Strain identifier

BacDive ID: 164192

Type strain: Yes

Species: Paraburkholderia panacisoli

Strain history: D.-C. Yang and Y.-J. Kim; Kyung Hee Univ., South Korea; DCY113.

NCBI tax ID(s): 2603818 (species)

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General

@ref: 67770

BacDive-ID: 164192

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

description: Paraburkholderia panacisoli JCM 32098 is an obligate aerobe, mesophilic, Gram-negative bacterium that forms circular colonies and was isolated from Ginseng cultivation soil in Gochang-gun.

NCBI tax id

  • NCBI tax id: 2603818
  • Matching level: species

strain history

  • @ref: 67770
  • history: D.-C. Yang and Y.-J. Kim; Kyung Hee Univ., South Korea; DCY113.

doi: 10.13145/bacdive164192.20250331.9.3

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Betaproteobacteria
  • order: Burkholderiales
  • family: Burkholderiaceae
  • genus: Paraburkholderia
  • species: Paraburkholderia panacisoli
  • full scientific name: Paraburkholderia panacisoli Huo et al. 2021

@ref: 67770

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Burkholderiaceae

genus: Paraburkholderia

species: Paraburkholderia panacisoli

full scientific name: Paraburkholderia panacisoli Huo et al.

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
68271negative1.2-2.0 µm0.7-0.8 µmrod-shapedno
125438negative98.482

colony morphology

  • @ref: 68271
  • colony size: 0.3-0.5 mm
  • colony color: yellow
  • colony shape: circular
  • incubation period: 3 days
  • medium used: Trypticase Soy Agar (TSA)

Culture and growth conditions

culture temp

@refgrowthtypetemperature
67770positivegrowth30
68271positivegrowth10-35
68271positiveoptimum30

culture pH

@refabilitytypepH
68271positivegrowth4.5-7.5
68271positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 68271
  • oxygen tolerance: obligate aerobe

halophily

@refsaltgrowthtested relationconcentration
68271NaClpositivegrowth0-3 %(w/v)
68271NaClpositiveoptimum0 %(w/v)

observation

  • @ref: 67770
  • observation: quinones: Q-8

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6827153426tween 80+hydrolysis
6827118186tyrosine+hydrolysis
68271casein-hydrolysis
6827116991dna-hydrolysis
682715291gelatin-hydrolysis
6827117234glucose+fermentation
682714853esculin+hydrolysis
6827116899D-mannitol+assimilation
68271506227N-acetyl-D-glucosamine+assimilation
6827132032potassium gluconate+assimilation
6827117120hexanoate+assimilation
6827117128adipate+assimilation
6827125115malate+assimilation
68271161933-hydroxybenzoate+assimilation
68271370543-hydroxybutyrate+assimilation
68271178794-hydroxybenzoate+assimilation
6827127689decanoate-assimilation
6827117634D-glucose-assimilation
6827116899D-mannitol-assimilation
6827116988D-ribose-assimilation
6827117924D-sorbitol+assimilation
6827128087glycogen-assimilation
6827117268myo-inositol-assimilation
6827117240itaconate-assimilation
6827124996lactate+assimilation
6827116977L-alanine+assimilation
6827130849L-arabinose-assimilation
6827118287L-fucose+assimilation
6827115971L-histidine+assimilation
6827117203L-proline+assimilation
6827162345L-rhamnose+assimilation
6827117115L-serine-assimilation
6827128053melibiose-assimilation
6827159640N-acetylglucosamine-assimilation
68271potassium 2-dehydro-D-gluconate+assimilation
68271potassium 5-dehydro-D-gluconate+assimilation
6827117272propionate-assimilation
6827117814salicin-assimilation
6827132954sodium acetate-assimilation
6827153258sodium citrate-assimilation
6827162983sodium malonate-assimilation
6827176282suberate+assimilation
6827117992sucrose-assimilation
6827131011valerate+assimilation

antibiotic resistance

@refChEBImetaboliteis antibioticis sensitivesensitivity conc.is resistantresistance conc.
682717507neomycinyesyes30 µg
6827127902tetracyclineyesyes30 µg
6827118208penicillin gyesyes10 Unit
6827148923erythromycinyesyes15 µg
6827128368novobiocinyesyes30 µg
682713508ceftazidimeyesyes30 µg
682713393carbenicillinyesyes100 µg
6827128077rifampicinyesyes5 µg
6827116869oleandomycinyesyes15 µg
6827128001vancomycinyesyes30 µg
682716472lincomycinyesyes15 µg

metabolite production

  • @ref: 68271
  • Chebi-ID: 16136
  • metabolite: hydrogen sulfide
  • production: no

enzymes

@refvalueactivityec
68271cytochrome oxidase+1.9.3.1
68271catalase+1.11.1.6
68271alkaline phosphatase+3.1.3.1
68271esterase (C 4)+
68271esterase Lipase (C 8)+
68271lipase (C 14)+
68271leucine arylamidase+3.4.11.1
68271valine arylamidase+
68271acid phosphatase+3.1.3.2
68271beta-glucosidase+3.2.1.21
68271naphthol-AS-BI-phosphohydrolase+

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    68271C14:03.6
    68271C16:030.7
    68271C17:0 cyclo13.8
    68271C16:1 2OH0.8
    68271C16:0 2OH1.3
    68271C16:0 3OH4.7
    68271C18:04.8
    68271C19:0 cyclo w8c9.2
    68271C12:0 aldehyde/Unknown 10.928/C14:0 3OH/iso-C16:1 I7.3
    68271C16:1 w7c/C16:1 w6c5.3
    68271C18:1 w7c/C18:1 w6c15.7
  • type of FA analysis: whole cell analysis
  • library/peak naming table: TSBA 6.1
  • system: MIS MIDI
  • instrument: Agilent GC 6890
  • method/protocol: Sasser, 1990
  • cutoff value:

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentgeographic locationenrichment cultureenrichment culture durationenrichment culture temperature
67770Ginseng cultivation soil in Gochang-gunRepublic of KoreaKORAsia
68271ginseng cultivation soilRepublic of KoreaKORAsiaGochang-gunTryptic soy agar3 days30

Sequence information

16S sequences

  • @ref: 67770
  • description: Paraburkholderia panacisoli 16S ribosomal RNA gene, partial sequence
  • accession: KY694398
  • length: 1468
  • database: nuccore
  • NCBI tax ID: 2603818

Genome sequences

  • @ref: 67770
  • description: Paraburkholderia panacisoli DCY113
  • accession: GCA_008369935
  • assembly level: scaffold
  • database: ncbi
  • NCBI tax ID: 2603818

GC content

  • @ref: 68271
  • GC-content: 62.2
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingno98.482yes
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no96.698no
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes88.781no
125438spore-formingspore-formingAbility to form endo- or exosporesno82.255no
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno97.424yes
125438motile2+flagellatedAbility to perform flagellated movementyes86.16no

External links

@ref: 67770

culture collection no.: JCM 32098, KCTC 52951, DCY 113

literature

  • topic: Phylogeny
  • Pubmed-ID: 32152645
  • title: Paraburkholderia panacisoli sp. nov., a potentially antagonistic bacterium against the root rot fungal pathogen Cylindrocarpon destructans, isolated from ginseng cultivation soil.
  • authors: Huo Y, Chokkalingam M, Kang JP, Ahn JC, Yang DC
  • journal: Arch Microbiol
  • DOI: 10.1007/s00203-020-01840-z
  • year: 2020
  • mesh: *Antibiosis, Bacterial Typing Techniques, Base Composition, Burkholderiaceae/*classification/genetics/*physiology, DNA, Bacterial/genetics, Fatty Acids/analysis, Hypocreales/*physiology, Panax/*microbiology, Phylogeny, RNA, Ribosomal, 16S/genetics, *Soil Microbiology, Species Specificity
  • topic2: Cultivation

Reference

@idauthorstitledoi/urljournal
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
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68271Yue Huo, Mohan Chokkalingam, Jong-Pyo Kang, Jong-Chan Ahn & Deok-Chun YangParaburkholderia panacisoli sp. nov., a potentially antagonistic bacterium against the root rot fungal pathogen Cylindrocarpon destructans, isolated from ginseng cultivation soil10.1007/s00203-020-01840-zArch Microbiol 202: 1341-1347 2020
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg OvermannPredicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets10.1101/2024.08.12.607695