Strain identifier

BacDive ID: 15311

Type strain: Yes

Species: Streptomyces hygroscopicus

Strain Designation: M5-13184

Strain history: CIP <- 2000, IFO <- Soc. Actinomycetes, Japan (SAJ) <- Ohio Wesleyan Univ., USA: strain ISP 5578

NCBI tax ID(s): 1912 (species)

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General

@ref: 9659

BacDive-ID: 15311

DSM-Number: 40578

keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, spore-forming, mesophilic, Gram-positive, antibiotic compound production

description: Streptomyces hygroscopicus M5-13184 is an obligate aerobe, spore-forming, mesophilic bacterium that produces antibiotic compounds.

NCBI tax id

  • NCBI tax id: 1912
  • Matching level: species

strain history

@refhistory
9659<- E.B. Shirling, ISP <- J.M. McGuire, Eli Lilly Res. Labs., M5-13184
67770KCC S-0772 <-- IFO 13472 <-- SAJ <-- ISP 5578 <-- Eli Lilly & Co.; M5-13184.
120019CIP <- 2000, IFO <- Soc. Actinomycetes, Japan (SAJ) <- Ohio Wesleyan Univ., USA: strain ISP 5578

doi: 10.13145/bacdive15311.20230509.8.1

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 hygroscopicus
  • full scientific name: Streptomyces hygroscopicus (Jensen 1931) Yüntsen et al. 1956 (Approved Lists 1980)

  • synonyms

    @refsynonym
    20215Actinomyces hygroscopicus
    20215Streptomyces hygroscopicus subsp. sporocinereus
    20215Streptomyces sporocinereus
    20215Streptomyces endus

@ref: 9659

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Streptomycetaceae

genus: Streptomyces

species: Streptomyces hygroscopicus subsp. hygroscopicus

full scientific name: Streptomyces hygroscopicus subsp. hygroscopicus (Jensen 1931) Yüntsen et al. 1956 emend. Komaki et al. 2017

strain designation: M5-13184

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480positive100
120019positivefilament-shapedno

colony morphology

  • @ref: 120019

pigmentation

  • @ref: 25185
  • production: no
  • name: melanin

multimedia

  • @ref: 9659
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_40578.jpg
  • caption: Medium 65 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
9659GYM 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
25185ISP 2 agaryes
25185ISP 3 agaryes
25185ISP 4 agaryes
25185ISP 5 agaryes
35999MEDIUM 116 - for Streptomyces, Nocardia, Streptosporangium and Mycobacterium chlorophenolicumyesDistilled water make up to (1000.000 ml);Agar (20.000 g);Glucose (4.000g);Yeast extract (4.000 g);Malt extract (10.000 g)
120019CIP Medium 116yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=116

culture temp

@refgrowthtypetemperaturerange
9659positivegrowth28mesophilic
25185positivegrowth15.0-45.0
35999positivegrowth30mesophilic
67770positivegrowth28mesophilic
120019positivegrowth25-41
120019nogrowth10psychrophilic
120019nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 120019
  • oxygen tolerance: obligate aerobe

spore formation

@reftype of sporespore formationconfidence
25185sporeyes
69481yes100
69480yes100

compound production

  • @ref: 9659
  • compound: hygromycin

halophily

@refsaltgrowthtested relationconcentration
120019NaClpositivegrowth0-4 %
120019NaClnogrowth6 %
120019NaClnogrowth8 %
120019NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
251856731melezitose-assimilation
2518516634raffinose-assimilation
2518517924D-sorbitol-assimilation
2518517632nitrate-reduction
2518515318xanthine-degradation
2518516708adenine+degradation
2518517057cellobiose+assimilation
2518515824D-fructose+assimilation
2518528847D-fucose+assimilation
2518512936D-galactose+assimilation
2518517634D-glucose+assimilation
2518516024D-mannose+assimilation
2518516988D-ribose+assimilation
2518565327D-xylose+assimilation
2518516235guanine+degradation
2518517368hypoxanthine+degradation
2518530849L-arabinose+assimilation
2518562345L-rhamnose+assimilation
2518517716lactose+assimilation
2518517306maltose+assimilation
2518529864mannitol+assimilation
2518517992sucrose+assimilation
2518553424tween 20+degradation
2518553426tween 80+degradation
1200194853esculin+hydrolysis
120019606565hippurate-hydrolysis
12001917632nitrate-reduction
12001916301nitrite-reduction
12001917632nitrate-respiration

antibiotic resistance

  • @ref: 120019
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

@refChebi-IDmetaboliteproduction
6777024753hygromycinyes
12001935581indoleno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12001915688acetoin-
12001917234glucose-

enzymes

@refvalueactivityec
120019oxidase-
120019beta-galactosidase+3.2.1.23
120019alcohol dehydrogenase-1.1.1.1
120019gelatinase+/-
120019amylase-
120019DNase+
120019caseinase+3.4.21.50
120019catalase+1.11.1.6
120019tween esterase+
120019gamma-glutamyltransferase+2.3.2.2
120019lecithinase-
120019lipase-
120019lysine decarboxylase-4.1.1.18
120019ornithine decarboxylase-4.1.1.17
120019phenylalanine ammonia-lyase-4.3.1.24
120019protease+
120019tryptophan deaminase-
120019urease+3.5.1.5

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
120019+++++----++++--++++++-+---+----+-++--+--++-++--++++--+++-+-++++-------+-++-+---++------+++++-++-++-

Isolation, sampling and environmental information

taxonmaps

  • @ref: 69479
  • File name: preview.99_359.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15;96_103;97_110;98_303;99_359&stattab=map
  • Last taxonomy: Streptomyces
  • 16S sequence: HQ244447
  • Sequence Identity:
  • Total samples: 834
  • soil counts: 635
  • aquatic counts: 65
  • animal counts: 94
  • plant counts: 40

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
96591Risk group (German classification)
1200191Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Streptomyces hygroscopicus subsp. hygroscopicus strain CGMCC 4.1527 16S ribosomal RNA gene, partial sequenceHQ2444471401ena68042
20218Streptomyces hygroscopicus subsp. hygroscopicus gene for 16S ribosomal RNA, partial sequence, strain: JCM 4772D44349121ena68042
20218Streptomyces hygroscopicus subsp. hygroscopicus gene for 16S rRNA, partial sequece, strain: PNK1-3AB2318031450ena68042
20218Streptomyces hygroscopicus subsp. hygroscopicus gene for 16S rRNA, partial sequece, strain: PNK1-5AB2318041451ena68042
20218Streptomyces hygroscopicus partial 16S rRNA gene, type strain NRRL 2387TAJ3918201465ena1912
9659Streptomyces hygroscopicus subsp. hygroscopicus gene for 16S rRNA, partial sequence, strain: NBRC 13472AB1844281470ena68042

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Streptomyces hygroscopicus subsp. hygroscopicus strain NBRC 1347268042.6wgspatric68042
66792Streptomyces hygroscopicus hygroscopicus NBRC 134722724679234draftimg68042
66792Streptomyces hygroscopicus hygroscopicus DSM 40578651716764draftimg68042
67770Streptomyces hygroscopicus subsp. hygroscopicus NBRC 13472GCA_001553455contigncbi68042

GC content

@refGC-contentmethod
2518572genome sequence analysis
965971.97sequence analysis
6777071.97genome sequence analysis
6777071.9thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
gram-positiveyes88.854no
anaerobicno99.109no
halophileno90.249no
spore-formingyes95.715yes
glucose-utilyes88.974yes
flagellatedno97.898no
thermophileno96.985no
aerobicyes93.35no
glucose-fermentno90.739no
motileno93.825no

External links

@ref: 9659

culture collection no.: DSM 40578, ATCC 27438, CBS 773.72, DSM 41148, ETH 28553, IFO 13472, ISP 5578, JCM 4772, NBRC 13472, NRRL 2387, RIA 1433, BCRC 11611, CGMCC 4.1313, CGMCC 4.1527, CGMCC 4.2118, CIP 106840, KACC 20099, LMG 19335, MTCC 1105, NBIMCC 1154, NBIMCC 803, VKM Ac-831

straininfo link

  • @ref: 84404
  • straininfo: 389289

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny7076575Cadeguomycin, a noval nucleoside analog antibiotic. I. The producing organism, production and isolation of cadeguomycin.Tanaka N, Wu RT, Okabe T, Yamashita H, Shimazu A, Nishimura TJ Antibiot (Tokyo)10.7164/antibiotics.35.2721982Anti-Bacterial Agents/*biosynthesis/isolation & purification/pharmacology, Cells, Cultured, Fermentation, Guanosine/analogs & derivatives/biosynthesis/isolation & purification/pharmacology, Streptomyces/classification/*metabolism, Thymidine/metabolism, Tubercidin/isolation & purificationEnzymology
Metabolism7688970Genetic relationships among actinomycetes that produce the immunosuppressant macrolides FK506, FK520/FK523 and rapamycin.Garrity GM, Heimbuch BK, Motamedi H, Shafiee AJ Ind Microbiol10.1007/BF015701271993Anti-Bacterial Agents/biosynthesis, Chromatography, Gas, DNA Probes, DNA, Bacterial/chemistry, Diaminopimelic Acid/metabolism, Fatty Acids/analysis, Genes, Bacterial, *Immunosuppressive Agents, Methyltransferases/genetics, Phenotype, *Polyenes, Sequence Homology, Nucleic Acid, Sirolimus, Streptomyces/classification/*genetics/metabolism, *Tacrolimus/analogs & derivativesPhenotype
Metabolism11976115Enzymatic synthesis of aminoglycoside antibiotics: novel adenosylmethionine:2-deoxystreptamine N-methyltransferase activities in hygromycin B- and spectinomycin-producing Streptomyces spp. and uses of the methylated products.Walker JBAppl Environ Microbiol10.1128/AEM.68.5.2404-2410.20022002Anti-Bacterial Agents/*biosynthesis, Carbon Radioisotopes, Hexosamines/metabolism, Hygromycin B/*metabolism, Methylation, Methyltransferases/*metabolism, Phosphorylation, Spectinomycin/*metabolism, Streptomyces/enzymology/*metabolism, Substrate Specificity, Transaminases/metabolismEnzymology
Pathogenicity22028855Lipoteichoic acid in Streptomyces hygroscopicus: structural model and immunomodulatory activities.Cot M, Ray A, Gilleron M, Vercellone A, Larrouy-Maumus G, Armau E, Gauthier S, Tiraby G, Puzo G, Nigou JPLoS One10.1371/journal.pone.00263162011Cytokines/biosynthesis, HEK293 Cells, Humans, Immunologic Factors/biosynthesis/*chemistry/isolation & purification/*pharmacology, Lipopolysaccharides/biosynthesis/*chemistry/isolation & purification/*pharmacology, *Models, Molecular, Signal Transduction/drug effects, Streptomyces/*chemistry/metabolism, Structure-Activity Relationship, Teichoic Acids/biosynthesis/*chemistry/isolation & purification/*pharmacology, Toll-Like Receptor 2/metabolismEnzymology
25191320An actinomycete isolate from solitary wasp mud nest having strong antibacterial activity and kills the Candida cells due to the shrinkage and the cytosolic loss.Kumar V, Naik B, Gusain O, Bisht GSFront Microbiol10.3389/fmicb.2014.004462014
Metabolism26448987[Storage of Actinobacteria of the Genera Streptomyces and Nonomuraea by Low Temperature Preservation].Sineva ON, Kulikova NG, Filippova SN, Terekhova LPAntibiot Khimioter2014Actinobacteria/*growth & development/metabolism, Cryopreservation/methods, Cryoprotective Agents/chemistry, Freezing, Preservation, Biological/*methods, Spores, Bacterial/growth & development, Streptomyces/growth & development/metabolism

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
9659Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 40578)https://www.dsmz.de/collection/catalogue/details/culture/DSM-40578
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
25185H. I. Komaki, N.,Oguchi, A.,Hamada, M.,Tamura, T.,Fujita, N.,Suzuki, K. I.10.1099/ijsem.0.001628Genome analysis-based reclassification of Streptomyces endus and Streptomyces sporocinereus as later heterotypic synonyms of Streptomyces hygroscopicus subsp. hygroscopicusIJSEM 67: 343-345 201727902297
35999Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/19015
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/
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
84404Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID389289.1StrainInfo: A central database for resolving microbial strain identifiers
120019Curators of the CIPCollection of Institut Pasteur (CIP 106840)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106840