Sphingobium fuliginis (DSM 16637, ATCC 27551, CIP 104270)

Name: Sphingobium fuliginis (DSM 16637, ATCC 27551, CIP 104270)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 14215

Type strain

Culture col. no. DSM 16637 ATCC 27551 CIP 104270

NCBI tax ID(s) 1208342 336203

Special Collections DSMZ CIP

Links

Sphingobium fuliginis DSM 16637 is a mesophilic, Gram-negative, rod-shaped prokaryote that was isolated from water from diazinon treated ricefield.

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

Name and taxonomic classification

SI-ID 39059

ATCC 27551,CIP 104270,CECT 4425,KCTC 2480,BCRC 15994,CCRC 15994,DSM 16637

@ref 20215

Last LPSN update 2025-12-16 09:50:17

Domain Pseudomonadati

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Sphingomonadales

Family Sphingomonadaceae

Genus Sphingobium

Species Sphingobium fuliginis

Full scientific name Sphingobium fuliginis Prakash and Lal 2006

Synonyms (1)

Sphingobium barthaii

BacDive ID	Other strains from **Sphingobium fuliginis** (2)	Type strain
14186	S. fuliginis TKP, DSM 18781, CCM 7327, MTCC 7295, CIP ... (type strain)
130669	S. fuliginis KK22, DSM 29313, JCM 30309 (type strain)

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Confidence
119483	negative	rod-shaped
125438	negative		93.833
125439	negative		95.9

Colony morphology

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
6540	MINERAL MEDIUM (NAGEL AND ANDREESEN) (DSMZ Medium 461)	Medium recipe at MediaDive	Name: MINERAL MEDIUM (NAGEL AND ANDREESEN) (DSMZ Medium 461) Composition: Na2HPO4 x 2 H2O 1.44135 g/l MgSO4 x 7 H2O 0.497018 g/l NH4Cl 0.298211 g/l KH2PO4 0.248509 g/l NaCl 0.0497018 g/l MnSO4 0.00994036 g/l CaCl2 0.00994036 g/l HCl 0.00248509 g/l FeCl2 x 4 H2O 0.00149105 g/l Thiamine-HCl x 2 H2O 0.000248509 g/l p-Aminobenzoic acid 0.000248509 g/l Vitamin B12 0.000248509 g/l Pantothenic acid 0.000248509 g/l Riboflavin 0.000248509 g/l alpha-lipoic acid 0.000248509 g/l CoCl2 x 6 H2O 0.000188867 g/l Nicotine amide 0.000124254 g/l Nicotinic acid 0.000124254 g/l Folic acid 9.94036e-05 g/l Biotin 9.94036e-05 g/l MnCl2 x 4 H2O 9.94036e-05 g/l ZnCl2 6.95825e-05 g/l Pyridoxamine hydrochloride 4.97018e-05 g/l Na2MoO4 x 2 H2O 3.57853e-05 g/l NiCl2 x 6 H2O 2.38569e-05 g/l H3BO3 5.96421e-06 g/l CuCl2 x 2 H2O 1.98807e-06 g/l Distilled water
6540	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
119483	CIP Medium 72	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
6540	positive	growth	28	mesophilic
119483	positive	growth	25-37	mesophilic
119483	negative	growth	5
119483	negative	growth	15
119483	negative	growth	41
119483	negative	growth	45

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	aerobe	94.3

Spore formation

@ref	Spore formation	Confidence
125439		93.5

Halophily

@ref	Salt	Growth	Tested relation	Concentration
119483	NaCl	positive	growth	0-2 %
119483	NaCl		growth	4 %
119483	NaCl		growth	6 %
119483	NaCl		growth	8 %
119483	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
119483	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
119483	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
119483	606565 ChEBI	hippurate	-	hydrolysis
68369	30849 ChEBI	L-arabinose	+	assimilation	from API 20NE
68369	25115 ChEBI	malate	-	assimilation	from API 20NE
119483	15792 ChEBI	malonate	-	assimilation
68369	17306 ChEBI	maltose	+	assimilation	from API 20NE
68369	59640 ChEBI	N-acetylglucosamine	-	assimilation	from API 20NE
119483	17632 ChEBI	nitrate	-	builds gas from
119483	17632 ChEBI	nitrate	-	reduction
119483	17632 ChEBI	nitrate	-	respiration
68369	17632 ChEBI	nitrate	-	reduction	from API 20NE
119483	16301 ChEBI	nitrite	-	builds gas from
119483	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
119483	0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)

Metabolite production

@ref	Chebi-ID	Metabolite	Production
68369	35581 ChEBI	indole		from API 20NE
119483	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Indole test	Voges-proskauer-test	Methylred-test
119483	15688 ChEBI	acetoin		-
119483	17234 ChEBI	glucose			-
68369	35581 ChEBI	indole	-			from API 20NE

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
119483	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
119483	amylase	-
68369	arginine dihydrolase	-	3.5.3.6	from API 20NE
68382	beta-galactosidase	-	3.2.1.23	from API zym
119483	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
119483	caseinase	-	3.4.21.50
119483	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
119483	DNase	+
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
119483	gamma-glutamyltransferase	+	2.3.2.2
119483	gelatinase	-
68369	gelatinase	-		from API 20NE
119483	lecithinase	-
68382	leucine arylamidase	+	3.4.11.1	from API zym
119483	lipase	-
68382	lipase (C 14)	-		from API zym
119483	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
119483	ornithine decarboxylase	-	4.1.1.17
119483	oxidase	+
119483	phenylalanine ammonia-lyase	-	4.3.1.24
119483	protease	-
68382	trypsin	-	3.4.21.4	from API zym
119483	tryptophan deaminase	-
119483	tween esterase	-
119483	urease	-	3.5.1.5
68369	urease	-	3.5.1.5	from API 20NE
68382	valine arylamidase	+		from API zym

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
119483	-	+	+	+	-	+	+	-	-	-	+	+	-	-	-	+	-	-	-	-

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
6540	-	-	-	-	-	+	-	-	+	+	-	-	-	+	-	-	-	-	-	-	+

API biotype100

@ref	ControlQ	D-glucose as carbon sourceGLU	D-fructose as carbon sourceFRU	D-galactose as carbon sourceGAL	D-trehalose as carbon sourceTRE	D-mannose as carbon sourceMNE	L-sorbose as carbon sourceSBE	D-melibiose as carbon sourceMEL	sucrose as carbon sourceSAC	D-raffinose as carbon sourceRAF	maltotriose as carbon sourceMTE	maltose as carbon sourceMAL	lactose as carbon sourceLAC	lactulose as carbon sourceLTE	1-O-methyl-beta-galactopyranoside as carbon sourceMbGa	1-O-methyl-alpha-galactopyranoside as carbon sourceMaGa	D-cellobiose as carbon sourceCEL	gentiobiose as carbon sourceGEN	1-O-methyl-beta-D-glucopyranoside as carbon sourceMbGu	esculin as carbon sourceESC	D-ribose as carbon sourceRIB	L-arabinose as carbon sourceARA	D-xylose as carbon sourceXYL	palatinose as carbon sourcePLE	L-rhamnose as carbon sourceRHA	L-fucose as carbon sourceFUC	D-melezitose as carbon sourceMLZ	D-arabitol as carbon sourceDARL	L-arabitol as carbon sourceLARL	xylitol as carbon sourceXLT	dulcitol as carbon sourceDUL	D-tagatose as carbon sourceTAG	glycerol as carbon sourceGLY	myo-inositol as carbon sourceINO	D-mannitol as carbon sourceMAN	maltitol as carbon sourceMTL	D-turanose as carbon sourceTUR	D-sorbitol as carbon sourceSOR	adonitol as carbon sourceADO	hydroxyquinoline-beta-glucuronide as carbon sourceHBG	D-lyxose as carbon sourceLYX	i-erythritol as carbon sourceERY	1-O-methyl-alpha-D-glucoside as carbon sourceMDG	3-O-methyl-D-glucose as carbon source3MDG	D-saccharate as carbon sourceSAT	mucate as carbon sourceMUC	L-tartrate as carbon sourceLTAT	D-tartrate as carbon sourceDTAT	meso-tartrate as carbon sourceMTAT	D-malate as carbon sourceDMLT	L-malate as carbon sourceLMLT	cis-aconitate as carbon sourceCATE	trans-aconitate as carbon sourceTATE	tricarballylate as carbon sourceTTE	citrate as carbon sourceCIT	D-glucuronate as carbon sourceGRT	D-galacturonate as carbon sourceGAT	2-ketogluconate as carbon source2KG	5-ketogluconate as carbon source5KG	tryptophan as carbon sourceTRY	N-acetyl-D-glucosamine as carbon sourceNAG	D-gluconate as carbon sourceGNT	phenylacetate as carbon sourcePAC	protocatechuate as carbon sourcePAT	4-hydroxybenzoate as carbon sourcepOBE	quinate as carbon sourceQAT	gentisate as carbon sourceGTE	3-hydroxybenzoate as carbon sourcemOBE	benzoate as carbon sourceBAT	3-phenylpropionate as carbon sourcePPAT	m-coumarate as carbon sourceCMT	trigonelline as carbon sourceTGE	betaine as carbon sourceBET	putrescine as carbon sourcePCE	4-aminobutyrate as carbon sourceABT	histamine as carbon sourceHIN	DL-lactate as carbon sourceLAT	caprate as carbon sourceCAP	caprylate as carbon sourceCYT	L-histidine as carbon sourceHIS	succinate as carbon sourceSUC	fumarate as carbon sourceFUM	glutarate as carbon sourceGRE	DL-glycerate as carbon sourceGYT	5-aminovalerate as carbon sourceAVT	ethanolamine as carbon sourceETN	tryptamine as carbon sourceTTN	D-glucosamine as carbon sourceGLN	itaconate as carbon sourceITA	3-hydroxybutyrate as carbon source3OBU	L-aspartate as carbon sourceAPT	L-glutamate as carbon sourceGTT	L-proline as carbon sourcePRO	D-alanine as carbon sourceDALA	L-alanine as carbon sourceLALA	L-serine as carbon sourceSER	malonate as carbon sourceMNT	propionate as carbon sourcePROP	L-tyrosine as carbon sourceTYR	2-ketoglutarate as carbon source2KT
119483	not determinedn.d.	+	-	+	+	-	-	-	-	-	+	+	-	-	-	-	+	+	-	+	-	+	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	-	-	-	-	-	-	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	+	+	-	-	-	-	-	-	-	+	-	+	+	-	+	-	-	+	-	+

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Agriculture	#Field
#Environmental	#Aquatic	-
#Host	#Plants	#Herbaceous plants (Grass,Crops)

Isolation

@ref	Sample type	Country	Country ISO 3 Code	Continent
6540	water from diazinon treated ricefield	Philippines	PHL	Asia
119483	Environment, Water of rice field

Taxonmaps

69479

Global distribution of 16S sequence AB465578 (>99% sequence identity) for Sphingobium quisquiliarum from Microbeatlas

Aquatic Samples	3
Soil Samples	35
Animal Samples
Plant Samples	2
Total Samples	40

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
6540	1	Risk group (German classification) According to TRBA 466
119483	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	ASM636387v1 assembly for Sphingobium fuliginis ATCC 27551	complete	GCA_006363875	1208342.6	2833940037	1208342	92.63

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
20218	Sphingobium fuliginis gene for 16S rRNA, partial sequence	AB465578	1414		1208342

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Sphingobium fuliginis ATCC 27551
PATRIC: 1208342.6

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	aerobe	94.30	no
125439	gram_stain	BacteriaNetⓘ	negative	95.90	no
125439	motility	BacteriaNetⓘ	yes	59.90	no
125439	spore_formation	BacteriaNetⓘ	no	93.50	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Sphingobium fuliginis ATCC 27551 ATCC 27551
NCBI: GCA_006363875.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	93.83	no
125438	anaerobic	anaerobicⓘ	no	95.41	no
125438	aerobic	aerobicⓘ	yes	89.73	no
125438	spore-forming	spore-formingⓘ	no	87.98	no
125438	thermophilic	thermophileⓘ	no	95.47	yes
125438	flagellated	motile2+ⓘ	yes	66.34	no

Literature

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	Microcystin shapes the Microcystis phycosphere through community filtering and by influencing cross-feeding interactions.	Grosse R, Heuser M, Teikari JE, Ramakrishnan DK, Abdelfattah A, Dittmann E.	ISME Commun	10.1093/ismeco/ycae170	2025
Genetics	Chemotactic response of p-nitrophenol degrading Pseudomonas asiatica strain PNPG3 through phenotypic and genome sequence-based in silico studies.	Alam SA, Saha P.	3 Biotech	10.1007/s13205-023-03809-3	2023
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Genetics	Genome Sequences of 72 Bacterial Strains Isolated from Ectocarpus subulatus: A Resource for Algal Microbiology.	Karimi E, Geslain E, KleinJan H, Tanguy G, Legeay E, Corre E, Dittami SM.	Genome Biol Evol	10.1093/gbe/evz278	2020
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Genetics	Genome Organization and Adaptive Potential of Archetypal Organophosphate Degrading Sphingobium fuliginis ATCC 27551.	Azam S, Parthasarathy S, Singh C, Kumar S, Siddavattam D	Genome Biol Evol	10.1093/gbe/evz189	2019
	Analysis of Polycaprolactone Microfibers as Biofilm Carriers for Biotechnologically Relevant Bacteria.	Tamayo-Ramos JA, Rumbo C, Caso F, Rinaldi A, Garroni S, Notargiacomo A, Romero-Santacreu L, Cuesta-Lopez S	ACS Appl Mater Interfaces	10.1021/acsami.8b07245	2018
Metabolism	Expression of recombinant organophosphorus hydrolase in the original producer of the enzyme, Sphingobium fuliginis ATCC 27551.	Nakayama K, Ohmori T, Ishikawa S, Iwata N, Seto Y, Kawahara K	Biosci Biotechnol Biochem	10.1080/09168451.2015.1123606	2016
Metabolism	Multiple mechanisms contribute to lateral transfer of an organophosphate degradation (opd) island in Sphingobium fuliginis ATCC 27551.	Pandeeti EV, Longkumer T, Chakka D, Muthyala VR, Parthasarathy S, Madugundu AK, Ghanta S, Medipally SR, Pantula SC, Yekkala H, Siddavattam D	G3 (Bethesda)	10.1534/g3.112.004051	2012
Phylogeny	Reclassification of a parathione-degrading Flavobacterium sp. ATCC 27551 as Sphingobium fuliginis.	Kawahara K, Tanaka A, Yoon J, Yokota A	J Gen Appl Microbiol	10.2323/jgam.56.249	2010

References

#6540	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 16637
#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 )
#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 .
#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 .
#119483	Collection of Institut Pasteur ; Curators of the CIP; CIP 104270
#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 fuliginis (DSM 16637, ATCC 27551, CIP 104270)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture medium

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Physiology and metabolism

Oxygen tolerance

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Halophily

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Genome browser: GCA_006363875

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