Strain identifier
BacDive ID: 15120
Type strain:
Species: Streptomyces daghestanicus
Strain history: KCC S-0365 <-- IFO 12762 <-- SAJ <-- ISP 5149 <-- INA 2656/55.
NCBI tax ID(s): 66885 (species)
General
@ref: 9349
BacDive-ID: 15120
DSM-Number: 40149
keywords: genome sequence, 16S sequence, Bacteria, spore-forming, mesophilic, Gram-positive, antibiotic compound production
description: Streptomyces daghestanicus DSM 40149 is a spore-forming, mesophilic, Gram-positive bacterium that produces antibiotic compounds and was isolated from soil.
NCBI tax id
- NCBI tax id: 66885
- Matching level: species
strain history
@ref | history |
---|---|
9349 | <- E.B. Shirling, ISP <- T.P. Preobrazhenskaya, INA |
67770 | KCC S-0365 <-- IFO 12762 <-- SAJ <-- ISP 5149 <-- INA 2656/55. |
doi: 10.13145/bacdive15120.20230509.8.1
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 daghestanicus
- full scientific name: Streptomyces daghestanicus (Sveshnikova 1957) Pridham et al. 1958 (Approved Lists 1980)
synonyms
- @ref: 20215
- synonym: Actinomyces daghestanicus
@ref: 9349
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Streptomycetaceae
genus: Streptomyces
species: Streptomyces daghestanicus
full scientific name: Streptomyces daghestanicus (Sveshnikova 1957) Pridham et al. 1958
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: positive
- confidence: 100
Culture and growth conditions
culture medium
- @ref: 9349
- name: GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)
- growth: yes
- link: https://mediadive.dsmz.de/medium/65
- composition: 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
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
18547 | positive | optimum | 28 | mesophilic |
9349 | 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: 9349
- compound: etamycin
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
18547 | 17234 | glucose | + | |
18547 | 22599 | arabinose | + | |
18547 | 17992 | sucrose | + | |
18547 | 18222 | xylose | + | |
18547 | 17268 | myo-inositol | + | |
18547 | 29864 | mannitol | + | |
18547 | 28757 | fructose | + | |
18547 | 26546 | rhamnose | + | |
18547 | 16634 | raffinose | + | |
18547 | 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 | etamycin | 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 |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
18547 | + | + | + | + | + | + | - | + | - | + | + | - | + | - | + | + | - | + | - |
API 20E
@ref | ONPG | ADH Arg | LDC Lys | ODC | CIT | H2S | URE | TDA Trp | IND | VP | GEL |
---|---|---|---|---|---|---|---|---|---|---|---|
18547 | + | - | - | - | + | - | + | - | - | - | + |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent |
---|---|---|---|---|---|
9349 | soil | Daghestan | Russia | RUS | Europe |
67770 | Soil | Russia | RUS |
isolation source categories
- Cat1: #Environmental
- Cat2: #Terrestrial
- Cat3: #Soil
taxonmaps
- @ref: 69479
- File name: preview.99_720.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15;96_91;97_287;98_384;99_720&stattab=map
- Last taxonomy: Streptomyces
- 16S sequence: DQ442497
- Sequence Identity:
- Total samples: 129
- soil counts: 39
- aquatic counts: 5
- animal counts: 85
Safety information
risk assessment
@ref | biosafety level | biosafety level comment |
---|---|---|
18547 | 1 | German classification |
9349 | 1 | Risk group (German classification) |
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Streptomyces daghestanicus gene for 16S ribosomal RNA, partial sequence, strain: JCM 4365 | D44082 | 120 | ena | 66885 |
20218 | Streptomyces griseoviridis gene for 16S rRNA, partial sequence, strain: NBRC 12762 | AB184125 | 1445 | ena | 45398 |
20218 | Streptomyces daghestanicus strain NRRL B-5418T 16S ribosomal RNA gene, partial sequence | DQ442497 | 1481 | ena | 66885 |
20218 | Streptomyces daghestanicus strain NRRL B-5418 16S ribosomal RNA gene, partial sequence | KJ027122 | 481 | ena | 66885 |
67770 | Streptomyces daghestanicus JCM 4365 gene for 16S rRNA, partial sequence | LC506592 | 1462 | ena | 66885 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Streptomyces daghestanicus JCM 4365 | GCA_014649475 | scaffold | ncbi | 66885 |
66792 | Streptomyces daghestanicus NBRC 12762 | GCA_020521275 | contig | ncbi | 66885 |
66792 | Streptomyces daghestanicus strain JCM 4365 | 66885.4 | wgs | patric | 66885 |
66792 | Streptomyces daghestanicus strain NBRC 12762 | 66885.7 | wgs | patric | 66885 |
66792 | Streptomyces daghestanicus strain NBRC 12762 | 66885.5 | wgs | patric | 66885 |
66792 | Streptomyces daghestanicus strain NBRC 12762 | 66885.6 | wgs | patric | 66885 |
GC content
- @ref: 67770
- GC-content: 73
- method: fluorimetric
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | yes | 100 | no |
flagellated | no | 97.773 | no |
gram-positive | yes | 89.358 | no |
anaerobic | no | 99.039 | no |
aerobic | yes | 93.963 | no |
halophile | no | 93.935 | no |
spore-forming | yes | 95.951 | no |
glucose-util | yes | 89.84 | yes |
thermophile | no | 97.084 | no |
motile | no | 93.87 | no |
glucose-ferment | no | 88.146 | no |
External links
@ref: 9349
culture collection no.: DSM 40149, ATCC 19747, ATCC 23620, CBS 486.68, IFO 12762, INA 2656/55, ISP 5149, JCM 4365, NBRC 12762, RIA 1028, BCRC 11468, CGMCC 4.1690, NRRL B-5418, VKM Ac-1722, VKM Ac-1862
straininfo link
- @ref: 84225
- straininfo: 386964
literature
- Pubmed-ID: 15835778
- title: [Cell wall teichoic acids from Streptomyces daghestanicus VKM Ac-1722T and Streptomyces murinus INA-00524T].
- authors: Streshinskaia GM, Koslova IuI, Alferova IV, Shashkov AS, Evtushenko LI
- journal: Mikrobiologiia
- year: 2005
- mesh: Cell Wall/chemistry, Nuclear Magnetic Resonance, Biomolecular, Streptomyces/*chemistry, Teichoic Acids/*chemistry
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
9349 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 40149) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-40149 | |||
18547 | Wink, J. | http://www.dsmz.de/microorganisms/wink_pdf/DSM40149.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 | |||
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 | |||||
68382 | Automatically annotated from API zym | |||||
69479 | João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich. | https://microbeatlas.org/ | MicrobeAtlas 1.0 beta | |||
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 | |||
84225 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID386964.1 | StrainInfo: A central database for resolving microbial strain identifiers |