Strain identifier

BacDive ID: 11062

Type strain: Yes

Species: Aeromicrobium ginsengisoli

Strain history: <- MK Kim, Kyunghee Uni.

NCBI tax ID(s): 363867 (species)

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General

@ref: 16219

BacDive-ID: 11062

DSM-Number: 22238

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

description: Aeromicrobium ginsengisoli DSM 22238 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from soil of a ginseng field.

NCBI tax id

  • NCBI tax id: 363867
  • Matching level: species

strain history

@refhistory
16219<- JCM/RIKEN <- D.-C. Yang; Gsoil 098
67770D.-C. Yang Gsoil 098.
67771<- MK Kim, Kyunghee Uni.

doi: 10.13145/bacdive11062.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Propionibacteriales
  • family: Nocardioidaceae
  • genus: Aeromicrobium
  • species: Aeromicrobium ginsengisoli
  • full scientific name: Aeromicrobium ginsengisoli Kim et al. 2008

@ref: 16219

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Nocardioidaceae

genus: Aeromicrobium

species: Aeromicrobium ginsengisoli

full scientific name: Aeromicrobium ginsengisoli Kim et al. 2008

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
32044positive0.5-1.2 µm0.3-0.4 µmcoccus-shapedno
67771positive
69480no94.215
69480positive100

pigmentation

  • @ref: 32044
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
16219R2A 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
16219TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)yeshttps://mediadive.dsmz.de/medium/92Name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Yeast extract 3.0 g/l Distilled water
16219TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)yeshttps://mediadive.dsmz.de/medium/535Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
16219positivegrowth28mesophilic
32044positivegrowth04-30
32044positiveoptimum30mesophilic
67770positivegrowth28mesophilic
67771positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
32044positivegrowth5-8.5alkaliphile
32044positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
32044aerobe
67771aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.983

halophily

@refsaltgrowthtested relationconcentration
32044NaClpositivegrowth03-04 %
32044NaClpositiveoptimum3 %

observation

@refobservation
32044aggregates in chains
67770quinones: MK-9(H4)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
32044370543-hydroxybutyrate+carbon source
3204430089acetate+carbon source
3204416449alanine+carbon source
3204422599arabinose+carbon source
3204422653asparagine+carbon source
3204417057cellobiose+carbon source
3204416236ethanol+carbon source
3204428757fructose+carbon source
3204433984fucose+carbon source
3204428260galactose+carbon source
3204424265gluconate+carbon source
3204417234glucose+carbon source
3204429987glutamate+carbon source
3204417754glycerol+carbon source
3204417716lactose+carbon source
3204425017leucine+carbon source
3204425115malate+carbon source
3204417306maltose+carbon source
3204437684mannose+carbon source
32044506227N-acetylglucosamine+carbon source
3204428044phenylalanine+carbon source
3204426271proline+carbon source
3204417272propionate+carbon source
3204415361pyruvate+carbon source
3204426546rhamnose+carbon source
3204417822serine+carbon source
3204430031succinate+carbon source
3204417992sucrose+carbon source
3204427082trehalose+carbon source
3204416296D-tryptophan+carbon source
3204431011valerate+carbon source
3204418222xylose+carbon source
3204417632nitrate+reduction

enzymes

  • @ref: 32044
  • value: cytochrome oxidase
  • activity: +
  • ec: 1.9.3.1

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
16219soil of a ginseng fieldDaejeonRepublic of KoreaKORAsia
67770Soil of a ginseng fieldDaejeonRepublic of KoreaKORAsia
67771From soil of ginseng fieldRepublic 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_5495.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_142;96_1793;97_2145;98_4103;99_5495&stattab=map
  • Last taxonomy: Aeromicrobium
  • 16S sequence: AB245394
  • Sequence Identity:
  • Total samples: 2046
  • soil counts: 1209
  • aquatic counts: 148
  • animal counts: 459
  • plant counts: 230

Safety information

risk assessment

  • @ref: 16219
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 16219
  • description: Aeromicrobium ginsengisoli gene for 16S rRNA, partial sequence, strain: Gsoil 098
  • accession: AB245394
  • length: 1483
  • database: ena
  • NCBI tax ID: 363867

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Aeromicrobium ginsengisoli strain JCM 14732363867.3wgspatric363867
66792Aeromicrobium ginsengisoli JCM 147322866597551draftimg363867
67770Aeromicrobium ginsengisoli JCM 14732GCA_004134905contigncbi363867

GC content

@refGC-contentmethod
1621966.8high performance liquid chromatography (HPLC)
3204466.8

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
gram-positiveyes91.09no
anaerobicno99.179no
halophileno92.126no
spore-formingno90.72no
glucose-utilyes88.061yes
aerobicyes95.543yes
motileno94.105yes
flagellatedno98.362yes
thermophileno98.791yes
glucose-fermentno88.659no

External links

@ref: 16219

culture collection no.: DSM 22238, JCM 14732, KCTC 19207, GBS 39, Gsoil 098

straininfo link

  • @ref: 80311
  • straininfo: 291516

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny18768598Aeromicrobium ginsengisoli sp. nov., isolated from a ginseng field.Kim MK, Park MJ, Im WT, Yang DCInt J Syst Evol Microbiol10.1099/ijs.0.64871-02008Actinomycetales/*classification/genetics/*isolation & purification/physiology, Bacterial Typing Techniques, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Genes, rRNA, Korea, Locomotion, Molecular Sequence Data, Nucleic Acid Hybridization, Panax/*microbiology, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, *Soil Microbiology, Spores, Bacterial/cytology, Vitamin K 2/analysisGenetics
Phylogeny20081024Aeromicrobium halocynthiae sp. nov., a taurocholic acid-producing bacterium isolated from the marine ascidian Halocynthia roretzi.Kim SH, Yang HO, Sohn YC, Kwon HCInt J Syst Evol Microbiol10.1099/ijs.0.016618-02010Actinomycetales/*classification/genetics/isolation & purification, Animals, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Taurocholic Acid/*biosynthesis, Urochordata/*microbiology, Vitamin K 2/analogs & derivatives/chemistryGenetics
Phylogeny26354190Aeromicrobium camelliae sp. nov., isolated from Pu'er tea.Niu L, Xiong M, Tang T, Song L, Hu X, Zhao M, Zhang KInt J Syst Evol Microbiol10.1099/ijsem.0.0005832015Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Tea/*microbiology, Vitamin K 2/analogs & derivatives/chemistryGenetics
Phylogeny29289978Aeromicrobium panacisoli sp. nov. Isolated from Soil of Ginseng Cultivating Field.Siddiqi MZ, Lee SY, Choi KD, Im WTCurr Microbiol10.1007/s00284-017-1426-42017Actinomycetales/classification/genetics/*isolation & purification/metabolism, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/chemistry/metabolism, Panax/*growth & development, Phylogeny, Republic of Korea, *Soil MicrobiologyMetabolism
Phylogeny32692642Aeromicrobium chenweiae sp. nov. and Aeromicrobium yanjiei sp. nov., isolated from Tibetan antelope (Pantholops hodgsonii) and plateau pika (Ochotona curzoniae), respectively.Li J, Lei W, Yang J, Lu S, Jin D, Lai XH, Zhang S, Cheng Y, Mi F, Huang Y, Pu J, Dong K, Tian Z, Wu X, Huang Y, Wang S, Xu JInt J Syst Evol Microbiol10.1099/ijsem.0.0043312020Actinobacteria/*classification/isolation & purification, Animals, Antelopes/*microbiology, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Feces/microbiology, Lagomorpha/*microbiology, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Tibet, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
16219Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 22238)https://www.dsmz.de/collection/catalogue/details/culture/DSM-22238
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
32044Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2829428776041
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)
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.https://microbeatlas.org/MicrobeAtlas 1.0 beta
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
80311Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID291516.1StrainInfo: A central database for resolving microbial strain identifiers