Massilia dura (DSM 17513, CCTCC AB 204070, KCTC 12342)

Name: Massilia dura (DSM 17513, CCTCC AB 204070, KCTC 12342)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 11328

Type strain

Strain Designation 16

Culture col. no. DSM 17513 CCTCC AB 204070 KCTC 12342 CCUG 52213 16 1 more

NCBI tax ID(s) 321982

Special Collections DSMZ CCUG KCTC CIP Literature strains

Links

Massilia dura 16 is an aerobe, mesophilic, Gram-negative prokaryote that was isolated from soil.

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

Name and taxonomic classification

SI-ID 232829

KCTC 12342,DSM 17513,CCUG 52213,CIP 109188

@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 dura

Full scientific name Massilia dura Zhang et al. 2006

Synonyms (1)

Pseudoduganella dura

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
31701	negative	1.8-2.2 µm	0.6-0.8 µm	rod-shaped
67771	negative
118978	negative			rod-shaped
125439	negative				99.7
125438	negative				97.875

Pigmentation

31701

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
7033	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
37474	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)
118978	CIP Medium 328	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
7033	positive	growth	30	mesophilic
31701	positive	growth	10-45
31701	positive	optimum	28-30	mesophilic
37474	positive	growth	30	mesophilic
59466	positive	growth	30	mesophilic
67771	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
59466	aerobe
67771	aerobe
118978	facultative anaerobe
125439	obligate aerobe	98.4

Spore formation

@ref	Spore formation	Confidence
31701
125439		98.5

Halophily

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

Observation

@ref	Observation
31701	aggregates in chains
67771	quinones: Q-8

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
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
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
31701	17632 ChEBI	nitrate	+	reduction
118978	17632 ChEBI	nitrate	-	reduction
68369	17632 ChEBI	nitrate	-	reduction	from API 20NE
118978	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
118978	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
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
68382	beta-glucuronidase	-	3.2.1.31	from API zym
31701	catalase	+	1.11.1.6
118978	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
68382	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
118978	oxidase	+
68382	trypsin	-	3.4.21.4	from API zym
31701	urease	+	3.5.1.5
118978	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
118978	-	+	+	+	-	+	+	-	-	-	+	+	+	-	-	-	-	-	-	-

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
7033	-	-	-	-	-	+/-	+	-	+	+	+	-	-	+	-	-	-	-	-	-	+
7033	-	-	-	-	-	+/-	+	-	+	-	+	-	-	+	-	-	-	-	-	-	+

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
7033	-	-	-	-	+	-	+	-	-	-	+	+	+	+	-	+	-	-	-	-	-	-	-	-	+	+	-	+	+	-	-	-	+	-	-	-	+	-	-	+	-	-	-	-	-	-	-	+	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Soil

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
7033	soil	Jiangsu province	China	CHN	Asia
67771	From soil	Jiangsu Province	China	CHN	Asia
118978	Environment, Heavy metal, polluted farm soil	Nanjing, Jiangsu	China	CHN	Asia

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
7033	1	Risk group (German classification) According to TRBA 466
118978	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	ASM972715v1 assembly for Pseudoduganella dura DSM 17513	contig	GCA_009727155	321982.3	2995933029	321982	78.74
66792	ASM1465139v1 assembly for Pseudoduganella dura KCTC 12342	scaffold	GCA_014651395	321982.4	8068501477	321982	54.12

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
31701	Massilia dura strain 16 16S ribosomal RNA gene, partial sequence	AY965998	1478	321982
124043	Massilia dura strain KCTC 12342 16S ribosomal RNA gene, partial sequence.	MT758057	1353	321982
124043	Massilia dura strain KCTC 12342 16S ribosomal RNA gene, partial sequence.	MT759898	1353	321982

GC content

31701

GC-content (mol%)65.9

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Pseudoduganella dura KCTC 12342
NCBI: GCA_014651395

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	98.50	no
125439	motility	BacteriaNetⓘ	yes	72.90	no
125439	gram_stain	BacteriaNetⓘ	negative	99.70	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	98.40	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Massilia dura KCTC 12342
NCBI: GCA_014651395.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	97.88	yes
125438	anaerobic	anaerobicⓘ	no	97.62	no
125438	aerobic	aerobicⓘ	yes	89.43	no
125438	spore-forming	spore-formingⓘ	no	81.41	yes
125438	thermophilic	thermophileⓘ	no	98.00	yes
125438	flagellated	motile2+ⓘ	yes	83.83	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Massilia lurida sp. nov., isolated from soil.	Luo X, Xie Q, Wang J, Pang H, Fan J, Zhang J	Int J Syst Evol Microbiol	10.1099/ijs.0.047068-0	2012
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

#7033	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 17513
#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)
#37474	; Curators of the CIP;
#59466	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 52213
#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) .
#67771	Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;
#68369	Automatically annotated from API 20NE .
#68371	Automatically annotated from API 50CH acid .
#68382	Automatically annotated from API zym .
#118978	Collection of Institut Pasteur ; Curators of the CIP; CIP 109188
#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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Massilia dura (DSM 17513, CCTCC AB 204070, KCTC 12342)

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 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_009727155

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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