Strain identifier

BacDive ID: 15454

Type strain: Yes

Species: Streptomyces parvulus

Strain history: KCC S-0068 <-- Y. Okami <-- NRRL B-1628 <-- S. A. Waksman IMRU 3677.

NCBI tax ID(s): 146923 (species)

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General

@ref: 9126

BacDive-ID: 15454

DSM-Number: 40048

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

description: Streptomyces parvulus DSM 40048 is a spore-forming, mesophilic bacterium that produces antibiotic compounds and was isolated from soil.

NCBI tax id

  • NCBI tax id: 146923
  • Matching level: species

strain history

@refhistory
9126<- E.B. Shirling, ISP <- S.A. Waksman, IMRU
67770KCC S-0068 <-- Y. Okami <-- NRRL B-1628 <-- S. A. Waksman IMRU 3677.

doi: 10.13145/bacdive15454.20230509.8.1

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 parvulus
  • full scientific name: Streptomyces parvulus corrig. Waksman and Gregory 1954 (Approved Lists 1980)

  • synonyms

    • @ref: 20215
    • synonym: Streptomyces parvullus

@ref: 9126

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Streptomycetaceae

genus: Streptomyces

species: Streptomyces parvulus

full scientific name: Streptomyces parvulus Waksman and Gregory 1954

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram stain
69480no92.169
69480100positive

multimedia

  • @ref: 9126
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_40048.jpg
  • caption: Medium 84 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
9126GYM 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
9126ROLLED OATS MINERAL MEDIUM (DSMZ Medium 84)yeshttps://mediadive.dsmz.de/medium/84Name: ROLLED OATS MINERAL MEDIUM (DSMZ Medium 84) Composition: Agar 20.0 g/l Rolled oats 20.0 g/l ZnSO4 x 7 H2O 0.001 g/l MnCl2 x 4 H2O 0.001 g/l FeSO4 x 7 H2O 0.001 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
18473positiveoptimum30mesophilic
9126positivegrowth28mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

tolerance

  • @ref: 18473
  • compound: Lysozyme
  • percentage: 0.1

spore formation

@refspore formationconfidence
69481yes100
69480yes100

compound production

@refcompound
9126actinomycin D
20216Actinomycin C1
20216Actinomycin D (Dactinomycin, Actinomycin1)

halophily

  • @ref: 18473
  • salt: NaCl
  • growth: positive
  • tested relation: maximum
  • concentration: 5 %

metabolite utilization

@refChebi-IDmetaboliteutilization activity
1847317234glucose+
1847322599arabinose+/-
1847317992sucrose-
1847318222xylose+
1847317268myo-inositol-
1847329864mannitol+
1847328757fructose+
1847326546rhamnose+
1847316634raffinose-
1847362968cellulose-

metabolite production

  • @ref: 67770
  • metabolite: actinomycin D
  • production: yes

Isolation, sampling and environmental information

isolation

@refsample type
9126soil
67770Soil

isolation source categories

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

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
184731German classification
91261Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Streptomyces parvulus gene for 16S rRNA, partial sequenceAB122767565ena146923
20218Streptomyces rochei gene for 16S ribosomal RNA, partial sequence, strain: JCM 4601D44257121ena1928
20218Streptomyces parvulus gene for 16S rRNA, partial sequence, strain: NBRC 13193AB1843261476ena146923
20218Streptomyces sp. NTRH11 gene for 16S ribosomal RNA, partial sequenceAB9205911286ena1571727

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Streptomyces parvulus JCM 4068GCA_014648855scaffoldncbi146923
66792Streptomyces parvulus strain JCM 4068146923.24wgspatric146923

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
flagellatedno98.171no
gram-positiveyes89.35no
anaerobicno99.387no
aerobicyes95.137no
halophileno91.797no
spore-formingyes95.16no
thermophileno98.565yes
glucose-utilyes89.749yes
motileno93.801no
glucose-fermentno88.948no

External links

@ref: 9126

culture collection no.: DSM 40048, ATCC 12434, ATCC 19796, CBS 548.68, ETH 12648, ETH 14318, IFO 13193, IMRU 3677, ISP 5048, JCM 4068, NBRC 13193, NCIMB 11240, NRRL B-1628, RIA 1075, RIA 307, BCRC 12046, CBS 418.59, CGMCC 4.0611, HUT 6081, ICMP 12845, ICMP 156, IMET 41380, JCM 4601, LMG 19312, RIA 507, VKM Ac-1063, VTT E-991419

straininfo link

  • @ref: 84542
  • straininfo: 13333

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny6369354Integrated DNA sequences in three streptomycetes form related autonomous plasmids after transfer to Streptomyces lividans.Hopwood DA, Hintermann G, Kieser T, Wright HMPlasmid10.1016/0147-619x(84)90002-71984Base Sequence, Chromosome Mapping, DNA, Bacterial/*genetics, Drug Resistance, Microbial, Escherichia coli/genetics, Nucleic Acid Hybridization, *Plasmids, Replicon, Species Specificity, Streptomyces/*genetics
9228745Electroporation of intact cells of Streptomyces parvulus and Streptomyces vinaceus.Mazy-Servais C, Baczkowski D, Dusart JFEMS Microbiol Lett10.1111/j.1574-6968.1997.tb12561.x1997*Electroporation, Muramidase/pharmacology, Polyethylene Glycols/pharmacology, Streptomyces/*genetics, *Transformation, Bacterial
Phylogeny20154329Streptomyces hyderabadensis sp. nov., an actinomycete isolated from soil.Reddy TVK, Mahmood S, Paris L, Reddy YHK, Wellington EMH, Idris MMInt J Syst Evol Microbiol10.1099/ijs.0.020446-02010Bacterial Typing Techniques, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, India, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Streptomyces/*classification/genetics/*isolation & purification/physiologyGenetics
Phylogeny24948949Production of polypeptide antibiotic from Streptomyces parvulus and its antibacterial activity.Shetty PR, Buddana SK, Tatipamula VB, Naga YV, Ahmad JBraz J Microbiol10.1590/S1517-838220140050000222014Anti-Bacterial Agents/chemistry/*isolation & purification/*pharmacology, Bacterial Typing Techniques, Chromatography, Liquid, Chromatography, Thin Layer, Cluster Analysis, DNA, Bacterial/chemistry/genetics, Geologic Sediments/microbiology, Gram-Negative Bacteria/drug effects, Gram-Positive Bacteria/drug effects, India, Magnetic Resonance Spectroscopy, Microbial Sensitivity Tests, Peptides/chemistry/*isolation & purification/*pharmacology, Phylogeny, RNA, Ribosomal/genetics, Sequence Analysis, DNA, Spectrophotometry, Ultraviolet, Spectroscopy, Fourier Transform Infrared, Streptomyces/isolation & purification/*metabolismEnzymology
Genetics27563047Complete Genome Sequence of Streptomyces parvulus 2297, Integrating Site-Specifically with Actinophage R4.Nishizawa T, Miura T, Harada C, Guo Y, Narisawa K, Ohta H, Takahashi H, Shirai MGenome Announc10.1128/genomeA.00875-162016
Metabolism28033726Optimization of desferrioxamine E production by Streptomyces parvulus.Gall T, Lehoczki G, Gyemant G, Emri T, Szigeti ZM, Balla G, Balla J, Pocsi IActa Microbiol Immunol Hung10.1556/030.63.2016.0292016Chromatography, High Pressure Liquid, Culture Media/chemistry/metabolism, Hydroxamic Acids/analysis/isolation & purification/*metabolism, Industrial Microbiology, Lactams/analysis/isolation & purification/*metabolism, Streptomyces/chemistry/*metabolismBiotechnology
Metabolism30058033Actinomycin-Producing Endophytic Streptomyces parvulus Associated with Root of Aloe vera and Optimization of Conditions for Antibiotic Production.Chandrakar S, Gupta AKProbiotics Antimicrob Proteins10.1007/s12602-018-9451-62019Aloe/*microbiology, Anti-Bacterial Agents/*metabolism/pharmacology, Culture Media/chemistry/metabolism, Dactinomycin/*analogs & derivatives/*metabolism/pharmacology, Endophytes/chemistry/genetics/isolation & purification/*metabolism, Microbial Sensitivity Tests, Plant Roots/microbiology, Pseudomonas aeruginosa/drug effects, Staphylococcus aureus/drug effects, Streptomyces/chemistry/genetics/isolation & purification/*metabolismEnzymology
Enzymology31654037Identification of actinomycin D as a specific inhibitor of the alternative pathway of peptidoglycan biosynthesis.Ogasawara Y, Shimizu Y, Sato Y, Yoneda T, Inokuma Y, Dairi TJ Antibiot (Tokyo)10.1038/s41429-019-0252-22019Anti-Bacterial Agents/isolation & purification/*pharmacology, Dactinomycin/isolation & purification/*pharmacology, Peptidoglycan/biosynthesis/*drug effects, Streptomyces/*metabolism, Xanthomonas/*drug effects/enzymologyPhylogeny

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
9126Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 40048)https://www.dsmz.de/collection/catalogue/details/culture/DSM-40048
18473Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM40048.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
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
84542Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID13333.1StrainInfo: A central database for resolving microbial strain identifiers