Sphingomonas endophytica (DSM 101535, CCTCC AA 209035, JCM 17394)

Name: Sphingomonas endophytica (DSM 101535, CCTCC AA 209035, JCM 17394)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 131250

Type strain

Culture col. no. DSM 101535 CCTCC AA 209035 JCM 17394 YIM 65583

NCBI tax ID(s) 869719

Special Collections DSMZ JCM Literature strains

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Sphingomonas endophytica DSM 101535 is an aerobe, mesophilic, Gram-negative prokaryote that was isolated from surface sterilized roots of Artemisia annua.

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

Name and taxonomic classification

SI-ID 403660

JCM 17394,DSM 101535

@ref 20215

Last LPSN update 2025-12-16 10:01:12

Domain Pseudomonadati

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Sphingomonadales

Family Sphingomonadaceae

Genus Sphingomonas

Species Sphingomonas endophytica

Full scientific name Sphingomonas endophytica Huang et al. 2012

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
30239	negative	1.8 µm	0.55 µm	rod-shaped
125439	negative				92.4
125438	negative				96.833

Pigmentation

30239

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
22478	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
22478	positive	growth	28	mesophilic
30239	positive	growth	12-45
30239	positive	optimum	29	mesophilic
67770	positive	growth	30	mesophilic

Culture pH

@ref	Ability	Type	PH
30239	positive	optimum	7

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
30239	aerobe
125439	obligate aerobe	99.1

Spore formation

@ref	Spore formation	Confidence
30239
125439		91.2
125438		92.064

Halophily

@ref	Salt	Growth	Tested relation	Concentration
30239	NaCl	positive	optimum	0.50 %

Observation

67770

Observationquinones: Q-10

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68369	17128 ChEBI	adipate	-	assimilation	from API 20NE
30239	22599 ChEBI	arabinose	+	carbon source
68369	29016 ChEBI	arginine	-	hydrolysis	from API 20NE
30239	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
68369	4853 ChEBI	esculin	+	hydrolysis	from API 20NE
30239	28260 ChEBI	galactose	+	carbon source
68369	5291 ChEBI	gelatin	-	hydrolysis	from API 20NE
68369	24265 ChEBI	gluconate	-	assimilation	from API 20NE
30239	17234 ChEBI	glucose	+	carbon source
68369	30849 ChEBI	L-arabinose	+	assimilation	from API 20NE
30239	17716 ChEBI	lactose	+	carbon source
68369	25115 ChEBI	malate	+	assimilation	from API 20NE
30239	17306 ChEBI	maltose	+	carbon source
68369	17306 ChEBI	maltose	+	assimilation	from API 20NE
30239	37684 ChEBI	mannose	+	carbon source
68369	59640 ChEBI	N-acetylglucosamine	+	assimilation	from API 20NE
68369	17632 ChEBI	nitrate	-	reduction	from API 20NE
30239	16634 ChEBI	raffinose	+	carbon source
30239	26546 ChEBI	rhamnose	+	carbon source
30239	17992 ChEBI	sucrose	+	carbon source
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
30239	catalase	+	1.11.1.6
68369	cytochrome oxidase	+	1.9.3.1	from API 20NE
30239	gelatinase	+
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
22478	-	-	-	-	-	+	-	+	+	+	+	-	+	+	-	-	-	+	-	-	+

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Plants	#Herbaceous plants (Grass,Crops)
#Host Body-Site	#Plant	#Root (Rhizome)
#Host Body-Site	#Plant	#Sterilized plant part

Isolation

@ref	Sample type	Host species	Geographic location	Country	Country ISO 3 Code	Continent
22478	surface sterilized roots of Artemisia annua	Artemisia annua	Yunnan province	China	CHN	Asia
67770	Tissue of Aremisia annua L. in Yunnan providence	Aremisia annua		China	CHN	Asia

Taxonmaps

69479

Global distribution of 16S sequence HM629444 (>99% sequence identity) for Sphingomonas from Microbeatlas

Aquatic Samples	128
Soil Samples	153
Animal Samples	324
Plant Samples	272
Total Samples	877

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
22478	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	ASM1419941v1 assembly for Sphingomonas endophytica DSM 101535	scaffold	GCA_014199415	869719.5	2828434831	869719	74.87
124043	ASM3953752v1 assembly for Sphingomonas endophytica JCM 17394	contig	GCA_039537525			869719	74.22

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
22478	Sphingomonas endophytica strain YIM 65583 16S ribosomal RNA gene, partial sequence	HM629444	1412		869719

GC content

@ref	GC-content (mol%)	Method
30239	63.3
67770	63.3	high performance liquid chromatography (HPLC)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Sphingomonas endophytica DSM 101535
NCBI: GCA_014199415

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	91.20	no
125439	motility	BacteriaNetⓘ	yes	59.40	no
125439	gram_stain	BacteriaNetⓘ	negative	92.40	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	99.10	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Sphingomonas endophytica DSM 101535
NCBI: GCA_014199415.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	96.83	no
125438	anaerobic	anaerobicⓘ	no	94.98	yes
125438	aerobic	aerobicⓘ	yes	87.48	yes
125438	spore-forming	spore-formingⓘ	no	92.06	no
125438	thermophilic	thermophileⓘ	no	97.80	yes
125438	flagellated	motile2+ⓘ	yes	70.85	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Synthetic bacterium-facilitated colonization of nitrogen-fixing bacteria for remodeling the rhizosphere microbiome and improving plant yield.	Liu S, Zhao Z, Ji Y, Zhu H, Sun Y, Li M, Yu Q.	Microbiome	10.1186/s40168-025-02189-5	2025
	The Dynamic Changes of Brassica napus Seed Microbiota across the Entire Seed Life in the Field.	Yao Y, Liu C, Zhang Y, Lin Y, Chen T, Xie J, Chang H, Fu Y, Cheng J, Li B, Yu X, Lyu X, Feng Y, Bian X, Jiang D.	Plants (Basel)	10.3390/plants13060912	2024
	Nodulation Experiment by Cross-Inoculation of Nitrogen-Fixing Bacteria Isolated from Root Nodules of Several Leguminous Plants.	Cho A, Joshi A, Hur HG, Lee JH.	J Microbiol Biotechnol	10.4014/jmb.2310.10025	2024
	Analysis of structural and metabolic changes in surface microorganisms following powdery mildew infection in wheat and assessment of their potential function in biological control.	Wu Z, Xue X.	PLoS One	10.1371/journal.pone.0320682	2025
	Using PacBio SMRT Sequencing Technology and Metabolomics to Explore the Microbiota-Metabolome Interaction Related to Silage Fermentation of Woody Plant.	Du Z, Sun L, Lin Y, Yang F, Cai Y.	Front Microbiol	10.3389/fmicb.2022.857431	2022
Genetics	Genomic Resource of Rice Seed Associated Bacteria.	Midha S, Bansal K, Sharma S, Kumar N, Patil PP, Chaudhry V, Patil PB.	Front Microbiol	10.3389/fmicb.2015.01551	2015
Phylogeny	Sphingomonas aeria sp. nov., isolated from air.	Xue H, Piao CG, Wang XZ, Lin CL, Guo MW, Li Y	Int J Syst Evol Microbiol	10.1099/ijsem.0.002910	2018
Phylogeny	Sphingomonas endophytica sp. nov., isolated from Artemisia annua L.	Huang HY, Li J, Zhao GZ, Zhu WY, Yang LL, Tang HY, Xu LH, Li WJ	Int J Syst Evol Microbiol	10.1099/ijs.0.031484-0	2011

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 )
#22478	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 101535
#26581	IJSEM 1576 2012 ( DOI 10.1099/ijs.0.031484-0 , PubMed 21873515 )
#30239	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 #26581
#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) .
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#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 .
#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 endophytica (DSM 101535, CCTCC AA 209035, JCM 17394)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

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

API 20NE

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_014199415

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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