Strain identifier
BacDive ID: 15428
Type strain:
Species: Streptomyces nodosus
Strain history: KCC S-0297 <-- ATCC 14899 <-- SC 2388.
NCBI tax ID(s): 40318 (species)
General
@ref: 9320
BacDive-ID: 15428
DSM-Number: 40109
keywords: genome sequence, 16S sequence, Bacteria, spore-forming, mesophilic, Gram-positive
description: Streptomyces nodosus DSM 40109 is a spore-forming, mesophilic, Gram-positive bacterium that was isolated from soil.
NCBI tax id
- NCBI tax id: 40318
- Matching level: species
strain history
@ref | history |
---|---|
9320 | <- E.B. Shirling, ISP <- W.H. Trejo, SC 2388 |
67770 | KCC S-0297 <-- ATCC 14899 <-- SC 2388. |
doi: 10.13145/bacdive15428.20230509.8.1
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 nodosus
- full scientific name: Streptomyces nodosus Trejo 1961 (Approved Lists 1980)
@ref: 9320
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Streptomycetaceae
genus: Streptomyces
species: Streptomyces nodosus
full scientific name: Streptomyces nodosus Trejo 1961 emend. Nouioui et al. 2018
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: positive
- confidence: 100
multimedia
- @ref: 9320
- multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_40109.jpg
- caption: Medium 252 28°C
- intellectual property rights: © Leibniz-Institut DSMZ
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
9320 | 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 |
9320 | 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 |
---|---|---|---|---|
18536 | positive | optimum | 28 | mesophilic |
9320 | positive | growth | 28 | mesophilic |
67770 | positive | growth | 28 | mesophilic |
Physiology and metabolism
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | yes | 100 |
69480 | yes | 100 |
compound production
@ref | compound |
---|---|
9320 | amphotericin A |
9320 | amphotericin A, B |
9320 | amphotericin B |
20216 | Amphotericin A (tetraenic) |
20216 | Amphotericin B (heptaenic) |
halophily
- @ref: 18536
- salt: NaCl
- growth: positive
- tested relation: maximum
- concentration: 2.5 %
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
18536 | 17234 | glucose | + | |
18536 | 22599 | arabinose | - | |
18536 | 17992 | sucrose | - | |
18536 | 18222 | xylose | + | |
18536 | 17268 | myo-inositol | +/- | |
18536 | 29864 | mannitol | +/- | |
18536 | 28757 | fructose | + | |
18536 | 26546 | rhamnose | - | |
18536 | 16634 | raffinose | - | |
18536 | 62968 | cellulose | - | |
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 | amphotericin A | yes | |
67770 | amphotericin B | 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 |
---|---|---|---|---|---|---|---|---|---|---|---|
18536 | + | - | + | + | - | - | + | - | - | - | + |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent |
---|---|---|---|---|---|
9320 | soil | ||||
67770 | Soil | Orinoco River region | Venezuela | VEN | Middle and South America |
isolation source categories
- Cat1: #Environmental
- Cat2: #Terrestrial
- Cat3: #Soil
Safety information
risk assessment
@ref | biosafety level | biosafety level comment |
---|---|---|
18536 | 1 | German classification |
9320 | 1 | Risk group (German classification) |
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Streptomyces nodosus rrnB operon 16S ribosomal RNA, 23S ribosomal RNA, and 5S ribosomal RNA, complete sequence | AF114033 | 6195 | ena | 40318 |
20218 | Streptomyces nodosus rrnD operon 16S ribosomal RNA, 23S ribosomal RNA, and 5S ribosomal RNA, complete sequence | AF114034 | 6169 | ena | 40318 |
20218 | Streptomyces nodosus rrnE operon 16S ribosomal RNA, 23S ribosomal RNA, and 5S ribosomal RNA, complete sequence | AF114035 | 6174 | ena | 40318 |
20218 | Streptomyces nodosus rrnF operon 16S ribosomal RNA, 23S ribosomal RNA, and 5S ribosomal RNA, complete sequence | AF114036 | 6175 | ena | 40318 |
20218 | Streptomyces nodosus gene for 16S ribosomal RNA, partial sequence, strain: JCM 4656 | D44288 | 120 | ena | 40318 |
20218 | Streptomyces nodosus gene for 16S rRNA, partial sequence, strain: NBRC 12895 | AB184226 | 1476 | ena | 40318 |
20218 | Streptomyces nodosus strain NRRL B-2371 16S ribosomal RNA gene, partial sequence | DQ026661 | 1495 | ena | 40318 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Streptomyces nodosus ATCC 14899 | GCA_008704995 | complete | ncbi | 40318 |
66792 | Streptomyces nodosus ATCC 14899 | GCA_000819545 | chromosome | ncbi | 40318 |
66792 | Streptomyces nodosus DSM 40109 | GCA_014205035 | contig | ncbi | 40318 |
66792 | Streptomyces nodosus ATCC 14899 | 40318.3 | complete | patric | 40318 |
66792 | Streptomyces nodosus strain ATCC 14899 | 40318.10 | complete | patric | 40318 |
66792 | Streptomyces nodosus strain ATCC 14899 | 40318.5 | wgs | patric | 40318 |
66792 | Streptomyces nodosus strain DSM 40109 | 40318.13 | wgs | patric | 40318 |
66792 | Streptomyces nodosus ATCC 14899 | 2563366705 | draft | img | 40318 |
66792 | Streptomyces nodosus ATCC 14899 | 2867064541 | complete | img | 40318 |
66792 | Streptomyces nodosus DSM 40109 | 2870767688 | draft | img | 40318 |
GC content
- @ref: 67770
- GC-content: 70.9
- method: genome sequence analysis
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | yes | 100 | no |
flagellated | no | 98.23 | no |
gram-positive | yes | 91.327 | no |
anaerobic | no | 98.797 | no |
aerobic | yes | 90.374 | no |
halophile | no | 96.247 | no |
spore-forming | yes | 96.029 | no |
thermophile | no | 96.31 | no |
glucose-util | yes | 89.69 | yes |
motile | no | 94.395 | no |
glucose-ferment | no | 86.865 | no |
External links
@ref: 9320
culture collection no.: DSM 40109, ATCC 14899, ATCC 23942, CBS 926.68, IFO 12895, ISP 5109, JCM 4297, JCM 4656, NBRC 12895, RIA 1123, SC 2388, BCRC 13768, CGMCC 4.1459, KCTC 9035, LMG 19340, NBIMCC 2208, NCIMB 12816, NRRL B-2371, RIA 831, VKM Ac-1224
straininfo link
- @ref: 84515
- straininfo: 13350
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Transcriptome | 10333524 | Molecular cloning and comparative sequence analyses of rRNA operons in Streptomyces nodosus ATCC 14899. | Yap WH, Wang Y | Gene | 10.1016/s0378-1119(99)00112-2 | 1999 | Base Sequence, Blotting, Southern, *Cloning, Molecular, Molecular Sequence Data, RNA, Bacterial/*genetics, RNA, Ribosomal, 16S/genetics, RNA, Ribosomal, 23S/genetics, RNA, Ribosomal, 5S/genetics, Restriction Mapping, Sequence Alignment, *Sequence Analysis, DNA, Streptomyces/*genetics, *rRNA Operon | Enzymology |
Enzymology | 11451671 | Amphotericin biosynthesis in Streptomyces nodosus: deductions from analysis of polyketide synthase and late genes. | Caffrey P, Lynch S, Flood E, Finnan S, Oliynyk M | Chem Biol | 10.1016/s1074-5521(01)00046-1 | 2001 | ATP-Binding Cassette Transporters/genetics, Amphotericin B/analogs & derivatives/*biosynthesis, Anti-Bacterial Agents/biosynthesis, Cloning, Molecular, Combinatorial Chemistry Techniques, Cytochrome P-450 Enzyme System/genetics, Genes, Fungal/genetics, Multienzyme Complexes/genetics, Multigene Family/genetics, Protein Engineering, Sequence Analysis, DNA, Streptomyces/enzymology/genetics/*metabolism, Transcription, Genetic | Transcriptome |
Metabolism | 33189073 | Enhanced amphotericin B production by genetically engineered Streptomyces nodosus. | Huang K, Zhang B, Shen ZY, Cai X, Liu ZQ, Zheng YG | Microbiol Res | 10.1016/j.micres.2020.126623 | 2020 | Acyl Coenzyme A, Amphotericin B/*biosynthesis, Antifungal Agents/metabolism, Base Sequence, Batch Cell Culture Techniques, Bioreactors, Biosynthetic Pathways/genetics, Fermentation, Gene Expression Regulation, Bacterial, Genes, Bacterial/genetics, Genetic Engineering/*methods, Multigene Family, Mutagenesis, Polyketides/metabolism, Secondary Metabolism/genetics, Streptomyces/*genetics/*metabolism | Biotechnology |
Transcriptome | 33598451 | Comparative Transcriptome Analysis of Streptomyces nodosus Mutant With a High-Yield Amphotericin B. | Huang K, Zhang B, Chen Y, Liu ZQ, Zheng YG | Front Bioeng Biotechnol | 10.3389/fbioe.2020.621431 | 2021 | Biotechnology | |
Biotechnology | 34194892 | Enhancing the production of amphotericin B by Strepyomyces nodosus in a 50-ton bioreactor based on comparative genomic analysis. | Huang K, Zhang B, Chen Y, Wu ZM, Liu ZQ, Zheng YG | 3 Biotech | 10.1007/s13205-021-02844-2 | 2021 |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
9320 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 40109) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-40109 | |||
18536 | Wink, J. | http://www.dsmz.de/microorganisms/wink_pdf/DSM40109.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) | |||
66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | 10.1093/nar/gkaa1025 | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | Nucleic Acids Res. 49: D498-D508 2020 | 33211880 | |
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 | |||
84515 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID13350.1 | StrainInfo: A central database for resolving microbial strain identifiers |