Strain identifier

BacDive ID: 132432

Type strain: Yes

Species: Streptomyces yangpuensis

Strain Designation: fd2-tb

Strain history: <- B. Tang, Fudan University, Shanghai, China; fd2-tb

NCBI tax ID(s): 1648182 (species)

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General

@ref: 24221

BacDive-ID: 132432

DSM-Number: 100336

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

description: Streptomyces yangpuensis fd2-tb is an aerobe, spore-forming, Gram-positive bacterium that was isolated from soil.

NCBI tax id

  • NCBI tax id: 1648182
  • Matching level: species

strain history

  • @ref: 24221
  • history: <- B. Tang, Fudan University, Shanghai, China; fd2-tb

doi: 10.13145/bacdive132432.20230509.8.1

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 yangpuensis
  • full scientific name: Streptomyces yangpuensis Tang et al. 2016

@ref: 24221

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Streptomycetaceae

genus: Streptomyces

species: Streptomyces yangpuensis

full scientific name: Streptomyces yangpuensis Tang et al. 2016

strain designation: fd2-tb

type strain: yes

Morphology

cell morphology

@refgram stainmotilityconfidence
43758positiveno
69480no91.989
69480positive100

multimedia

  • @ref: 24221
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_100336.jpg
  • caption: Medium 65 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
24221ROLLED OATS MINERAL MEDIUM (DSMZ Medium 84)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium84.pdf
43758Gause's mediumyes
43758GYMyes
43758ISP 2yes
43758ISP 3yes
43758ISP 4yes
43758ISP 5no
43758ISP 6no
43758Nutrient agar (NA)no
24221GYM 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
43758positivegrowth10-40
43758positiveoptimum28-30mesophilic
24221positivegrowth28mesophilic

culture pH

  • @ref: 43758
  • ability: positive
  • type: growth
  • pH: 5-10
  • PH range: alkaliphile

Physiology and metabolism

oxygen tolerance

  • @ref: 43758
  • oxygen tolerance: aerobe

spore formation

@refspore descriptiontype of sporespore formationconfidence
43758Oval with a line pattern on their surfacesporeyes
69481yes100
69480yes100

halophily

@refsaltgrowthtested relationconcentration
43758NaClpositivegrowth0-4 %(w/v)
43758NaClpositiveoptimum0-2 %(w/v)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
4375815824D-fructose-carbon source
4375812936D-galactose-carbon source
4375830849L-arabinose-carbon source
4375817992sucrose-carbon source
4375828225D-leucine-nitrogen source
4375816449dl-alanine-nitrogen source
4375824898isoleucine-nitrogen source
4375817561L-cysteine-nitrogen source
4375815971L-histidine-nitrogen source
4375815603L-leucine-nitrogen source
4375816643L-methionine-nitrogen source
4375817203L-proline-nitrogen source
4375817115L-serine-nitrogen source
4375816857L-threonine-nitrogen source
4375817895L-tyrosine-nitrogen source
4375817057cellobiose+carbon source
4375817634D-glucose+carbon source
4375823652dextrin+carbon source
4375862345L-rhamnose+carbon source
4375817306maltose+carbon source
4375828017starch+carbon source
4375829016arginine+nitrogen source
4375815428glycine+nitrogen source
4375817196L-asparagine+nitrogen source

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitudeisolation date
24221soilShanghai, Yangpu district, Fudan University (31° 30' N 121° 51' E)ChinaCHNAsia31.5121.85
43758Soil collected from Fudan UniversityShanghai, Yangpu districtChinaCHNAsia31.5121.852013-09

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_1810.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15;96_102;97_109;98_144;99_1810&stattab=map
  • Last taxonomy: Streptomyces
  • 16S sequence: KP893387
  • Sequence Identity:
  • Total samples: 6072
  • soil counts: 4236
  • aquatic counts: 230
  • animal counts: 299
  • plant counts: 1307

Safety information

risk assessment

  • @ref: 24221
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 24221
  • description: Streptomyces sp. fd2-tb 16S ribosomal RNA gene, partial sequence
  • accession: KP893387
  • length: 1485
  • database: ena
  • NCBI tax ID: 1648182

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Streptomyces yangpuensis fd2-tbGCA_001005295scaffoldncbi1648182
66792Streptomyces yangpuensis fd2-tb2627853788draftimg1648182

GC content

@refGC-contentmethod
4375872genome sequence analysis
2422172sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileno94.757yes
flagellatedno97.429yes
gram-positiveyes88.196no
anaerobicno98.809yes
aerobicyes89.091no
halophileno95.18no
spore-formingyes93.293yes
thermophileno99.226no
glucose-utilyes88.174yes
glucose-fermentno87.436no

External links

@ref: 24221

culture collection no.: DSM 100336, CGMCC 4.7256

straininfo link

  • @ref: 90771
  • straininfo: 405620

literature

  • topic: Phylogeny
  • Pubmed-ID: 26703868
  • title: Streptomyces yangpuensis sp. nov., isolated from soil.
  • authors: Tang B, Yu Y, Zhi X, Yang L, Cen X, Zhao G, Ding X
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.000861
  • year: 2015

Reference

@idauthorstitledoi/urlcataloguejournalpubmed
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
24221Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-100336Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 100336)
43758Biao Tang, Yucong Yu, Xiaoyang Zhi, Lingling Yang, Xufeng Cen, Guoping Zhao, Xiaoming DingStreptomyces yangpuensis sp. nov., isolated from soil10.1099/ijsem.0.000861IJSEM 66: 1224-1229 201626703868
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
90771Reimer, 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-ID405620.1