Strain identifier

BacDive ID: 133241

Type strain: Yes

Species: Phycicoccus ginsengisoli

Strain history: D.-C. Yang and Y.-J. Kim; Kyung Hee Univ., South Korea; DCY87.

NCBI tax ID(s): 1462998 (species)

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General

@ref: 25082

BacDive-ID: 133241

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

description: Phycicoccus ginsengisoli DCY 87 is an aerobe, Gram-positive, rod-shaped bacterium that forms circular colonies and was isolated from Bulky and rhizosphere soil samples were obtained from a ginseng field.

NCBI tax id

  • NCBI tax id: 1462998
  • Matching level: species

strain history

  • @ref: 67770
  • history: D.-C. Yang and Y.-J. Kim; Kyung Hee Univ., South Korea; DCY87.

doi: 10.13145/bacdive133241.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Intrasporangiaceae
  • genus: Phycicoccus
  • species: Phycicoccus ginsengisoli
  • full scientific name: Phycicoccus ginsengisoli Kang et al. 2016

@ref: 25082

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Micrococcales

family: Intrasporangiaceae

genus: Phycicoccus

species: Phycicoccus ginsengisoli

type strain: yes

Morphology

cell morphology

  • @ref: 25082
  • gram stain: positive
  • cell length: 1.0-2.1 µm
  • cell width: 0.5-0.6 µm
  • cell shape: rod-shaped
  • motility: no

colony morphology

  • @ref: 25082
  • colony size: 0.7-0.8 mm
  • colony color: white
  • colony shape: circular
  • incubation period: 2 days
  • medium used: R2A agar (Reasoner's 2A agar)

Culture and growth conditions

culture medium

@refnamegrowth
25082NA (Nutrient Agar)yes
25082Reasoner's 2A agar (R2A)yes
25082LB (lysogeny broth) agaryes
25082TSA (Trypticase soy agar)yes

culture temp

@refgrowthtypetemperaturerange
25082positivegrowth10.0-37.0
25082positiveoptimum30mesophilic
67770positivegrowth28mesophilic

culture pH

@refabilitytypepHPH range
25082positivegrowth6.0-9.0alkaliphile
25082positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 25082
  • oxygen tolerance: aerobe

halophily

@refsaltgrowthtested relationconcentration
25082NaClpositivegrowth0.0-3.0 %(w/v)
25082NaCloptimum2 %(w/v)

murein

  • @ref: 25082
  • murein short key: A31
  • type: A1gamma m-Dpm-direct

observation

  • @ref: 67770
  • observation: quinones: MK-8(H4)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
25082168082-dehydro-D-gluconate-builds acid from
25082581435-dehydro-D-gluconate-builds acid from
2508227613amygdalin-builds acid from
2508222599arabinose-builds acid from
2508222599arabinose-assimilation
2508218305arbutin-builds acid from
2508218305arbutin-assimilation
2508216947citrate-carbon source
2508215963ribitol-builds acid from
2508217113erythritol-builds acid from
2508233984fucose-builds acid from
2508216813galactitol-builds acid from
2508217234glucose-fermentation
2508217268myo-inositol-builds acid from
2508217268myo-inositol-assimilation
2508215443inulin-builds acid from
2508215443inulin-assimilation
2508230849L-arabinose-builds acid from
2508218403L-arabitol-builds acid from
2508218287L-fucose-builds acid from
2508218287L-fucose-assimilation
2508215729L-ornithine-assimilation
2508262345L-rhamnose-builds acid from
2508262345L-rhamnose-assimilation
2508217266L-sorbose-builds acid from
2508217266L-sorbose-assimilation
2508265328L-xylose-builds acid from
2508225097lyxose-builds acid from
2508225097lyxose-assimilation
2508243943methyl alpha-D-mannoside-builds acid from
2508243943methyl alpha-D-mannoside-assimilation
2508274863methyl beta-D-xylopyranoside-builds acid from
2508232032potassium gluconate-builds acid from
2508216634raffinose-builds acid from
2508216634raffinose-assimilation
2508253258sodium citrate-assimilation
2508233954tagatose-builds acid from
2508233954tagatose-assimilation
2508253424tween 20-hydrolysis
2508216199urea-hydrolysis
2508218222xylose-builds acid from
25082casein+hydrolysis
2508217057cellobiose+builds acid from
2508217057cellobiose+assimilation
2508218333D-arabitol+builds acid from
2508218333D-arabitol+assimilation
2508215824D-fructose+builds acid from
2508212936D-galactose+builds acid from
2508217634D-glucose+builds acid from
2508216899D-mannitol+builds acid from
2508216899D-mannitol+assimilation
2508216024D-mannose+builds acid from
2508216988D-ribose+builds acid from
2508217924D-sorbitol+builds acid from
2508217924D-sorbitol+assimilation
2508216991dna+hydrolysis
250824853esculin+hydrolysis
250824853esculin+builds acid from
250825291gelatin+hydrolysis
2508228066gentiobiose+builds acid from
2508228066gentiobiose+assimilation
2508217754glycerol+assimilation
2508214336glycerol 1-phosphate+builds acid from
2508230849L-arabinose+assimilation
2508217895L-tyrosine+hydrolysis
2508217716lactose+builds acid from
2508217306maltose+builds acid from
250826731melezitose+assimilation
2508228053melibiose+builds acid from
2508228053melibiose+assimilation
25082320061methyl alpha-D-glucopyranoside+builds acid from
25082320061methyl alpha-D-glucopyranoside+assimilation
25082506227N-acetylglucosamine+builds acid from
25082506227N-acetylglucosamine+assimilation
2508233942ribose+assimilation
2508217814salicin+builds acid from
2508228017starch+hydrolysis
2508228017starch+assimilation
2508217992sucrose+assimilation
2508232528turanose+builds acid from
2508232528turanose+assimilation
2508253423tween 40+hydrolysis
2508253426tween 80+hydrolysis
2508217151xylitol+assimilation

metabolite production

@refChebi-IDmetaboliteproduction
2508215688acetoinno
2508216136hydrogen sulfideno
2508226672siderophoreyes

metabolite tests

@refChebi-IDmetabolitemethylred-testvoges-proskauer-testcitrate test
2508217234glucose-
2508215688acetoin-
2508216947citrate-

enzymes

@refvalueactivityec
250826-phospho-beta-galactosidase+3.2.1.85
25082acid phosphatase+3.1.3.2
25082alkaline phosphatase+3.1.3.1
25082alpha-chymotrypsin-3.4.21.1
25082alpha-fucosidase-3.2.1.51
25082alpha-galactosidase+3.2.1.22
25082alpha-glucosidase+3.2.1.20
25082alpha-mannosidase+3.2.1.24
25082arginine dihydrolase+3.5.3.6
25082beta-glucosidase+3.2.1.21
25082beta-glucuronidase-3.2.1.31
25082catalase+1.11.1.6
25082cystine arylamidase+3.4.11.3
25082cytochrome oxidase-1.9.3.1
25082esterase (C 4)+
25082esterase Lipase (C 8)+
25082gelatinase+
25082leucine arylamidase+3.4.11.1
25082lipase-
25082lysine decarboxylase-4.1.1.18
25082N-acetyl-beta-glucosaminidase+3.2.1.52
25082naphthol-AS-BI-phosphohydrolase+
25082ornithine decarboxylase-4.1.1.17
25082phenylalanine deaminase-4.3.1.5
25082trypsin+3.4.21.4
25082tryptophan deaminase+4.1.99.1
25082urease-3.5.1.5
25082valine arylamidase+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitudeenrichment cultureenrichment culture durationenrichment culture temperature
25082Bulky and rhizosphere soil samples were obtained from a ginseng fieldGochang CountyRepublic of KoreaKORAsia35126R2A agar (Reasoner's 2A agar)5 days30
67770Ginseng-cultivated soilGochang CountyRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Engineered#Agriculture#Field
#Environmental#Terrestrial#Soil
#Host Body-Site#Plant#Rhizosphere

taxonmaps

  • @ref: 69479
  • File name: preview.99_14961.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_670;97_776;98_900;99_14961&stattab=map
  • Last taxonomy: Intrasporangiaceae
  • 16S sequence: KF915798
  • Sequence Identity:
  • Total samples: 344
  • soil counts: 148
  • aquatic counts: 17
  • animal counts: 133
  • plant counts: 46

Sequence information

16S sequences

  • @ref: 25082
  • description: Phycicoccus sp. DCY87 16S ribosomal RNA gene, partial sequence
  • accession: KF915798
  • length: 1466
  • database: nuccore
  • NCBI tax ID: 1462998

GC content

  • @ref: 67770
  • GC-content: 72.7
  • method: high performance liquid chromatography (HPLC)

External links

@ref: 25082

culture collection no.: DCY 87, KCTC 39635, JCM 31016

literature

  • topic: Phylogeny
  • Pubmed-ID: 27666743
  • title: Phycicoccus ginsengisoli sp. nov., isolated from cultivated ginseng soil.
  • authors: Kang JP, Kim YJ, Nguyen NL, Hoang VA, Farh ME, Joo SC, Quan LH, Yang DC
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.001515
  • year: 2016
  • mesh: Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Nucleic Acid Hybridization, Panax/*microbiology, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, 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
25082J. P. K. Kang, Y. J.,Nguyen, N. L.,Hoang, V. A.,Farh, M. E.,Joo, S. C.,Quan, L. H.,Yang, D. C.Phycicoccus ginsengisoli sp. nov., isolated from cultivated ginseng soil10.1099/ijsem.0.001515IJSEM 66: 5320-5327 201627666743
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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/