Massilia umbonata (DSM 26121, CECT 7753, LP01)

Name: Massilia umbonata (DSM 26121, CECT 7753, LP01)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 24262

Type strain

Strain Designation LP01

Culture col. no. DSM 26121 CECT 7753 LP01

NCBI tax ID(s) 864828

Special Collections DSMZ

Links

Massilia umbonata LP01 is a mesophilic prokaryote that was isolated from mixture of soil and sewage sludge compost.

mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 391806

CECT 7753,DSM 26121

@ref 20215

Last LPSN update 2025-12-16 09:52:49

Domain Pseudomonadati

Phylum Pseudomonadota

Class Betaproteobacteria

Order Burkholderiales

Family Oxalobacteraceae

Genus Massilia

Species Massilia umbonata

Full scientific name Massilia umbonata Rodríguez-Díaz et al. 2014

Synonyms (1)

Pseudoduganella umbonata

Morphology

Cell morphology

@ref	Gram stain	Confidence
125439	negative	99.7

Colony morphology

20644

Incubation period2-3 days

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
20644	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
20644	positive	growth	30	mesophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	obligate aerobe	98.8

Spore formation

@ref	Spore formation	Confidence
125439		98.5

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68369	17128 ChEBI	adipate	-	assimilation	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	30849 ChEBI	L-arabinose	+	assimilation	from API 20NE
68369	25115 ChEBI	malate	+	assimilation	from API 20NE
68369	17632 ChEBI	nitrate	-	reduction	from API 20NE
68369	27897 ChEBI	tryptophan	-	energy source	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	beta-glucosidase	+	3.2.1.21	from API 20NE
20644	catalase	+	1.11.1.6
68369	cytochrome oxidase	+	1.9.3.1	from API 20NE
20644	cytochrome-c oxidase	+	1.9.3.1

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
20644	-	-	-	+	+	+	+	+	+	+	+	+	+	-	+	-	-	+	+	-	+
20644	-	-	-	-	-	+	+	+	+	+	+	+	-	+	-	-	-	+	+	-	not determinedn.d.
20644	-	-	-	-	-	+	-	+	+	+	+	+	-	+	-	-	-	+	+	-	not determinedn.d.

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Biodegradation	#Composting
#Engineered	#Waste	#Sewage sludge
#Environmental	#Terrestrial	#Soil

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
20644	mixture of soil and sewage sludge compost	province of Jaén, nearby Guadalimar (soil) and Granada	Spain	ESP	Europe

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
20644	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	ASM528031v1 assembly for Pseudoduganella umbonata DSMZ 26121	complete	GCA_005280315	864828.3	2848879641	864828	93.65
66792	ASM1419222v1 assembly for Pseudoduganella umbonata CECT 7753	scaffold	GCA_014192225	864828.4	2824420946	864828	66.46

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
20644	Massilia umbonata strain LP01 16S ribosomal RNA gene, partial sequence	HM053474	1434		864828

GC content

@ref	GC-content (mol%)	Method
20644	66.0	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: Pseudoduganella umbonata CECT 7753
NCBI: GCA_014192225

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	98.50	no
125439	motility	BacteriaNetⓘ	yes	76.20	no
125439	gram_stain	BacteriaNetⓘ	negative	99.70	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	98.80	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Massilia umbonata sp. nov., able to accumulate poly-beta-hydroxybutyrate, isolated from a sewage sludge compost-soil microcosm.	Rodriguez-Diaz M, Cerrone F, Sanchez-Peinado M, SantaCruz-Calvo L, Pozo C, Lopez JG	Int J Syst Evol Microbiol	10.1099/ijs.0.049874-0	2013

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 )
#20644	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 26121
#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 .
#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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Massilia umbonata (DSM 26121, CECT 7753, LP01)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

API 20NE

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_005280315

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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