Massilia ginsengisoli (KCTC 42409, JCM 30745, DCY 83)

Name: Massilia ginsengisoli (KCTC 42409, JCM 30745, DCY 83)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 141131

Type strain

Culture col. no. KCTC 42409 JCM 30745 DCY 83

NCBI tax ID(s) 1462440

Special Collections JCM KCTC Literature strains

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Massilia ginsengisoli KCTC 42409 is an aerobe, Gram-negative, motile prokaryote that forms circular colonies and was isolated from soil of a ginseng field.

Gram-negative motile rod-shaped colony-forming aerobe genome sequence 16S sequence

Name and taxonomic classification

SI-ID 27975

JCM 30745,KCTC 42409

@ref 20215

Last LPSN update 2025-12-16 10:03:46

Domain Pseudomonadati

Phylum Pseudomonadota

Class Betaproteobacteria

Order Burkholderiales

Family Oxalobacteraceae

Genus Massilia

Species Massilia ginsengisoli

Full scientific name Massilia ginsengisoli (Zhang et al. 2016) Lu et al. 2020

Synonyms (2)

Pseudoduganella ginsengisoli
Duganella ginsengisoli

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
44043	negative	1.1 µm	0.8 µm	rod-shaped
125438	negative				98.5
125439	negative				90.4

Colony morphology

@ref	Colony size	Colony color	Colony shape	Incubation period	Medium used
44043	0.3-1.5 mm	white-cream	circular	2 days	Nutrient agar

Culture and growth conditions

Culture medium

@ref	Name	Growth
44043	Nutrient agar (NA)
44043	Reasoner's 2A agar (R2A)
44043	LB (Luria-Bertani) MEDIUM
44043	MacConkey
44043	PDA
44043	Trypticase Soy Agar (TSA)

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
44043	positive	growth	4-40
44043	positive	optimum	30	mesophilic
67770	positive	growth	30	mesophilic

Culture pH

@ref	Ability	Type	PH
44043	positive	optimum	7
44043	positive	growth	6-8

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
44043	aerobe
125438	aerobe	90.305

Spore formation

@ref	Spore formation	Confidence
125439		98.2

Halophily

@ref	Salt	Growth	Tested relation	Concentration
44043	NaCl	positive	growth	0-0.4 %(w/v)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
44043	16808 ChEBI	2-dehydro-D-gluconate	-	assimilation
44043	16193 ChEBI	3-hydroxybenzoate	-	assimilation
44043	37054 ChEBI	3-hydroxybutyrate	+	assimilation
44043	17879 ChEBI	4-hydroxybenzoate	-	assimilation
44043	58143 ChEBI	5-dehydro-D-gluconate	-	assimilation
44043	17128 ChEBI	adipate	-	assimilation
44043	17634 ChEBI	D-glucose	+	assimilation
44043	16899 ChEBI	D-mannitol	-	assimilation
44043	16024 ChEBI	D-mannose	-	assimilation
44043	16988 ChEBI	D-ribose	-	assimilation
44043	17924 ChEBI	D-sorbitol	-	assimilation
44043	27689 ChEBI	decanoate	-	assimilation
44043	16991 ChEBI	dna	-	hydrolysis
44043	4853 ChEBI	esculin	-	hydrolysis
44043	5291 ChEBI	gelatin	+	hydrolysis
44043	17234 ChEBI	glucose	-	fermentation
44043	28087 ChEBI	glycogen	+	assimilation
44043	17240 ChEBI	itaconate	-	assimilation
44043	16977 ChEBI	L-alanine	-	assimilation
44043	30849 ChEBI	L-arabinose	-	assimilation
44043	18287 ChEBI	L-fucose	-	assimilation
44043	15971 ChEBI	L-histidine	-	assimilation
44043	17203 ChEBI	L-proline	-	assimilation
44043	62345 ChEBI	L-rhamnose	-	assimilation
44043	17115 ChEBI	L-serine	+	assimilation
44043	24996 ChEBI	lactate	+	assimilation
44043	25115 ChEBI	malate	-	assimilation
44043	17306 ChEBI	maltose	-	assimilation
44043	17306 ChEBI	maltose	+	assimilation
44043	28053 ChEBI	melibiose	-	assimilation
44043	17268 ChEBI	myo-inositol	-	assimilation
44043	506227 ChEBI	N-acetylglucosamine	-	assimilation
44043	17632 ChEBI	nitrate	+	reduction
44043	18401 ChEBI	phenylacetate	-	assimilation
44043	32032 ChEBI	potassium gluconate	-	assimilation
44043	17272 ChEBI	propionate	-	assimilation
44043	17814 ChEBI	salicin	-	assimilation
44043		skimmed milk	+	hydrolysis
44043	32954 ChEBI	sodium acetate	-	assimilation
44043	53258 ChEBI	sodium citrate	-	assimilation
44043	62983 ChEBI	sodium malonate	-	assimilation
44043	28017 ChEBI	starch	+	hydrolysis
44043	9300 ChEBI	suberic acid	-	assimilation
44043	17992 ChEBI	sucrose	+	assimilation
44043	53424 ChEBI	tween 20	-	hydrolysis
44043	53426 ChEBI	tween 80	-	hydrolysis
44043	16199 ChEBI	urea	-	hydrolysis
44043	31011 ChEBI	valerate	-	assimilation

Antibiotic resistance

@ref	ChEBI	Metabolite	Resistance conc.	Sensitivity conc.
44043	3393	carbenicillin	100 µg (disc)
44043	474053	cefazolin	30 µg (disc)
44043	3508	ceftazidime	30 µg (disc)
44043	48923	erythromycin	15 µg (disc)
44043	7507	neomycin	30 µg (disc)
44043	28368	novobiocin	34 µg (disc)
44043	16869	oleandomycin	5 µg (disc)
44043	17334	penicillin	10 µg (disc)
44043	28077	rifampicin	5 µg (disc)
44043	27902	tetracycline		30 µg (disc)

Metabolite production

@ref	Chebi-ID	Metabolite	Production
44043	35581 ChEBI	indole
44043	26672 ChEBI	siderophore

Enzymes

@ref	Value	Activity	Ec
44043	acid phosphatase	+/-	3.1.3.2
44043	alkaline phosphatase	+	3.1.3.1
44043	alpha-chymotrypsin	-	3.4.21.1
44043	alpha-fucosidase	-	3.2.1.51
44043	alpha-galactosidase	-	3.2.1.22
44043	alpha-glucosidase	+	3.2.1.20
44043	alpha-mannosidase	-	3.2.1.24
44043	arginine dihydrolase	-	3.5.3.6
44043	beta-galactosidase	-	3.2.1.23
44043	beta-glucosidase	-	3.2.1.21
44043	beta-glucuronidase	-	3.2.1.31
44043	catalase	-	1.11.1.6
44043	cystine arylamidase	-	3.4.11.3
44043	cytochrome oxidase	-	1.9.3.1
44043	esterase (C 4)	+
44043	esterase Lipase (C 8)	+
44043	leucine arylamidase	+	3.4.11.1
44043	lipase (C 14)	-
44043	N-acetyl-beta-glucosaminidase	-	3.2.1.52
44043	naphthol-AS-BI-phosphohydrolase	+/-
44043	trypsin	-	3.4.21.4
44043	urease	-	3.5.1.5
44043	valine arylamidase	+

Fatty acid profile

Metadata FA analysis

@ref

44043

Fatty acid	Percentage
C16:1ω6c / C16:1ω7c	43.1
C16:0	31.2
C10:0 3OH	6.4
C18:0	5.1
C12:0	4.7
C18:1ω7c / C18:1ω6c	4.4
C12:0 3OH	2.4
C8:0-3-OH	0.8
C14:0	0.6
C14:0 anteiso	0.5
C19:0 anteiso	0.5
C14:1ω5c	0.4

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Agriculture	#Field
#Environmental	#Terrestrial	#Soil
#Host	#Plants	#Herbaceous plants (Grass,Crops)

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Enrichment culture	Enrichment culture composition	Enrichment culture duration	Enrichment culture temperature
44043	soil of a ginseng field	Gwangju Province	Republic of Korea	KOR	Asia	R2A	fivefold diluted	7 days	25
67770	Soil of a ginseng field in Gwangju Province		Republic of Korea	KOR	Asia

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
67770	ASM972086v1 assembly for Pseudoduganella ginsengisoli KCTC 42409	contig	GCA_009720865	1462440.3	2915254074	1462440	50.24

16S sequences

@ref	Description	Accession	Database
44043	Pseudoduganella ginsengisoli 16S ribosomal RNA gene, partial sequence	KJ186108

GC content

@ref	GC-content (mol%)	Method
67770	55.3	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 ginsengisoli KCTC 42409
NCBI: GCA_009720865

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	98.20	no
125439	motility	BacteriaNetⓘ	yes	70.90	no
125439	gram_stain	BacteriaNetⓘ	negative	90.40	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	87.30	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Duganella ginsengisoli strain KCTC 42409
PATRIC: 1462440.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	98.50	yes
125438	anaerobic	anaerobicⓘ	no	96.08	yes
125438	spore-forming	spore-formingⓘ	no	82.24	no
125438	aerobic	aerobicⓘ	yes	90.31	yes
125438	thermophilic	thermophileⓘ	no	99.00	no
125438	flagellated	motile2+ⓘ	yes	84.18	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	A small step to discover candidate biological control agents from preexisting bioresources by using novel nonribosomal peptide synthetases hidden in activated sludge metagenomes.	Tomita S, Kuroda K, Narihiro T.	PLoS One	10.1371/journal.pone.0294843	2023
Phylogeny	Duganella lactea sp. nov., Duganella guangzhouensis sp. nov., Duganella flavida sp. nov. and Massilia rivuli sp. nov., isolated from a subtropical stream in PR China and proposal to reclassify Duganella ginsengisoli as Massilia ginsengisoli comb. nov.	Lu H, Deng T, Liu F, Wang Y, Yang X, Xu M	Int J Syst Evol Microbiol	10.1099/ijsem.0.004355	2020

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 )
#44043	Jinglou Zhang, Yeon-Ju Kim, Van-An Hoang, Ngoc Lan Nguyen, Chao Wang, Jong-Pyo Kang, Dandan Wang and Deok-Chun Yang: Duganella ginsengisoli sp. nov., isolated from ginseng soil. IJSEM 66: 56 - 61 2016 ( DOI 10.1099/ijsem.0.000669 , PubMed 26449233 )
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#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 ginsengisoli (KCTC 42409, JCM 30745, DCY 83)

Name and taxonomic classification