Strain identifier

BacDive ID: 16438

Type strain: Yes

Species: Streptomyces vietnamensis

Strain Designation: GIMV4.0001

Strain history: IAM 15340 <-- CCTCC M 205143 <-- H.-H. Zhu et al. GIMV4.0001.

NCBI tax ID(s): 362257 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 8.1 (current version)

General

@ref: 15468

BacDive-ID: 16438

DSM-Number: 41927

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

description: Streptomyces vietnamensis GIMV4.0001 is an aerobe, spore-forming, mesophilic bacterium that was isolated from forest soil sample.

NCBI tax id

  • NCBI tax id: 362257
  • Matching level: species

strain history

@refhistory
15468<- JCM/RIKEN <- IAM <- CCTCC <- H.-H. Zhu et al.; GIMV4.0001
67770IAM 15340 <-- CCTCC M 205143 <-- H.-H. Zhu et al. GIMV4.0001.

doi: 10.13145/bacdive16438.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Kitasatosporales
  • family: Streptomycetaceae
  • genus: Streptomyces
  • species: Streptomyces vietnamensis
  • full scientific name: Streptomyces vietnamensis Zhu et al. 2007

@ref: 15468

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Streptomycetaceae

genus: Streptomyces

species: Streptomyces vietnamensis

full scientific name: Streptomyces vietnamensis Zhu et al. 2007 emend. Nouioui et al. 2018

strain designation: GIMV4.0001

type strain: yes

Morphology

cell morphology

  • @ref: 31991
  • gram stain: positive
  • cell shape: rod-shaped

pigmentation

  • @ref: 31991
  • production: yes

multimedia

  • @ref: 15468
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_41927.jpg
  • caption: Medium 65 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

  • @ref: 15468
  • name: GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/65
  • composition: Name: 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
15468positivegrowth28mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 31991
  • oxygen tolerance: aerobe

spore formation

  • @ref: 31991
  • spore formation: yes

observation

  • @ref: 31991
  • observation: aggregates in chains

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3199122599arabinose+carbon source
3199128757fructose+carbon source
3199128260galactose+carbon source
3199117234glucose+carbon source
3199128053melibiose+carbon source
3199116634raffinose+carbon source
3199126546rhamnose+carbon source
3199117992sucrose+carbon source
3199118222xylose+carbon source

metabolite production

@refChebi-IDmetaboliteproduction
3199116136hydrogen sulfideyes
677705533granaticinyes

enzymes

  • @ref: 31991
  • value: catalase
  • activity: +
  • ec: 1.11.1.6

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentgeographic location
15468forest soil sampleVietnamVNMAsia
67770Forest soilVietnamVNMAsiaDo Xongpha

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Forest
#Environmental#Terrestrial#Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_2484.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15;96_102;97_109;98_766;99_2484&stattab=map
  • Last taxonomy: Streptomyces
  • 16S sequence: DQ311081
  • Sequence Identity:
  • Total samples: 971
  • soil counts: 718
  • aquatic counts: 54
  • animal counts: 76
  • plant counts: 123

Safety information

risk assessment

  • @ref: 15468
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 15468
  • description: Streptomyces vietnamensis strain GIMV4.0001 16S ribosomal RNA gene, partial sequence
  • accession: DQ311081
  • length: 1419
  • database: ena
  • NCBI tax ID: 362257

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Streptomyces vietnamensis GIMV4.00012582581575draftimg362257
66792Streptomyces vietnamensis GIMV4.00012872942632completeimg362257
67770Streptomyces vietnamensis GIMV4.0001GCA_000830005completencbi362257

GC content

@refGC-contentmethod
1546873.9
6777073.9thermal denaturation, midpoint method (Tm)
6777072.09genome sequence analysis
6777072genome sequence analysis

External links

@ref: 15468

culture collection no.: DSM 41927, CCTCC M205143, IAM 15340, JCM 21785, CCTCC M 205143, NBRC 104153

straininfo link

  • @ref: 85477
  • straininfo: 309500

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny17684254Streptomyces vietnamensis sp. nov., a streptomycete with violet blue diffusible pigment isolated from soil in Vietnam.Zhu HH, Guo J, Yao Q, Yang SZ, Deng MR, Phuong LTB, Hanh VT, Ryan MJInt J Syst Evol Microbiol10.1099/ijs.0.64774-02007DNA, Bacterial, DNA, Ribosomal/genetics, Molecular Sequence Data, Phylogeny, Pigments, Biological/biosynthesis, RNA, Ribosomal, 16S/genetics, *Soil Microbiology, Streptomyces/*classification/genetics/*isolation & purification/physiology, Trees, VietnamGenetics
Genetics25687102Complete genome sequence of Streptomyces vietnamensis GIMV4.0001 T, a genetically manipulable producer of the benzoisochromanequinone antibiotic granaticin.Deng MR, Guo J, Ma LY, Li YX, Feng GD, Mo CY, Zhu HHJ Biotechnol10.1016/j.jbiotec.2015.02.0092015Anti-Bacterial Agents/*biosynthesis, Base Sequence, *Chromosomes, Bacterial, *Genome, Bacterial, Molecular Sequence Data, Naphthoquinones/metabolism, Streptomyces/*genetics/*metabolismMetabolism
Metabolism31925390An aberrant metabolic flow toward early shunt products in the granaticin biosynthetic machinery of Streptomyces vietnamensis GIMV4.0001.Deng MR, Li Y, He HH, Zhou X, Zheng XL, Wang YH, Zhu HJ Antibiot (Tokyo)10.1038/s41429-019-0267-82020Naphthoquinones/isolation & purification/metabolism, Secondary Metabolism, Streptomyces/*metabolismEnzymology
35004619Discovery of Mycothiogranaticins from Streptomyces vietnamensis GIMV4.0001 and the Regulatory Effect of Mycothiol on the Granaticin Biosynthesis.Deng MR, Li Y, Luo X, Zheng XL, Chen Y, Zhang YL, Zhang W, Zhou H, Zhu HFront Chem10.3389/fchem.2021.8022792021
Phylogeny35258449Characterization of Streptomyces nymphaeiformis sp. nov., and its taxonomic relatedness to other polyhydroxybutyrate-degrading streptomycetes.Hix GR, Khan MS, Miller MT, Napier EC, O'Brien AL, White RP, Baron SFInt J Syst Evol Microbiol10.1099/ijsem.0.0052662022Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, *Fatty Acids/chemistry, Nucleic Acid Hybridization, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Streptomyces/geneticsTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
15468Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 41927)https://www.dsmz.de/collection/catalogue/details/culture/DSM-41927
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
31991Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2824528776041
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
85477Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID309500.1StrainInfo: A central database for resolving microbial strain identifiers