Strain identifier

BacDive ID: 16031

Type strain: Yes

Species: Streptomyces sulphureus

Strain Designation: Gasperini IPV 510

Strain history: KCC S-0085 <-- H. Yonehara <-- NRRL B-1627 <-- E. Baldacci.

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General

@ref: 9315

BacDive-ID: 16031

DSM-Number: 40104

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

description: Streptomyces sulphureus Gasperini IPV 510 is a spore-forming, mesophilic, Gram-positive bacterium that builds an aerial mycelium.

NCBI tax id

NCBI tax idMatching level
1123321strain
47758species

strain history

@refhistory
9315<- E.B. Shirling, ISP <- E. Baldacci, IPV 510 "strain Gasperini"
67770KCC S-0085 <-- H. Yonehara <-- NRRL B-1627 <-- E. Baldacci.

doi: 10.13145/bacdive16031.20230509.8.1

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 sulphureus
  • full scientific name: Streptomyces sulphureus (Gasperini 1894) Waksman 1953 (Approved Lists 1980)
  • synonyms

    • @ref: 20215
    • synonym: Actinomyces sulphureus

@ref: 9315

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Streptomycetaceae

genus: Streptomyces

species: Streptomyces sulphureus

full scientific name: Streptomyces sulphureus (Gasperini 1894) Waksman 1953 emend. Nouioui et al. 2018

strain designation: Gasperini IPV 510

type strain: yes

Morphology

cell morphology

  • @ref: 69480
  • gram stain: positive
  • confidence: 100

colony morphology

@refcolony colorincubation periodmedium used
19805Yellow brown10-14 daysISP 2
19805Brown10-14 daysISP 3
19805Yellow10-14 daysISP 4
19805Yellow10-14 daysISP 5
19805Yellow10-14 daysISP 6
19805Yellow10-14 daysISP 7

multicellular morphology

@refforms multicellular complexcomplex namecomplex colormedium name
19805yesAerial MyceliumYellowISP 2
19805yesAerial MyceliumYellowISP 3
19805yesAerial MyceliumYellowISP 4
19805yesAerial MyceliumYellowISP 5
19805yesAerial MyceliumYellowISP 6
19805yesAerial MyceliumYellowISP 7

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
9315GYM 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
19805ISP 2yesName: ISP 2 / Yeast Malt Agar (5265); 5265 Composition Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l Agar 15.0 g/l Preparation: Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.0 Usage: Maintenance and Taxonomy Organisms: All Actinomycetes
19805ISP 3yesName: ISP 3; 5315 Composition Dog oat flakes 20.0 g/l Trace element solution (5314) 2.5 ml/l Agar 18.0 g/l Preparation: Oat flakes are cooked for 20 minutes, trace element solution and agar are added (in the case of non rolled oat flakes the suspension has to bee filtrated). Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.8 Usage: Maintenance and taxonomy (e.g. SEM As liquid medium for metabolite production) Organisms: All Actinomycetes Trace element solution 5314 Name: Trace element solution 5314; 5314 Composition CaCl2 x H2O 3.0 g/l Fe-III-citrate 1.0 g/l MnSO4 0.2 g/l ZnCl2 0.1 g/l CuSO4 x 5 H2O 0.025 g/l Sodium tetra borate 0.2 g/l CoCl2 x 6 H2O 0.004 g/l Sodium molybdate 0.01 g/l Preparation: Use double destillated water. Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Trace element solution for different media Organisms:
19805ISP 4yesName: ISP 4; DSM 547 Solution I: Difco soluble starch, 10.0 g. Make a paste of the starch with a small amount of cold distilled water and bring to a volume of 500 ml. Solution II: CaCO3 2.0 g K2HPO4 (anhydrous) 1.0 g MgSO4 x 7 H2O 1.0 g NaCl 1.0 g (NH4)2SO4 2.0 g Distilled water 500.0 ml Trace salt solution (see below) 1.0 ml The pH should be between 7.0 and 7.4. Do not adjust if it is within this range. Mix solutions I and II together. Add 20.0 g agar. Liquify agar by steaming at 100°C for 10 to 20 min. Trace element solution: FeSO4 x 7 H2O 0.1 g MnCl2 x 4 H2O 0.1 g ZnSO4 x 7 H2O 0.1 g Distilled water 100.0 ml
19805ISP 5yesName: ISP 5 (5323) Composition L-Asparagine 1.0 g/l Glycerol 10.0 g/l K2HPO4 1.0 g/l Salt solution (see preparation) 1.0 ml/l Agar 20.0 g/l Preparation: Salt solution 1.0 g FeSO4 x 7 H2O 1.0 g MnCl2 x 4 H2O 1.0 g ZNSO4 x 7 H2O in 100 ml water Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.2 Usage: Maintenance and taxonomy Organisms: All Actinomycetes
19805ISP 6yesName: ISP 6 (5318) Composition Peptone 15.0 g/l Proteose peptose 5.0 g/l Ferric ammonium citrate 0.5 g/l Sodium glycerophosphate 1.0 g/l Sodium thiosulfate 0.08 g/l Yeast extract 1.0 g/l Agar 15.0 g/l Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigments Organisms: All Actinomycetes
19805ISP 7yesName: ISP 7 (5322) Composition Glycerol 15.0 g/l L-Tyrosine 0.5 g/l L-Asparagine 1.0 g/l K2HPO4 0.5 g/l NaCl 0.5 g/l FeSO4 x 7 H2O 0.01 g/l Trace element solution 5343 1.0 ml/l Agar 20.0 Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.3 Usage: Production of melanoid pigments Organisms: All Actinomycetes

culture temp

@refgrowthtypetemperaturerange
9315positivegrowth28mesophilic
19805positiveoptimum28mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

spore formation

@refspore descriptionspore formationconfidence
19805Formation of spore chains: spira, spore surface: smoothyes
69481yes100
69480yes100

halophily

  • @ref: 19805
  • salt: NaCl
  • growth: positive
  • tested relation: maximum
  • concentration: 5 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1980562968cellulose-
1980516634raffinose-
1980526546rhamnose+
1980528757fructose+
1980529864mannitol+
1980517268myo-inositol-
1980518222xylose+
1980517992sucrose-
1980522599arabinose+
1980517234glucose+
683685291gelatin+hydrolysis
6836827897tryptophan-energy source
6836816199urea-hydrolysis
6836816947citrate-assimilation
6836818257ornithine-degradation
6836825094lysine-degradation
6836829016arginine-hydrolysis

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinyes
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
19805---------++

Isolation, sampling and environmental information

taxonmaps

  • @ref: 69479
  • File name: preview.99_7562.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15;96_1755;97_4329;98_5542;99_7562&stattab=map
  • Last taxonomy: Streptomyces
  • 16S sequence: DQ442546
  • Sequence Identity:
  • Total samples: 2104
  • soil counts: 626
  • aquatic counts: 129
  • animal counts: 1133
  • plant counts: 216

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
93151Risk group (German classification)
198051Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Streptomyces sulphureus 16S-23S ribosomal RNA gene spacer, complete sequenceU93350300ena1123321
20218Streptomyces sulphureus gene for 16S ribosomal RNA, partial sequence, strain: JCM 4835D44397120ena1123321
20218Streptomyces sulphureus gene for 16S rRNA, partial sequence, strain: NBRC 13345AB2499651344ena1123321
20218Streptomyces sulphureus strain NRRL B-1627T 16S ribosomal RNA gene, partial sequenceDQ4425461418ena1123321

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Streptomyces sulphureus DSM 401041123321.3wgspatric1123321
66792Streptomyces sulphureus DSM 401042518645610draftimg1123321
67770Streptomyces sulphureus DSM 40104GCA_000381025scaffoldncbi1123321

GC content

  • @ref: 67770
  • GC-content: 71.7
  • method: genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileno94.389no
flagellatedno97.785no
gram-positiveyes90.978no
anaerobicno99.29no
aerobicyes94.634no
halophileno80.255no
spore-formingyes93.388yes
thermophileno94.053yes
glucose-utilyes89.848no
glucose-fermentno89.616no

External links

@ref: 9315

culture collection no.: DSM 40104, ATCC 27468, CBS 646.72, IFO 13345, ISP 5104, NBRC 13345, NRRL B-1627, RIA 1306, JCM 4085, BCRC 13764, CGMCC 4.0627, HUT 6080, IMET 40623, JCM 4835, LMG 19355, NRRL B-2195, VKM Ac-1820

straininfo link

  • @ref: 85104
  • straininfo: 13359

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Genetics22843605Draft genome sequence of the marine actinomycete Streptomyces sulphureus L180, isolated from marine sediment.Zhao X, Geng X, Chen C, Chen L, Jiao W, Yang CJ Bacteriol10.1128/JB.00900-122012China, DNA, Bacterial/*chemistry/*genetics, *Genome, Bacterial, Geologic Sediments/*microbiology, Molecular Sequence Data, RNA, Ribosomal, 16S/genetics, *Sequence Analysis, DNA, Streptomyces/classification/*genetics/isolation & purificationPhylogeny
Phylogeny23291896Streptomyces halophytocola sp. nov., an endophytic actinomycete isolated from the surface-sterilized stems of a coastal halophyte Tamarix chinensis Lour.Qin S, Bian GK, Tamura T, Zhang YJ, Zhang WD, Cao CL, Jiang JHInt J Syst Evol Microbiol10.1099/ijs.0.047456-02013Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Endophytes/classification/genetics/isolation & purification, Fatty Acids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/analysis, *Phylogeny, Plant Stems/microbiology, RNA, Ribosomal, 16S/genetics, Salt-Tolerant Plants/*microbiology, Sequence Analysis, DNA, Streptomyces/*classification/genetics/isolation & purification, Tamaricaceae/*microbiologyEnzymology
Phylogeny25488288Streptomyces xiaopingdaonensis sp. nov., a novel marine actinomycete isolated from the sediment of Xiaopingdao in Dalian, China.Chen C, Feng WW, Qin S, Zhao XQAntonie Van Leeuwenhoek10.1007/s10482-014-0347-52014Bacterial Typing Techniques, China, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Geologic Sediments/*microbiology, Microscopy, Electron, Scanning, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Streptomyces/*classification/genetics/*isolation & purification/physiologyGenetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
9315Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 40104)https://www.dsmz.de/collection/catalogue/details/culture/DSM-40104
19805Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM40104.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
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/
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
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
85104Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID13359.1StrainInfo: A central database for resolving microbial strain identifiers