Massilia buxea (DSM 103547, CGMCC 1.15931, KCTC 52429)

Name: Massilia buxea (DSM 103547, CGMCC 1.15931, KCTC 52429)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 158678

Type strain

Strain Designation A9

Culture col. no. DSM 103547 CGMCC 1.15931 KCTC 52429 A9

NCBI tax ID(s) 1949069

Special Collections DSMZ KCTC Literature strains

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Massilia buxea A9 is an aerobe, Gram-negative, motile prokaryote that forms circular colonies and was isolated from the surface of rock collected from the shore.

Gram-negative motile rod-shaped colony-forming aerobe genome sequence

Name and taxonomic classification

SI-ID 28297

KCTC 52429

@ref 20215

Last LPSN update 2026-02-09 11:38:23

Domain Bacteria

Phylum Pseudomonadota

Class Betaproteobacteria

Order Burkholderiales

Family Oxalobacteraceae

Genus Massilia

Species Massilia buxea

Full scientific name Massilia buxea Sun et al. 2017

Synonyms (1)

Pseudoduganella buxea

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
65410	negative	1.3-2.1 µm	0.6-0.9 µm	rod-shaped
125439	negative				99.5
125438	negative				98.375

Colony morphology

@ref	Colony size	Colony color	Colony shape	Incubation period	Medium used
65410	2-4 mm	pale yellow	circular	3 days	R2A agar

Pigmentation

65410

Productionno

Culture and growth conditions

Culture medium

@ref	Name	Growth
65410	Reasoner's 2A agar (R2A)

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
65410	positive	growth	10-37
65410	positive	optimum	28-30	mesophilic

Culture pH

@ref	Ability	Type	PH	PH range
65410	positive	optimum	7
65410	positive	growth	6-9	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
65410	aerobe
125439	obligate aerobe	98.6

Spore formation

@ref	Spore formation	Confidence
65410
125439		98

Halophily

@ref	Salt	Growth	Tested relation	Concentration
65410	NaCl	positive	growth	0-1 %(w/v)
65410	NaCl	positive	optimum	0 %(w/v)

Observation

@ref	Observation
65410	colonies are circular to irregular, crimped, convex, opaque, not smooth
65410	growth occurs on ISP2 agar, nutrient agar and trypticase soy agar
65410	predominant ubiquinone is Q-8
65410	major polar lipids are diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and aminophospholipid

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
65410		1-o-methyl alpha-galactopyranoside	+	assimilation
65410	30089 ChEBI	acetate	+	assimilation
65410	17128 ChEBI	adipate	-	assimilation
65410	17925 ChEBI	alpha-D-glucose	+	assimilation
65410	73706 ChEBI	bromosuccinate	+	assimilation
65410		casein	+	assimilation
65410	17057 ChEBI	cellobiose	+	assimilation
65410	15824 ChEBI	D-fructose	+	assimilation
65410	78697 ChEBI	D-fructose 6-phosphate	+	assimilation
65410	15895 ChEBI	D-galactonic acid lactone	+	assimilation
65410	12936 ChEBI	D-galactose	+	assimilation
65410	18024 ChEBI	D-galacturonic acid	+	assimilation
65410	8391 ChEBI	D-gluconate	+	assimilation
65410	17634 ChEBI	D-glucose	+	assimilation
65410	17634 ChEBI	D-glucose	+	fermentation
65410	14314 ChEBI	D-glucose 6-phosphate	+	assimilation
65410	15748 ChEBI	D-glucuronate	+	assimilation
65410	16899 ChEBI	D-mannitol	-	assimilation
65410	16024 ChEBI	D-mannose	+	assimilation
65410	27689 ChEBI	decanoate	-	assimilation
65410	23652 ChEBI	dextrin	+	assimilation
65410		esculin ferric citrate	+	assimilation
65410	5291 ChEBI	gelatin	+	assimilation
65410	28066 ChEBI	gentiobiose	+	assimilation
65410	32323 ChEBI	glucuronamide	+	assimilation
65410	17754 ChEBI	glycerol	+	assimilation
65410	70744 ChEBI	glycine-proline	+	assimilation
65410	17596 ChEBI	inosine	+	assimilation
65410	16977 ChEBI	L-alanine	+	assimilation
65410	30849 ChEBI	L-arabinose	+	assimilation
65410	16467 ChEBI	L-arginine	+	assimilation
65410	29991 ChEBI	L-aspartate	+	assimilation
65410	18287 ChEBI	L-fucose	+	assimilation
65410	29985 ChEBI	L-glutamate	+	assimilation
65410	15971 ChEBI	L-histidine	+	assimilation
65410	18183 ChEBI	L-pyroglutamic acid	+	assimilation
65410	62345 ChEBI	L-rhamnose	+	assimilation
65410	17115 ChEBI	L-serine	+	assimilation
65410	25115 ChEBI	malate	+	assimilation
65410	17306 ChEBI	maltose	+	assimilation
65410	28053 ChEBI	melibiose	+	assimilation
65410	37657 ChEBI	methyl D-glucoside	+	assimilation
65410	51850 ChEBI	methyl pyruvate	+	assimilation
65410	28037 ChEBI	N-acetylgalactosamine	+	assimilation
65410	506227 ChEBI	N-acetylglucosamine	-	assimilation
65410	506227 ChEBI	N-acetylglucosamine	+	assimilation
65410	35418 ChEBI	n-acetylneuraminate	+	assimilation
65410	17632 ChEBI	nitrate	+	reduction
65410	17309 ChEBI	pectin	+	assimilation
65410	18401 ChEBI	phenylacetate	-	assimilation
65410	32032 ChEBI	potassium gluconate	-	assimilation
65410	17814 ChEBI	salicin	+	assimilation
65410	53258 ChEBI	sodium citrate	-	assimilation
65410	28017 ChEBI	starch	+	assimilation
65410	17992 ChEBI	sucrose	+	assimilation
65410	27082 ChEBI	trehalose	+	assimilation
65410	32528 ChEBI	turanose	-	assimilation
65410	53424 ChEBI	tween 20	+	assimilation
65410	53423 ChEBI	tween 40	+	assimilation

Antibiotic resistance

@ref	ChEBI	Metabolite
65410	161680	aztreonam
65410	16523	d-serine
65410	71321	fusidate
65410	32735	guanidinium chloride
65410	48607	lithium chloride
65410	50694	minocycline
65410	100147	nalidixic acid
65410	75273	niaproof
65410	75248	potassium tellurite
65410	29673	rifamycin sv
65410	80025	salinomycin
65410	75229	sodium bromate
65410	64103	sodium butyrate
65410	75198	tetrazolium blue
65410	75193	tetrazolium violet
65410	45735	troleandomycin
65410	28001	vancomycin

Metabolite production

@ref	Chebi-ID	Metabolite	Production
65410	35581 ChEBI	indole
65410	15138 ChEBI	sulfide

Enzymes

@ref	Value	Activity	Ec
65410	acid phosphatase	+	3.1.3.2
65410	alkaline phosphatase	+	3.1.3.1
65410	alpha-chymotrypsin	-	3.4.21.1
65410	alpha-fucosidase	-	3.2.1.51
65410	alpha-galactosidase	+	3.2.1.22
65410	alpha-glucosidase	+	3.2.1.20
65410	alpha-mannosidase	-	3.2.1.24
65410	arginine dihydrolase	-	3.5.3.6
65410	beta-galactosidase	+	3.2.1.23
65410	beta-glucosidase	-	3.2.1.21
65410	beta-glucuronidase	-	3.2.1.31
65410	catalase	+	1.11.1.6
65410	cystine arylamidase	+	3.4.11.3
65410	cytochrome oxidase	+	1.9.3.1
65410	esterase (C 4)	+
65410	esterase Lipase (C 8)	+
65410	leucine arylamidase	+	3.4.11.1
65410	lipase (C 14)	-
65410	N-acetyl-beta-glucosaminidase	-	3.2.1.52
65410	naphthol-AS-BI-phosphohydrolase	+
65410	trypsin	-	3.4.21.4
65410	urease	+	3.5.1.5
65410	valine arylamidase	+

Fatty acid profile

Metadata FA analysis

@ref

65410

Fatty acid	Percentage
C16:1ω7c and/or iso-C 15:0 2-OH	51.4
C16:0	28.4
C18:1ω7c	7.8
C10:0 3OH	4.7
C12:0	3.6
C14:0 2OH	1.6
C12:0 2OH	1.3
C14:0	0.9

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Coast
#Environmental	#Terrestrial	#Geologic

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
65410	the surface of rock collected from the shore	Nvshan Lake in Mingguang city, Anhui province	China	CHN	Asia

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM1464415v1 assembly for Pseudoduganella buxea CGMCC 1.15931	scaffold	GCA_014644155	1949069.4	8068485948	1949069	62.59
66792	ASM972083v1 assembly for Pseudoduganella buxea KCTC 52429	scaffold	GCA_009720835	1949069.3	2920891533	1949069	6.47

GC content

@ref	GC-content (mol%)	Method
65410	69.9	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 buxea CGMCC 1.15931
NCBI: GCA_014644155

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	98.00	no
125439	motility	BacteriaNetⓘ	yes	79.40	no
125439	gram_stain	BacteriaNetⓘ	negative	99.50	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	98.60	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Massilia buxea CGMCC 1.15931
NCBI: GCA_014644155.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	98.38	yes
125438	anaerobic	anaerobicⓘ	no	97.77	yes
125438	aerobic	aerobicⓘ	yes	88.88	no
125438	spore-forming	spore-formingⓘ	no	81.86	yes
125438	thermophilic	thermophileⓘ	no	98.50	no
125438	flagellated	motile2+ⓘ	yes	85.13	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Massilia aquatica sp. nov., Isolated from a Subtropical Stream in China.	Lu HB, Deng TC, Xu MY	Curr Microbiol	10.1007/s00284-020-02104-1	2020
Phylogeny	Massilia buxea sp. nov., isolated from a rock surface.	Sun LN, Yang ED, Cui DX, Ni YW, Wang YB, Sun DD, Wang WY	Int J Syst Evol Microbiol	10.1099/ijsem.0.002301	2017

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 )
#65410	Le-Ni Sun, En-Dong Yang, Dan-Xi Cui, Ye-Wen Ni, Yu-Bo Wang, Dong-Dong Sun, Wei-Yun Wang: Massilia buxea sp. nov., isolated from a rock surface. IJSEM 67: 4390 - 4396 2017 ( DOI 10.1099/ijsem.0.002301 , PubMed 28933315 )
#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) .
#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 buxea (DSM 103547, CGMCC 1.15931, KCTC 52429)

Name and taxonomic classification