Sphingomonas sp. (DSM 102732, Leaf357)

Name: Sphingomonas sp. (DSM 102732, Leaf357)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 131949

Type strain

Strain Designation Leaf357

Culture col. no. DSM 102732 Leaf357

NCBI tax ID(s) 28214

Special Collections DSMZ Arabidopsis

History DSMZ <- J. A. Vorholt, Institute of Microbiology, ETH Zurich, Switzerland; Leaf357 <- D. B. Müller, E. Potthoff and M. Remus-Emsermann

Links

Leaf357 is a bacterium that was isolated from leaf of wild-type Arabidopsis thaliana.

genome sequence Bacteria

Name and taxonomic classification

SI-ID 396539

DSM 102732

@ref 20215

Last LPSN update 2026-05-29 08:37:44

Domain Bacteria

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Sphingomonadales

Family Sphingomonadaceae

Genus Sphingomonas

Full scientific name Sphingomonas Yabuuchi et al. 1990

Synonyms (18)

Alterirhizorhabdus
Paraquisediminimonas
Novistakelama
Parastakelama
Alteristakelama
Pseudostakelama
Alterisphingomonas
Solisphingomonas
Parayabuuchia
Humisphingomonas
Pseudosphingomonas
Neorhizorhabdus
Parasphingomonas
Flavisphingomonas
Edaphosphingomonas
Pararhizorhabdus
Alteriyabuuchia
Alterisphingopyxis

Morphology

Cell morphology

@ref	Gram stain	Confidence
125439	negative	94.886
125438	negative	95.542

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
23741	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)
23741	positive	growth	28

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	obligate aerobe	98.548

Spore formation

@ref	Spore formation	Confidence
125438		91.738
125439		97.19

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
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	27689 ChEBI	decanoate	-	assimilation	from API 20NE
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	17306 ChEBI	maltose	-	assimilation	from API 20NE
68369	17632 ChEBI	nitrate	-	reduction	from API 20NE
68369	27897 ChEBI	tryptophan	-	energy source	from API 20NE
68369	16199 ChEBI	urea	-	hydrolysis	from API 20NE

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
68369	beta-glucosidase	-	3.2.1.21	from API 20NE
68369	cytochrome oxidase	+	1.9.3.1	from API 20NE
68369	gelatinase	+		from API 20NE
68369	urease	-	3.5.1.5	from API 20NE

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
23741	-	-	-	-	-	-	+	+	+	+	+/-	-	+/-	-	-	-	-	+/-	-	-	+

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Plants	#Herbaceous plants (Grass,Crops)
#Host Body-Site	#Plant	#Leaf (Phyllosphere)

Isolation

@ref	Sample type	Host species	Geographic location	Country	Country ISO 3 Code	Continent	Latitude	Longitude
23741	leaf of wild-type Arabidopsis thaliana	Arabidopsis thaliana	Tuebingen Farm (48.5560194N 9.134944444E)	Germany	DEU	Europe	48.556	9.1349 48.556/9.1349

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	Leaf357 assembly for Sphingomonas sp. Leaf357	contig	GCA_001423845	1736350.3	2643221813	1736350	78.75

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Leaf357 assembly for Sphingomonas sp. Leaf357
BV-BRC: 1736350.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	gram_stain	BacteriaNetⓘ	negative	94.89	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	98.55	no
125439	motility	BacteriaNetⓘ	yes	62.07	no
125439	spore_formation	BacteriaNetⓘ	no	97.19	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Sphingomonas sp. Leaf357
PATRIC: 1736350.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	95.54	no
125438	anaerobic	anaerobicⓘ	no	94.27	no
125438	spore-forming	spore-formingⓘ	no	91.74	no
125438	aerobic	aerobicⓘ	yes	88.08	no
125438	thermophilic	thermophileⓘ	no	96.89	yes
125438	flagellated	motile2+ⓘ	yes	69.85	no

Literature

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 )
#23741	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 102732
#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 .
#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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