Strain identifier

BacDive ID: 130440

Type strain: Yes

Species: Actinoplanes siamensis

Strain Designation: A-T 6646

Strain history: <- C Suriyachadkun, BCC; BCC 46194 <- C Suriyachadkun; A-T 6646

NCBI tax ID(s): 1223317 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 21460

BacDive-ID: 130440

DSM-Number: 46706

keywords: genome sequence, 16S sequence, Bacteria, aerobe, spore-forming, Gram-positive, motile, ovoid-shaped

description: Actinoplanes siamensis A-T 6646 is an aerobe, spore-forming, Gram-positive bacterium that was isolated from Bamboo forest soil.

NCBI tax id

  • NCBI tax id: 1223317
  • Matching level: species

strain history

  • @ref: 21460
  • history: <- C Suriyachadkun, BCC; BCC 46194 <- C Suriyachadkun; A-T 6646

doi: 10.13145/bacdive130440.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micromonosporales
  • family: Micromonosporaceae
  • genus: Actinoplanes
  • species: Actinoplanes siamensis
  • full scientific name: Actinoplanes siamensis Suriyachadkun et al. 2013

@ref: 21460

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Micromonosporaceae

genus: Actinoplanes

species: Actinoplanes siamensis

full scientific name: Actinoplanes siamensis Suriyachadkun et al. 2013

strain designation: A-T 6646

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
30942positiveovoid-shapedyes
69480positive100

pigmentation

  • @ref: 30942
  • production: yes

multimedia

  • @ref: 21460
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_46706.jpg
  • caption: Medium 65 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
21460CZAPEK PEPTONE AGAR (DSMZ Medium 83)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium83.pdf
21460GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)yeshttps://mediadive.dsmz.de/medium/65Name: GYM STREPTOMYCES MEDIUM (DSMZ Medium 65) Composition: Agar 18.0 g/l Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l CaCO3 2.0 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
30942positivegrowth25-40
30942positiveoptimum27.5mesophilic
21460positivegrowth28mesophilic

culture pH

@refabilitytypepHPH range
30942positivegrowth06-11alkaliphile
30942positiveoptimum8.5

Physiology and metabolism

oxygen tolerance

  • @ref: 30942
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
30942yes
69481yes100
69480yes100

halophily

  • @ref: 30942
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-1 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3094217057cellobiose+carbon source
3094228757fructose+carbon source
3094228260galactose+carbon source
3094217234glucose+carbon source
3094237684mannose+carbon source
3094218222xylose+carbon source

enzymes

@refvalueactivityec
30942acid phosphatase+3.1.3.2
30942alkaline phosphatase+3.1.3.1
30942catalase+1.11.1.6
30942gelatinase+

Isolation, sampling and environmental information

isolation

  • @ref: 21460
  • sample type: Bamboo forest soil
  • geographic location: Khorn Kaen Province
  • country: Thailand
  • origin.country: THA
  • continent: Asia

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Forest
#Environmental#Terrestrial#Soil
#Host#Plants#Herbaceous plants (Grass,Crops)

taxonmaps

  • @ref: 69479
  • File name: preview.99_60515.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_94;96_240;97_262;98_42945;99_60515&stattab=map
  • Last taxonomy: Actinoplanes siamensis subclade
  • 16S sequence: JX283293
  • Sequence Identity:
  • Total samples: 5
  • soil counts: 5

Safety information

risk assessment

  • @ref: 21460
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 21460
  • description: Actinoplanes siamensis strain A-T 6646 16S ribosomal RNA gene, partial sequence
  • accession: JX283293
  • length: 1451
  • database: ena
  • NCBI tax ID: 1223317

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Actinoplanes siamensis NBRC 109076GCA_016862395contigncbi1223317
66792Actinoplanes siamensis strain NBRC 1090761223317.3wgspatric1223317

GC content

  • @ref: 21460
  • GC-content: 72

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileyes61.781no
gram-positiveyes90.252no
anaerobicno99.191yes
aerobicyes95.525no
halophileno96.24no
spore-formingyes92.452no
glucose-utilyes90.157yes
flagellatedno90.186no
thermophileno98.298no
glucose-fermentno90.195no

External links

@ref: 21460

culture collection no.: DSM 46706, BCC 46194, NBRC 109076

straininfo link

  • @ref: 88970
  • straininfo: 399657

literature

  • topic: Phylogeny
  • Pubmed-ID: 23396720
  • title: Actinoplanes siamensis sp. nov., isolated from soil.
  • authors: Suriyachadkun C, Ngaemthao W, Chunhametha S, Thawai C, Sanglier JJ
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.048017-0
  • year: 2013
  • mesh: Bacterial Typing Techniques, Bambusa/*microbiology, DNA, Bacterial/genetics, Fatty Acids/analysis, Micromonosporaceae/*classification/genetics/isolation & purification, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/analysis, Phospholipids/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Thailand, Vitamin K 2/analogs & derivatives/analysis
  • topic2: Genetics

Reference

@idauthorstitledoi/urlcatalogueID_cross_referencepubmed
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
21460Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-46706Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 46706)
30942Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172727228776041
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1
88970Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID399657.1