Massilia sp. (DSM 102448, Root335)

Name: Massilia sp. (DSM 102448, Root335)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 132756

Type strain

Strain Designation Root335

Culture col. no. DSM 102448 Root335

NCBI tax ID(s) 1882437

Special Collections DSMZ Arabidopsis

Links

Root335 is a mesophilic prokaryote that was isolated from roots of Arabidopsis thaliana ecotype Shakdara .

mesophilic genome sequence

Name and taxonomic classification

SI-ID 406783

DSM 102448

@ref 20215

Last LPSN update 2025-12-16 10:01:35

Domain Pseudomonadati

Phylum Pseudomonadota

Class Betaproteobacteria

Order Burkholderiales

Family Oxalobacteraceae

Genus Massilia

Full scientific name Massilia La Scola et al. 2000

Synonyms (2)

Mokoshia
Naxibacter

Morphology

Cell morphology

@ref	Gram stain	Confidence
125439	negative	97.2
125438	negative	97.75

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
24546	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)	Range
24546	positive	growth	30	mesophilic

Physiology and metabolism

Spore formation

@ref	Spore formation	Confidence
125439		98

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	16024 ChEBI	D-mannose	+	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	30849 ChEBI	L-arabinose	+	assimilation	from API 20NE
68369	25115 ChEBI	malate	+	assimilation	from API 20NE
68369	17306 ChEBI	maltose	+	assimilation	from API 20NE
68369	59640 ChEBI	N-acetylglucosamine	-	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
24546	-	-	-	-	-	+	+	+	+	+	+	-	-	+	+/-	-	-	+	-	+	+

Isolation, sampling and environmental information

Isolation source categories

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

Isolation

@ref	Sample type	Host species	Geographic location	Country	Country ISO 3 Code	Continent	Latitude	Longitude
24546	roots of Arabidopsis thaliana ecotype Shakdara (Sha)	Arabidopsis thaliana	Cologne (50.958N 6.856E)	Germany	DEU	Europe	50.958	6.856 50.958/6.856

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	Root335 assembly for Massilia sp. Root335	scaffold	GCA_001425685	1736517.3	2713896890	1736517	12.71

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Massilia sp. Root335
NCBI: GCA_001425685

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	98.00	no
125439	motility	BacteriaNetⓘ	yes	83.50	no
125439	gram_stain	BacteriaNetⓘ	negative	97.20	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	86.10	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Massilia sp. Root335 Root335
NCBI: GCA_001425685.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	97.75	no
125438	anaerobic	anaerobicⓘ	no	94.88	no
125438	aerobic	aerobicⓘ	yes	85.30	no
125438	spore-forming	spore-formingⓘ	no	84.35	no
125438	thermophilic	thermophileⓘ	no	98.00	no
125438	flagellated	motile2+ⓘ	yes	82.24	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 )
#24546	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 102448
#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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