Strain identifier

BacDive ID: 11853

Type strain: Yes

Species: Aminobacter aganoensis

Strain Designation: TH-3

Strain history: T. Urakami TH-3.

NCBI tax ID(s): 83264 (species)

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General

@ref: 2961

BacDive-ID: 11853

DSM-Number: 7051

keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-negative

description: Aminobacter aganoensis TH-3 is a mesophilic, Gram-negative bacterium that was isolated from soil.

NCBI tax id

  • NCBI tax id: 83264
  • Matching level: species

strain history

@refhistory
2961<- JCM <- T. Urakami, TH-3
67770T. Urakami TH-3.

doi: 10.13145/bacdive11853.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Hyphomicrobiales
  • family: Phyllobacteriaceae
  • genus: Aminobacter
  • species: Aminobacter aganoensis
  • full scientific name: Aminobacter aganoensis Urakami et al. 1992

@ref: 2961

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhizobiales

family: Phyllobacteriaceae

genus: Aminobacter

species: Aminobacter aganoensis

full scientific name: Aminobacter aganoensis Urakami et al. 1992

strain designation: TH-3

type strain: yes

Morphology

cell morphology

  • @ref: 69480
  • gram stain: negative
  • confidence: 99.987

Culture and growth conditions

culture medium

  • @ref: 2961
  • name: NUTRIENT AGAR (DSMZ Medium 1)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/1
  • composition: Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
2961positivegrowth30mesophilic
67770positivegrowth30mesophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481no100
69480no99.995

observation

  • @ref: 67770
  • observation: quinones: Q-10

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
2961soil
67770SoilNiigata Pref.JapanJPNAsia

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_1038.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_5;96_220;97_697;98_812;99_1038&stattab=map
  • Last taxonomy: Mesorhizobium
  • 16S sequence: AJ011760
  • Sequence Identity:
  • Total samples: 1264
  • soil counts: 780
  • aquatic counts: 308
  • animal counts: 145
  • plant counts: 31

Safety information

risk assessment

  • @ref: 2961
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 20218
  • description: Aminobacter aganoensis strain DSM7051T, 16S rRNA gene, partial
  • accession: AJ011760
  • length: 1467
  • database: ena
  • NCBI tax ID: 83264

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Aminobacter aganoensis DSM 7051GCA_014206975contigncbi83264
66792Aminobacter aganoensis strain DSM 705183264.4wgspatric83264
66792Aminobacter aganoensis DSM 70512829777543draftimg83264

GC content

@refGC-contentmethod
6777063.5
6777063.8high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes85.648no
flagellatedno77.799no
gram-positiveno97.699no
anaerobicno98.513no
halophileno89.839no
spore-formingno95.406no
glucose-utilyes92.716no
aerobicyes92.733no
thermophileno98.818yes
glucose-fermentno90.049no

External links

@ref: 2961

culture collection no.: DSM 7051, ATCC 49933, JCM 7854, CCM 4328, IAM 15266

straininfo link

  • @ref: 81071
  • straininfo: 46132

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
2961Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 7051)https://www.dsmz.de/collection/catalogue/details/culture/DSM-7051
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
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
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/
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
81071Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID46132.1StrainInfo: A central database for resolving microbial strain identifiers