Massilia lutea (DSM 17473, CCTCC AB 204073, KCTC 12345)

Name: Massilia lutea (DSM 17473, CCTCC AB 204073, KCTC 12345)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 11326

Type strain

Strain Designation 101

Culture col. no. DSM 17473 CCTCC AB 204073 KCTC 12345 CCUG 52216 101 1 more

NCBI tax ID(s) 321985

Special Collections DSMZ CCUG KCTC Literature strains CIP

Links

Massilia lutea 101 is an aerobe, mesophilic, Gram-negative prokaryote that was isolated from heavy-metal-polluted farm soil.

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

Name and taxonomic classification

SI-ID 232832

KCTC 12345,DSM 17473,CCUG 52216,CIP 109190

@ref 20215

Last LPSN update 2025-12-16 09:49:33

Domain Pseudomonadati

Phylum Pseudomonadota

Class Betaproteobacteria

Order Burkholderiales

Family Oxalobacteraceae

Genus Massilia

Species Massilia lutea

Full scientific name Massilia lutea Zhang et al. 2006

Synonyms (1)

Pseudoduganella lutea

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
31701	negative	3-3.5 µm	1.8-2 µm	rod-shaped
120683	negative			rod-shaped
125438	negative				96.375
125439	negative				99.4

Colony morphology

59468

Incubation period3 days

Pigmentation

31701

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
7008	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
33280	MEDIUM 328- for nutrient agar		Distilled water make up to (1000.000 ml);Agar (15.000 g);Peptone (5.000g);Beef extract (3.000 g)
120683	CIP Medium 328	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
7008	positive	growth	30	mesophilic
31701	positive	growth	10-45
31701	positive	optimum	28-30	mesophilic
33280	positive	growth	30	mesophilic
59468	positive	growth	30	mesophilic

Culture pH

@ref	Ability	Type	PH	PH range
31701	positive	optimum	7-7.5
31701	positive	growth	6.5-8.5	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
31701	aerobe
59468	aerobe
120683	facultative anaerobe
125439	aerobe	94.5

Spore formation

@ref	Spore formation	Confidence
31701
125439		97.9

Halophily

@ref	Salt	Growth	Tested relation	Concentration
31701	NaCl	positive	growth	0-1 %
31701	NaCl	positive	optimum	0-1 %

Observation

31701

Observationaggregates in chains

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68369	17128 ChEBI	adipate	-	assimilation	from API 20NE
68371	27613 ChEBI	amygdalin	+	builds acid from	from API 50CH acid
68371	18305 ChEBI	arbutin	+	builds acid from	from API 50CH acid
68369	29016 ChEBI	arginine	-	hydrolysis	from API 20NE
68371	17057 ChEBI	cellobiose	+	builds acid from	from API 50CH acid
68371	17108 ChEBI	D-arabinose	-	builds acid from	from API 50CH acid
68371	18333 ChEBI	D-arabitol	-	builds acid from	from API 50CH acid
68371	15824 ChEBI	D-fructose	+	builds acid from	from API 50CH acid
68371	28847 ChEBI	D-fucose	-	builds acid from	from API 50CH acid
68371	12936 ChEBI	D-galactose	+	builds acid from	from API 50CH acid
68371	17634 ChEBI	D-glucose	+	builds acid from	from API 50CH acid
68369	17634 ChEBI	D-glucose	+	assimilation	from API 20NE
68369	17634 ChEBI	D-glucose	-	fermentation	from API 20NE
68371	62318 ChEBI	D-lyxose	-	builds acid from	from API 50CH acid
68371	16899 ChEBI	D-mannitol	-	builds acid from	from API 50CH acid
68369	16899 ChEBI	D-mannitol	-	assimilation	from API 20NE
68371	16024 ChEBI	D-mannose	+	builds acid from	from API 50CH acid
68369	16024 ChEBI	D-mannose	+	assimilation	from API 20NE
68371	16988 ChEBI	D-ribose	-	builds acid from	from API 50CH acid
68371	17924 ChEBI	D-sorbitol	-	builds acid from	from API 50CH acid
68371	16443 ChEBI	D-tagatose	-	builds acid from	from API 50CH acid
68371	65327 ChEBI	D-xylose	+	builds acid from	from API 50CH acid
68369	27689 ChEBI	decanoate	-	assimilation	from API 20NE
68371	17113 ChEBI	erythritol	-	builds acid from	from API 50CH acid
68371	4853 ChEBI	esculin	+	builds acid from	from API 50CH acid
68369	4853 ChEBI	esculin	+	hydrolysis	from API 20NE
68371	16813 ChEBI	galactitol	-	builds acid from	from API 50CH acid
68369	5291 ChEBI	gelatin	+	hydrolysis	from API 20NE
68371	28066 ChEBI	gentiobiose	+	builds acid from	from API 50CH acid
68371	24265 ChEBI	gluconate	+	builds acid from	from API 50CH acid
68369	24265 ChEBI	gluconate	-	assimilation	from API 20NE
31701	17234 ChEBI	glucose	+	carbon source
68371	17754 ChEBI	glycerol	-	builds acid from	from API 50CH acid
68371	28087 ChEBI	glycogen	+	builds acid from	from API 50CH acid
68371	15443 ChEBI	inulin	+	builds acid from	from API 50CH acid
68371	30849 ChEBI	L-arabinose	+	builds acid from	from API 50CH acid
68369	30849 ChEBI	L-arabinose	-	assimilation	from API 20NE
68371	18403 ChEBI	L-arabitol	-	builds acid from	from API 50CH acid
68371	18287 ChEBI	L-fucose	-	builds acid from	from API 50CH acid
68371	62345 ChEBI	L-rhamnose	+	builds acid from	from API 50CH acid
68371	17266 ChEBI	L-sorbose	-	builds acid from	from API 50CH acid
68371	65328 ChEBI	L-xylose	-	builds acid from	from API 50CH acid
68371	17716 ChEBI	lactose	-	builds acid from	from API 50CH acid
68369	25115 ChEBI	malate	-	assimilation	from API 20NE
68371	17306 ChEBI	maltose	+	builds acid from	from API 50CH acid
68369	17306 ChEBI	maltose	+	assimilation	from API 20NE
68371	6731 ChEBI	melezitose	-	builds acid from	from API 50CH acid
68371	28053 ChEBI	melibiose	-	builds acid from	from API 50CH acid
68371	320061 ChEBI	methyl alpha-D-glucopyranoside	-	builds acid from	from API 50CH acid
68371	43943 ChEBI	methyl alpha-D-mannoside	-	builds acid from	from API 50CH acid
68371	74863 ChEBI	methyl beta-D-xylopyranoside	-	builds acid from	from API 50CH acid
68371	17268 ChEBI	myo-inositol	-	builds acid from	from API 50CH acid
68371	59640 ChEBI	N-acetylglucosamine	-	builds acid from	from API 50CH acid
68369	59640 ChEBI	N-acetylglucosamine	-	assimilation	from API 20NE
120683	17632 ChEBI	nitrate	-	reduction
68369	17632 ChEBI	nitrate	-	reduction	from API 20NE
120683	16301 ChEBI	nitrite	-	reduction
68371		Potassium 2-ketogluconate	-	builds acid from	from API 50CH acid
68371		Potassium 5-ketogluconate	-	builds acid from	from API 50CH acid
68371	16634 ChEBI	raffinose	-	builds acid from	from API 50CH acid
68371	15963 ChEBI	ribitol	-	builds acid from	from API 50CH acid
68371	17814 ChEBI	salicin	-	builds acid from	from API 50CH acid
68371	28017 ChEBI	starch	+	builds acid from	from API 50CH acid
31701	17992 ChEBI	sucrose	+	carbon source
68371	17992 ChEBI	sucrose	+	builds acid from	from API 50CH acid
68371	27082 ChEBI	trehalose	+	builds acid from	from API 50CH acid
68369	27897 ChEBI	tryptophan	-	energy source	from API 20NE
68371	32528 ChEBI	turanose	-	builds acid from	from API 50CH acid
68369	16199 ChEBI	urea	-	hydrolysis	from API 20NE
68371	17151 ChEBI	xylitol	-	builds acid from	from API 50CH acid

Metabolite production

@ref	Chebi-ID	Metabolite	Production
68369	35581 ChEBI	indole		from API 20NE
120683	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Indole test
68369	35581 ChEBI	indole	-	from API 20NE

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
120683	alcohol dehydrogenase	-	1.1.1.1
68382	alkaline phosphatase	+	3.1.3.1	from API zym
68382	alpha-chymotrypsin	-	3.4.21.1	from API zym
68382	alpha-fucosidase	-	3.2.1.51	from API zym
68382	alpha-galactosidase	+	3.2.1.22	from API zym
68382	alpha-glucosidase	-	3.2.1.20	from API zym
68382	alpha-mannosidase	-	3.2.1.24	from API zym
68369	arginine dihydrolase	-	3.5.3.6	from API 20NE
68382	beta-galactosidase	-	3.2.1.23	from API zym
68382	beta-glucosidase	+	3.2.1.21	from API zym
68369	beta-glucosidase	+	3.2.1.21	from API 20NE
68382	beta-glucuronidase	-	3.2.1.31	from API zym
31701	catalase	+	1.11.1.6
120683	catalase	+	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
31701	cytochrome oxidase	+	1.9.3.1
68369	cytochrome oxidase	+	1.9.3.1	from API 20NE
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
68369	gelatinase	+		from API 20NE
68382	leucine arylamidase	+	3.4.11.1	from API zym
68382	lipase (C 14)	-		from API zym
120683	lysine decarboxylase	-	4.1.1.18
68382	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
120683	ornithine decarboxylase	-	4.1.1.17
120683	oxidase	+
68382	trypsin	-	3.4.21.4	from API zym
120683	urease	+	3.5.1.5
68369	urease	-	3.5.1.5	from API 20NE
68382	valine arylamidase	+		from API zym

API zym

@ref	Control	Alkaline phosphatase	Esterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	Lipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	Trypsin	alpha- Chymotrypsin	Acid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	alpha- Galactosidase	beta- Galactosidase	beta- Glucuronidase	alpha- Glucosidase	beta- Glucosidase	N-acetyl-beta- glucosaminidase	alpha- Mannosidase	alpha- Fucosidase
120683	-	+	+	+	-	+	+	-	-	-	+	+	+	-	-	-	+	-	-	-

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
7008	-	-	-	-	-	+	+	+	+	-	+	-	-	+	-	-	-	-	-	+	+

API 50CHac

@ref	ControlQ	GLY	ERY	DARA	LARA	RIB	DXYL	LXYL	ADO	MDX	GAL	GLU	FRU	MNE	SBE	RHA	DUL	INO	MAN	SOR	MDM	MDG	NAG	AMY	ARB	ESC	SAL	CEL	MAL	LAC	MEL	SAC	TRE	INU	MLZ	RAF	AMD	GLYG	XLT	GEN	TUR	LYX	TAG	DFUC	LFUC	DARL	LARL	GNT	2KG	5KG
7008	-	-	-	-	+	-	+	-	-	-	+	+	+	+	-	+	-	-	-	-	-	-	-	+	+	+	-	+	+	-	-	+	+	+	-	-	+	+	-	+	-	-	-	-	-	-	-	+	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Agriculture	-
#Engineered	#Contamination	#Heavy metal
#Environmental	#Terrestrial	#Soil

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
7008	heavy-metal-polluted farm soil	Nanjing, Jiangsu province	China	CHN	Asia
120683	Environment, Heavy metal, polluted farm soil	Nanjing, Jiangsu	China	CHN	Asia

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
7008	1	Risk group (German classification) According to TRBA 466
120683	1	Risk group (French classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM420975v1 assembly for Pseudoduganella lutea DSM 17473	chromosome	GCA_004209755	321985.3	2843750665	321985	83.94

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
7008	Massilia lutea strain 101 16S ribosomal RNA gene, partial sequence	AY966001	1464		321985

GC content

7008

GC-content (mol%)63.3

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Massilia lutea DSM 17473
IMG: 2843750665

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	97.90	no
125439	motility	BacteriaNetⓘ	yes	74.70	no
125439	gram_stain	BacteriaNetⓘ	negative	99.40	no
125439	oxygen_tolerance	BacteriaNetⓘ	aerobe	94.50	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Massilia lutea strain DSM 17473
PATRIC: 321985.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	96.38	yes
125438	anaerobic	anaerobicⓘ	no	97.53	yes
125438	spore-forming	spore-formingⓘ	no	80.44	yes
125438	aerobic	aerobicⓘ	yes	88.88	no
125438	thermophilic	thermophileⓘ	no	98.50	yes
125438	flagellated	motile2+ⓘ	yes	85.08	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Massilia flava sp. nov., isolated from soil.	Wang J, Zhang J, Pang H, Zhang Y, Li Y, Fan J	Int J Syst Evol Microbiol	10.1099/ijs.0.031344-0	2011
Phylogeny	Massilia jejuensis sp. nov. and Naxibacter suwonensis sp. nov., isolated from air samples.	Weon HY, Yoo SH, Kim SJ, Kim YS, Anandham R, Kwon SW	Int J Syst Evol Microbiol	10.1099/ijs.0.015479-0	2009
Phylogeny	Massilia dura sp. nov., Massilia albidiflava sp. nov., Massilia plicata sp. nov. and Massilia lutea sp. nov., isolated from soils in China.	Zhang YQ, Li WJ, Zhang KY, Tian XP, Jiang Y, Xu LH, Jiang CL, Lai R	Int J Syst Evol Microbiol	10.1099/ijs.0.64083-0	2006

References

#7008	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 17473
#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 )
#31701	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 #27978 (see below)
#33280	; Curators of the CIP;
#59468	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 52216
#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 .
#68371	Automatically annotated from API 50CH acid .
#68382	Automatically annotated from API zym .
#120683	Collection of Institut Pasteur ; Curators of the CIP; CIP 109190
#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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Massilia lutea (DSM 17473, CCTCC AB 204073, KCTC 12345)

Name and taxonomic classification

Morphology

Cell morphology

Colony 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 zym

API 20NE

API 50CHac

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_004209755

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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