Strain identifier

BacDive ID: 14881

Type strain: Yes

Species: Streptomyces achromogenes subsp. achromogenes

Strain Designation: Z-4-1

Strain history: KCC S-0121 <-- Y. Okami Z-4-1 (NIHJ 213).

NCBI tax ID(s): 67255 (species), 67256 (subspecies)

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General

@ref: 9227

BacDive-ID: 14881

DSM-Number: 40028

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

description: Streptomyces achromogenes subsp. achromogenes Z-4-1 is an aerobe, spore-forming, mesophilic bacterium that builds an aerial mycelium and produces antibiotic compounds.

NCBI tax id

NCBI tax idMatching level
67256subspecies
67255species

strain history

@refhistory
9227<- E.B. Shirling, ISP <- Y. Okami, Z-4-1
67770KCC S-0121 <-- Y. Okami Z-4-1 (NIHJ 213).

doi: 10.13145/bacdive14881.20250331.9.3

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 achromogenes subsp. achromogenes
  • full scientific name: Streptomyces achromogenes subsp. achromogenes (Okami and Umezawa 1953) Bhuyan et al. 1965 (Approved Lists 1980)

@ref: 9227

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Streptomycetaceae

genus: Streptomyces

species: Streptomyces achromogenes subsp. achromogenes

full scientific name: Streptomyces achromogenes subsp. achromogenes (Okami and Umezawa 1953) Bhuyan et al. 1965

strain designation: Z-4-1

type strain: yes

Morphology

colony morphology

@refcolony colorincubation periodmedium used
19389Maize yellow10-14 daysISP 2
19389Beige10-14 daysISP 3
19389Beige10-14 daysISP 4
19389Beige10-14 daysISP 5
19389Brown beige10-14 daysISP 6
19389Beige10-14 daysISP 7

multicellular morphology

@refforms multicellular complexcomplex namecomplex colormedium name
19389yesAerial MyceliumCreamISP 2
19389yesAerial MyceliumLight greyISP 3
19389yesAerial MyceliumCreamISP 4
19389noISP 5
19389noISP 6
19389yesAerial MyceliumCreamISP 7

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
9227GYM 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
19389ISP 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
19389ISP 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:
19389ISP 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
19389ISP 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
19389ISP 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
19389ISP 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
9227ROLLED 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

culture temp

@refgrowthtypetemperature
19389positiveoptimum28
9227positivegrowth37
67770positivegrowth28

Physiology and metabolism

oxygen tolerance

  • @ref: 125438
  • oxygen tolerance: aerobe
  • confidence: 91.661

spore formation

  • @ref: 125438
  • spore formation: yes
  • confidence: 92.876

compound production

@refcompound
9227achromoviromycin
9227restriction endonuclease SacI
9227sarcidin
20216Achromoviromycin
20216Sarcidin
20216Endonuclease SacI
20216Endonuclease SacII
20216Endonuclease SacIII

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1938962968cellulose+
1938916634raffinose-
1938926546rhamnose+
1938928757fructose+
1938929864mannitol+
1938917268myo-inositol-
1938918222xylose-
1938917992sucrose-
1938922599arabinose+
1938917234glucose+
683685291gelatin+hydrolysis
6836827897tryptophan-energy source
6836816199urea+hydrolysis
6836816947citrate+assimilation
6836818257ornithine+degradation
6836825094lysine+degradation
6836829016arginine+hydrolysis

metabolite production

@refmetaboliteproductionChebi-ID
67770achromoviromycinyes
67770sarcidinyes
68368acetoinyes15688
68368indoleno35581
68368hydrogen sulfideyes16136

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole test
6836815688acetoin+
6836835581indole-

enzymes

@refvalueactivityec
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51
68382alpha-glucosidase+3.2.1.20
68382beta-galactosidase-3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-chymotrypsin+3.4.21.1
68382acid phosphatase+3.1.3.2
68382trypsin+3.4.21.4
68382cystine arylamidase-3.4.11.3
68382valine arylamidase+
68382leucine arylamidase+3.4.11.1
68382esterase lipase (C 8)+
68382esterase (C 4)-
68382alkaline phosphatase+3.1.3.1
68382N-acetyl-beta-glucosaminidase+3.2.1.52
68382beta-glucosidase-3.2.1.21
68382beta-glucuronidase-3.2.1.31
68382lipase (C 14)-
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 zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
19389+-+-++-++++---+-+--

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
19389+++++++--++

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
9227garden soil
67770Garden soilSuginami-ku, TokyoJapanJPNAsia

isolation source categories

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

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
92271Risk group (German classification)
193891Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Streptomyces achromogenes strain ATCC 12767 16S ribosomal RNA gene, partial sequenceDQ012961577nuccore67255
20218Streptomyces achromogenes subsp. achromogenes gene for 16S ribosomal RNA, partial sequence, strain: JCM 4561D44232120nuccore67256
20218Streptomyces achromogenes subsp. achromogenes gene for 16S rRNA, partial sequence, strain: NBRC 12735AB1841091460nuccore67256
20218Streptomyces achromogenes subsp. achromogenes strain NRRL B-2120 16S ribosomal RNA gene, partial sequenceEF6540911395nuccore67256

Genome sequences

  • @ref: 67770
  • description: Streptomyces achromogenes subsp. achromogenes NRRL B-2120
  • accession: GCA_000720835
  • assembly level: contig
  • database: ncbi
  • NCBI tax ID: 67256

GC content

  • @ref: 67770
  • GC-content: 72.5
  • method: genome sequence analysis

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingyes86.36no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no97.896no
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes91.661no
125438spore-formingspore-formingAbility to form endo- or exosporesyes92.876no
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno97.491yes
125438motile2+flagellatedAbility to perform flagellated movementno88.1no

External links

@ref: 9227

culture collection no.: DSM 40028, ATCC 12767, ATCC 19719, CBS 458.68, IFO 12735, ISP 5028, JCM 4121, NBRC 12735, RIA 1000, BCRC 11618, CECT 3074, CGMCC 4.1075, IAM 12360, IFM 1173, IFO 16791, IMET 43080, IMSNU 20130, JCM 4561, KCTC 1740, MTCC 931, NBRC 16791, NRRL B-2120, PCM 2365, RIA 756, VKM Ac-1258

straininfo link

  • @ref: 83990
  • straininfo: 389313

literature

topicPubmed-IDtitleauthorsjournalyearmeshtopic2DOI
Enzymology3033630[Isolation and purification of restriction endonuclease SacI from Streptomyces achromogenes ATCC 12767].Zhuravleva LI, Oreshkin EN, Bezborodov AMPrikl Biokhim Mikrobiol1987Chromatography, Ion Exchange, DNA Restriction Enzymes/*isolation & purification, *Deoxyribonucleases, Type II Site-Specific, Electrophoresis, Polyacrylamide Gel, Isoelectric Point, Molecular Weight, Streptomyces/*enzymologyPhylogeny
Phylogeny33174827Streptomyces phaeolivaceus sp. nov. and Streptomyces broussonetiae sp. nov., isolated from the leaves and rhizosphere soil of Broussonetia papyrifera.Mo P, Liu J, Zhao Y, Xu ZInt J Syst Evol Microbiol2020Bacterial Typing Techniques, Base Composition, Broussonetia/*microbiology, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, *Phylogeny, Plant Leaves, RNA, Ribosomal, 16S/genetics, Rhizosphere, Sequence Analysis, DNA, *Soil Microbiology, Streptomyces/*classification/isolation & purificationTranscriptome10.1099/ijsem.0.004556

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
9227Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 40028)https://www.dsmz.de/collection/catalogue/details/culture/DSM-40028
19389Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM40028.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
20216Curators of the HKIhttp://www.leibniz-hki.de/de/Collection Description Leibniz-Institut für Naturstoff-Forschung und Infektionsbiologie e. V. Hans-Knöll-Institut (HKI)
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
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68368Automatically annotated from API 20E
68382Automatically annotated from API zym
83990Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID389313.1StrainInfo: A central database for resolving microbial strain identifiers
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann10.1101/2024.08.12.607695Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets