Sphingomonas melonis (DSM 24958, Fr1)

Name: Sphingomonas melonis (DSM 24958, Fr1)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 24560

Type strain

Strain Designation Fr1

Culture col. no. DSM 24958 Fr1

NCBI tax ID(s) 152682

Special Collections DSMZ

History <- A. Francez-Charlot, ETH, Zürich, Switzerland; FR1 <- C. Knief

Links

Sphingomonas melonis Fr1 is a plant pathogen that was isolated from Arabidopsis thaliana fruit.

plant pathogen genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 403417

DSM 24958

@ref 20215

Last LPSN update 2026-02-09 11:24:00

Domain Bacteria

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Sphingomonadales

Family Sphingomonadaceae

Genus Sphingomonas

Species Sphingomonas melonis

Full scientific name Sphingomonas melonis Buonaurio et al. 2002

BacDive ID	Other strains from **Sphingomonas melonis** (3)	Type strain
14230	S. melonis EY 4350, DSM 14444, LMG 19484, DAPP-PG 224, ... (type strain)
14231	S. melonis DSM 14445, LMG 19485, DAPP-PG 228, CIP 107881
24559	S. melonis C3, DSM 24957

Morphology

Cell morphology

@ref	Gram stain	Confidence
125438	negative	97.313
125439	negative	98.7

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
20817	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

Culture temp

@ref	Growth	Type	Temperature (°C)
20817	positive	growth	28

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	obligate aerobe	99.1

Spore formation

@ref	Spore formation	Confidence
125439		93.1

Isolation, sampling and environmental information

Isolation source categories

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

Isolation

@ref	Sample type	Host species	Geographic location	Country	Country ISO 3 Code	Continent
20817	Arabidopsis thaliana fruit	Arabidopsis thaliana	Madrid	Spain	ESP	Europe

Taxonmaps

69479

Global distribution of 16S sequence FR696367 (>99% sequence identity) for Sphingomonas from Microbeatlas

Aquatic Samples	1091
Soil Samples	447
Animal Samples	1087
Plant Samples	307
Total Samples	2932

Interaction and safety

Risk assessment

@ref	Pathogenicity plant	Biosafety level	Biosafety level comment
20817		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	ASM41956v1 assembly for Sphingomonas melonis FR1	contig	GCA_000419565	1090317.4	2517093015	1090317	77.43

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
20817	Sphingomonas sp. Fr1 partial 16S rRNA gene, strain Fr1	FR696367	1401		907061

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Sphingomonas melonis FR1
NCBI: GCA_000419565

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	99.10	no
125439	gram_stain	BacteriaNetⓘ	negative	98.70	no
125439	motility	BacteriaNetⓘ	yes	74.10	no
125439	spore_formation	BacteriaNetⓘ	no	93.10	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Sphingomonas melonis FR1
PATRIC: 1090317.4

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	97.31	no
125438	anaerobic	anaerobicⓘ	no	94.84	no
125438	spore-forming	spore-formingⓘ	no	86.40	no
125438	aerobic	aerobicⓘ	yes	84.80	no
125438	thermophilic	thermophileⓘ	no	96.84	yes
125438	flagellated	motile2+ⓘ	yes	67.34	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 )
#20817	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 24958
#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) .
#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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