Strain identifier

BacDive ID: 16485

Type strain: Yes

Species: Streptomyces indicus

Strain Designation: IH32-1

Strain history: CGMCC 4.5727 <-- Y. Luo et al. IH32-1.

NCBI tax ID(s): 417292 (species)

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General

@ref: 16602

BacDive-ID: 16485

DSM-Number: 42001

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

description: Streptomyces indicus IH32-1 is a spore-forming, mesophilic, Gram-positive bacterium that builds an aerial mycelium and was isolated from deep-sea sediment sample.

NCBI tax id

  • NCBI tax id: 417292
  • Matching level: species

strain history

@refhistory
16602<- J. Xu, Marine Biogenetic Resources, Third Inst. Oceanography, SOA, China; IH32-1 <- J. Xu and Y. Luo
67770CGMCC 4.5727 <-- Y. Luo et al. IH32-1.

doi: 10.13145/bacdive16485.20230509.8.1

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 indicus
  • full scientific name: Streptomyces indicus Luo et al. 2011

@ref: 16602

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Streptomycetaceae

genus: Streptomyces

species: Streptomyces indicus

full scientific name: Streptomyces indicus Luo et al. 2011

strain designation: IH32-1

type strain: yes

Morphology

cell morphology

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

colony morphology

@refcolony colormedium used
69319Beige (1001)suter with tyrosine
69319Ivory (1014)ISP 5
69319Ivory (1014)ISP 7
69319Light ivory (1015)ISP 3
69319Light ivory (1015)suter without tyrosine
69319Sand yellow (1002)ISP 4
69319Sand yellow (1002)ISP 6

multicellular morphology

@refforms multicellular complexcomplex namecomplex colormedium name
69319yesAerial myceliumPure white (9010)ISP 2
69319yesAerial myceliumPure white (9010)ISP 3
69319yesAerial myceliumPure white (9010)ISP 4
69319yesAerial myceliumSignal white (9003)ISP 5
69319noAerial myceliumISP 6
69319yesAerial myceliumLight ivory (1015)ISP 7
69319noAerial myceliumsuter with tyrosine
69319noAerial myceliumsuter without tyrosine

pigmentation

@refproductionnamecolor
69319noMelanin
69319yessoluble pigmentSand yellow (1002), ivory (1014)

multimedia

@refmultimedia contentcaptionintellectual property rights
69319DSM_42001_image3.jpegPlates (65, ISP2, ISP3, ISP4, ISP5, ISP7)Helmholtz-Zentrum für Infektionsforschung GmbH
69319DSM_42001_image4.jpegPlates (65, ISP2, ISP3, ISP4, ISP5, ISP7)Helmholtz-Zentrum für Infektionsforschung GmbH

Culture and growth conditions

culture temp

  • @ref: 67770
  • growth: positive
  • type: growth
  • temperature: 28
  • range: mesophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481yes100
69480yes100

halophily

  • @ref: 69319
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-7.5 %

observation

  • @ref: 67770
  • observation: quinones: MK-9(H6), MK-9(H4), MK-9(H8)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6931922599arabinose+growth
6931962968cellulose-growth
6931928757fructose+growth
6931917234glucose-growth
6931917268inositol+growth
6931937684mannose-growth
6931916634raffinose+/-growth
6931926546rhamnose+/-growth
6931917992sucrose+growth
6931918222xylose+growth
6837917632nitrate+reduction
683794853esculin+hydrolysis
6837916199urea+hydrolysis
683795291gelatin+hydrolysis
6837917634D-glucose+fermentation
6837916988D-ribose-fermentation
6837965327D-xylose-fermentation
6837916899D-mannitol-fermentation
6837917306maltose-fermentation
6837917716lactose-fermentation
6837917992sucrose-fermentation
6837928087glycogen-fermentation

enzymes

@refvalueactivityec
68379gelatinase+
68379urease+3.5.1.5
68379beta-glucosidase+3.2.1.21
68379N-acetyl-beta-glucosaminidase+3.2.1.52
68379alpha-glucosidase+3.2.1.20
68379beta-galactosidase+3.2.1.23
68379beta-glucuronidase-3.2.1.31
68379alkaline phosphatase+3.1.3.1
68379pyrrolidonyl arylamidase-3.4.19.3
68379pyrazinamidase-3.5.1.B15
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase+
68382cystine arylamidase-3.4.11.3
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 coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
69319+--+-+++++++-------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
69319+++/--++-+/--++++-++++-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitude
16602deep-sea (2434 m) sediment sampleIndian Ocean (25.3206° S, 70.0402° E)IndiaINDAsia-25.320670.0402
67770Deep-sea sediment from the Indian Ocean

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Marine
#Environmental#Aquatic#Sediment

Safety information

risk assessment

  • @ref: 16602
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 16602
  • description: Streptomyces indicus strain IH32-1 16S ribosomal RNA gene, partial sequence
  • accession: EF157833
  • length: 1488
  • database: ena
  • NCBI tax ID: 417292

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Streptomyces indicus strain CGMCC 4.5727417292.4wgspatric417292
66792Streptomyces indicus CGMCC 4.57272675903130draftimg417292
67770Streptomyces indicus CGMCC 4.5727GCA_900100315scaffoldncbi417292

GC content

@refGC-contentmethod
1660271.3high performance liquid chromatography (HPLC)
6777071.4genome sequence analysis
6777070.3-72.3high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
gram-positiveyes88.807no
anaerobicno99.385no
halophileno91.364no
spore-formingyes94.89no
glucose-utilyes87.052yes
aerobicyes90.484no
flagellatedno97.439no
motileno90.034no
thermophileno98.814yes
glucose-fermentno80.203yes

External links

@ref: 16602

culture collection no.: DSM 42001, CGMCC 4.5727, MCCC IA03308, JCM 18323

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny21169463Streptomyces indicus sp. nov., an actinomycete isolated from deep-sea sediment.Luo Y, Xiao J, Wang Y, Xu J, Xie S, Xu JInt J Syst Evol Microbiol10.1099/ijs.0.029389-02010DNA, Bacterial/genetics, Fatty Acids/metabolism, Geologic Sediments/*microbiology, Indian Ocean, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Streptomyces/*classification/genetics/*isolation & purification/metabolismMetabolism
Phylogeny33666547Streptomyces ureilyticus sp. nov. and Streptomyces mesophilus sp. nov., two novel Actinobacteria with antimicrobial activity isolated from lake sediment.Tokatli A, Idil O, Saygin H, Sahin NInt J Syst Evol Microbiol10.1099/ijsem.0.0047382021
Phylogeny33738648Streptomyces polyasparticus sp. nov. isolated from cotton field soil by a medium applied with polyaspartic acid.Liu W, Zeng H, Xia Z, Luo X, Zhang L, Wan CAntonie Van Leeuwenhoek10.1007/s10482-021-01557-z2021Bacterial Typing Techniques, DNA, Bacterial/genetics, Fatty Acids/analysis, Peptides, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil, Soil Microbiology, *Streptomyces/geneticsTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
16602Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 42001)https://www.dsmz.de/collection/catalogue/details/culture/DSM-42001
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
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68379Automatically annotated from API Coryne
68382Automatically annotated from API zym
69319Wink, J.https://cdn.dsmz.de/wink/DSM%2042001.pdfCompendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig
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