Strain identifier

BacDive ID: 141131

Type strain: Yes

Species: Massilia ginsengisoli

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

NCBI tax ID(s): 1462440 (species)

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General

@ref: 44043

BacDive-ID: 141131

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

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

NCBI tax id

  • NCBI tax id: 1462440
  • Matching level: species

strain history

  • @ref: 67770
  • history: D.-C. Yang and Y.-J. Kim; Kyung Hee Univ., South Korea; DCY83.

doi: 10.13145/bacdive141131.20241212.9.2

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • 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

    @refsynonym
    20215Duganella ginsengisoli
    20215Pseudoduganella ginsengisoli

@ref: 44043

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Oxalobacteraceae

genus: Duganella

species: Duganella ginsengisoli

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
44043negative1.1 µm0.8 µmrod-shapedyes
69480negative98.5

colony morphology

  • @ref: 44043
  • colony size: 0.3-1.5 mm
  • colony color: white-cream
  • colony shape: circular
  • incubation period: 2 days
  • medium used: Nutrient agar

Culture and growth conditions

culture medium

@refnamegrowth
44043LB (Luria-Bertani) MEDIUMno
44043MacConkeyno
44043Nutrient agar (NA)yes
44043PDAno
44043Reasoner's 2A agar (R2A)yes
44043Trypticase Soy Agar (TSA)no

culture temp

@refgrowthtypetemperature
44043positivegrowth4-40
44043positiveoptimum30
67770positivegrowth30

culture pH

@refabilitytypepH
44043positivegrowth6-8
44043positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
44043aerobe
69480aerobe90.305

spore formation

  • @ref: 69481
  • spore formation: no
  • confidence: 100

halophily

  • @ref: 44043
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-0.4 %(w/v)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
44043168082-dehydro-D-gluconate-assimilation
44043161933-hydroxybenzoate-assimilation
44043178794-hydroxybenzoate-assimilation
44043581435-dehydro-D-gluconate-assimilation
4404317128adipate-assimilation
4404327689decanoate-assimilation
4404316899D-mannitol-assimilation
4404316024D-mannose-assimilation
4404316988D-ribose-assimilation
4404317924D-sorbitol-assimilation
4404317240itaconate-assimilation
4404316977L-alanine-assimilation
4404330849L-arabinose-assimilation
4404318287L-fucose-assimilation
4404315971L-histidine-assimilation
4404317203L-proline-assimilation
4404362345L-rhamnose-assimilation
4404325115malate-assimilation
4404317306maltose-assimilation
4404328053melibiose-assimilation
4404317268myo-inositol-assimilation
44043506227N-acetylglucosamine-assimilation
4404318401phenylacetate-assimilation
4404332032potassium gluconate-assimilation
4404317272propionate-assimilation
4404317814salicin-assimilation
4404332954sodium acetate-assimilation
4404353258sodium citrate-assimilation
4404362983sodium malonate-assimilation
440439300suberic acid-assimilation
4404331011valerate-assimilation
4404317234glucose-fermentation
4404316991dna-hydrolysis
440434853esculin-hydrolysis
4404353424tween 20-hydrolysis
4404353426tween 80-hydrolysis
4404316199urea-hydrolysis
44043370543-hydroxybutyrate+assimilation
4404317634D-glucose+assimilation
4404328087glycogen+assimilation
4404317115L-serine+assimilation
4404324996lactate+assimilation
4404317306maltose+assimilation
4404317992sucrose+assimilation
440435291gelatin+hydrolysis
44043skimmed milk+hydrolysis
4404328017starch+hydrolysis
4404317632nitrate+reduction

antibiotic resistance

@refChEBImetaboliteis antibioticis sensitivesensitivity conc.is resistantresistance conc.
4404327902tetracyclineyesyes30 µg (disc)
4404348923erythromycinyesyes15 µg (disc)
4404316869oleandomycinyesyes5 µg (disc)
440433508ceftazidimeyesyes30 µg (disc)
4404328077rifampicinyesyes5 µg (disc)
4404328368novobiocinyesyes34 µg (disc)
4404317334penicillinyesyes10 µg (disc)
44043474053cefazolinyesyes30 µg (disc)
440437507neomycinyesyes30 µg (disc)
440433393carbenicillinyesyes100 µg (disc)

metabolite production

@refChebi-IDmetaboliteproduction
4404335581indoleno
4404326672siderophoreyes

enzymes

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

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    44043C14:0 anteiso0.5
    44043C19:0 anteiso0.5
    44043C10:0 3OH6.4
    44043C12:04.7
    44043C12:0 3OH2.4
    44043C14:00.6
    44043C14:1ω5c0.4
    44043C16:031.2
    44043C16:1ω6c / C16:1ω7c43.1
    44043C18:05.1
    44043C18:1ω7c / C18:1ω6c4.4
    44043C8:0-3-OH0.8
  • type of FA analysis: whole cell analysis
  • incubation medium: NA
  • incubation temperature: 30
  • incubation time: 1
  • library/peak naming table: TSBA6.1
  • system: MIS MIDI
  • method/protocol: Sasser, 1990

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentenrichment cultureenrichment culture compositionenrichment culture durationenrichment culture temperature
44043soil of a ginseng fieldGwangju ProvinceRepublic of KoreaKORAsiaR2Afivefold diluted7 days25
67770Soil of a ginseng field in Gwangju ProvinceRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Engineered#Agriculture#Field
#Environmental#Terrestrial#Soil
#Host#Plants#Herbaceous plants (Grass,Crops)

Sequence information

16S sequences

  • @ref: 44043
  • description: Pseudoduganella ginsengisoli 16S ribosomal RNA gene, partial sequence
  • accession: KJ186108
  • database: nuccore

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Duganella ginsengisoli strain KCTC 424091462440.3wgspatric1462440
66792Duganella ginsengisoli KCTC 424092915254074draftimg1462440
67770Pseudoduganella ginsengisoli KCTC 42409GCA_009720865contigncbi1462440

GC content

  • @ref: 67770
  • GC-content: 55.3
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69481spore-formingspore-formingAbility to form endo- or exosporesno100no
69480gram-positivegram-positivePositive reaction to Gram-stainingno98.5yes
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no96.081yes
69480spore-formingspore-formingAbility to form endo- or exosporesno82.244no
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes90.305yes
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno99no
69480flagellatedmotile2+Ability to perform flagellated movementyes84.177no

External links

@ref: 44043

culture collection no.: KCTC 42409, JCM 30745, DCY 83

literature

  • topic: Phylogeny
  • Pubmed-ID: 32706332
  • title: 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.
  • authors: Lu H, Deng T, Liu F, Wang Y, Yang X, Xu M
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.004355
  • year: 2020
  • mesh: Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, Oxalobacteraceae/*classification/isolation & purification, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rivers/*microbiology, Sequence Analysis, DNA
  • topic2: Transcriptome

Reference

@idauthorstitledoi/urljournalpubmed
20215Parte, 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 DSMZ10.1099/ijsem.0.004332
44043Jinglou Zhang, Yeon-Ju Kim, Van-An Hoang, Ngoc Lan Nguyen, Chao Wang, Jong-Pyo Kang, Dandan Wang and Deok-Chun YangDuganella ginsengisoli sp. nov., isolated from ginseng soil10.1099/ijsem.0.000669IJSEM 66: 56-61 201626449233
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1