Strain identifier

BacDive ID: 140959

Type strain: Yes

Species: Daejeonia ginsenosidivorans

Strain Designation: NP5

NCBI tax ID(s): 1813881 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 43859

BacDive-ID: 140959

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

description: Daejeonia ginsenosidivorans NP5 is an aerobe, Gram-negative, rod-shaped bacterium that forms circular colonies and was isolated from water of Kaist Duck Lake in Daejeon city, Korea.

NCBI tax id

  • NCBI tax id: 1813881
  • Matching level: species

doi: 10.13145/bacdive140959.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Flavobacteriia
  • order: Flavobacteriales
  • family: Flavobacteriaceae
  • genus: Daejeonia
  • species: Daejeonia ginsenosidivorans
  • full scientific name: Daejeonia ginsenosidivorans Siddiqi et al. 2017

@ref: 43859

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Flavobacteriaceae

genus: Daejeonia

species: Daejeonia ginsenosidivorans

strain designation: NP5

type strain: yes

Morphology

cell morphology

  • @ref: 43859
  • gram stain: negative
  • cell length: 1.2-3.0 µm
  • cell width: 0.2-0.5 µm
  • cell shape: rod-shaped
  • motility: no

colony morphology

  • @ref: 43859
  • colony color: light-yellow
  • colony shape: circular
  • incubation period: 2-3 days
  • medium used: Tryptic soy agar

pigmentation

  • @ref: 43859
  • production: no
  • name: Flexirubin-type pigment

Culture and growth conditions

culture medium

@refnamegrowth
43859LB (Luria-Bertani) MEDIUMno
43859MacConkey agarno
43859Nutrient agar (NA)yes
43859Reasoner's 2A agar (R2A)yes
43859Tryptic soy agaryes

culture temp

@refgrowthtypetemperaturerange
43859positivegrowth18-37
43859positiveoptimum30mesophilic

culture pH

@refabilitytypepH
43859positivegrowth5.5-8.0
43859positiveoptimum6.0-7.0

Physiology and metabolism

oxygen tolerance

  • @ref: 43859
  • oxygen tolerance: aerobe

spore formation

  • @ref: 43859
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
43859NaClpositivegrowth0.5-3 %(w/v)
43859NaClpositiveoptimum0-0.5 %(w/v)

observation

  • @ref: 43859
  • observation: quinone MK-6

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
43859168082-dehydro-D-gluconate-builds acid from
43859161933-hydroxybenzoate-builds acid from
43859370543-hydroxybutyrate-builds acid from
43859178794-hydroxybenzoate-builds acid from
43859581435-dehydro-D-gluconate-builds acid from
4385917128adipate-builds acid from
4385927689decanoate-builds acid from
4385916947citrate-builds acid from
4385916899D-mannitol-builds acid from
4385916988D-ribose-builds acid from
4385917924D-sorbitol-builds acid from
4385924265gluconate-builds acid from
4385917268myo-inositol-builds acid from
4385917240itaconate-builds acid from
4385930849L-arabinose-builds acid from
4385918287L-fucose-builds acid from
4385915971L-histidine-builds acid from
4385962345L-rhamnose-builds acid from
4385925115malate-builds acid from
4385918401phenylacetate-builds acid from
4385917814salicin-builds acid from
438599300suberic acid-builds acid from
4385917992sucrose-builds acid from
43859581435-dehydro-D-gluconate-carbon source
4385916947citrate-carbon source
4385924265gluconate-carbon source
4385925115malate-carbon source
4385917814salicin-carbon source
4385985146carboxymethylcellulose-hydrolysis
4385953424tween 20-hydrolysis
4385917632nitrate-reduction
4385930089acetate+builds acid from
4385917634D-glucose+builds acid from
4385916024D-mannose+builds acid from
4385928087glycogen+builds acid from
43859L-alanine 4-nitroanilide+builds acid from
4385917203L-proline+builds acid from
4385917115L-serine+builds acid from
4385924996lactate+builds acid from
4385915792malonate+builds acid from
4385917306maltose+builds acid from
4385928053melibiose+builds acid from
43859506227N-acetylglucosamine+builds acid from
4385917272propionate+builds acid from
4385931011valerate+builds acid from
4385930089acetate+carbon source
4385917634D-glucose+carbon source
4385916024D-mannose+carbon source
4385928087glycogen+carbon source
4385916977L-alanine+carbon source
4385917203L-proline+carbon source
4385917115L-serine+carbon source
4385924996lactate+carbon source
4385915792malonate+carbon source
4385917306maltose+carbon source
4385928053melibiose+carbon source
43859506227N-acetylglucosamine+carbon source
4385917272propionate+carbon source
4385931011valerate+carbon source
43859casein+hydrolysis
4385916991dna+hydrolysis
438594853esculin+hydrolysis
4385928017starch+hydrolysis
438595291gelatin+/-hydrolysis

metabolite production

  • @ref: 43859
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
43859cytochrome oxidase+1.9.3.1
43859catalase+1.11.1.6
43859alkaline phosphatase+3.1.3.1
43859esterase (C 4)+
43859esterase Lipase (C 8)+
43859lipase (C 14)+
43859leucine arylamidase+3.4.11.1
43859valine arylamidase+
43859cystine arylamidase+3.4.11.3
43859trypsin+3.4.21.4
43859alpha-chymotrypsin+3.4.21.1
43859acid phosphatase+3.1.3.2
43859naphthol-AS-BI-phosphohydrolase+
43859alpha-glucosidase+3.2.1.20
43859beta-glucosidase+3.2.1.21
43859alpha-galactosidase-3.2.1.22
43859beta-galactosidase-3.2.1.23
43859beta-glucuronidase-3.2.1.31
43859alpha-mannosidase-3.2.1.24
43859alpha-fucosidase-3.2.1.51
43859N-acetyl-beta-glucosaminidase-3.2.1.52
43859urease-3.5.1.5

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    43859C15:0 anteiso7.5
    43859C15:0 2OH0.5
    43859C16:01.1
    43859C16:0 3OH0.6
    43859C16:1ω7c / C16:1ω6c6.3
    43859C17:0 2OH0.9
    43859C17:1ω6c0.6
    43859C18:0 3OH8.5
    43859C18:1ω5c1
    43859C13:0 iso3.4
    43859C14:0 iso3.5
    43859C14:0 iso 3OH0.5
    43859C15:0 iso27.7
    43859C15:0 iso 3OH2.9
    43859C16:0 iso4.6
    43859C16:0 iso 3OH11.1
    43859C16:1 iso H2
    43859C17:0 iso 3OH13.6
    43859C17:1 iso I /C17:1 anteiso B1.2
    43859iso-C17:1ω9c/C16:0 10-methyl2.8
  • type of FA analysis: whole cell analysis
  • incubation medium: R2A agar
  • agar/liquid: agar
  • software version: Sherlock 6.1
  • library/peak naming table: TSBA6.1
  • system: MIS MIDI
  • instrument: Hewlett Packard 6890 gas chromatograph
  • cutoff value:

Isolation, sampling and environmental information

isolation

  • @ref: 43859
  • sample type: water of Kaist Duck Lake in Daejeon city, Korea
  • geographic location: Daejeon city
  • country: Republic of Korea
  • origin.country: KOR
  • continent: Asia
  • enrichment culture: R2A agar
  • enrichment culture duration: 7 days
  • enrichment culture temperature: 30

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Aquatic
  • Cat3: #Lake (large)

Sequence information

16S sequences

  • @ref: 43859
  • description: 16S rRNA gene sequence
  • accession: KT950745
  • database: nuccore

GC content

  • @ref: 43859
  • GC-content: 44.8
  • method: high performance liquid chromatography (HPLC)

External links

@ref: 43859

culture collection no.: KACC 18626, LMG 29198

literature

  • topic: Phylogeny
  • Pubmed-ID: 28809138
  • title: Daejeonia ginsenosidivorans gen. nov., sp. nov., a ginsenoside-transforming bacterium isolated from lake water.
  • authors: Siddiqi MZ, Choi GM, Kim MS, Im WT
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.001994
  • year: 2017
  • mesh: Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Flavobacteriaceae/*classification/genetics/isolation & purification, Ginsenosides/*metabolism, Lakes/*microbiology, Phospholipids/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry
  • 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
43859Muhammad Zubair Siddiqi, Gyu-Min Choi, Mi-Sun Kim, Wan-Taek ImDaejeonia ginsenosidivorans gen. nov., sp. nov., a ginsenoside-transforming bacterium isolated from lake water10.1099/ijsem.0.001994IJSEM 67: 2665-2671 201728809138