Strain identifier

BacDive ID: 7280

Type strain: Yes

Species: Agromyces terreus

Strain Designation: DS-10

Strain history: <- JH Yoon, KRIBB

NCBI tax ID(s): 424795 (species)

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General

@ref: 16104

BacDive-ID: 7280

DSM-Number: 22016

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

description: Agromyces terreus DS-10 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from soil.

NCBI tax id

  • NCBI tax id: 424795
  • Matching level: species

strain history

@refhistory
16104<- JCM/RIKEN <- J.-H. Yoon, Korea Res. Inst. Biosci. & Biotechnol. (KRIBB), Taejon, South Korea; DS-10
67770J.-H. Yoon DS-10.
67771<- JH Yoon, KRIBB

doi: 10.13145/bacdive7280.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Microbacteriaceae
  • genus: Agromyces
  • species: Agromyces terreus
  • full scientific name: Agromyces terreus Yoon et al. 2008

@ref: 16104

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Microbacteriaceae

genus: Agromyces

species: Agromyces terreus

full scientific name: Agromyces terreus Yoon et al. 2008

strain designation: DS-10

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
32172positive2.85 µm0.35 µmrod-shapedno
67771positive

Culture and growth conditions

culture medium

  • @ref: 16104
  • name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/92
  • composition: Name: 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

culture temp

@refgrowthtypetemperaturerange
16104positivegrowth25mesophilic
32172positivegrowth10-35
32172positiveoptimum25mesophilic
67770positivegrowth25mesophilic
67771positivegrowth25mesophilic

culture pH

@refabilitytypepHPH range
32172positivegrowth05-10alkaliphile
32172positiveoptimum7.5

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
32172aerobe
67771aerobe

halophily

@refsaltgrowthtested relationconcentration
32172NaClpositivegrowth0-6 %
32172NaClpositiveoptimum0.75 %

observation

  • @ref: 67770
  • observation: quinones: MK-11, MK-12, MK-10

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3217222599arabinose+carbon source
3217217057cellobiose+carbon source
3217228757fructose+carbon source
3217233984fucose+carbon source
3217228260galactose+carbon source
3217217234glucose+carbon source
3217217754glycerol+carbon source
3217228087glycogen+carbon source
3217217306maltose+carbon source
3217237684mannose+carbon source
32172506227N-acetylglucosamine+carbon source
3217218401phenylacetate+carbon source
3217216634raffinose+carbon source
3217226546rhamnose+carbon source
3217217814salicin+carbon source
3217217992sucrose+carbon source
3217227082trehalose+carbon source
3217218222xylose+carbon source

enzymes

@refvalueactivityec
32172gelatinase+
32172cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
16104soilDokdoRepublic of KoreaKORAsia
67770Soil
67771From soilDokdoRepublic of KoreaKORAsia

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_6092.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_852;97_1358;98_4520;99_6092&stattab=map
  • Last taxonomy: Agromyces
  • 16S sequence: EF363711
  • Sequence Identity:
  • Total samples: 413
  • soil counts: 271
  • aquatic counts: 38
  • animal counts: 92
  • plant counts: 12

Safety information

risk assessment

  • @ref: 16104
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 16104
  • description: Agromyces terreus strain DS-10 16S ribosomal RNA gene, partial sequence
  • accession: EF363711
  • length: 1449
  • database: ena
  • NCBI tax ID: 424795

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Agromyces terreus JCM 14581GCA_009749465contigncbi424795
66792Agromyces terreus DSM 220162844602033draftimg424795
66792Agromyces terreus DSM 22016GCA_024172065contigncbi424795

GC content

@refGC-contentmethod
1610471.1high performance liquid chromatography (HPLC)
3217271.1

External links

@ref: 16104

culture collection no.: DSM 22016, JCM 14581, KCTC 19216

straininfo link

  • @ref: 76731
  • straininfo: 407133

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny18523170Agromyces terreus sp. nov., isolated from soil.Yoon JH, Schumann P, Kang SJ, Park S, Oh TKInt J Syst Evol Microbiol10.1099/ijs.0.65072-02008Actinomycetales/*classification/genetics/*isolation & purification/physiology, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Genes, rRNA, Genotype, Korea, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Species SpecificityGenetics
Phylogeny33779960Agromyces laixinhei sp. nov. isolated from bat feces in China.Cheng Y, Bai Y, Huang Y, Yang J, Lu S, Jin D, Pu J, Zheng H, Li J, Huang Y, Wang S, Xu JJ Microbiol10.1007/s12275-021-0546-52021Actinobacteria, Actinomycetales/*classification/genetics/*isolation & purification/physiology, Animals, Base Composition, China, Chiroptera/*microbiology, DNA, Bacterial/genetics, Fatty Acids/analysis, Feces/*microbiology, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Whole Genome SequencingTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
16104Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 22016)https://www.dsmz.de/collection/catalogue/details/culture/DSM-22016
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
32172Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2841428776041
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
76731Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID407133.1StrainInfo: A central database for resolving microbial strain identifiers