Sphingobium xanthum (DSM 100901, ATCC 51296, NL9)

Name: Sphingobium xanthum (DSM 100901, ATCC 51296, NL9)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 131277

Type strain

Strain Designation NL9

Culture col. no. DSM 100901 ATCC 51296 NL9 LMG 12560

NCBI tax ID(s) 1387165

Special Collections DSMZ

History <- LMG <- K. N. Jochimsen, Department of Plant Pathology, University of Florida; NL9

Links

Sphingobium xanthum NL9 is a plant pathogen that was isolated from soil.

plant pathogen genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 7191

LMG 12560,ATCC 51296,DSM 100901

@ref 20215

Last LPSN update 2026-02-09 11:31:25

Domain Bacteria

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Sphingomonadales

Family Sphingomonadaceae

Genus Sphingobium

Species Sphingobium xanthum

Full scientific name Sphingobium xanthum Francis et al. 2014

Synonyms (1)

Parasphingobium xanthum

Morphology

Cell morphology

@ref	Gram stain	Confidence
125439	negative	93.1

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
22504	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

Culture temp

@ref	Growth	Type	Temperature (°C)
22504	positive	growth	28

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	obligate aerobe	98.4

Spore formation

@ref	Spore formation	Confidence
125439		95.5

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Soil

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
22504	soil	Maasland	Netherlands	NLD	Europe

Interaction and safety

Risk assessment

@ref	Pathogenicity plant	Biosafety level	Biosafety level comment
22504		1	Risk group (German classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	Sphingobium xanthum DSM 100901	complete			2828427071	1387165	95.59
66792	ASM1973761v1 assembly for Sphingobium xanthum NL9	contig	GCA_019737615	1387165.3	8047984571	1387165	70.81
124043	ASM5043314v1 assembly for Sphingobium xanthum DSM 100901	contig	GCA_050433145			1387165	62.45

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
22504	Sphingobium xanthum strain NL9 16S ribosomal RNA gene, partial sequence	KF437579	1453		1387165

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Sphingobium xanthum NL9
NCBI: GCA_019737615

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	95.50	no
125439	motility	BacteriaNetⓘ	yes	60.80	no
125439	gram_stain	BacteriaNetⓘ	negative	93.10	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	98.40	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Reclassification of rhizosphere bacteria including strains causing corky root of lettuce and proposal of Rhizorhapis suberifaciens gen. nov., comb. nov., Sphingobium mellinum sp. nov., Sphingobium xanthum sp. nov. and Rhizorhabdus argentea gen. nov., sp. nov.	Francis IM, Jochimsen KN, De Vos P, van Bruggen AHC	Int J Syst Evol Microbiol	10.1099/ijs.0.058909-0	2014

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 )
#22504	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 100901
#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) .
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#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 xanthum (DSM 100901, ATCC 51296, NL9)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_019737615

16S sequences

Genome-based predictions

Predictions

Literature

Literature

References

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