Name: Massilia ginsengisoli KCTC 42409
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 141131

Type strain:

Species: Massilia ginsengisoli

Culture col. no.: KCTC 42409, JCM 30745, DCY 83

Strain history: D.-C. Yang and Y.-J. Kim; Kyung Hee Univ., South Korea; DCY83.

NCBI tax ID(s): 1462440 (species)

Section

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

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

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Pseudomonadota*
	Class	*Betaproteobacteria*
	Order	*Burkholderiales*
	Family	*Oxalobacteraceae*
	Genus	*Massilia*
	Species	**Massilia ginsengisoli**
	Full Scientific Name (LPSN)	Massilia ginsengisoli (Zhang et al. 2016) Lu et al. 2020

	Synonym	Pseudoduganella ginsengisoli
	Synonym	Duganella ginsengisoli

Information on morphological and physiological properties Morphology

[Ref.: #44043]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.995

[Ref.: #44043]	Cell length	1.1 µm

[Ref.: #44043]	Cell width	0.8 µm

[Ref.: #44043]	Cell shape	rod-shaped

[Ref.: #44043]	Motility	yes
[Ref.: #69480]	Motility	yes Confidence in %94.98

[Ref.: #44043]	Colony size	0.3-1.5 mm
[Ref.: #44043]	Colony color	white-cream
[Ref.: #44043]	Colony shape	circular
[Ref.: #44043]	Incubation period	2 days
[Ref.: #44043]	Cultivation medium used	Nutrient agar

Information on culture and growth conditions Culture and growth conditions

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Culture medium

Nutrient agar (NA)

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Culture medium growth

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Culture medium

Reasoner's 2A agar (R2A)

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Culture medium growth

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Culture medium

LB (Luria-Bertani) MEDIUM

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Culture medium growth

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Culture medium

MacConkey

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Culture medium growth

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Culture medium

PDA

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Culture medium growth

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Culture medium

Trypticase Soy Agar (TSA)

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Culture medium growth

		Temperature
[Ref.: #44043]	growth	4-40 °C
[Ref.: #44043]	optimum	30 °C
[Ref.: #67770]	growth	30 °C

[Ref.: #44043]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #44043]			optimum	7
[Ref.: #44043]			growth	6-8

Information on physiology and metabolism Physiology and metabolism

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Oxygen tolerance

aerobe

[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.993

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #44043]		NaCl		growth	0-0.4	%(w/v)

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #44043]	2-dehydro-D-gluconate ChEBI	-	assimilation
[Ref.: #44043]	3-hydroxybenzoate ChEBI	-	assimilation
[Ref.: #44043]	3-hydroxybutyrate ChEBI	+	assimilation
[Ref.: #44043]	4-hydroxybenzoate ChEBI	-	assimilation
[Ref.: #44043]	5-dehydro-D-gluconate ChEBI	-	assimilation
[Ref.: #44043]	adipate ChEBI	-	assimilation
[Ref.: #44043]	D-glucose ChEBI	+	assimilation
[Ref.: #44043]	D-mannitol ChEBI	-	assimilation
[Ref.: #44043]	D-mannose ChEBI	-	assimilation
[Ref.: #44043]	D-ribose ChEBI	-	assimilation
[Ref.: #44043]	D-sorbitol ChEBI	-	assimilation
[Ref.: #44043]	decanoate ChEBI	-	assimilation
[Ref.: #44043]	dna ChEBI	-	hydrolysis
[Ref.: #44043]	esculin ChEBI	-	hydrolysis
[Ref.: #44043]	gelatin ChEBI	+	hydrolysis
[Ref.: #44043]	glucose ChEBI	-	fermentation
[Ref.: #44043]	glycogen ChEBI	+	assimilation
[Ref.: #44043]	itaconate ChEBI	-	assimilation
[Ref.: #44043]	L-alanine ChEBI	-	assimilation
[Ref.: #44043]	L-arabinose ChEBI	-	assimilation
[Ref.: #44043]	L-fucose ChEBI	-	assimilation
[Ref.: #44043]	L-histidine ChEBI	-	assimilation
[Ref.: #44043]	L-proline ChEBI	-	assimilation
[Ref.: #44043]	L-rhamnose ChEBI	-	assimilation
[Ref.: #44043]	L-serine ChEBI	+	assimilation
[Ref.: #44043]	lactate ChEBI	+	assimilation
[Ref.: #44043]	malate ChEBI	-	assimilation
[Ref.: #44043]	maltose ChEBI	-	assimilation
[Ref.: #44043]	maltose ChEBI	+	assimilation
[Ref.: #44043]	melibiose ChEBI	-	assimilation
[Ref.: #44043]	myo-inositol ChEBI	-	assimilation
[Ref.: #44043]	N-acetylglucosamine ChEBI	-	assimilation
[Ref.: #44043]	nitrate ChEBI	+	reduction
[Ref.: #44043]	phenylacetate ChEBI	-	assimilation
[Ref.: #44043]	potassium gluconate ChEBI	-	assimilation
[Ref.: #44043]	propionate ChEBI	-	assimilation
[Ref.: #44043]	salicin ChEBI	-	assimilation
[Ref.: #44043]	skimmed milk	+	hydrolysis
[Ref.: #44043]	sodium acetate ChEBI	-	assimilation
[Ref.: #44043]	sodium citrate ChEBI	-	assimilation
[Ref.: #44043]	sodium malonate ChEBI	-	assimilation
[Ref.: #44043]	starch ChEBI	+	hydrolysis
[Ref.: #44043]	suberic acid ChEBI	-	assimilation
[Ref.: #44043]	sucrose ChEBI	+	assimilation
[Ref.: #44043]	tween 20 ChEBI	-	hydrolysis
[Ref.: #44043]	tween 80 ChEBI	-	hydrolysis
[Ref.: #44043]	urea ChEBI	-	hydrolysis
[Ref.: #44043]	valerate ChEBI	-	assimilation
	Only first 10 entries are displayed. Click here to see all.

	Metabolite	Antibiotic sensitivity	Concentration		Antibiotic resistance	Concentration
[Ref.: #44043]	carbenicillin ChEBI				yes	100	µg (disc)
[Ref.: #44043]	cefazolin ChEBI				yes	30	µg (disc)
[Ref.: #44043]	ceftazidime ChEBI				yes	30	µg (disc)
[Ref.: #44043]	erythromycin ChEBI				yes	15	µg (disc)
[Ref.: #44043]	neomycin ChEBI				yes	30	µg (disc)
[Ref.: #44043]	novobiocin ChEBI				yes	34	µg (disc)
[Ref.: #44043]	oleandomycin ChEBI				yes	5	µg (disc)
[Ref.: #44043]	penicillin ChEBI				yes	10	µg (disc)
[Ref.: #44043]	rifampicin ChEBI				yes	5	µg (disc)
[Ref.: #44043]	tetracycline ChEBI	yes	30	µg (disc)

	Metabolite production	Metabolite	Production
[Ref.: #44043]		indole ChEBI	no
[Ref.: #44043]		siderophore ChEBI	yes

	Enzyme	Enzyme activity	EC number
[Ref.: #44043]	acid phosphatase	+/-	3.1.3.2
[Ref.: #44043]	alkaline phosphatase	+	3.1.3.1
[Ref.: #44043]	alpha-chymotrypsin	-	3.4.21.1
[Ref.: #44043]	alpha-fucosidase	-	3.2.1.51
[Ref.: #44043]	alpha-galactosidase	-	3.2.1.22
[Ref.: #44043]	alpha-glucosidase	+	3.2.1.20
[Ref.: #44043]	alpha-mannosidase	-	3.2.1.24
[Ref.: #44043]	arginine dihydrolase	-	3.5.3.6
[Ref.: #44043]	beta-galactosidase	-	3.2.1.23
[Ref.: #44043]	beta-glucosidase	-	3.2.1.21
[Ref.: #44043]	beta-glucuronidase	-	3.2.1.31
[Ref.: #44043]	catalase	-	1.11.1.6
[Ref.: #44043]	cystine arylamidase	-	3.4.11.3
[Ref.: #44043]	cytochrome oxidase	-	1.9.3.1
[Ref.: #44043]	esterase (C 4)	+
[Ref.: #44043]	esterase Lipase (C 8)	+
[Ref.: #44043]	leucine arylamidase	+	3.4.11.1
[Ref.: #44043]	lipase (C 14)	-
[Ref.: #44043]	N-acetyl-beta-glucosaminidase	-	3.2.1.52
[Ref.: #44043]	naphthol-AS-BI-phosphohydrolase	+/-
[Ref.: #44043]	trypsin	-	3.4.21.4
[Ref.: #44043]	urease	-	3.5.1.5
[Ref.: #44043]	valine arylamidase	+
	Only first 10 entries are displayed. Click here to see all.

Fatty acid profile

Metadata FA analysis

Reference

[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

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #44043]	Sample type/isolated from	soil of a ginseng field
[Ref.: #44043]	Geographic location (country and/or sea, region)	Gwangju Province
[Ref.: #44043]	Country	Republic of Korea
[Ref.: #44043]	Country ISO 3 Code	KOR
[Ref.: #44043]	Continent	Asia
[Ref.: #44043]	Enrichment culture	R2A
[Ref.: #44043]	Enrichment culture composition	fivefold diluted
[Ref.: #44043]	Enrichment culture duration	7 days
[Ref.: #44043]	Enrichment culture temperature	25 ̊C

[Ref.: #67770]	Sample type/isolated from	Soil of a ginseng field in Gwangju Province
[Ref.: #67770]	Country	Republic of Korea
[Ref.: #67770]	Country ISO 3 Code	KOR
[Ref.: #67770]	Continent	Asia
* marker position based on {}

Isolation sources categories

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

What are isolation sources categories?

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #44043]	16S rRNA gene sequence	KJ186108		GenBank

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Pseudoduganella ginsengisoli KCTC 42409	GCA_009720865	contig	GenBank	1462440 tax ID
[Ref.: #66792]	Duganella ginsengisoli strain KCTC 42409	1462440.3	wgs	PATRIC	1462440 tax ID	*
[Ref.: #66792]	Duganella ginsengisoli KCTC 42409	2915254074	draft	JGI IMG/M	1462440 tax ID	*

[Ref.: #67770]

GC-content

55.3 mol%

high performance liquid chromatography (HPLC)

Data predicted using genome information as a basis Genome-based predictions

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Duganella ginsengisoli strain KCTC 42409 PATRIC: 1462440.3
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Duganella ginsengisoli strain KCTC 42409 PATRIC: 1462440.3
[Ref.: #69480]	motile	yes	91.501	no
[Ref.: #69480]	gram-positive	no	98.608	yes
[Ref.: #69480]	anaerobic	no	99.015	yes
[Ref.: #69480]	aerobic	yes	90.348	yes
[Ref.: #69480]	halophile	no	95.223	no
[Ref.: #69480]	spore-forming	no	93.727	no
[Ref.: #69480]	thermophile	no	99.171	yes
[Ref.: #69480]	glucose-util	yes	88.951	yes
[Ref.: #69480]	flagellated	yes	81.092	no
[Ref.: #69480]	glucose-ferment	no	88.104	no

Availability in culture collections External links

[Ref.: #44043]

Culture collection no.

KCTC 42409, JCM 30745, DCY 83

Literature:

Topic	Title	Authors	Journal	DOI	Year
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 )

#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) .

#67770 Japan Collection of Microorganism (JCM) ; Curators of the JCM;

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

* These data were automatically processed and therefore are not curated

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Duganella ginsengisoli strain KCTC 42409

Duganella ginsengisoli strain KCTC 42409

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