Strain identifier

BacDive ID: 15419

Type strain: Yes

Species: Streptomyces naganishii

Strain Designation: H-4871

Strain history: KCC S-0190 <-- H. Yonehara <-- T. Yamaguchi H-4871.

NCBI tax ID(s): 1306179 (strain), 285447 (species)

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General

@ref: 9433

BacDive-ID: 15419

DSM-Number: 40282

keywords: genome sequence, 16S sequence, Bacteria, spore-forming, mesophilic

description: Streptomyces naganishii H-4871 is a spore-forming, mesophilic bacterium that was isolated from soil.

NCBI tax id

NCBI tax idMatching level
1306179strain
285447species

strain history

@refhistory
9433<- E.B. Shirling, ISP <- T. Yamaguchi, H-4871
67770KCC S-0190 <-- H. Yonehara <-- T. Yamaguchi H-4871.

doi: 10.13145/bacdive15419.20230509.8.1

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 naganishii
  • full scientific name: Streptomyces naganishii Yamaguchi and Saburi 1955 (Approved Lists 1980)

@ref: 9433

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Streptomycetaceae

genus: Streptomyces

species: Streptomyces naganishii

full scientific name: Streptomyces naganishii Yamaguchi and Saburi 1955

strain designation: H-4871

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram stain
69480no92.222
6948099.719positive

multimedia

  • @ref: 9433
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_40282.jpg
  • caption: Medium 65 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

  • @ref: 9433
  • 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
9433positivegrowth28mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481yes100
69480no98.804

Isolation, sampling and environmental information

isolation

  • @ref: 9433
  • sample type: soil
  • country: Japan
  • origin.country: JPN
  • continent: Asia

isolation source categories

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

Safety information

risk assessment

  • @ref: 9433
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Streptomyces naganishii gene for 16S rRNA, partial sequence, strain: NBRC 12892AB1842241472ena1306179
20218Streptomyces naganishii strain NRRL B-1816T 16S ribosomal RNA gene, partial sequenceDQ4425291501ena1306179

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Streptomyces naganishii JCM 4654GCA_014650575contigncbi1306179
66792Streptomyces naganishii JCM 4654GCA_001315425contigncbi1306179
66792Streptomyces naganishii JCM 46541306179.6wgspatric1306179
66792Streptomyces naganishii JCM 46541306179.5wgspatric1306179
66792Streptomyces naganishii JCM 46542734481987draftimg1306179

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileno94.578no
gram-positiveyes89.971no
anaerobicno98.56no
halophileno94.936no
spore-formingyes94.9no
thermophileno98.281yes
glucose-utilyes87.976no
aerobicyes85.42no
flagellatedno98.34no
glucose-fermentno89.882no

External links

@ref: 9433

culture collection no.: DSM 40282, ATCC 23939, CBS 923.68, IFO 12892, ISP 5282, NBRC 12892, RIA 1196, JCM 4190, BCRC 15130, JCM 4654, NRRL B-1816

straininfo link

  • @ref: 84507
  • straininfo: 389333

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny29624162Streptomyces boninensis sp. nov., isolated from soil from a limestone cave in the Ogasawara Islands.Take A, Inahashi Y, Omura S, Takahashi Y, Matsumoto AInt J Syst Evol Microbiol10.1099/ijsem.0.0027532018Bacterial Typing Techniques, Base Composition, *Calcium Carbonate, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, *Islands, Japan, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Streptomyces/*classification/genetics/isolation & purification, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny31613740Streptomyces triticagri sp. nov. and Streptomyces triticirhizae sp. nov., two novel Actinobacteria isolated from the rhizosphere soil of wheat (Triticum aestivum L.).Han C, Yu Z, Zhao J, Shi H, Hu J, Yu B, Song J, Shen Y, Xiang W, Wang XInt J Syst Evol Microbiol10.1099/ijsem.0.0037272020Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Genes, Bacterial, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, *Rhizosphere, Sequence Analysis, DNA, *Soil Microbiology, Streptomyces/*classification/isolation & purification, Triticum/*microbiologyTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
9433Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 40282)https://www.dsmz.de/collection/catalogue/details/culture/DSM-40282
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/
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
84507Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID389333.1StrainInfo: A central database for resolving microbial strain identifiers