Strain identifier

BacDive ID: 133396

Type strain: Yes

Species: Arachidicoccus ginsenosidivorans

Strain history: <- ST Lee, KAIST

NCBI tax ID(s): 496057 (species)

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General

@ref: 64148

BacDive-ID: 133396

DSM-Number: 22792

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

description: Arachidicoccus ginsenosidivorans DSM 22792 is an aerobe, Gram-negative, rod-shaped bacterium that forms circular colonies and was isolated from ginseng cultivating soil.

NCBI tax id

  • NCBI tax id: 496057
  • Matching level: species

strain history

@refhistory
64148<- S.-T. Lee, KAIST <- W.-T. Im; Gsoil 809
67770W.-T. Im; Hankyong Natl. Univ., South Korea; Gsoil 809.
67771<- ST Lee, KAIST

doi: 10.13145/bacdive133396.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Chitinophagia
  • order: Chitinophagales
  • family: Chitinophagaceae
  • genus: Arachidicoccus
  • species: Arachidicoccus ginsenosidivorans
  • full scientific name: Arachidicoccus ginsenosidivorans Siddiqi et al. 2017

@ref: 64148

domain: Bacteria

phylum: Bacteroidetes

class: Chitinophagia

order: Chitinophagales

family: Chitinophagaceae

genus: Arachidicoccus

species: Arachidicoccus ginsenosidivorans

full scientific name: Arachidicoccus ginsenosidivorans Siddiqi et al. 2017

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
25254negative1.5-3.0 µm0.4-1.0 µmrod-shapedno
67771rod-shapedno
67771negative

colony morphology

  • @ref: 25254
  • colony size: 2.0-3.5 mm
  • colony color: yellow
  • colony shape: circular
  • incubation period: 2 days
  • medium used: NA

pigmentation

  • @ref: 25254
  • production: no
  • name: Flexirubin-type

Culture and growth conditions

culture medium

@refnamegrowth
25254Nutrient agar (NA)yes
25254Trypticase Soy Agar (TSA)no
25254LB (Luria-Bertani) MEDIUMno
25254MacConkey agarno

culture temp

@refgrowthtypetemperaturerange
25254positivegrowth10-37
25254positiveoptimum30mesophilic
67770positivegrowth30mesophilic
67771positivegrowth30mesophilic

culture pH

@refabilitytypepH
25254positivegrowth5-7
25254positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
25254aerobe
67771aerobe

halophily

@refsaltgrowthtested relationconcentration
25254NaClpositivegrowth0-4 %(w/v)
25254NaCloptimum0-1 %(w/v)

observation

  • @ref: 67771
  • observation: quinones: MK-7

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
25254161933-hydroxybenzoate-assimilation
25254370543-hydroxybutyrate-assimilation
25254178794-hydroxybenzoate-assimilation
2525417128adipate-assimilation
2525417634D-glucose-carbon source
2525416899D-mannitol-assimilation
2525416024D-mannose-carbon source
2525416988D-ribose-assimilation
2525417924D-sorbitol-carbon source
2525427689decanoate-assimilation
2525416991dna-hydrolysis
252545291gelatin-hydrolysis
2525428087glycogen-assimilation
2525428087glycogen-carbon source
2525417268myo-inositol-assimilation
2525417240itaconate-assimilation
2525416977L-alanine-assimilation
2525418287L-fucose-carbon source
2525417203L-proline-carbon source
2525417115L-serine-assimilation
2525416828L-tryptophan-assimilation
2525424996lactate-assimilation
2525425115malate-assimilation
2525417306maltose-assimilation
2525418401phenylacetate-assimilation
25254potassium 2-dehydro-D-gluconate-assimilation
25254potassium 5-dehydro-D-gluconate-assimilation
2525432032potassium gluconate-assimilation
2525417272propionate-carbon source
2525417814salicin-carbon source
2525432954sodium acetate-assimilation
2525453258sodium citrate-assimilation
2525462983sodium malonate-assimilation
252549300suberic acid-assimilation
2525416199urea-hydrolysis
2525431011valerate-assimilation
252543557154-nitrophenyl beta-D-galactopyranoside+assimilation
2525427570histidine+carbon source
2525430849L-arabinose+assimilation
2525462345L-rhamnose+assimilation
2525428053melibiose+assimilation
2525417632nitrate+reduction
2525463043potassium nitrate+assimilation
2525417992sucrose+assimilation

metabolite production

@refChebi-IDmetaboliteproduction
2525415688acetoinno
2525435581indoleno

metabolite tests

  • @ref: 25254
  • Chebi-ID: 15688
  • metabolite: acetoin
  • voges-proskauer-test: -

enzymes

@refvalueactivityec
25254acid phosphatase+3.1.3.2
25254alkaline phosphatase+3.1.3.1
25254alpha-chymotrypsin+3.4.21.1
25254alpha-fucosidase+3.2.1.51
25254alpha-galactosidase+3.2.1.22
25254alpha-glucosidase+3.2.1.20
25254alpha-mannosidase-3.2.1.24
25254arginine dihydrolase-3.5.3.6
25254beta-galactosidase+3.2.1.23
25254beta-glucuronidase-3.2.1.31
25254catalase+1.11.1.6
25254cystine arylamidase+3.4.11.3
25254cytochrome oxidase+1.9.3.1
25254esterase+
25254leucine arylamidase+3.4.11.1
25254lipase (C 14)-
25254N-acetyl-beta-glucosaminidase+3.2.1.52
25254naphthol-AS-BI-phosphohydrolase+
25254trypsin-3.4.21.4
25254urease-3.5.1.5
25254valine arylamidase+

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    25254C15:0 anteiso0.9
    25254C14:00.3
    25254C16:03.8
    25254C16:0 2OH0.3
    25254C16:0 3OH3.8
    25254C16:1ω7c / C16:1ω6c9.3
    25254C18:00.3
    25254C13:0 iso0.1
    25254C15:0 iso42.7
    25254C15:0 iso 3OH2.7
    25254C15:1 iso G14.9
    25254C17:0 iso0.2
    25254C17:0 iso 3OH20.7
  • type of FA analysis: whole cell analysis
  • incubation medium: R2A
  • agar/liquid: agar
  • incubation temperature: 30
  • incubation time: 2
  • library/peak naming table: TSBA 60
  • system: MIS MIDI
  • method/protocol: Sasser 1990

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
25254ginseng cultivating soilPocheon province, Republic of KoreaRepublic of KoreaKORAsia
64148soil of a ginseng fieldPocheon provinceRepublic of KoreaKORAsia
67770Soil of a ginseng field in Pocheon ProvinceRepublic of KoreaKORAsia
67771From ginseng cultivating soilDaejeonRepublic of KoreaKORAsia

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_147786.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_700;96_10751;97_34126;98_68145;99_147786&stattab=map
  • Last taxonomy: Arachidicoccus ginsenosidivorans
  • 16S sequence: EU370955
  • Sequence Identity:
  • Total samples: 536
  • soil counts: 209
  • aquatic counts: 83
  • animal counts: 81
  • plant counts: 163

Safety information

risk assessment

  • @ref: 64148
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 64148
  • description: Arachidicoccus ginsenosidivorans strain Gsoil 809 16S ribosomal RNA gene, partial sequence
  • accession: EU370955
  • length: 1470
  • database: ena
  • NCBI tax ID: 496057

Genome sequences

  • @ref: 67770
  • description: Arachidicoccus ginsenosidivorans Gsoil 809
  • accession: GCA_007971385
  • assembly level: complete
  • database: ncbi
  • NCBI tax ID: 496057

GC content

@refGC-contentmethod
6414839.4high performance liquid chromatography (HPLC)
6777139.4

External links

@ref: 64148

culture collection no.: DSM 22792, JCM 30984, KCTC 22820, Gsoil 809

straininfo link

  • @ref: 91425
  • straininfo: 406212

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny27974091Arachidicoccus ginsenosidivorans sp. nov., with ginsenoside-converting activity isolated from ginseng cultivating soil.Siddiqi MZ, Aslam Z, Im WTInt J Syst Evol Microbiol10.1099/ijsem.0.0017202017Bacterial Typing Techniques, Bacteroidetes/*classification/genetics/isolation & purification, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Ginsenosides/*metabolism, Nucleic Acid Hybridization, Panax/*microbiology, Phosphatidylethanolamines/chemistry, *Phylogeny, Polyamines/chemistry, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny33206036Arachidicoccus soli sp. nov., a bacterium isolated from soil.Lee SA, Kim TW, Sang MK, Song J, Kwon SW, Weon HYInt J Syst Evol Microbiol10.1099/ijsem.0.0045662020Bacterial Typing Techniques, Bacteroidetes/*classification, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Islands, Nucleic Acid Hybridization, Phosphatidylethanolamines/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny35621997Arachidicoccus terrestris sp. nov., isolated from greenhouse soil.Won M, Weon HY, Hong SB, Han BH, Kwon SWInt J Syst Evol Microbiol10.1099/ijsem.0.0053912022Bacterial Typing Techniques, Bacteroidetes, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil, *Soil MicrobiologyTranscriptome

Reference

@idauthorstitledoi/urljournalpubmedcatalogue
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
25254M. Z. A. Siddiqi, Z.,Im, W. T.Arachidicoccus ginsenosidivorans sp. nov., with ginsenoside-converting activity isolated from ginseng cultivating soil10.1099/ijsem.0.001720IJSEM 67: 1005-1010 201727974091
64148Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-22792Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 22792)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
69479João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
91425Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID406212.1