Sphingomonas sanxanigenens (DSM 19645, CGMCC 1.6417, CIP 110406)

Name: Sphingomonas sanxanigenens (DSM 19645, CGMCC 1.6417, CIP 110406)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 14256

Type strain

Strain Designation NX02

Culture col. no. DSM 19645 CGMCC 1.6417 CIP 110406 NX02

NCBI tax ID(s) 1123269 397260

Special Collections DSMZ CIP Literature strains

Links

Sphingomonas sanxanigenens NX02 is a mesophilic, Gram-negative, rod-shaped prokaryote that was isolated from cornfield soil.

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

Name and taxonomic classification

SI-ID 362326

CGMCC 1.6417,DSM 19645,CIP 110406

@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 sanxanigenens

Full scientific name Sphingomonas sanxanigenens Huang et al. 2009

Synonyms (1)

Alteriyabuuchia sanxanigenens

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
28879	negative	1.75 µm	0.75 µm	rod-shaped
122484	negative			rod-shaped
125438	negative				91.065
125439	negative				95.8

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
8232	REACTIVATION WITH LIQUID MEDIUM (DSMZ Medium 535b)	Medium recipe at MediaDive	Name: REACTIVATION WITH LIQUID MEDIUM (DSMZ Medium 535b) Composition: Trypticase soy broth 30.0 g/l Casein peptone 17.0 g/l Agar 15.0 g/l NaCl 5.0 g/l Soy peptone 3.0 g/l K2HPO4 2.5 g/l D(+)-Glucose 2.5 g/l Distilled water
39797	MEDIUM 72- for trypto casein soja agar		Distilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
122484	CIP Medium 72	Medium recipe at CIP
8232	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)	Range
8232	positive	growth	28	mesophilic
28879	positive	optimum	29	mesophilic
39797	positive	growth	30	mesophilic

Culture pH

@ref	Ability	Type	PH
28879	positive	optimum	7.25

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	obligate aerobe	99.5

Spore formation

28879

Spore formationno

Halophily

@ref	Salt	Growth	Tested relation	Concentration
28879	NaCl	positive	optimum	0.025 %

Observation

28879

Observationaggregates in clumps

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68369	17128 ChEBI	adipate	-	assimilation	from API 20NE
28879	22599 ChEBI	arabinose	+	carbon source
68369	29016 ChEBI	arginine	-	hydrolysis	from API 20NE
28879	17057 ChEBI	cellobiose	+	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
28879	23652 ChEBI	dextrin	+	carbon source
28879	4853 ChEBI	esculin	+	hydrolysis
28879	28260 ChEBI	galactose	+	carbon source
28879	5291 ChEBI	gelatin	+	carbon source
68369	5291 ChEBI	gelatin	-	hydrolysis	from API 20NE
68369	24265 ChEBI	gluconate	+	assimilation	from API 20NE
28879	17234 ChEBI	glucose	+	carbon source
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
28879	37684 ChEBI	mannose	+	carbon source
28879	28053 ChEBI	melibiose	+	carbon source
28879	51850 ChEBI	methyl pyruvate	+	carbon source
68369	59640 ChEBI	N-acetylglucosamine	-	assimilation	from API 20NE
28879	17632 ChEBI	nitrate	+	reduction
68369	17632 ChEBI	nitrate	-	reduction	from API 20NE
28879	16634 ChEBI	raffinose	+	carbon source
28879	17992 ChEBI	sucrose	+	carbon source
28879	27082 ChEBI	trehalose	+	carbon source
68369	27897 ChEBI	tryptophan	-	energy source	from API 20NE
68369	16199 ChEBI	urea	-	hydrolysis	from API 20NE
28879	27248 ChEBI	urocanic acid	+	carbon source

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
28879	catalase	+	1.11.1.6
68369	cytochrome oxidase	+	1.9.3.1	from API 20NE
68369	gelatinase	-		from API 20NE
68369	urease	-	3.5.1.5	from API 20NE

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	palmitate biosynthesis	100	22 of 22
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	sulfopterin metabolism	100	4 of 4
66794	coenzyme A metabolism	100	4 of 4
66794	adipate degradation	100	2 of 2
66794	formaldehyde oxidation	100	3 of 3
66794	acetate fermentation	100	4 of 4
66794	biotin biosynthesis	100	4 of 4
66794	starch degradation	100	10 of 10
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	Entner Doudoroff pathway	100	10 of 10
66794	valine metabolism	100	9 of 9
66794	butanoate fermentation	100	4 of 4
66794	methylglyoxal degradation	100	5 of 5
66794	threonine metabolism	100	10 of 10
66794	ppGpp biosynthesis	100	4 of 4
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	folate polyglutamylation	100	1 of 1
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	tetrahydrofolate metabolism	100	14 of 14
66794	suberin monomers biosynthesis	100	2 of 2
66794	cellulose degradation	100	5 of 5
66794	creatinine degradation	100	5 of 5
66794	lactate fermentation	100	4 of 4
66794	gluconeogenesis	100	8 of 8
66794	C4 and CAM-carbon fixation	100	8 of 8
66794	taurine degradation	100	1 of 1
66794	NAD metabolism	94.44	17 of 18
66794	citric acid cycle	92.86	13 of 14
66794	phenylalanine metabolism	92.31	12 of 13
66794	proline metabolism	90.91	10 of 11
66794	pentose phosphate pathway	90.91	10 of 11
66794	propionate fermentation	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	serine metabolism	88.89	8 of 9
66794	molybdenum cofactor biosynthesis	88.89	8 of 9
66794	degradation of sugar acids	88	22 of 25
66794	isoleucine metabolism	87.5	7 of 8
66794	reductive acetyl coenzyme A pathway	85.71	6 of 7
66794	ubiquinone biosynthesis	85.71	6 of 7
66794	propanol degradation	85.71	6 of 7
66794	photosynthesis	85.71	12 of 14
66794	glutamate and glutamine metabolism	85.71	24 of 28
66794	purine metabolism	85.11	80 of 94
66794	leucine metabolism	84.62	11 of 13
66794	d-xylose degradation	81.82	9 of 11
66794	methionine metabolism	80.77	21 of 26
66794	glycogen metabolism	80	4 of 5
66794	peptidoglycan biosynthesis	80	12 of 15
66794	ethylmalonyl-CoA pathway	80	4 of 5
66794	phenylacetate degradation (aerobic)	80	4 of 5
66794	gallate degradation	80	4 of 5
66794	pyrimidine metabolism	80	36 of 45
66794	heme metabolism	78.57	11 of 14
66794	allantoin degradation	77.78	7 of 9
66794	alanine metabolism	75.86	22 of 29
66794	histidine metabolism	75.86	22 of 29
66794	arginine metabolism	75	18 of 24
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	dTDPLrhamnose biosynthesis	75	6 of 8
66794	CMP-KDO biosynthesis	75	3 of 4
66794	glycogen biosynthesis	75	3 of 4
66794	tryptophan metabolism	73.68	28 of 38
66794	3-phenylpropionate degradation	73.33	11 of 15
66794	flavin biosynthesis	73.33	11 of 15
66794	metabolism of disaccharids	72.73	8 of 11
66794	chlorophyll metabolism	72.22	13 of 18
66794	glutathione metabolism	71.43	10 of 14
66794	tyrosine metabolism	71.43	10 of 14
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	lipid metabolism	70.97	22 of 31
66794	glycolysis	70.59	12 of 17
66794	isoprenoid biosynthesis	69.23	18 of 26
66794	vitamin B1 metabolism	69.23	9 of 13
66794	androgen and estrogen metabolism	68.75	11 of 16
66794	degradation of sugar alcohols	68.75	11 of 16
66794	non-pathway related	68.42	26 of 38
66794	4-hydroxymandelate degradation	66.67	6 of 9
66794	acetyl CoA biosynthesis	66.67	2 of 3
66794	cyanate degradation	66.67	2 of 3
66794	sulfoquinovose degradation	66.67	2 of 3
66794	octane oxidation	66.67	2 of 3
66794	degradation of hexoses	66.67	12 of 18
66794	acetoin degradation	66.67	2 of 3
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	enterobactin biosynthesis	66.67	2 of 3
66794	phenol degradation	65	13 of 20
66794	vitamin B6 metabolism	63.64	7 of 11
66794	ketogluconate metabolism	62.5	5 of 8
66794	phosphatidylethanolamine bioynthesis	61.54	8 of 13
66794	cysteine metabolism	61.11	11 of 18
66794	degradation of pentoses	60.71	17 of 28
66794	myo-inositol biosynthesis	60	6 of 10
66794	3-chlorocatechol degradation	60	3 of 5
66794	factor 420 biosynthesis	60	3 of 5
66794	lipoate biosynthesis	60	3 of 5
66794	degradation of aromatic, nitrogen containing compounds	58.33	7 of 12
66794	d-mannose degradation	55.56	5 of 9
66794	lipid A biosynthesis	55.56	5 of 9
66794	nitrate assimilation	55.56	5 of 9
66794	sulfate reduction	53.85	7 of 13
66794	urea cycle	53.85	7 of 13
66794	oxidative phosphorylation	52.75	48 of 91
66794	lysine metabolism	52.38	22 of 42
66794	kanosamine biosynthesis II	50	1 of 2
66794	glycolate and glyoxylate degradation	50	3 of 6
66794	vitamin E metabolism	50	2 of 4
66794	ribulose monophosphate pathway	50	1 of 2
66794	cyclohexanol degradation	50	2 of 4
66794	4-hydroxyphenylacetate degradation	50	5 of 10
66794	coenzyme M biosynthesis	50	5 of 10
66794	toluene degradation	50	2 of 4
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	arachidonic acid metabolism	50	9 of 18
66794	pantothenate biosynthesis	50	3 of 6
66794	alginate biosynthesis	50	2 of 4
66794	phenylmercury acetate degradation	50	1 of 2
66794	quinate degradation	50	1 of 2
66794	glycine metabolism	50	5 of 10
66794	ethanol fermentation	50	1 of 2
66794	vitamin B12 metabolism	47.06	16 of 34
66794	bile acid biosynthesis, neutral pathway	47.06	8 of 17
66794	arachidonate biosynthesis	40	2 of 5
66794	glycine betaine biosynthesis	40	2 of 5
66794	carnitine metabolism	37.5	3 of 8
66794	carotenoid biosynthesis	36.36	8 of 22
66794	ascorbate metabolism	36.36	8 of 22
66794	polyamine pathway	34.78	8 of 23
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	selenocysteine biosynthesis	33.33	2 of 6
66794	sphingosine metabolism	33.33	2 of 6
66794	IAA biosynthesis	33.33	1 of 3
66794	methane metabolism	33.33	1 of 3
66794	aclacinomycin biosynthesis	28.57	2 of 7
66794	benzoyl-CoA degradation	28.57	2 of 7
66794	methanogenesis from CO2	25	3 of 12
66794	catecholamine biosynthesis	25	1 of 4

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
8232	-	-	-	-	-	-	-	+	+	+	+	-	-	+	+	-	-	+	+	-	+
8232	-	-	-	-	-	-	-	-	+	+	+	-	-	+	+	-	-	+	+	-	+
8232	-	-	-	-	-	+	-	+	+	+	+	-	-	+	+	-	-	+	+	-	+

Isolation, sampling and environmental information

Isolation source categories

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

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
8232	cornfield soil	Xinhe County	China	CHN	Asia
122484	Environment, Cornfield soil	Xinhe	China	CHN	Asia

Taxonmaps

69479

Global distribution of 16S sequence DQ789172 (>99% sequence identity) for Sphingomonas sanxanigenens from Microbeatlas

Aquatic Samples	340
Soil Samples	135
Animal Samples	85
Plant Samples	20
Total Samples	580

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
8232	1	Risk group (German classification) According to TRBA 466
122484	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	ASM51220v2 assembly for Sphingomonas sanxanigenens DSM 19645 = NX02	complete	GCA_000512205	1123269.5	2558860262	1123269	96.51
66792	Sphingomonas sanxanigenens DSM 19645	complete			2574179733	1123269	73.92

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
8232	Sphingomonas sanxanigenens strain NX02 16S ribosomal RNA gene, partial sequence	DQ789172	1480		397260
124043	Sphingomonas sanxanigenens partial 16S rRNA gene, isolate strain #16 (MBG-DUTH)/DSM 19645 (ELTE)	OU548670	800		397260

GC content

8232

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: Sphingomonas sanxanigenens DSM 19645 = NX02
NCBI: GCA_000512205

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	99.50	no
125439	gram_stain	BacteriaNetⓘ	negative	95.80	no
125439	motility	BacteriaNetⓘ	yes	61.80	no
125439	spore_formation	BacteriaNetⓘ	no	89.20	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Sphingomonas sanxanigenens DSM 19645 = NX02 NX02
NCBI: GCA_000512205.2

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	91.07	yes
125438	anaerobic	anaerobicⓘ	no	93.05	no
125438	aerobic	aerobicⓘ	yes	89.92	no
125438	spore-forming	spore-formingⓘ	no	84.79	yes
125438	thermophilic	thermophileⓘ	no	96.97	yes
125438	flagellated	motile2+ⓘ	yes	71.04	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Identification and characterization of two CRISPR/Cas systems associated with the mosquito microbiome.	Hegde S, Rauch HE, Hughes GL, Shariat N.	Access Microbiol	10.1099/acmi.0.000599.v4	2023
	The evolutionary life cycle of the polysaccharide biosynthetic gene cluster based on the Sphingomonadaceae.	Wu M, Huang H, Li G, Ren Y, Shi Z, Li X, Dai X, Gao G, Ren M, Ma T.	Sci Rep	10.1038/srep46484	2017
	Genome Sequence and Characterization of a Xanthorhodopsin-Containing, Aerobic Anoxygenic Phototrophic Rhodobacter Species, Isolated from Mesophilic Conditions at Yellowstone National Park.	Kyndt JA, Robertson S, Shoffstall IB, Ramaley RF, Meyer TE.	Microorganisms	10.3390/microorganisms10061169	2022
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
	Evolutionary Genomics of an Ancient Prophage of the Order Sphingomonadales.	Viswanathan V, Narjala A, Ravichandran A, Jayaprasad S, Siddaramappa S.	Genome Biol Evol	10.1093/gbe/evx024	2017
	Diversity of Phototrophic Genes Suggests Multiple Bacteria May Be Able to Exploit Sunlight in Exposed Soils from the Sør Rondane Mountains, East Antarctica.	Tahon G, Tytgat B, Willems A.	Front Microbiol	10.3389/fmicb.2016.02026	2016
Genetics	Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of Alphaproteobacteria.	Hordt A, Lopez MG, Meier-Kolthoff JP, Schleuning M, Weinhold LM, Tindall BJ, Gronow S, Kyrpides NC, Woyke T, Goker M.	Front Microbiol	10.3389/fmicb.2020.00468	2020
Phylogeny	Sphingomonas gilva sp. nov., isolated from mountain soil.	Zhu D, Niu Y, Liu D, Wang G, Zheng S	Int J Syst Evol Microbiol	10.1099/ijsem.0.003645	2019
Phylogeny	Sphingomonaszeicaulis sp. nov., an endophytic bacterium isolated from maize root.	Gao JL, Sun P, Wang XM, Cheng S, Lv F, Qiu TL, Yuan M, Sun JG	Int J Syst Evol Microbiol	10.1099/ijsem.0.001262	2016
Phylogeny	Hephaestia caeni gen. nov., sp. nov., a novel member of the family Sphingomonadaceae isolated from activated sludge.	Felfoldi T, Vengring A, Marialigeti K, Andras J, Schumann P, Toth EM	Int J Syst Evol Microbiol	10.1099/ijs.0.053736-0	2013
Phylogeny	Sphingomonas sanxanigenens sp. nov., isolated from soil.	Huang HD, Wang W, Ma T, Li GQ, Liang FL, Liu RL	Int J Syst Evol Microbiol	10.1099/ijs.0.000257-0	2009

References

#8232	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 19645
#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 )
#25319	IJSEM 719 2009 ( DOI 10.1099/ijs.0.000257-0 , PubMed 19329595 )
#28879	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 #25319
#39797	; 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 .
#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 .
#122484	Collection of Institut Pasteur ; Curators of the CIP; CIP 110406
#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 sanxanigenens (DSM 19645, CGMCC 1.6417, CIP 110406)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Observation

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

Pathway annotation

API 20NE

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000512205

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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