Strain identifier

BacDive ID: 16142

Type strain: Yes

Species: Streptomyces abikoensis

Strain Designation: AS-803

Strain history: CIP <- 2003, JCM <- 1983, KCC <- H. Yonehara, IAM <- Y. Okami Z-1-6

NCBI tax ID(s): 97398 (species)

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General

@ref: 9834

BacDive-ID: 16142

DSM-Number: 40831

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

description: Streptomyces abikoensis AS-803 is an obligate aerobe, spore-forming, mesophilic bacterium that builds an aerial mycelium and produces antibiotic compounds.

NCBI tax id

  • NCBI tax id: 97398
  • Matching level: species

strain history

@refhistory
9834<- H.D. Tresner, AS-803
67770KCC S-0002 <-- H. Yonehara (IAM 0001) <-- Y. Okami Z-1-6.
115976CIP <- 2003, JCM <- 1983, KCC <- H. Yonehara, IAM <- Y. Okami Z-1-6

doi: 10.13145/bacdive16142.20230509.8.1

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 abikoensis
  • full scientific name: Streptomyces abikoensis corrig. Umezawa et al. 1951

  • synonyms

    @refsynonym
    20215Streptoverticillium luteoverticillatum
    20215Streptomyces olivoreticuli
    20215Streptoverticillium olivoreticulum subsp. cellulophilum
    20215Streptomyces abikoensum
    20215Streptomyces abikoensis
    20215Streptomyces luteoverticillatus
    20215Streptomyces parvisporogenes
    20215Streptoverticillium abikoense
    20215Streptoverticillium olivoreticuli
    20215Streptoverticillium parvisporogenum
    20215Streptoverticillium olivoreticuli subsp. cellulophilum
    20215Streptoverticillium ehimense
    20215Streptoverticillium parvisporogenes
    20215Streptoverticillium olivoreticulum
    20215Streptomyces ehimensis
    20215Streptomyces ekimensis

@ref: 9834

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Streptomycetaceae

genus: Streptomyces

species: Streptomyces abikoensis

full scientific name: Streptomyces abikoensis (Umezawa et al. 1951) Witt and Stackebrandt 1991

strain designation: AS-803

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480no94.298
69480100positive
115976nopositiverod-shaped

colony morphology

@refcolony colorincubation periodmedium usedhemolysis ability
18678Brown10-14 daysISP 2
18678Brown10-14 daysISP 3
18678Brown10-14 daysISP 4
18678Brown10-14 daysISP 5
18678Brown10-14 daysISP 6
18678Brown10-14 daysISP 7
1159761

multicellular morphology

@refforms multicellular complexcomplex namecomplex colormedium name
18678yesAerial MyceliumLight grey (7035)ISP 2
18678yesAerial MyceliumWhiteISP 3
18678yesAerial MyceliumWhiteISP 4
18678yesAerial MyceliumISP 5
18678noISP 6
18678yesAerial MyceliumWhiteISP 7

multimedia

  • @ref: 9834
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_40831.jpg
  • caption: Medium 65 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
9834GYM 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
18678ISP 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
18678ISP 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:
18678ISP 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
18678ISP 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
18678ISP 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
18678ISP 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
38258MEDIUM 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)
9834ROLLED OATS MINERAL MEDIUM (DSMZ Medium 84)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium84.pdf
115976CIP Medium 57yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=57

culture temp

@refgrowthtypetemperaturerange
9834positivegrowth28mesophilic
18678positiveoptimum28mesophilic
38258positivegrowth30mesophilic
67770positivegrowth28mesophilic
115976positivegrowth25-45
115976nogrowth10psychrophilic

Physiology and metabolism

tolerance

  • @ref: 18678
  • compound: Lysozyme
  • percentage: 1

oxygen tolerance

  • @ref: 115976
  • oxygen tolerance: obligate aerobe

spore formation

@refspore descriptionspore formationconfidence
18678Formation of spore chains (verticillati)(Ve), spore surface smoothyes
69481yes100
69480yes100

compound production

  • @ref: 9834
  • compound: abikoviromycin

halophily

@refsaltgrowthtested relationconcentration
18678NaClpositivemaximum5 %
115976NaClpositivegrowth0-2 %
115976NaClnogrowth4 %
115976NaClnogrowth6 %
115976NaClnogrowth8 %
115976NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1867817234glucose+
1867822599arabinose-
1867817992sucrose-
1867818222xylose-
1867817268myo-inositol+
1867829864mannitol+
1867828757fructose+
1867826546rhamnose-
1867816634raffinose-
1867862968cellulose-
683685291gelatin+hydrolysis
6836827897tryptophan-energy source
6836816199urea-hydrolysis
6836816947citrate-assimilation
6836818257ornithine-degradation
6836825094lysine-degradation
6836829016arginine-hydrolysis
11597616947citrate-carbon source
1159764853esculin-hydrolysis
115976606565hippurate+hydrolysis
11597617632nitrate-reduction
11597616301nitrite-reduction
11597617632nitrate-respiration

metabolite production

@refmetaboliteproductionChebi-ID
67770abikoviromycinyes
68368acetoinyes15688
68368indoleno35581
68368hydrogen sulfideyes16136
115976indoleno35581

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole testmethylred-test
6836815688acetoin+
6836835581indole-
11597615688acetoin-
11597617234glucose-

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
115976oxidase-
115976beta-galactosidase-3.2.1.23
115976alcohol dehydrogenase-1.1.1.1
115976gelatinase+
115976amylase+
115976DNase+
115976caseinase+3.4.21.50
115976catalase+1.11.1.6
115976tween esterase-
115976gamma-glutamyltransferase+2.3.2.2
115976lecithinase+
115976lipase-
115976lysine decarboxylase-4.1.1.18
115976ornithine decarboxylase-4.1.1.17
115976phenylalanine ammonia-lyase-4.3.1.24
115976tryptophan deaminase-
115976urease-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
115976-++--+++--++---+----

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
18678-----+---++

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
115976++--+----++--------+-----------++----------------++--+-----++-----------++----+++---+++--+++--+-++-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
9834garden soil
67770Garden soilAbiko, Chiba Pref.JapanJPNAsia
115976Environment, Garden soilAbikoJapanJPNAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Soil
#Engineered#Agriculture#Garden

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
186781German classification
98341Risk group (German classification)
1159761Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Streptomyces abikoensis strain CGMCC 4.1662 16S ribosomal RNA gene, partial sequenceHQ2444501488ena97398
20218Streptomyces abikoensis strain DSM 40831 16S ribosomal RNA gene, partial sequenceKC9545561347ena97398
20218Streptoverticillium abikoense partial 16S rRNAX531681358ena97398
20218Micrococcus luteus gene for 16S ribosomal RNA, partial sequence, strain: AIAM01AB7489751386ena1270
20218Spiroplasma endosymbiont of Irenimus aequalis clone IAM1 16S ribosomal RNA gene, partial sequenceKJ494866483ena1519525
20218Streptomyces abikoensis gene for 16S rRNA, partial sequence, strain: NBRC 13860AB1845371456ena97398
20218Streptomyces abikoensis strain NBRC 13860 clone 1 16S ribosomal RNA gene, partial sequenceJN5660401488ena97398
20218Streptomyces abikoensis strain NBRC 13860 clone 2 16S ribosomal RNA gene, partial sequenceJN5660411488ena97398

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Streptomyces abikoensis JCM 4002GCA_014648775contigncbi97398
66792Streptomyces abikoensis strain JCM 400297398.3wgspatric97398

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileno92.925no
flagellatedno97.863no
gram-positiveyes88.314no
anaerobicno98.956no
halophileno92.722no
spore-formingyes93.622yes
thermophileno96.555no
glucose-utilyes90.099no
aerobicyes87.205no
glucose-fermentno90.145no

External links

@ref: 9834

culture collection no.: DSM 40831, ATCC 12766, CBS 487.62, NRRL B-1518, RIA 497, JCM 4002, BCRC 12461, CGMCC 4.1662, CIP 108146, IFO 13860, KCTC 9662, KCTC 9741, NBIMCC 1606, NBRC 13860, NCB 260, NRRL B-2113, PCM 2364, CCRC 12461, KCC S-0002, IAM 0001, AS 4.1162

straininfo link

  • @ref: 85207
  • straininfo: 45528

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
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
Phylogeny27405543Streptomyces palmae sp. nov., isolated from oil palm (Elaeis guineensis) rhizosphere soil.Sujarit K, Kudo T, Ohkuma M, Pathom-Aree W, Lumyong SInt J Syst Evol Microbiol10.1099/ijsem.0.0012982016Arecaceae/*microbiology, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, *Rhizosphere, Sequence Analysis, DNA, *Soil Microbiology, Streptomyces/*classification/genetics/isolation & purification, Thailand, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
9834Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 40831)https://www.dsmz.de/collection/catalogue/details/culture/DSM-40831
18678Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM40831.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
38258Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5736
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
85207Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID45528.1StrainInfo: A central database for resolving microbial strain identifiers
115976Curators of the CIPCollection of Institut Pasteur (CIP 108146)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108146