Sphingomonas jeddahensis (DSM 103790, LMG 29955, G39)

Name: Sphingomonas jeddahensis (DSM 103790, LMG 29955, G39)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 141053

Type strain

Strain Designation G39

Culture col. no. DSM 103790 LMG 29955 G39

NCBI tax ID(s) 1915074

Special Collections DSMZ Literature strains

History <- J. H. Wübbeler, Univ. Münster, Germany; G39 <- A. Röttig, Institute of Molecular Microbiology, Westfälische Wilhelms-University, Münster, Germany

Links

Sphingomonas jeddahensis G39 is an aerobe, Gram-negative, motile bacterium that forms circular colonies and was isolated from arid dry sand sample collected at a depth of 3 cm next to a highway near Jeddah, Saudi Arabia.

Gram-negative motile rod-shaped colony-forming aerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 407035

LMG 29955,DSM 103790

@ref 20215

Last LPSN update 2026-02-09 11:33:48

Domain Bacteria

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Sphingomonadales

Family Sphingomonadaceae

Genus Sphingomonas

Species Sphingomonas jeddahensis

Full scientific name Sphingomonas jeddahensis Wübbeler et al. 2017

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
43933	negative	2 µm	0.9 µm	rod-shaped
125439	negative				95.9
125438	negative				96.833

Colony morphology

@ref	Type of hemolysis	Hemolysis ability	Colony color	Colony shape
43933	alpha	1	yellow	circular

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
64910	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
64910	NUTRIENT AGAR (DSMZ Medium 1)	Medium recipe at MediaDive	Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
64910	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

Culture temp

@ref	Growth	Type	Temperature (°C)
43933	positive	growth	20-35
43933	positive	optimum	30
64910	positive	growth	28

Culture pH

@ref	Ability	Type	PH
43933	positive	growth	6.5-8.0

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
43933	aerobe
125439	obligate aerobe	98.5

Spore formation

@ref	Spore formation	Confidence
43933
125439		93.3
125438		91.623

Halophily

@ref	Salt	Growth	Tested relation	Concentration
43933	NaCl	positive	growth	0-4 %(w/v)

Observation

43933

Observationquinone Q-10

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
43933	30089 ChEBI	acetate	+	carbon source
43933	17128 ChEBI	adipate	-	assimilation
68369	17128 ChEBI	adipate	+	assimilation	from API 20NE
43933	16449 ChEBI	alanine	-	carbon source
68369	29016 ChEBI	arginine	-	hydrolysis	from API 20NE
43933	35391 ChEBI	aspartate	-	carbon source
43933	17057 ChEBI	cellobiose	+	carbon source
43933	16947 ChEBI	citrate	-	assimilation
43933	16947 ChEBI	citrate	-	carbon source
68369	17634 ChEBI	D-glucose	+	assimilation	from API 20NE
68369	17634 ChEBI	D-glucose	-	fermentation	from API 20NE
43933	16899 ChEBI	D-mannitol	-	assimilation
68369	16899 ChEBI	D-mannitol	-	assimilation	from API 20NE
43933	16024 ChEBI	D-mannose	-	assimilation
68369	16024 ChEBI	D-mannose	+	assimilation	from API 20NE
43933	27689 ChEBI	decanoate	-	assimilation
68369	27689 ChEBI	decanoate	-	assimilation	from API 20NE
43933	4853 ChEBI	esculin	+	hydrolysis
68369	4853 ChEBI	esculin	+	hydrolysis	from API 20NE
43933	28757 ChEBI	fructose	+	carbon source
43933	28260 ChEBI	galactose	-	carbon source
68369	5291 ChEBI	gelatin	-	hydrolysis	from API 20NE
43933	24265 ChEBI	gluconate	-	assimilation
68369	24265 ChEBI	gluconate	-	assimilation	from API 20NE
43933	17234 ChEBI	glucose	-	fermentation
43933	17234 ChEBI	glucose	+	assimilation
43933	17234 ChEBI	glucose	+	carbon source
43933	29987 ChEBI	glutamate	+	carbon source
43933	16087 ChEBI	isocitrate	+	carbon source
43933	30849 ChEBI	L-arabinose	-	assimilation
68369	30849 ChEBI	L-arabinose	-	assimilation	from API 20NE
43933	17716 ChEBI	lactose	-	carbon source
68369	25115 ChEBI	malate	-	assimilation	from API 20NE
43933	17306 ChEBI	maltose	-	assimilation
68369	17306 ChEBI	maltose	-	assimilation	from API 20NE
43933	28053 ChEBI	melibiose	-	carbon source
43933	506227 ChEBI	N-acetylglucosamine	-	assimilation
68369	59640 ChEBI	N-acetylglucosamine	-	assimilation	from API 20NE
43933	17632 ChEBI	nitrate	-	reduction
68369	17632 ChEBI	nitrate	-	reduction	from API 20NE
43933	18401 ChEBI	phenylacetate	-	assimilation
43933	26271 ChEBI	proline	+	carbon source
43933	15361 ChEBI	pyruvate	+	carbon source
43933	26546 ChEBI	rhamnose	-	carbon source
43933	30911 ChEBI	sorbitol	-	carbon source
43933	17992 ChEBI	sucrose	-	carbon source
43933	27082 ChEBI	trehalose	+	carbon source
68369	27897 ChEBI	tryptophan	-	energy source	from API 20NE
68369	16199 ChEBI	urea	-	hydrolysis	from API 20NE
43933	18222 ChEBI	xylose	-	carbon source

Antibiotic resistance

@ref	ChEBI	Metabolite	Sensitivity conc.	Resistance conc.
43933	28971	ampicillin	10 µg (disc)
43933	3393	carbenicillin	100 µg (disc)
43933	124991	cefalotin	30 µg (disc)
43933	17698	chloramphenicol	30 µg (disc)
43933	48923	erythromycin	5 µg (disc)
43933	17833	gentamicin	10 µg (disc)
43933	6104	kanamycin	30 µg (disc)
43933	28368	novobiocin		5 µg (disc)
43933	17334	penicillin	6 µg (disc)
43933	59062	polymyxin	180 µg (disc)
43933	28077	rifampicin	30 µg (disc)
43933	17076	streptomycin		10 µg (disc)
43933	27902	tetracycline	30 µg (disc)
43933	28001	vancomycin	30 µg (disc)

Metabolite production

@ref	Chebi-ID	Metabolite	Production
43933	35581 ChEBI	indole
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
43933	alkaline phosphatase	+	3.1.3.1
43933	arginine dihydrolase	-	3.5.3.6
68369	arginine dihydrolase	-	3.5.3.6	from API 20NE
43933	beta-galactosidase	-	3.2.1.23
43933	beta-glucosidase	+	3.2.1.21
68369	beta-glucosidase	+	3.2.1.21	from API 20NE
43933	catalase	+	1.11.1.6
43933	cytochrome oxidase	+	1.9.3.1
68369	cytochrome oxidase	+	1.9.3.1	from API 20NE
43933	esterase	+
43933	gelatinase	-
68369	gelatinase	-		from API 20NE
43933	leucine arylamidase	+	3.4.11.1
43933	trypsin	+	3.4.21.4
43933	urease	-	3.5.1.5
68369	urease	-	3.5.1.5	from API 20NE
43933	valine arylamidase	+

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	adipate degradation	100	2 of 2
66794	Entner Doudoroff pathway	100	10 of 10
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	reductive acetyl coenzyme A pathway	100	7 of 7
66794	palmitate biosynthesis	100	22 of 22
66794	ppGpp biosynthesis	100	4 of 4
66794	methylglyoxal degradation	100	5 of 5
66794	glycogen metabolism	100	5 of 5
66794	valine metabolism	100	9 of 9
66794	ethylmalonyl-CoA pathway	100	5 of 5
66794	suberin monomers biosynthesis	100	2 of 2
66794	folate polyglutamylation	100	1 of 1
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	coenzyme A metabolism	100	4 of 4
66794	formaldehyde oxidation	100	3 of 3
66794	ceramide biosynthesis	100	1 of 1
66794	tetrahydrofolate metabolism	92.86	13 of 14
66794	starch degradation	90	9 of 10
66794	chorismate metabolism	88.89	8 of 9
66794	CO2 fixation in Crenarchaeota	88.89	8 of 9
66794	aspartate and asparagine metabolism	88.89	8 of 9
66794	C4 and CAM-carbon fixation	87.5	7 of 8
66794	photosynthesis	85.71	12 of 14
66794	citric acid cycle	85.71	12 of 14
66794	NAD metabolism	83.33	15 of 18
66794	glutamate and glutamine metabolism	82.14	23 of 28
66794	pentose phosphate pathway	81.82	9 of 11
66794	threonine metabolism	80	8 of 10
66794	metabolism of amino sugars and derivatives	80	4 of 5
66794	phenylacetate degradation (aerobic)	80	4 of 5
66794	peptidoglycan biosynthesis	80	12 of 15
66794	molybdenum cofactor biosynthesis	77.78	7 of 9
66794	serine metabolism	77.78	7 of 9
66794	phenylalanine metabolism	76.92	10 of 13
66794	leucine metabolism	76.92	10 of 13
66794	alanine metabolism	75.86	22 of 29
66794	acetate fermentation	75	3 of 4
66794	butanoate fermentation	75	3 of 4
66794	toluene degradation	75	3 of 4
66794	gluconeogenesis	75	6 of 8
66794	glycogen biosynthesis	75	3 of 4
66794	sulfopterin metabolism	75	3 of 4
66794	cysteine metabolism	72.22	13 of 18
66794	heme metabolism	71.43	10 of 14
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	ubiquinone biosynthesis	71.43	5 of 7
66794	propanol degradation	71.43	5 of 7
66794	propionate fermentation	70	7 of 10
66794	vitamin B1 metabolism	69.23	9 of 13
66794	purine metabolism	68.09	64 of 94
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	octane oxidation	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	cyanate degradation	66.67	2 of 3
66794	acetyl CoA biosynthesis	66.67	2 of 3
66794	flavin biosynthesis	66.67	10 of 15
66794	d-mannose degradation	66.67	6 of 9
66794	isoprenoid biosynthesis	65.38	17 of 26
66794	methionine metabolism	65.38	17 of 26
66794	lipid metabolism	64.52	20 of 31
66794	tyrosine metabolism	64.29	9 of 14
66794	glutathione metabolism	64.29	9 of 14
66794	metabolism of disaccharids	63.64	7 of 11
66794	vitamin B6 metabolism	63.64	7 of 11
66794	proline metabolism	63.64	7 of 11
66794	non-pathway related	63.16	24 of 38
66794	isoleucine metabolism	62.5	5 of 8
66794	myo-inositol biosynthesis	60	6 of 10
66794	factor 420 biosynthesis	60	3 of 5
66794	glycolysis	58.82	10 of 17
66794	degradation of aromatic, nitrogen containing compounds	58.33	7 of 12
66794	degradation of sugar alcohols	56.25	9 of 16
66794	pyrimidine metabolism	55.56	25 of 45
66794	lipid A biosynthesis	55.56	5 of 9
66794	histidine metabolism	55.17	16 of 29
66794	d-xylose degradation	54.55	6 of 11
66794	arginine metabolism	54.17	13 of 24
66794	phosphatidylethanolamine bioynthesis	53.85	7 of 13
66794	urea cycle	53.85	7 of 13
66794	sulfate reduction	53.85	7 of 13
66794	tryptophan metabolism	52.63	20 of 38
66794	CMP-KDO biosynthesis	50	2 of 4
66794	ethanol fermentation	50	1 of 2
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	50	4 of 8
66794	ketogluconate metabolism	50	4 of 8
66794	lysine metabolism	50	21 of 42
66794	biotin biosynthesis	50	2 of 4
66794	cyclohexanol degradation	50	2 of 4
66794	oxidative phosphorylation	47.25	43 of 91
66794	nitrate assimilation	44.44	4 of 9
66794	androgen and estrogen metabolism	43.75	7 of 16
66794	benzoyl-CoA degradation	42.86	3 of 7
66794	glycine metabolism	40	4 of 10
66794	glycine betaine biosynthesis	40	2 of 5
66794	lipoate biosynthesis	40	2 of 5
66794	arachidonate biosynthesis	40	2 of 5
66794	arachidonic acid metabolism	38.89	7 of 18
66794	degradation of hexoses	38.89	7 of 18
66794	dTDPLrhamnose biosynthesis	37.5	3 of 8
66794	carotenoid biosynthesis	36.36	8 of 22
66794	IAA biosynthesis	33.33	1 of 3
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	enterobactin biosynthesis	33.33	1 of 3
66794	glycolate and glyoxylate degradation	33.33	2 of 6
66794	selenocysteine biosynthesis	33.33	2 of 6
66794	pantothenate biosynthesis	33.33	2 of 6
66794	ascorbate metabolism	31.82	7 of 22
66794	phenol degradation	30	6 of 20
66794	bile acid biosynthesis, neutral pathway	29.41	5 of 17
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	polyamine pathway	26.09	6 of 23
66794	carnitine metabolism	25	2 of 8
66794	methanogenesis from CO2	25	3 of 12
66794	lactate fermentation	25	1 of 4
66794	degradation of pentoses	25	7 of 28
66794	catecholamine biosynthesis	25	1 of 4
66794	alginate biosynthesis	25	1 of 4
66794	vitamin B12 metabolism	23.53	8 of 34
66794	4-hydroxymandelate degradation	22.22	2 of 9

Fatty acid profile

Metadata FA analysis

@ref

43933

Fatty acid	Percentage
C18:1ω7c	60.47
C16:1ω7c / C16:1ω6c	14.5
C14:0 2OH	8.36
C16:0	6.29
C16:1ω5c	4.94
11-methyl C18:1ω7c	2.34
C14:0	1.68
C17:0 cyclo	0.69
C18:1 2OH	0.34
C19:0ω8c cyclo	0.15
C16:0 iso 3OH	0.1
C12:0 2OH	0.09
C12:0	0.06

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
64910	-	-	-	-	-	+	-	-	+	-	+	-	-	-	-	-	+	-	-	-	+

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Desert
#Environmental	#Terrestrial	#Soil
#Condition	#Xerophilic	-

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Latitude	Longitude	Enrichment culture	Enrichment culture composition
43933	arid dry sand sample collected at a depth of 3 cm next to a highway near Jeddah, Saudi Arabia	Jeddah	Saudi Arabia	SAU	Asia	21.379	39.5119 21.379/39.5119	Mineral salt medium	containing 0.5 % (w/v) glucose, 150 µg/mL cycloheximide
64910	desert soil	near Jeddah (21° 22' 44.4'' N 39° 30' 42.8'' E)	Saudi Arabia	SAU	Asia	21.379	39.5119 21.379/39.5119

Taxonmaps

69479

Global distribution of 16S sequence KY032004 (>99% sequence identity) for Sphingomonas sp. from Microbeatlas

Aquatic Samples	82
Soil Samples	38
Animal Samples	210
Plant Samples	93
Total Samples	423

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
64910	1	Risk group (German classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	NCBI tax ID	Score
66792	ASM198152v1 assembly for Sphingomonas jeddahensis G39	contig	GCA_001981525	1915074	71.22

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
64910	Sphingomonas jeddahensis strain G39 16S ribosomal RNA gene, partial sequence	KY032004	1476		1915074

GC content

@ref	GC-content (mol%)	Method
43933	65.8	genome sequence analysis
64910	65.84	sequence analysis

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Sphingomonas jeddahensis G39
NCBI: GCA_001981525

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	93.30	no
125439	motility	BacteriaNetⓘ	yes	70.40	no
125439	gram_stain	BacteriaNetⓘ	negative	95.90	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	98.50	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Sphingomonas jeddahensis G39
NCBI: GCA_001981525.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	96.83	yes
125438	anaerobic	anaerobicⓘ	no	94.35	yes
125438	aerobic	aerobicⓘ	yes	85.99	yes
125438	spore-forming	spore-formingⓘ	no	91.62	yes
125438	thermophilic	thermophileⓘ	no	94.34	no
125438	flagellated	motile2+ⓘ	yes	65.98	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Sphingomonas jeddahensis sp. nov., isolated from Saudi Arabian desert soil.	Wubbeler JH, Oppermann-Sanio FB, Ockenfels A, Rottig A, Osthaar-Ebker A, Verbarg S, Poehlein A, Madkour MH, Al-Ansari AM, Almakishah NH, Daniel R, Steinbuchel A	Int J Syst Evol Microbiol	10.1099/ijsem.0.002249	2017

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 )
#43933	Jan Hendrik Wübbeler, Fred Bernd Oppermann-Sanio, Andrea Ockenfels, Annika Röttig, Alena Osthaar-Ebker, Susanne Verbarg, Anja Poehlein, Mohamed H. Madkour, Ahmed M. Al-Ansari, Naief H. Almakishah, Rolf Daniel, Alexander Steinbüchel: Sphingomonas jeddahensis sp. nov., isolated from Saudi Arabian desert soil. IJSEM 67: 4057 - 4063 2017 ( DOI 10.1099/ijsem.0.002249 , PubMed 28905699 )
#64910	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 103790
#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 .
#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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Sphingomonas jeddahensis (DSM 103790, LMG 29955, G39)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Observation

Metabolite utilization

Antibiotic resistance

Metabolite production

Metabolite tests

Enzymes

Pathway annotation

Fatty acid profile

API 20NE

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_001981525

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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