Strain identifier
BacDive ID: 15452
Type strain: 
Species: Streptomyces pactus
Strain history: KCC S-0288 <-- NCIB 9445 <-- Upjohn Co., USA; UC 2432.
NCBI tax ID(s): 68249 (species)
version 8.1 (current version)
General
@ref: 9619
BacDive-ID: 15452
DSM-Number: 40530
keywords: genome sequence, 16S sequence, Bacteria, spore-forming, mesophilic, antibiotic compound production
description: Streptomyces pactus DSM 40530 is a spore-forming, mesophilic bacterium that builds an aerial mycelium and produces antibiotic compounds.
NCBI tax id
- NCBI tax id: 68249
- Matching level: species
strain history
| @ref | history |
|---|---|
| 9619 | <- E.B. Shirling, ISP <- NRRL <- Upjohn Co., UC 2432 |
| 67770 | KCC S-0288 <-- NCIB 9445 <-- Upjohn Co., USA; UC 2432. |
doi: 10.13145/bacdive15452.20230509.8.1
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 pactus
- full scientific name: Streptomyces pactus corrig. Bhuyan et al. 1962 (Approved Lists 1980)
synonyms
- @ref: 20215
- synonym: Streptomyces pactum
@ref: 9619
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Streptomycetaceae
genus: Streptomyces
species: Streptomyces pactum
full scientific name: Streptomyces pactum Bhuyan et al. 1962
type strain: yes
Morphology
cell morphology
| @ref | motility | confidence | gram stain |
|---|---|---|---|
| 69480 | no | 96.262 | |
| 69480 | 100 | positive |
colony morphology
| @ref | colony color | incubation period | medium used |
|---|---|---|---|
| 19472 | Grey | 10-14 days | ISP 2 |
| 19472 | 10-14 days | ISP 3 | |
| 19472 | Beige | 10-14 days | ISP 4 |
| 19472 | Beige | 10-14 days | ISP 5 |
| 19472 | 10-14 days | ISP 6 | |
| 19472 | Beige | 10-14 days | ISP 7 |
multicellular morphology
| @ref | forms multicellular complex | complex name | complex color | medium name |
|---|---|---|---|---|
| 19472 | yes | Aerial Mycelium | Beige | ISP 2 |
| 19472 | yes | Aerial Mycelium | ISP 3 | |
| 19472 | yes | Aerial Mycelium | Grey | ISP 4 |
| 19472 | yes | Aerial Mycelium | Grey | ISP 5 |
| 19472 | no | ISP 6 | ||
| 19472 | yes | Aerial Mycelium | Grey beige | ISP 7 |
multimedia
- @ref: 9619
- multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_40530.jpg
- caption: Medium 65 28°C
- intellectual property rights: © Leibniz-Institut DSMZ
Culture and growth conditions
culture medium
| @ref | name | growth | link | composition |
|---|---|---|---|---|
| 9619 | 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 |
| 19472 | 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 | |
| 19472 | 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: | |
| 19472 | 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 | |
| 19472 | 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 | |
| 19472 | 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 | |
| 19472 | 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 | |
| 9619 | STARCH - MINERAL SALT - AGAR (STMS) (DSMZ Medium 252) | yes | https://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium252.pdf |
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 19472 | positive | optimum | 28 | mesophilic |
| 9619 | positive | growth | 28 | mesophilic |
| 67770 | positive | growth | 28 | mesophilic |
Physiology and metabolism
spore formation
| @ref | spore description | type of spore | spore formation | confidence |
|---|---|---|---|---|
| 19472 | Formation of spore chains (retinaculiapetri b), spore surface smooth | spore | yes | |
| 69481 | yes | 100 | ||
| 69480 | yes | 100 |
compound production
| @ref | compound |
|---|---|
| 9619 | pactamycin |
| 9619 | piericidins |
| 20216 | Pactamycin (Pactacin, NSC52947) |
| 20216 | Pieridacin |
| 19472 | Actinopyrones |
| 19472 | Lonomycin A |
| 19472 | Pactamycin |
| 19472 | Piericidin A |
| 67770 | piericidins |
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 19472 | 62968 | cellulose | - | |
| 19472 | 16634 | raffinose | - | |
| 19472 | 26546 | rhamnose | - | |
| 19472 | 28757 | fructose | - | |
| 19472 | 29864 | mannitol | - | |
| 19472 | 17268 | myo-inositol | - | |
| 19472 | 18222 | xylose | - | |
| 19472 | 17992 | sucrose | - | |
| 19472 | 22599 | arabinose | - | |
| 19472 | 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 | pactamycin | yes | |
| 68368 | acetoin | no | 15688 |
| 68368 | indole | no | 35581 |
| 68368 | hydrogen sulfide | no | 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 |
API 20E
| @ref | ONPG | ADH Arg | LDC Lys | ODC | CIT | H2S | URE | TDA Trp | IND | VP | GEL |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 19472 | + | + | + | + | - | - | + | - | - | - | + |
Safety information
risk assessment
| @ref | biosafety level | biosafety level comment |
|---|---|---|
| 9619 | 1 | Risk group (German classification) |
| 19472 | 1 | Risk group (German classification) |
Sequence information
16S sequences
| @ref | description | accession | length | database | NCBI tax ID |
|---|---|---|---|---|---|
| 20218 | Streptomyces pactum strain NRRL ISP-5530 16S ribosomal RNA gene, partial sequence | EF654095 | 1479 | ena | 68249 |
| 20218 | Streptomyces pactum gene for 16S ribosomal RNA, partial sequence, strain: JCM 4809 | D44377 | 121 | ena | 68249 |
| 20218 | Streptomyces pactum gene for 16S rRNA, partial sequence, strain: NBRC 13433 | AB184398 | 1464 | ena | 68249 |
| 20218 | Streptomyces pactum gene for 16S ribosomal RNA, partial sequence, strain: NBRC 13433 | AB915617 | 1302 | ena | 68249 |
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Streptomyces pactum ATCC 27456 | GCA_016031615 | contig | ncbi | 68249 |
| 66792 | Streptomyces pactum strain ATCC 27456 | 68249.10 | wgs | patric | 68249 |
| 66792 | Streptomyces pactum NBRC 13433 | 2563366709 | draft | img | 68249 |
| 66792 | Streptomyces pactum ATCC 27456 | 2563366708 | draft | img | 68249 |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | yes | 100 | no |
| gram-positive | yes | 93.581 | no |
| anaerobic | no | 98.797 | no |
| halophile | no | 93.222 | no |
| spore-forming | yes | 96.688 | yes |
| glucose-util | yes | 91.871 | yes |
| thermophile | no | 97.322 | yes |
| flagellated | no | 98.462 | no |
| motile | no | 94.853 | no |
| aerobic | yes | 90.91 | no |
| glucose-ferment | no | 88.737 | no |
External links
@ref: 9619
culture collection no.: DSM 40530, ATCC 27456, CBS 461.69, CBS 734.72, DSM 41250, IFO 13433, ISP 5530, JCM 4288, JCM 4809, KCC S-0288, KCC S-0809, NBRC 13433, NCIB 9445, NRRL 2939, RIA 1394, UC 2432, BCRC 12076, CGMCC 4.1443, IMET 43357, KCTC 9165, LMG 19357, NCIMB 9445, VKM Ac-1911, VTT E-073029
straininfo link
- @ref: 84540
- straininfo: 126008
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Enzymology | 7487006 | Characterization of a keratinolytic serine proteinase from Streptomyces pactum DSM 40530. | Bockle B, Galunsky B, Muller R | Appl Environ Microbiol | 10.1128/aem.61.10.3705-3710.1995 | 1995 | Amino Acid Sequence, Animals, Chickens, Chromatography, Affinity, Feathers/metabolism, In Vitro Techniques, Isoelectric Point, Keratins/metabolism, Kinetics, Molecular Sequence Data, Molecular Weight, Oligopeptides/chemistry, Oxidation-Reduction, Peptide Hydrolases/chemistry/*isolation & purification/metabolism, Serine Endopeptidases/chemistry/*isolation & purification/metabolism, Streptomyces/*enzymology, Substrate Specificity | Metabolism |
| Metabolism | 17827660 | Cloning of the pactamycin biosynthetic gene cluster and characterization of a crucial glycosyltransferase prior to a unique cyclopentane ring formation. | Kudo F, Kasama Y, Hirayama T, Eguchi T | J Antibiot (Tokyo) | 10.1038/ja.2007.63 | 2007 | Bacterial Proteins/*genetics/metabolism, Cyclopentanes/chemistry/*metabolism, Genes, Bacterial/*genetics, Glucosides/metabolism, Glycosylation, Glycosyltransferases/*genetics/*metabolism, *Multigene Family, Open Reading Frames/physiology, Pactamycin/*biosynthesis/chemistry, Salicylates/metabolism, Streptomyces/*genetics/metabolism | Enzymology |
| Metabolism | 19670201 | Deciphering pactamycin biosynthesis and engineered production of new pactamycin analogues. | Ito T, Roongsawang N, Shirasaka N, Lu W, Flatt PM, Kasanah N, Miranda C, Mahmud T | Chembiochem | 10.1002/cbic.200900339 | 2009 | Anti-Bacterial Agents/*biosynthesis/chemistry/pharmacology, Antibiotics, Antineoplastic/*chemistry/metabolism/toxicity, Cell Line, Tumor, Humans, Molecular Sequence Data, Multigene Family, Pactamycin/*analogs & derivatives/biosynthesis/pharmacology, Polyketide Synthases/genetics/metabolism, Structure-Activity Relationship | Pathogenicity |
| Phylogeny | 20154329 | Streptomyces hyderabadensis sp. nov., an actinomycete isolated from soil. | Reddy TVK, Mahmood S, Paris L, Reddy YHK, Wellington EMH, Idris MM | Int J Syst Evol Microbiol | 10.1099/ijs.0.020446-0 | 2010 | Bacterial Typing Techniques, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, India, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Streptomyces/*classification/genetics/*isolation & purification/physiology | Genetics |
| Pathogenicity | 23521145 | Mutasynthesis of fluorinated pactamycin analogues and their antimalarial activity. | Almabruk KH, Lu W, Li Y, Abugreen M, Kelly JX, Mahmud T | Org Lett | 10.1021/ol4004614 | 2013 | Antimalarials/*chemical synthesis/chemistry/*pharmacology, Chloroquine/pharmacology, Drug Resistance/drug effects, Drug Resistance, Multiple/drug effects, Hydrocarbons, Fluorinated/*chemical synthesis/chemistry/*pharmacology, Molecular Structure, Pactamycin/*analogs & derivatives/*chemical synthesis/chemistry/*pharmacology, Plasmodium falciparum/drug effects, Streptomyces/chemistry/genetics/metabolism, meta-Aminobenzoates | Metabolism |
| Metabolism | 33284588 | Biosynthesis of the Nuclear Factor of Activated T Cells Inhibitor NFAT-133 in Streptomyces pactum. | Zhou W, Posri P, Abugrain ME, Weisberg AJ, Chang JH, Mahmud T | ACS Chem Biol | 10.1021/acschembio.0c00775 | 2020 | Computational Biology, Genes, Bacterial, Genome, Bacterial, Magnetic Resonance Spectroscopy, Multigene Family, Pentanols/*metabolism, Pentanones/*metabolism, Polyketide Synthases/genetics, Streptomyces/enzymology/genetics/*metabolism | Genetics |
| Metabolism | 33601889 | Natural Occurrence of Hybrid Polyketides from Two Distinct Biosynthetic Pathways in Streptomyces pactum. | Zhou W, Posri P, Mahmud T | ACS Chem Biol | 10.1021/acschembio.0c00982 | 2021 | Genes, Bacterial, Multigene Family, Polyketide Synthases/chemistry/metabolism, Polyketides/chemistry/*metabolism, Protein Domains, Streptomyces/genetics/*metabolism, Thiolester Hydrolases/chemistry/metabolism | |
| 34519213 | Identification and Biological Activity of NFAT-133 Congeners from Streptomyces pactum. | Zhou W, Posri P, Liu XJ, Ju Z, Lan WJ, Mahmud T | J Nat Prod | 10.1021/acs.jnatprod.1c00152 | 2021 | Animals, Biological Products, Mice, Molecular Structure, Pentanols/*pharmacology, Pentanones/*pharmacology, Polyketides/*pharmacology, RAW 264.7 Cells, Streptomyces/*chemistry | ||
| Metabolism | 34723462 | Modulation of Specialized Metabolite Production in Genetically Engineered Streptomyces pactum. | Ju Z, Zhou W, Alharbi HA, Howell DC, Mahmud T | ACS Chem Biol | 10.1021/acschembio.1c00718 | 2021 | Anti-Bacterial Agents/pharmacology, Antineoplastic Agents/pharmacology, Cell Line, Tumor, Drug Screening Assays, Antitumor, Genes, Bacterial, HSP90 Heat-Shock Proteins/metabolism, Humans, Microbial Sensitivity Tests, Molecular Structure, *Organisms, Genetically Modified, Oxazoles/chemistry/metabolism/pharmacology, Polyketide Synthases/metabolism, Polyketides/chemistry, Protein Binding, Streptomyces/genetics/*metabolism, Substrate Specificity | Biotechnology |
| Metabolism | 35904416 | Functional Studies and Revision of the NFAT-133/TM-123 Biosynthetic Pathway in Streptomyces pactum. | Zhou W, Alharbi HA, Hummingbird E, Keatinge-Clay AT, Mahmud T | ACS Chem Biol | 10.1021/acschembio.2c00454 | 2022 | *Biosynthetic Pathways, Multigene Family, Pentanols, Pentanones, Polyketide Synthases/genetics/metabolism, *Streptomyces/genetics/metabolism |
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 9619 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 40530) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-40530 | |||
| 19472 | Wink, J. | http://www.dsmz.de/microorganisms/wink_pdf/DSM40530.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 | |
| 66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
| 67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
| 68368 | Automatically annotated from API 20E | |||||
| 69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
| 69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 | |||
| 84540 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID126008.1 | StrainInfo: A central database for resolving microbial strain identifiers |