
116330	positive	growth	25-30
116330	negative	growth	5
116330	negative	growth	10
116330	negative	growth	37
116330	negative	growth	41

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
116330	obligate aerobe
125439	aerobe	96.1

Spore formation

@ref	Spore formation	Confidence
125439		96.5
125438		90.302

Halophily

@ref	Salt	Growth	Tested relation	Concentration
116330	NaCl	positive	growth	0-2 %
116330	NaCl		growth	4 %
116330	NaCl		growth	6 %
116330	NaCl		growth	8 %
116330	NaCl		growth	10 %

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
116330	16947 ChEBI	citrate	-	carbon source
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
116330	4853 ChEBI	esculin	-	hydrolysis
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
116330	17632 ChEBI	nitrate	-	reduction
116330	17632 ChEBI	nitrate	-	respiration
68369	17632 ChEBI	nitrate	-	reduction	from API 20NE
116330	16301 ChEBI	nitrite	-	reduction
68369	27897 ChEBI	tryptophan	-	energy source	from API 20NE
68369	16199 ChEBI	urea	-	hydrolysis	from API 20NE

Antibiotic resistance

@ref	Metabolite	Is sensitive	Is resistant
116330	0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)

Metabolite production

@ref	Chebi-ID	Metabolite	Production
68369	35581 ChEBI	indole		from API 20NE
116330	35581 ChEBI	indole

Metabolite tests

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

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
116330	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
116330	amylase	+
68369	arginine dihydrolase	-	3.5.3.6	from API 20NE
68382	beta-galactosidase	-	3.2.1.23	from API zym
116330	beta-galactosidase	+	3.2.1.23
68382	beta-glucosidase	-	3.2.1.21	from API zym
68369	beta-glucosidase	-	3.2.1.21	from API 20NE
68382	beta-glucuronidase	-	3.2.1.31	from API zym
116330	caseinase	-	3.4.21.50
116330	catalase	+	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
68369	cytochrome oxidase	+	1.9.3.1	from API 20NE
116330	DNase	-
68382	esterase (C 4)	-		from API zym
68382	esterase lipase (C 8)	-		from API zym
116330	gelatinase	-
68369	gelatinase	-		from API 20NE
116330	lecithinase	-
68382	leucine arylamidase	+	3.4.11.1	from API zym
116330	lipase	-
68382	lipase (C 14)	-		from API zym
116330	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
116330	ornithine decarboxylase	-	4.1.1.17
116330	oxidase	+
68382	trypsin	+	3.4.21.4	from API zym
116330	tryptophan deaminase	-
116330	tween esterase	-
116330	urease	-	3.5.1.5
68369	urease	-	3.5.1.5	from API 20NE
68382	valine arylamidase	-		from API zym

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	cellulose degradation	100	5 of 5
66794	gluconeogenesis	100	8 of 8
66794	C4 and CAM-carbon fixation	100	8 of 8
66794	methylglyoxal degradation	100	5 of 5
66794	ppGpp biosynthesis	100	4 of 4
66794	palmitate biosynthesis	100	22 of 22
66794	glycogen metabolism	100	5 of 5
66794	biotin biosynthesis	100	4 of 4
66794	adipate degradation	100	2 of 2
66794	Entner Doudoroff pathway	100	10 of 10
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	threonine metabolism	100	10 of 10
66794	formaldehyde oxidation	100	3 of 3
66794	coenzyme A metabolism	100	4 of 4
66794	valine metabolism	100	9 of 9
66794	suberin monomers biosynthesis	100	2 of 2
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	folate polyglutamylation	100	1 of 1
66794	denitrification	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	butanoate fermentation	100	4 of 4
66794	resorcinol degradation	100	2 of 2
66794	tetrahydrofolate metabolism	92.86	13 of 14
66794	aspartate and asparagine metabolism	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	molybdenum cofactor biosynthesis	88.89	8 of 9
66794	serine metabolism	88.89	8 of 9
66794	isoleucine metabolism	87.5	7 of 8
66794	photosynthesis	85.71	12 of 14
66794	glutamate and glutamine metabolism	85.71	24 of 28
66794	leucine metabolism	84.62	11 of 13
66794	glycolate and glyoxylate degradation	83.33	5 of 6
66794	NAD metabolism	83.33	15 of 18
66794	d-xylose degradation	81.82	9 of 11
66794	peptidoglycan biosynthesis	80	12 of 15
66794	starch degradation	80	8 of 10
66794	gallate degradation	80	4 of 5
66794	3-phenylpropionate degradation	80	12 of 15
66794	ethylmalonyl-CoA pathway	80	4 of 5
66794	phenylacetate degradation (aerobic)	80	4 of 5
66794	citric acid cycle	78.57	11 of 14
66794	CO2 fixation in Crenarchaeota	77.78	7 of 9
66794	vitamin B1 metabolism	76.92	10 of 13
66794	phenylalanine metabolism	76.92	10 of 13
66794	alanine metabolism	75.86	22 of 29
66794	glycogen biosynthesis	75	3 of 4
66794	acetate fermentation	75	3 of 4
66794	sulfopterin metabolism	75	3 of 4
66794	dTDPLrhamnose biosynthesis	75	6 of 8
66794	CMP-KDO biosynthesis	75	3 of 4
66794	ketogluconate metabolism	75	6 of 8
66794	proline metabolism	72.73	8 of 11
66794	metabolism of disaccharids	72.73	8 of 11
66794	pentose phosphate pathway	72.73	8 of 11
66794	vitamin B6 metabolism	72.73	8 of 11
66794	ubiquinone biosynthesis	71.43	5 of 7
66794	glutathione metabolism	71.43	10 of 14
66794	reductive acetyl coenzyme A pathway	71.43	5 of 7
66794	tyrosine metabolism	71.43	10 of 14
66794	heme metabolism	71.43	10 of 14
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	propanol degradation	71.43	5 of 7
66794	propionate fermentation	70	7 of 10
66794	polyamine pathway	69.57	16 of 23
66794	purine metabolism	69.15	65 of 94
66794	pyrimidine metabolism	68.89	31 of 45
66794	flavin biosynthesis	66.67	10 of 15
66794	octane oxidation	66.67	2 of 3
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	nitrate assimilation	66.67	6 of 9
66794	cyanate degradation	66.67	2 of 3
66794	cysteine metabolism	66.67	12 of 18
66794	acetoin degradation	66.67	2 of 3
66794	tryptophan metabolism	65.79	25 of 38
66794	methionine metabolism	65.38	17 of 26
66794	glycolysis	64.71	11 of 17
66794	lipid metabolism	64.52	20 of 31
66794	degradation of sugar acids	64	16 of 25
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
66794	androgen and estrogen metabolism	62.5	10 of 16
66794	lysine metabolism	61.9	26 of 42
66794	sulfate reduction	61.54	8 of 13
66794	isoprenoid biosynthesis	61.54	16 of 26
66794	non-pathway related	60.53	23 of 38
66794	lipoate biosynthesis	60	3 of 5
66794	hydrogen production	60	3 of 5
66794	arginine metabolism	58.33	14 of 24
66794	degradation of sugar alcohols	56.25	9 of 16
66794	d-mannose degradation	55.56	5 of 9
66794	histidine metabolism	55.17	16 of 29
66794	phenol degradation	55	11 of 20
66794	urea cycle	53.85	7 of 13
66794	phosphatidylethanolamine bioynthesis	53.85	7 of 13
66794	cyclohexanol degradation	50	2 of 4
66794	toluene degradation	50	2 of 4
66794	mannosylglycerate biosynthesis	50	1 of 2
66794	myo-inositol biosynthesis	50	5 of 10
66794	ribulose monophosphate pathway	50	1 of 2
66794	pantothenate biosynthesis	50	3 of 6
66794	4-hydroxyphenylacetate degradation	50	5 of 10
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	glycine metabolism	50	5 of 10
66794	degradation of aromatic, nitrogen containing compounds	50	6 of 12
66794	quinate degradation	50	1 of 2
66794	kanosamine biosynthesis II	50	1 of 2
66794	selenocysteine biosynthesis	50	3 of 6
66794	ethanol fermentation	50	1 of 2
66794	degradation of pentoses	46.43	13 of 28
66794	oxidative phosphorylation	46.15	42 of 91
66794	carotenoid biosynthesis	45.45	10 of 22
66794	4-hydroxymandelate degradation	44.44	4 of 9
66794	lipid A biosynthesis	44.44	4 of 9
66794	degradation of hexoses	44.44	8 of 18
66794	metabolism of amino sugars and derivatives	40	2 of 5
66794	arachidonate biosynthesis	40	2 of 5
66794	creatinine degradation	40	2 of 5
66794	glycine betaine biosynthesis	40	2 of 5
66794	vitamin K metabolism	40	2 of 5
66794	3-chlorocatechol degradation	40	2 of 5
66794	arachidonic acid metabolism	38.89	7 of 18
66794	vitamin B12 metabolism	38.24	13 of 34
66794	sphingosine metabolism	33.33	2 of 6
66794	IAA biosynthesis	33.33	1 of 3
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	enterobactin biosynthesis	33.33	1 of 3
66794	ascorbate metabolism	31.82	7 of 22
66794	bile acid biosynthesis, neutral pathway	29.41	5 of 17
66794	aclacinomycin biosynthesis	28.57	2 of 7
66794	benzoyl-CoA degradation	28.57	2 of 7
66794	carnitine metabolism	25	2 of 8
66794	alginate biosynthesis	25	1 of 4
66794	lactate fermentation	25	1 of 4
66794	catecholamine biosynthesis	25	1 of 4
66794	vitamin E metabolism	25	1 of 4

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
116330	-	+	-	-	-	+	-	-	+	+	+	+	-	-	-	-	-	-	-	-

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
6275	-	-	-	-	-	-	-	-	+	-	+	+	-	+	+	-	-	+	-	-	+

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#River (Creek)
#Environmental	#Aquatic	#Sediment

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Isolation date
6275	river sediment	Ibaraki	Japan	JPN	Asia
116330	Environment, River sediment sample	Ibaraki	Japan	JPN	Asia	1999

Taxonmaps

69479

Global distribution of 16S sequence AB047364 (>99% sequence identity) for Sphingobium amiense from Microbeatlas

Aquatic Samples	60
Soil Samples	6
Animal Samples	7
Plant Samples	60
Total Samples	133

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
6275	1	Risk group (German classification) According to TRBA 466
116330	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
66792	ASM396707v1 assembly for Sphingobium amiense DSM 16289	complete	GCA_003967075	135719.3	2843241807	135719	93.14

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
6275	Sphingomonas sp. YT gene for 16S rRNA	AB047364	1448		135719
124043	Sphingobium amiense strain DSM 16289 16S ribosomal RNA gene, partial sequence.	PP737887	1423		135719

GC content

6275

GC-content (mol%)66.4

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Sphingobium amiense DSM 16289
IMG: 2843241807

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	96.50	no
125439	motility	BacteriaNetⓘ	yes	60.60	no
125439	gram_stain	BacteriaNetⓘ	negative	98.20	no
125439	oxygen_tolerance	BacteriaNetⓘ	aerobe	96.10	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Sphingobium amiense DSM 16289
NCBI: GCA_003967075.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	96.57	no
125438	anaerobic	anaerobicⓘ	no	94.03	yes
125438	aerobic	aerobicⓘ	yes	86.56	no
125438	spore-forming	spore-formingⓘ	no	90.30	no
125438	thermophilic	thermophileⓘ	no	97.39	yes
125438	flagellated	motile2+ⓘ	yes	65.28	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	DNA regions responsible for maintenance of Shingobium plasmid pYAN-2.	Hayashi H, Kurusu Y.	Microbes Environ	10.1264/jsme2.me13135	2014
Metabolism	Comparative Analysis of the Genetic Basis of Branched Nonylphenol Degradation by Sphingobium amiense DSM 16289(T) and Sphingobium cloacae JCM 10874(T).	Ootsuka M, Nishizawa T, Hasegawa M, Kurusu Y, Ohta H	Microbes Environ	10.1264/jsme2.ME18077	2018
Phylogeny	Sphingobium limneticum sp. nov. and Sphingobium boeckii sp. nov., two freshwater planktonic members of the family Sphingomonadaceae, and reclassification of Sphingomonas suberifaciens as Sphingobium suberifaciens comb. nov.	Chen H, Jogler M, Rohde M, Klenk HP, Busse HJ, Tindall BJ, Sproer C, Overmann J	Int J Syst Evol Microbiol	10.1099/ijs.0.040105-0	2012
Phylogeny	Sphingobium scionense sp. nov., an aromatic hydrocarbon-degrading bacterium isolated from contaminated sawmill soil.	Liang Q, Lloyd-Jones G	Int J Syst Evol Microbiol	10.1099/ijs.0.008144-0	2009
Phylogeny	Sphingobium quisquiliarum sp. nov., a hexachlorocyclohexane (HCH)-degrading bacterium isolated from an HCH-contaminated soil.	Bala K, Sharma P, Lal R	Int J Syst Evol Microbiol	10.1099/ijs.0.010868-0	2009
Phylogeny	Sphingobium amiense sp. nov., a novel nonylphenol-degrading bacterium isolated from a river sediment.	Ushiba Y, Takahara Y, Ohta H	Int J Syst Evol Microbiol	10.1099/ijs.0.02581-0	2003

References

#6275	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 16289
#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 )
#40728	; Curators of the CIP;
#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) .
#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 )
#68369	Automatically annotated from API 20NE .
#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 .
#116330	Collection of Institut Pasteur ; Curators of the CIP; CIP 107839
#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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Sphingobium amiense (DSM 16289, CIP 107839, IAM 15006)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Metabolite utilization

Antibiotic resistance

Metabolite production

Metabolite tests

Enzymes

Pathway annotation

API zym

API 20NE

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_003967075

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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