Strain identifier

BacDive ID: 15293

Type strain: Yes

Species: Streptomyces hiroshimensis

Strain Designation: 201

Strain history: CIP <- 2003, JCM <- 1983, KCC <- R. Shinobu: strain 201

NCBI tax ID(s): 66424 (species)

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General

@ref: 9116

BacDive-ID: 15293

DSM-Number: 40037

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

description: Streptomyces hiroshimensis 201 is an obligate aerobe, spore-forming, mesophilic bacterium that builds an aerial mycelium and was isolated from soil.

NCBI tax id

  • NCBI tax id: 66424
  • Matching level: species

strain history

@refhistory
9116<- E.B. Shirling, ISP <- R. Shinobu, OEU, 201
67770KCC S-0098 <-- R. Shinobu 201.
119910CIP <- 2003, JCM <- 1983, KCC <- R. Shinobu: strain 201

doi: 10.13145/bacdive15293.20230509.8.1

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 hiroshimensis
  • full scientific name: Streptomyces hiroshimensis (Shinobu 1955) Witt and Stackebrandt 1991

  • synonyms

    @refsynonym
    20215Actinomyces biverticillatus
    20215Actinomyces rectiverticillatus
    20215Streptomyces fervens
    20215Streptomyces hiroshimensis
    20215Streptoverticillium salmonicida
    20215Streptoverticillium fervens
    20215Streptoverticillium hiroshimense
    20215Streptoverticillium roseoverticillatum
    20215Streptoverticillium rectiverticillatum
    20215Streptomyces roseoverticillatus
    20215Streptomyces spitsbergensis
    20215Streptoverticillium aureoversales
    20215Streptoverticillium fervens subsp. melrosporus
    20215Streptoverticillium aureoversile
    20215Streptoverticillium salmonis
    20215Streptoverticillium biverticillatum
    20215Streptomyces aureoversales
    20215Streptomyces biverticillatus
    20215Streptomyces fervens subsp. melrosporus
    20215Streptomyces salmonis
    20215Streptomyces aureoversilis
    20215Streptomyces rectiverticillatus

@ref: 9116

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Streptomycetaceae

genus: Streptomyces

species: Streptomyces hiroshimensis

full scientific name: Streptomyces hiroshimensis (Shinobu 1955) Witt and Stackebrandt 1991

strain designation: 201

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480no93.936
69480100positive
119910nopositiverod-shaped

colony morphology

@refcolony colorincubation periodmedium usedhemolysis ability
19391Red10-14 daysISP 2
19391Red10-14 daysISP 3
19391Red10-14 daysISP 4
19391Red10-14 daysISP 5
19391Red10-14 daysISP 6
19391Red10-14 daysISP 7
1199101

multicellular morphology

@refforms multicellular complexcomplex namecomplex colormedium name
19391yesAerial MyceliumWhiteISP 2
19391yesAerial MyceliumRoseISP 3
19391yesAerial MyceliumRedISP 4
19391yesAerial MyceliumWhiteISP 5
19391yesAerial MyceliumWhiteISP 6
19391yesAerial MyceliumWhiteISP 7

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
9116GYM 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
19391ISP 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
19391ISP 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:
19391ISP 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
19391ISP 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
19391ISP 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
19391ISP 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
37416MEDIUM 57 - for Streptomyces, Nocardioides, Lentzea albidocapillata and Streptoverticillium reticulumyesDistilled water make up to (1000.000 ml);Agar (15.000 g);Glucose (4.000g);Yeast extract (4.000 g);Malt extract (10.000 g);Calcium carbonate (2.000 g)
9116ROLLED 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
119910CIP Medium 57yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=57

culture temp

@refgrowthtypetemperaturerange
19391positiveoptimum28mesophilic
9116positivegrowth28mesophilic
37416positivegrowth30mesophilic
67770positivegrowth28mesophilic
119910positivegrowth10-37
119910nogrowth41thermophilic
119910nogrowth45thermophilic

Physiology and metabolism

tolerance

  • @ref: 19391
  • compound: Lysozyme
  • percentage: 1

oxygen tolerance

  • @ref: 119910
  • oxygen tolerance: obligate aerobe

spore formation

@refspore descriptionspore formationconfidence
19391Formation of spore chains: Verticillus, spore surface: smoothyes
69481yes100
69480yes100

halophily

@refsaltgrowthtested relationconcentration
19391NaClpositivemaximum2.5 %
119910NaClpositivegrowth0-2 %
119910NaClnogrowth4 %
119910NaClnogrowth6 %
119910NaClnogrowth8 %
119910NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1939162968cellulose-
1939116634raffinose-
1939126546rhamnose-
1939128757fructose-
1939129864mannitol-
1939117268myo-inositol-
1939118222xylose-
1939117992sucrose-
1939122599arabinose-
1939117234glucose+
683685291gelatin-hydrolysis
6836827897tryptophan-energy source
6836816199urea-hydrolysis
6836816947citrate-assimilation
6836818257ornithine-degradation
6836825094lysine-degradation
6836829016arginine-hydrolysis
11991016947citrate-carbon source
1199104853esculin+hydrolysis
11991017632nitrate-reduction
11991016301nitrite-reduction
11991017632nitrate-respiration

antibiotic resistance

  • @ref: 119910
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinno
6836835581indoleno
6836816136hydrogen sulfideno
11991035581indoleno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole testmethylred-test
6836815688acetoin-
6836835581indole-
11991015688acetoin-
11991017234glucose-

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
119910oxidase-
119910beta-galactosidase-3.2.1.23
119910alcohol dehydrogenase-1.1.1.1
119910gelatinase+/-
119910amylase+
119910DNase-
119910caseinase-3.4.21.50
119910catalase+1.11.1.6
119910tween esterase+
119910lecithinase+
119910lipase-
119910lysine decarboxylase-4.1.1.18
119910ornithine decarboxylase-4.1.1.17
119910phenylalanine ammonia-lyase-4.3.1.24
119910tryptophan deaminase-
119910urease-3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase-
68382cystine arylamidase-3.4.11.3
68382trypsin-3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase-3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase-3.2.1.20
68382beta-glucosidase-3.2.1.21
68382N-acetyl-beta-glucosaminidase+3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
119910-+++-+----++-----+--

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
19391-----------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
119910+--++----++--------+-----------++---------------+++--+-----+++----------++-+---++---+---++++++--+-+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
9116soil
67770SoilHiroshimaJapanJPNAsia
119910Environment, SoilHiroshimaJapanJPNAsia

isolation source categories

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

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
91161Risk group (German classification)
193911Risk group (German classification)
1199101Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Streptomyces hiroshimensis strain CGMCC 4.1948 16S ribosomal RNA gene, partial sequenceHQ2444591488ena66424
20218Streptomyces hiroshimensis gene for 16S ribosomal RNA, partial sequence, strain: JCM 4098D44005120ena66424
20218Streptomyces hiroshimensis gene for 16S rRNA, partial sequence, strain: NBRC 12785AB1841441429ena66424
20218Streptomyces hiroshimensis strain NBRC 12785 16S ribosomal RNA gene, partial sequenceJN5660331488ena66424
20218Streptomyces hiroshimensis gene for 16S rRNA, partial sequence, strain: NBRC 3720AB1847891467ena66424
20218Streptomyces hiroshimensis gene for 16S rRNA, partial sequence, strain: NBRC 3839AB1848021454ena66424
20218Streptomyces hiroshimensis strain NRRL B-1823 16S ribosomal RNA gene, partial sequenceEF1786771325ena66424

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Streptomyces hiroshimensis JCM 4586GCA_014650335scaffoldncbi66424
66792Streptomyces hiroshimensis strain JCM 458666424.5wgspatric66424

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
flagellatedno97.906no
gram-positiveyes89.186no
anaerobicno99.301no
aerobicyes92.211no
halophileno93.163no
spore-formingyes94.55yes
glucose-utilyes89.941yes
thermophileno98.184yes
motileno92.963no
glucose-fermentno90.611no

External links

@ref: 9116

culture collection no.: DSM 40037, ATCC 19772, CBS 510.68, IFO 12785, ISP 5037, KCC S-0098, KCC S-0586, NBRC 12785, NRRL B-1823, RIA 1052, OEU 201, JCM 4098, BCRC 13375, CECT 3261, CGMCC 4.1948, CIP 108157, HUT 6033, IFO 3839, IMET 43546, JCM 4586, KCTC 9781, NBRC 3839, NCIMB 9838, NRRL B-5484, RIA 592, VKM Ac-902, CCRC 13375

straininfo link

  • @ref: 84387
  • straininfo: 38289

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Enzymology12132653A novel protein with alkaline phosphatase and protease inhibitor activities in Streptomyces hiroshimensis.Nitta M, Goto M, Shibuya N, Okawa YBiol Pharm Bull10.1248/bpb.25.8332002Alkaline Phosphatase/chemistry/*isolation & purification/pharmacology, Amino Acid Sequence, Bacterial Proteins/chemistry/*isolation & purification/pharmacology, Catalysis, Chromatography, Gel, Electrophoresis, Polyacrylamide Gel, Isoelectric Point, Molecular Sequence Data, Molecular Weight, Protease Inhibitors/chemistry/*isolation & purification/pharmacology, Streptomyces/*chemistry/growth & development, Substrate Specificity, Subtilisin/antagonists & inhibitors, Trypsin Inhibitors/chemistry/isolation & purification/pharmacologyPhylogeny
Phylogeny25030519Streptomyces zagrosensis sp. nov., isolated from soil.Mohammadipanah F, Hamedi J, Sproer C, Rohde M, Montero-Calasanz MDC, Klenk HPInt J Syst Evol Microbiol10.1099/ijs.0.064527-02014Bacterial Typing Techniques, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Iran, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhizosphere, Sequence Analysis, DNA, *Soil Microbiology, Streptomyces/*classification/genetics/isolation & purificationGenetics
Phylogeny28005217Streptomyces gamaensis sp. nov., a novel actinomycete with antifungal activity isolated from soil in Gama, Chad.Zhao S, Ye L, Liu C, Abagana AY, Zheng W, Sun P, Li J, Xiang W, Wang XAntonie Van Leeuwenhoek10.1007/s10482-016-0816-02016Antifungal Agents/*metabolism, Chad, Fungi/*drug effects, Microbial Sensitivity Tests, RNA, Ribosomal, 16S/genetics, *Soil Microbiology, Streptomyces/genetics/isolation & purification/*metabolismMetabolism
Phylogeny30625109Polyphasic classification of the gifted natural product producer Streptomyces roseifaciens sp. nov.van der Aart LT, Nouioui I, Kloosterman A, Igual JM, Willemse J, Goodfellow M, van Wezel GPInt J Syst Evol Microbiol10.1099/ijsem.0.0032152019Bacterial Typing Techniques, Base Composition, Biological Products, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Genes, Bacterial, Multilocus Sequence Typing, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Streptomyces/*classification/isolation & purification, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
9116Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 40037)https://www.dsmz.de/collection/catalogue/details/culture/DSM-40037
19391Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM40037.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
37416Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5748
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
68382Automatically annotated from API zym
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
84387Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID38289.1StrainInfo: A central database for resolving microbial strain identifiers
119910Curators of the CIPCollection of Institut Pasteur (CIP 108157)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108157