Strain identifier

BacDive ID: 364

Type strain: Yes

Species: Allopusillimonas ginsengisoli

Strain history: <- DC Yang, Kyunghee Univ.

NCBI tax ID(s): 453575 (species)

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General

@ref: 17925

BacDive-ID: 364

DSM-Number: 25164

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

description: Allopusillimonas ginsengisoli DSM 25164 is an aerobe, mesophilic, Gram-negative bacterium that forms circular colonies and was isolated from soil from ginseng field.

NCBI tax id

  • NCBI tax id: 453575
  • Matching level: species

strain history

@refhistory
17925<- KCTC <- D.-C. Yang, Korean Ginseng Center and Ginseng Genetic Resource Bank, Gyeonggi-do
67770D.-C. Yang DCY25.
67771<- DC Yang, Kyunghee Univ.

doi: 10.13145/bacdive364.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Betaproteobacteria
  • order: Burkholderiales
  • family: Alcaligenaceae
  • genus: Allopusillimonas
  • species: Allopusillimonas ginsengisoli
  • full scientific name: Allopusillimonas ginsengisoli (Srinivasan et al. 2010) Babich et al. 2023

  • synonyms

    • @ref: 20215
    • synonym: Pusillimonas ginsengisoli

@ref: 17925

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Alcaligenaceae

genus: Pusillimonas

species: Pusillimonas ginsengisoli

full scientific name: Pusillimonas ginsengisoli Srinivasan et al. 2010

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
23278negative0.5-0.8 µm0.3-0.6 µmrod-shapedyes
67771negative
69480yes93.106
69480negative99.999

colony morphology

  • @ref: 23278
  • colony color: pale yellow
  • colony shape: circular
  • incubation period: 5 days
  • medium used: nutrient agar

multimedia

  • @ref: 17925
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_25164.jpg
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
17925REACTIVATION WITH LIQUID MEDIUM 830 (DSMZ Medium 830c)yeshttps://mediadive.dsmz.de/medium/830cName: REACTIVATION WITH LIQUID MEDIUM 830 (DSMZ Medium 830c) Composition: Agar 15.0 g/l Yeast extract 0.5 g/l Proteose peptone 0.5 g/l Casamino acids 0.5 g/l Glucose 0.5 g/l Starch 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
17925REACTIVATION WITH LIQUID MEDIUM 1 (DSMZ Medium 1a)yeshttps://mediadive.dsmz.de/medium/1aName: REACTIVATION WITH LIQUID MEDIUM 1 (DSMZ Medium 1a) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
23278Nutrient agar (NA)yes

culture temp

@refgrowthtypetemperaturerange
17925positivegrowth28mesophilic
23278positivegrowth15-40
23278nogrowth4psychrophilic
23278nogrowth42thermophilic
23278positiveoptimum30mesophilic
67770positivegrowth30mesophilic
67771positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
23278positivegrowth5.5-9.0alkaliphile
23278positiveoptimum7.0

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
23278aerobe
67771aerobe

spore formation

@refspore formationconfidence
23278no
69481no100
69480no99.979

observation

@refobservation
67770quinones: Q-8
67771quinones: Q-8

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
23278161933-hydroxybenzoate-assimilation
23278178794-hydroxybenzoate-assimilation
2327827689decanoate-assimilation
2327816988D-ribose-assimilation
2327817924D-sorbitol-assimilation
232788391D-gluconate-assimilation
2327815971L-histidine-assimilation
2327862345L-rhamnose-assimilation
2327817306maltose-assimilation
2327837684mannose-assimilation
2327817268myo-inositol-assimilation
232789300suberic acid-assimilation
23278168082-dehydro-D-gluconate-growth
23278174265-dehydro-D-gluconate-growth
2327817634D-glucose-growth
2327816899D-mannitol-growth
2327816024D-mannose-growth
2327824265gluconate-growth
2327828087glycogen-growth
2327830849L-arabinose-growth
2327818287L-fucose-growth
2327817306maltose-growth
2327828053melibiose-growth
23278506227N-acetylglucosamine-growth
2327817814salicin-growth
2327817992sucrose-growth
232784853esculin-hydrolysis
232785291gelatin-hydrolysis
2327828017starch-hydrolysis
23278370543-hydroxybutyrate+assimilation
23278167244-hydroxybutyrate+assimilation
2327817128adipate+assimilation
2327816947citrate+assimilation
2327817240itaconate+assimilation
2327816977L-alanine+assimilation
2327817203L-proline+assimilation
2327817115L-serine+assimilation
2327825115malate+assimilation
2327815792malonate+assimilation
2327818401phenylacetate+assimilation
2327817272propionate+assimilation
2327831011valerate+assimilation
2327830089acetate+growth
2327824996lactate+growth

enzymes

@refvalueactivityec
23278acid phosphatase+3.1.3.2
23278alkaline phosphatase+3.1.3.1
23278alpha-chymotrypsin+3.4.21.1
23278alpha-fucosidase-3.2.1.51
23278alpha-galactosidase-3.2.1.22
23278alpha-glucosidase-3.2.1.20
23278alpha-mannosidase-3.2.1.24
23278arginine dihydrolase-3.5.3.6
23278beta-galactosidase-3.2.1.23
23278beta-glucosidase-3.2.1.21
23278beta-glucuronidase-3.2.1.31
23278catalase+1.11.1.6
23278cystine arylamidase+3.4.11.3
23278cytochrome oxidase+1.9.3.1
23278esterase (C 4)+
23278esterase lipase (C 8)+
23278leucine arylamidase+3.4.11.1
23278lipase (C 14)-
23278N-acetyl-beta-glucosaminidase-3.2.1.52
23278naphthol-AS-BI-phosphohydrolase+
23278trypsin+3.4.21.4
23278urease-3.5.1.5
23278valine arylamidase+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
17925soil from ginseng fieldnear DaejeonRepublic of KoreaKORAsia
67770Soil of a ginseng field near Daejeon CityRepublic of KoreaKORAsia
67771From soil, ginseng fieldRepublic of KoreaKORAsia

isolation source categories

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

Safety information

risk assessment

  • @ref: 17925
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 17925
  • description: Pusillimonas ginsengisoli strain DCY25 16S ribosomal RNA gene, partial sequence
  • accession: EF672088
  • length: 1479
  • database: ena
  • NCBI tax ID: 453575

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pusillimonas ginsengisoli strain KCTC 22046453575.4wgspatric453575
66792Pusillimonas ginsengisoli KCTC 220462891648259draftimg453575
67770Allopusillimonas ginsengisoli KCTC 22046GCA_004153455contigncbi453575

GC content

@refGC-contentmethod
2327857.3high performance liquid chromatography (HPLC)
6777157.3

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
gram-positiveno97.864yes
anaerobicno99.308no
halophileno80.228no
spore-formingno94.33yes
glucose-utilno77.507yes
aerobicyes91.689no
flagellatedno70.223no
thermophileno98.949no
motileyes86.369yes
glucose-fermentno91.755no

External links

@ref: 17925

culture collection no.: DSM 25164, JCM 14767, KCTC 22046, DCY 25

straininfo link

  • @ref: 70044
  • straininfo: 399770

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19749028Pusillimonas ginsengisoli sp. nov., isolated from soil of a ginseng field.Srinivasan S, Kim MK, Sathiyaraj G, Kim YJ, Yang DCInt J Syst Evol Microbiol10.1099/ijs.0.018358-02009Alcaligenaceae/*classification/genetics/*isolation & purification/metabolism, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/metabolism, Molecular Sequence Data, Panax/*microbiology, Phylogeny, RNA, Ribosomal, 16S/genetics, *Soil MicrobiologyMetabolism
Phylogeny19933592Pusillimonas soli sp. nov., isolated from farm soil.Lee M, Woo SG, Chae M, Ten LNInt J Syst Evol Microbiol10.1099/ijs.0.020404-02009Alcaligenaceae/*classification/genetics/*isolation & purification/physiology, Bacterial Typing Techniques, Base Composition, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Locomotion, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/analysis, Phylogeny, Polyamines/analysis, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil MicrobiologyGenetics
Phylogeny21257696Pusillimonas harenae sp. nov., isolated from a sandy beach, and emended description of the genus Pusillimonas.Park MS, Park YJ, Jung JY, Lee SH, Park W, Lee K, Jeon COInt J Syst Evol Microbiol10.1099/ijs.0.029892-02011Alcaligenaceae/*classification/genetics/*isolation & purification/metabolism, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/metabolism, Geologic Sediments/*microbiology, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of KoreaMetabolism
Phylogeny27744638Pusillimonas caeni sp. nov., isolated from a sludge sample of a biofilm reactor.Jin L, Ko SR, Cui Y, Lee CS, Oh HM, Ahn CY, Lee HGAntonie Van Leeuwenhoek10.1007/s10482-016-0782-62016Alcaligenaceae/classification/genetics/*isolation & purification/metabolism, Bacterial Typing Techniques, Base Composition, *Biofilms, DNA, Bacterial/genetics, Fatty Acids/chemistry/metabolism, Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sewage/*microbiologyMetabolism
Phylogeny32369004Pusillimonas maritima sp. nov., isolated from surface seawater.Li J, Qi M, Lai Q, Dong C, Liu X, Wang G, Shao ZInt J Syst Evol Microbiol10.1099/ijsem.0.0042022020Alcaligenaceae/*classification/isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Indian Ocean, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*chemistry, Sequence Analysis, DNA, Ubiquinone/chemistryTranscriptome
Phylogeny36123413Paracandidimonas lactea sp. nov., a urea-utilizing bacterium isolated from landfill.Zhang C, Pu Q, Ying JJ, Chen Y, Li CZ, Wu HT, Wang BJ, Zhang YH, Zeng GH, Li O, Hu XF, Sun CArch Microbiol10.1007/s00203-022-03190-42022Bacterial Typing Techniques, DNA, Bacterial/genetics, Glycerol, *Phosphatidylethanolamines, Phosphatidylglycerols, Phylogeny, Quinones, RNA, Ribosomal, 16S/genetics, Sodium Chloride, *Urea, Waste Disposal Facilities

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
17925Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 25164)https://www.dsmz.de/collection/catalogue/details/culture/DSM-25164
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
23278Sathiyaraj Srinivasan, Myung Kyum Kim, Gayathri Sathiyaraj, Yeon-Ju Kim,Deok-Chun Yang10.1099/ijs.0.018358-0Pusillimonas ginsengisoli sp. nov., isolated from soil of a ginseng fieldIJSEM 60: 1783-1787 201019749028
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
70044Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID399770.1StrainInfo: A central database for resolving microbial strain identifiers