Strain identifier

BacDive ID: 6304

Type strain: Yes

Species: Pedococcus ginsenosidimutans

Strain Designation: BXN5-13

Strain history: <- ST Lee, KAIST

NCBI tax ID(s): 490570 (species)

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General

@ref: 9079

BacDive-ID: 6304

DSM-Number: 21006

keywords: 16S sequence, Bacteria, aerobe, mesophilic, Gram-positive, coccus-shaped

description: Pedococcus ginsenosidimutans BXN5-13 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from soil of a ginseng field.

NCBI tax id

  • NCBI tax id: 490570
  • Matching level: species

strain history

@refhistory
9079<- S. T. Lee, KAIST <- D.-S. An; BXN5-13
67770LMG 24462 <-- S.-T. Lee BXN5-13 <-- W.-T. Im.
67771<- ST Lee, KAIST

doi: 10.13145/bacdive6304.20241212.9.2

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Intrasporangiaceae
  • genus: Pedococcus
  • species: Pedococcus ginsenosidimutans
  • full scientific name: Pedococcus ginsenosidimutans (Wang et al. 2011) Nouioui et al. 2018

  • synonyms

    • @ref: 20215
    • synonym: Phycicoccus ginsenosidimutans

@ref: 9079

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Intrasporangiaceae

genus: Pedococcus

species: Pedococcus ginsenosidimutans

full scientific name: Pedococcus ginsenosidimutans (Wang et al. 2011) Nouioui et al. 2018

strain designation: BXN5-13

type strain: yes

Morphology

cell morphology

@refgram staincell widthcell shapemotility
29835positive0.5 µmcoccus-shapedno
67771positive

colony morphology

@refcolony colorincubation periodmedium used
21352Brown beige (1011)10-14 daysISP 2
21352Maize yellow (1006)10-14 daysISP 3
2135210-14 daysISP 4
2135210-14 daysISP 5
2135210-14 daysISP 7
2135210-14 dayssuter with tyrosine
2135210-14 dayssuter without tyrosine

multicellular morphology

@refforms multicellular complexmedium name
21352noISP 2
21352noISP 3
21352noISP 4
21352noISP 5
21352noISP 7
21352noSuter with tyrosine
21352noSuter without tyrosine

pigmentation

  • @ref: 29835
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
9079R2A MEDIUM (DSMZ Medium 830)yeshttps://mediadive.dsmz.de/medium/830Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water
21352ISP 2yesName: ISP 2 / Yeast Malt Agar (5265); 5265 Composition Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l Agar 15.0 g/l Preparation: Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.0 Usage: Maintenance and Taxonomy Organisms: All Actinomycetes
21352ISP 3yesName: ISP 3; 5315 Composition Dog oat flakes 20.0 g/l Trace element solution (5314) 2.5 ml/l Agar 18.0 g/l Preparation: Oat flakes are cooked for 20 minutes, trace element solution and agar are added (in the case of non rolled oat flakes the suspension has to bee filtrated). Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.8 Usage: Maintenance and taxonomy (e.g. SEM As liquid medium for metabolite production) Organisms: All Actinomycetes Trace element solution 5314 Name: Trace element solution 5314; 5314 Composition CaCl2 x H2O 3.0 g/l Fe-III-citrate 1.0 g/l MnSO4 0.2 g/l ZnCl2 0.1 g/l CuSO4 x 5 H2O 0.025 g/l Sodium tetra borate 0.2 g/l CoCl2 x 6 H2O 0.004 g/l Sodium molybdate 0.01 g/l Preparation: Use double destillated water. Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Trace element solution for different media Organisms:
21352ISP 4yesName: ISP 4; DSM 547 Solution I: Difco soluble starch, 10.0 g. Make a paste of the starch with a small amount of cold distilled water and bring to a volume of 500 ml. Solution II: CaCO3 2.0 g K2HPO4 (anhydrous) 1.0 g MgSO4 x 7 H2O 1.0 g NaCl 1.0 g (NH4)2SO4 2.0 g Distilled water 500.0 ml Trace salt solution (see below) 1.0 ml The pH should be between 7.0 and 7.4. Do not adjust if it is within this range. Mix solutions I and II together. Add 20.0 g agar. Liquify agar by steaming at 100°C for 10 to 20 min. Trace element solution: FeSO4 x 7 H2O 0.1 g MnCl2 x 4 H2O 0.1 g ZnSO4 x 7 H2O 0.1 g Distilled water 100.0 ml
21352ISP 5yesName: ISP 5 (5323) Composition L-Asparagine 1.0 g/l Glycerol 10.0 g/l K2HPO4 1.0 g/l Salt solution (see preparation) 1.0 ml/l Agar 20.0 g/l Preparation: Salt solution 1.0 g FeSO4 x 7 H2O 1.0 g MnCl2 x 4 H2O 1.0 g ZNSO4 x 7 H2O in 100 ml water Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.2 Usage: Maintenance and taxonomy Organisms: All Actinomycetes
21352ISP 7yesName: ISP 7 (5322) Composition Glycerol 15.0 g/l L-Tyrosine 0.5 g/l L-Asparagine 1.0 g/l K2HPO4 0.5 g/l NaCl 0.5 g/l FeSO4 x 7 H2O 0.01 g/l Trace element solution 5343 1.0 ml/l Agar 20.0 Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.3 Usage: Production of melanoid pigments Organisms: All Actinomycetes
21352suter with tyrosineyesName: Synthetically suter medium (5337) with and without tyrosine - see Kutzner,H.J., R. M. Kroppensted and F. Korn-Wendisch. (1986) Composition: Glycerol 15.0 g/l Tyrosine 1.0 (optional, see preparation comment) L-arginine 5.0 g/l L-glutamic acid 5.0 g/l L-methionine 0.3 g/l L-isoleucine 0.3 g/l K2HPO4 0.5 g/l MgSO4 x 7 H2O 0.2 g/l Agar 20.0 g/l Trace element solution (5341) 1.0 ml Composition of Trace element solution (5341): CuSO4 x 5 H2O 10.0 g/l CaCl2 x 2 H2O 10.0 g/l FeSO4 x 7 H2O 10.0 g/l ZnSO4 x 7 H2O 10.0 g/l MnSO4 x 7 H2O 40.0 g/l Preparation: Control medium is prepared without tyrosine Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigment Organisms: All Actinomycetes
21352suter without tyrosineyesName: Synthetically suter medium (5337) with and without tyrosine - see Kutzner,H.J., R. M. Kroppensted and F. Korn-Wendisch. (1986) Composition: Glycerol 15.0 g/l Tyrosine 1.0 (optional, see preparation comment) L-arginine 5.0 g/l L-glutamic acid 5.0 g/l L-methionine 0.3 g/l L-isoleucine 0.3 g/l K2HPO4 0.5 g/l MgSO4 x 7 H2O 0.2 g/l Agar 20.0 g/l Trace element solution (5341) 1.0 ml Composition of Trace element solution (5341): CuSO4 x 5 H2O 10.0 g/l CaCl2 x 2 H2O 10.0 g/l FeSO4 x 7 H2O 10.0 g/l ZnSO4 x 7 H2O 10.0 g/l MnSO4 x 7 H2O 40.0 g/l Preparation: Control medium is prepared without tyrosine Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigment Organisms: All Actinomycetes

culture temp

@refgrowthtypetemperature
9079positivegrowth28
29835positivegrowth10-37
29835positiveoptimum30
67770positivegrowth28
67771positivegrowth30

culture pH

@refabilitytypepHPH range
29835positivegrowth05-10alkaliphile
29835positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
29835aerobe
67771aerobe

spore formation

  • @ref: 29835
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
21352NaClpositivegrowth0 %
29835NaClpositivegrowth0-5 %
29835NaClpositiveoptimum0-2 %

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2135217234glucose-
2135222599arabinose-
2135217992sucrose-
2135218222xylose-
2135217268myo-inositol-
2135237684mannose-
2135228757fructose-
2135226546rhamnose-
2135216634raffinose-
2135262968cellulose-
2983517234glucose+carbon source
2983525115malate+carbon source
2983529864mannitol+carbon source
2983517632nitrate+reduction
6837928087glycogen-fermentation
6837917306maltose-fermentation
6837916899D-mannitol-fermentation
6837965327D-xylose-fermentation
6837916988D-ribose-fermentation
6837917634D-glucose-fermentation
683795291gelatin-hydrolysis
6837916199urea-hydrolysis
683794853esculin+hydrolysis
6837917632nitrate-reduction
6837917716lactose-fermentation

enzymes

@refvalueactivityec
29835catalase+1.11.1.6
29835cytochrome oxidase+1.9.3.1
29835urease+3.5.1.5
68382alpha-mannosidase+3.2.1.24
68382alpha-fucosidase-3.2.1.51
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucosidase-3.2.1.21
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase+3.2.1.20
68382beta-galactosidase+3.2.1.23
68382alpha-galactosidase+3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase+3.1.3.2
68382trypsin-3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382esterase lipase (C 8)+
68382esterase (C 4)+
68382alkaline phosphatase+3.1.3.1
68379gelatinase-
68379urease-3.5.1.5
68379beta-glucosidase+3.2.1.21
68379beta-galactosidase+3.2.1.23
68379beta-glucuronidase-3.2.1.31
68379alkaline phosphatase+3.1.3.1
68379pyrrolidonyl arylamidase-3.4.19.3
68379pyrazinamidase-3.5.1.B15

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
21352---+-++/-+/-+--------+/--

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
21352+++-++/-+/---++++-+--+-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
9079soil of a ginseng fieldJilin district, Baekdu MountainChinaCHNAsia
67770Soil of a ginseng field of Baekdu MountainJinlin DistrictChinaCHNAsia
67771From soil of ginseng fieldBaekdu Mountain in Jilin districtRepublic of KoreaKORAsia

isolation source categories

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

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: EU332824
  • Sequence Identity:
  • Total samples: 344
  • soil counts: 148
  • aquatic counts: 17
  • animal counts: 133
  • plant counts: 46

Safety information

risk assessment

  • @ref: 9079
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 9079
  • description: Phycicoccus ginsenosidimutans strain BXN5-13 16S ribosomal RNA gene, partial sequence
  • accession: EU332824
  • length: 1405
  • database: nuccore
  • NCBI tax ID: 490570

GC content

@refGC-contentmethod
907970.8high performance liquid chromatography (HPLC)
2983570.8

External links

@ref: 9079

culture collection no.: DSM 21006, KCTC 19419, LMG 24462, JCM 18961

straininfo link

  • @ref: 75779
  • straininfo: 323917

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny20382795Phycicoccus ginsenosidimutans sp. nov., isolated from soil of a ginseng field.Wang L, An DS, Jin FX, Lee ST, Im WT, Bae HMInt J Syst Evol Microbiol10.1099/ijs.0.022137-02010Actinomycetales/*classification/genetics/*isolation & purification/physiology, Bacterial Typing Techniques, Base Composition, China, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Diaminopimelic Acid/analysis, Fatty Acids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Panax, Phospholipids/analysis, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil MicrobiologyGenetics
Phylogeny27666743Phycicoccus ginsengisoli sp. nov., isolated from cultivated ginseng soil.Kang JP, Kim YJ, Nguyen NL, Hoang VA, Farh ME, Joo SC, Quan LH, Yang DCInt J Syst Evol Microbiol10.1099/ijsem.0.0015152016Actinomycetales/*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/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
9079Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21006)https://www.dsmz.de/collection/catalogue/details/culture/DSM-21006
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
21352Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM21006.pdfCompendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig
29835Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2621128776041
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
68379Automatically annotated from API Coryne
68382Automatically annotated from API zym
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.https://microbeatlas.org/MicrobeAtlas 1.0 beta
75779Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID323917.1StrainInfo: A central database for resolving microbial strain identifiers