Strain identifier

BacDive ID: 15054

Type strain: Yes

Species: Streptomyces bobili

Strain history: KCC S-0012 <-- T. Yamaguchi (IAM 0002) <-- ATU <-- ATCC 3310 <-- IMRU 3310.

NCBI tax ID(s): 67280 (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: 9239

BacDive-ID: 15054

DSM-Number: 40056

keywords: genome sequence, 16S sequence, Bacteria, mesophilic

description: Streptomyces bobili DSM 40056 is a mesophilic bacterium that was isolated from adobe, garden soil.

NCBI tax id

  • NCBI tax id: 67280
  • Matching level: species

strain history

@refhistory
9239<- E.B. Shirling, ISP <- S.A. Waksman
67770KCC S-0012 <-- T. Yamaguchi (IAM 0002) <-- ATU <-- ATCC 3310 <-- IMRU 3310.

doi: 10.13145/bacdive15054.20230509.8.1

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 bobili
  • full scientific name: Streptomyces bobili (Waksman and Curtis 1916) Waksman and Henrici 1948 (Approved Lists 1980)

  • synonyms

    @refsynonym
    20215Streptomyces galilaeus
    20215Actinomyces bobili

@ref: 9239

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Streptomycetaceae

genus: Streptomyces

species: Streptomyces bobili

full scientific name: Streptomyces bobili (Waksman and Curtis 1916) Waksman and Henrici 1948

type strain: yes

Morphology

multimedia

  • @ref: 9239
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_40056.jpg
  • caption: Medium 65 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
9239GYM 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
9239ROLLED OATS MINERAL MEDIUM (DSMZ Medium 84)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium84.pdf

culture temp

@refgrowthtypetemperaturerange
18475positiveoptimum28mesophilic
9239positivegrowth28mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

compound production

@refcompound
9239cinerubin-like antibiotic
9239restriction endonuclease SboI
20216Cinerubin-like antibiotic

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1847517234glucose+
1847522599arabinose+
1847517992sucrose+
1847518222xylose+
1847517268myo-inositol+
1847529864mannitol-
1847528757fructose+
1847526546rhamnose+
1847516634raffinose+
1847562968cellulose+
683685291gelatin-hydrolysis
6836827897tryptophan-energy source
6836816199urea-hydrolysis
6836816947citrate-assimilation
6836818257ornithine-degradation
6836825094lysine+degradation
6836829016arginine-hydrolysis

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinno
6836835581indoleno
6836816136hydrogen sulfideno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole test
6836815688acetoin-
6836835581indole-

enzymes

@refvalueactivityec
68368gelatinase-
68368tryptophan deaminase+4.1.99.1
68368urease-3.5.1.5
68368ornithine decarboxylase-4.1.1.17
68368lysine decarboxylase+4.1.1.18
68368arginine dihydrolase-3.5.3.6
68368beta-galactosidase+3.2.1.23

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
18475+-+----+---

Isolation, sampling and environmental information

isolation

  • @ref: 9239
  • sample type: adobe, garden soil

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_1501.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15;96_102;97_109;98_118;99_1501&stattab=map
  • Last taxonomy: Streptomyces
  • 16S sequence: AB249925
  • Sequence Identity:
  • Total samples: 802
  • soil counts: 664
  • aquatic counts: 35
  • animal counts: 54
  • plant counts: 49

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
92391Risk group (German classification)
184751German classification

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Streptomyces bobili gene for 16S ribosomal RNA, partial sequence, strain: JCM 4627D44274120ena67280
20218Streptomyces bobili gene for 16S rRNA, partial sequence, strain: NBRC 13199AB1843281475ena67280
20218Streptomyces bobili gene for 16S rRNA, partial sequence, strain: NBRC 16166AB2499251451ena67280

Genome sequences

  • @ref: 67770
  • description: Streptomyces bobili NRRL B-1338
  • accession: GCA_002154575
  • assembly level: scaffold
  • database: ncbi
  • NCBI tax ID: 67280

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
flagellatedno97.578no
gram-positiveyes89.43no
anaerobicno99.32no
halophileno95.752no
spore-formingyes93.982no
glucose-utilyes88.449no
aerobicyes92.985no
thermophileno99.107yes
glucose-fermentno90.785no
motileno93.451no

External links

@ref: 9239

culture collection no.: DSM 40056, ATCC 23889, ATCC 3310, CBS 675.68, IFO 13199, IMRU 3310, ISP 5056, NBRC 13199, RIA 1116, JCM 4012, BCRC 13671, CBS 419.34, CGMCC 4.1624, IFO 16166, IMET 41372, JCM 4627, NBRC 16166, NRRL B-1338, NRRL B-2097, VKM Ac-1756

straininfo link

  • @ref: 84160
  • straininfo: 92661

literature

  • topic: Phylogeny
  • Pubmed-ID: 27298302
  • title: Streptomyces rhizosphaerihabitans sp. nov. and Streptomyces adustus sp. nov., isolated from bamboo forest soil.
  • authors: Lee HJ, Whang KS
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.001236
  • year: 2016
  • mesh: Bacterial Typing Techniques, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Forests, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sasa/*microbiology, Sequence Analysis, DNA, *Soil Microbiology, Streptomyces/*classification/genetics/isolation & purification, Vitamin K 2/analogs & derivatives/chemistry
  • topic2: Transcriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
9239Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 40056)https://www.dsmz.de/collection/catalogue/details/culture/DSM-40056
18475Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM40056.pdfCompendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig
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
20216Curators of the HKIhttp://www.leibniz-hki.de/de/Collection Description Leibniz-Institut für Naturstoff-Forschung und Infektionsbiologie e. V. Hans-Knöll-Institut (HKI)
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
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68368Automatically annotated from API 20E
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
84160Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID92661.1StrainInfo: A central database for resolving microbial strain identifiers