Strain identifier
BacDive ID: 14881
Type strain:
Species: Streptomyces achromogenes
Strain Designation: Z-4-1
Strain history: KCC S-0121 <-- Y. Okami Z-4-1 (NIHJ 213).
NCBI tax ID(s): 67255 (species)
General
@ref: 9227
BacDive-ID: 14881
DSM-Number: 40028
keywords: genome sequence, 16S sequence, Bacteria, mesophilic, antibiotic compound production
description: Streptomyces achromogenes Z-4-1 is a mesophilic bacterium that builds an aerial mycelium and produces antibiotic compounds.
NCBI tax id
- NCBI tax id: 67255
- Matching level: species
strain history
@ref | history |
---|---|
9227 | <- E.B. Shirling, ISP <- Y. Okami, Z-4-1 |
67770 | KCC S-0121 <-- Y. Okami Z-4-1 (NIHJ 213). |
doi: 10.13145/bacdive14881.20230509.8.1
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 achromogenes
- full scientific name: Streptomyces achromogenes Okami and Umezawa 1953 (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
@ref | colony color | incubation period | medium used |
---|---|---|---|
19389 | Maize yellow | 10-14 days | ISP 2 |
19389 | Beige | 10-14 days | ISP 3 |
19389 | Beige | 10-14 days | ISP 4 |
19389 | Beige | 10-14 days | ISP 5 |
19389 | Brown beige | 10-14 days | ISP 6 |
19389 | Beige | 10-14 days | ISP 7 |
multicellular morphology
@ref | forms multicellular complex | complex name | complex color | medium name |
---|---|---|---|---|
19389 | yes | Aerial Mycelium | Cream | ISP 2 |
19389 | yes | Aerial Mycelium | Light grey | ISP 3 |
19389 | yes | Aerial Mycelium | Cream | ISP 4 |
19389 | no | ISP 5 | ||
19389 | no | ISP 6 | ||
19389 | yes | Aerial Mycelium | Cream | ISP 7 |
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
9227 | GYM STREPTOMYCES MEDIUM (DSMZ Medium 65) | yes | https://mediadive.dsmz.de/medium/65 | Name: 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 |
19389 | ISP 2 | yes | Name: 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 | |
19389 | ISP 3 | yes | Name: 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: | |
19389 | ISP 4 | yes | Name: 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 | |
19389 | ISP 5 | yes | Name: 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 | |
19389 | ISP 6 | yes | Name: 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 | |
19389 | ISP 7 | yes | Name: 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 | |
9227 | ROLLED OATS MINERAL MEDIUM (DSMZ Medium 84) | yes | https://mediadive.dsmz.de/medium/84 | Name: 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
@ref | growth | type | temperature | range |
---|---|---|---|---|
19389 | positive | optimum | 28 | mesophilic |
9227 | positive | growth | 37 | mesophilic |
67770 | positive | growth | 28 | mesophilic |
Physiology and metabolism
compound production
@ref | compound |
---|---|
9227 | achromoviromycin |
9227 | restriction endonuclease SacI |
9227 | sarcidin |
20216 | Achromoviromycin |
20216 | Sarcidin |
20216 | Endonuclease SacI |
20216 | Endonuclease SacII |
20216 | Endonuclease SacIII |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
19389 | 62968 | cellulose | + | |
19389 | 16634 | raffinose | - | |
19389 | 26546 | rhamnose | + | |
19389 | 28757 | fructose | + | |
19389 | 29864 | mannitol | + | |
19389 | 17268 | myo-inositol | - | |
19389 | 18222 | xylose | - | |
19389 | 17992 | sucrose | - | |
19389 | 22599 | arabinose | + | |
19389 | 17234 | glucose | + | |
68368 | 5291 | gelatin | + | hydrolysis |
68368 | 27897 | tryptophan | - | energy source |
68368 | 16199 | urea | + | hydrolysis |
68368 | 16947 | citrate | + | assimilation |
68368 | 18257 | ornithine | + | degradation |
68368 | 25094 | lysine | + | degradation |
68368 | 29016 | arginine | + | hydrolysis |
metabolite production
@ref | metabolite | production | Chebi-ID |
---|---|---|---|
67770 | achromoviromycin | yes | |
67770 | sarcidin | yes | |
68368 | acetoin | yes | 15688 |
68368 | indole | no | 35581 |
68368 | hydrogen sulfide | yes | 16136 |
metabolite tests
@ref | Chebi-ID | metabolite | voges-proskauer-test | indole test |
---|---|---|---|---|
68368 | 15688 | acetoin | + | |
68368 | 35581 | indole | - |
enzymes
@ref | value | activity | ec |
---|---|---|---|
68368 | gelatinase | + | |
68368 | tryptophan deaminase | - | 4.1.99.1 |
68368 | urease | + | 3.5.1.5 |
68368 | ornithine decarboxylase | + | 4.1.1.17 |
68368 | lysine decarboxylase | + | 4.1.1.18 |
68368 | arginine dihydrolase | + | 3.5.3.6 |
68368 | beta-galactosidase | + | 3.2.1.23 |
68382 | alkaline phosphatase | + | 3.1.3.1 |
68382 | esterase (C 4) | - | |
68382 | esterase lipase (C 8) | + | |
68382 | lipase (C 14) | - | |
68382 | leucine arylamidase | + | 3.4.11.1 |
68382 | valine arylamidase | + | |
68382 | cystine arylamidase | - | 3.4.11.3 |
68382 | trypsin | + | 3.4.21.4 |
68382 | alpha-chymotrypsin | + | 3.4.21.1 |
68382 | acid phosphatase | + | 3.1.3.2 |
68382 | naphthol-AS-BI-phosphohydrolase | + | |
68382 | alpha-galactosidase | - | 3.2.1.22 |
68382 | beta-galactosidase | - | 3.2.1.23 |
68382 | beta-glucuronidase | - | 3.2.1.31 |
68382 | alpha-glucosidase | + | 3.2.1.20 |
68382 | beta-glucosidase | - | 3.2.1.21 |
68382 | N-acetyl-beta-glucosaminidase | + | 3.2.1.52 |
68382 | alpha-mannosidase | - | 3.2.1.24 |
68382 | alpha-fucosidase | - | 3.2.1.51 |
API zym
@ref | Alkaline phosphatase | Esterase | Esterase Lipase | Lipase | Leucine arylamidase | Valine arylamidase | Cystine arylamidase | Trypsin | alpha- Chymotrypsin | Acid phosphatase | Naphthol-AS-BI-phosphohydrolase | alpha- Galactosidase | beta- Galactosidase | beta- Glucuronidase | alpha- Glucosidase | beta- Glucosidase | N-acetyl-beta- glucosaminidase | alpha- Mannosidase | alpha- Fucosidase |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
19389 | + | - | + | - | + | + | - | + | + | + | + | - | - | - | + | - | + | - | - |
API 20E
@ref | ONPG | ADH Arg | LDC Lys | ODC | CIT | H2S | URE | TDA Trp | IND | VP | GEL |
---|---|---|---|---|---|---|---|---|---|---|---|
19389 | + | + | + | + | + | + | + | - | - | + | + |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent |
---|---|---|---|---|---|
9227 | garden soil | ||||
67770 | Garden soil | Suginami-ku, Tokyo | Japan | JPN | Asia |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Environmental | #Terrestrial | #Soil |
#Engineered | #Agriculture | #Garden |
Safety information
risk assessment
@ref | biosafety level | biosafety level comment |
---|---|---|
9227 | 1 | Risk group (German classification) |
19389 | 1 | Risk group (German classification) |
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Streptomyces achromogenes strain ATCC 12767 16S ribosomal RNA gene, partial sequence | DQ012961 | 577 | ena | 67255 |
20218 | Streptomyces achromogenes subsp. achromogenes gene for 16S ribosomal RNA, partial sequence, strain: JCM 4561 | D44232 | 120 | ena | 67256 |
20218 | Streptomyces achromogenes subsp. achromogenes gene for 16S rRNA, partial sequence, strain: NBRC 12735 | AB184109 | 1460 | ena | 67256 |
20218 | Streptomyces achromogenes subsp. achromogenes strain NRRL B-2120 16S ribosomal RNA gene, partial sequence | EF654091 | 1395 | ena | 67256 |
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
trait | prediction | confidence | training_data |
---|---|---|---|
motile | no | 94.641 | no |
flagellated | no | 98.532 | no |
gram-positive | yes | 91.358 | no |
anaerobic | no | 99.306 | no |
aerobic | yes | 94.516 | no |
halophile | no | 93.682 | no |
spore-forming | yes | 96.993 | no |
thermophile | no | 97.749 | yes |
glucose-util | yes | 89.821 | yes |
glucose-ferment | no | 90.542 | no |
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
topic | Pubmed-ID | title | authors | journal | year | mesh | topic2 | DOI |
---|---|---|---|---|---|---|---|---|
Enzymology | 3033630 | [Isolation and purification of restriction endonuclease SacI from Streptomyces achromogenes ATCC 12767]. | Zhuravleva LI, Oreshkin EN, Bezborodov AM | Prikl Biokhim Mikrobiol | 1987 | Chromatography, Ion Exchange, DNA Restriction Enzymes/*isolation & purification, *Deoxyribonucleases, Type II Site-Specific, Electrophoresis, Polyacrylamide Gel, Isoelectric Point, Molecular Weight, Streptomyces/*enzymology | Phylogeny | |
Phylogeny | 33174827 | Streptomyces 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 Z | Int J Syst Evol Microbiol | 2020 | Bacterial 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 & purification | Transcriptome | 10.1099/ijsem.0.004556 |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
9227 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 40028) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-40028 | |||
19389 | Wink, J. | http://www.dsmz.de/microorganisms/wink_pdf/DSM40028.pdf | Compendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig | |||
20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | |||
20216 | Curators of the HKI | http://www.leibniz-hki.de/de/ | Collection Description Leibniz-Institut für Naturstoff-Forschung und Infektionsbiologie e. V. Hans-Knöll-Institut (HKI) | |||
20218 | Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P. | 10.1016/j.syapm.2013.11.002 | StrainInfo introduces electronic passports for microorganisms. | Syst Appl Microbiol. 37: 42-50 2014 | 24321274 | |
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
68368 | Automatically annotated from API 20E | |||||
68382 | Automatically annotated from API zym | |||||
83990 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID389313.1 | StrainInfo: A central database for resolving microbial strain identifiers |