Strain identifier
BacDive ID: 13488
Type strain: 
Species: Saccharothrix ecbatanensis
Strain Designation: HM 537
Strain history: <- J. Hamedi, Univ. Tehran, Iran <- F. Mohammadipanah; UTMC 537
NCBI tax ID(s): 1105145 (species)
version 8.1 (current version)
General
@ref: 17344
BacDive-ID: 13488
DSM-Number: 45486
keywords: genome sequence, 16S sequence, Bacteria, aerobe, spore-forming, mesophilic, Gram-positive
description: Saccharothrix ecbatanensis HM 537 is an aerobe, spore-forming, mesophilic bacterium that was isolated from rhizospheric soil.
NCBI tax id
- NCBI tax id: 1105145
- Matching level: species
strain history
- @ref: 17344
- history: <- J. Hamedi, Univ. Tehran, Iran <- F. Mohammadipanah; UTMC 537
doi: 10.13145/bacdive13488.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/actinomycetota
- domain: Bacteria
- phylum: Actinomycetota
- class: Actinomycetes
- order: Pseudonocardiales
- family: Pseudonocardiaceae
- genus: Saccharothrix
- species: Saccharothrix ecbatanensis
- full scientific name: Saccharothrix ecbatanensis Mohammadipanah et al. 2015
@ref: 17344
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Pseudonocardiaceae
genus: Saccharothrix
species: Saccharothrix ecbatanensis
full scientific name: Saccharothrix ecbatanensis Mohammadipanah et al. 2015
strain designation: HM 537
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: positive
- confidence: 100
colony morphology
| @ref | colony color | incubation period | medium used |
|---|---|---|---|
| 21431 | Light ivory (1015) | 10-14 days | ISP 2 |
| 21431 | Ivory (1014) | 10-14 days | ISP 3 |
| 21431 | Ivory (1014) | 10-14 days | ISP 4 |
| 21431 | Pastel yellow (1034) | 10-14 days | ISP 5 |
| 21431 | Light ivory (1015) | 10-14 days | ISP 6 |
| 21431 | 10-14 days | ISP 7 | |
| 21431 | Light ivory (1015) | 10-14 days | Suter with tyrosine |
| 21431 | Light ivory (1015) | 10-14 days | Suter without tyrosine |
| 62934 | 2 days |
multimedia
| @ref | multimedia content | caption | intellectual property rights |
|---|---|---|---|
| 66793 | EM_DSM_45486_1.jpg | electron microscopic image | © HZI/Manfred Rohde |
| 66793 | EM_DSM_45486_2.jpg | electron microscopic image | © HZI/Manfred Rohde |
| 66793 | EM_DSM_45486_3.jpg | electron microscopic image | © HZI/Manfred Rohde |
| 66793 | EM_DSM_45486_4.jpg | electron microscopic image | © HZI/Manfred Rohde |
| 66793 | EM_DSM_45486_5.jpg | electron microscopic image | © HZI/Manfred Rohde |
Culture and growth conditions
culture medium
| @ref | name | growth | composition | link |
|---|---|---|---|---|
| 21431 | 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 | |
| 21431 | 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: | |
| 21431 | 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 | |
| 21431 | 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 | |
| 21431 | 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 | |
| 21431 | 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 | |
| 21431 | Suter with tyrosine | yes | Name: Synthetically suter medium (5337) with and without tyrosine - see Kutzner,H.J., R. M. Kroppensted and F. Korn-Wendisch. (1986) Composition: Glycerol 15.0 g/l Tyrosine 1.0 (optional, see preparation comment) L-arginine 5.0 g/l L-glutamic acid 5.0 g/l L-methionine 0.3 g/l L-isoleucine 0.3 g/l K2HPO4 0.5 g/l MgSO4 x 7 H2O 0.2 g/l Agar 20.0 g/l Trace element solution (5341) 1.0 ml Composition of Trace element solution (5341): CuSO4 x 5 H2O 10.0 g/l CaCl2 x 2 H2O 10.0 g/l FeSO4 x 7 H2O 10.0 g/l ZnSO4 x 7 H2O 10.0 g/l MnSO4 x 7 H2O 40.0 g/l Preparation: Control medium is prepared without tyrosine Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigment Organisms: All Actinomycetes | |
| 21431 | Suter without tyrosine | yes | Name: Synthetically suter medium (5337) with and without tyrosine - see Kutzner,H.J., R. M. Kroppensted and F. Korn-Wendisch. (1986) Composition: Glycerol 15.0 g/l Tyrosine 1.0 (optional, see preparation comment) L-arginine 5.0 g/l L-glutamic acid 5.0 g/l L-methionine 0.3 g/l L-isoleucine 0.3 g/l K2HPO4 0.5 g/l MgSO4 x 7 H2O 0.2 g/l Agar 20.0 g/l Trace element solution (5341) 1.0 ml Composition of Trace element solution (5341): CuSO4 x 5 H2O 10.0 g/l CaCl2 x 2 H2O 10.0 g/l FeSO4 x 7 H2O 10.0 g/l ZnSO4 x 7 H2O 10.0 g/l MnSO4 x 7 H2O 40.0 g/l Preparation: Control medium is prepared without tyrosine Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigment Organisms: All Actinomycetes | |
| 17344 | GYM STREPTOMYCES MEDIUM (DSMZ Medium 65) | yes | 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 | https://mediadive.dsmz.de/medium/65 |
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 62934 | positive | growth | 30 | mesophilic |
| 17344 | positive | growth | 28 | mesophilic |
Physiology and metabolism
oxygen tolerance
- @ref: 62934
- oxygen tolerance: aerobe
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | yes | 100 |
| 69480 | yes | 100 |
halophily
- @ref: 21431
- salt: NaCl
- growth: positive
- tested relation: maximum
- concentration: 7.5 %
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 21431 | 17234 | glucose | + | |
| 21431 | 22599 | arabinose | + | |
| 21431 | 17992 | sucrose | + | |
| 21431 | 18222 | xylose | + | |
| 21431 | 17268 | myo-inositol | + | |
| 21431 | 37684 | mannose | + | |
| 21431 | 28757 | fructose | + | |
| 21431 | 26546 | rhamnose | + | |
| 21431 | 16634 | raffinose | + | |
| 21431 | 62968 | cellulose | - | |
| 68379 | 17632 | nitrate | - | reduction |
| 68379 | 4853 | esculin | + | hydrolysis |
| 68379 | 16199 | urea | + | hydrolysis |
| 68379 | 5291 | gelatin | + | hydrolysis |
| 68379 | 17634 | D-glucose | - | fermentation |
| 68379 | 16988 | D-ribose | - | fermentation |
| 68379 | 65327 | D-xylose | - | fermentation |
| 68379 | 16899 | D-mannitol | - | fermentation |
| 68379 | 17306 | maltose | - | fermentation |
| 68379 | 17716 | lactose | - | fermentation |
| 68379 | 17992 | sucrose | - | fermentation |
enzymes
| @ref | value | activity | ec |
|---|---|---|---|
| 68379 | gelatinase | + | |
| 68379 | urease | + | 3.5.1.5 |
| 68379 | beta-glucosidase | + | 3.2.1.21 |
| 68379 | N-acetyl-beta-glucosaminidase | + | 3.2.1.52 |
| 68379 | alpha-glucosidase | + | 3.2.1.20 |
| 68379 | beta-galactosidase | + | 3.2.1.23 |
| 68379 | beta-glucuronidase | - | 3.2.1.31 |
| 68379 | alkaline phosphatase | + | 3.1.3.1 |
| 68379 | pyrrolidonyl arylamidase | - | 3.4.19.3 |
| 68379 | pyrazinamidase | - | 3.5.1.B15 |
| 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 | trypsin | + | 3.4.21.4 |
| 68382 | alpha-chymotrypsin | + | 3.4.21.1 |
| 68382 | acid phosphatase | + | 3.1.3.2 |
| 68382 | alpha-galactosidase | + | 3.2.1.22 |
| 68382 | beta-galactosidase | + | 3.2.1.23 |
| 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 coryne
| @ref | NIT | PYZ | PYRA | PAL | beta GUR | beta GAL | alpha GLU | beta NAG | ESC | URE | GEL | GLU | RIB | XYL | MAN | MAL | LAC | SAC | GLYG |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 21431 | - | - | - | + | - | + | + | + | + | + | + | - | - | - | - | - | - | - | +/- |
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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 21431 | + | + | + | + | + | + | +/- | + | + | + | +/- | + | + | +/- | + | + | + | - | - |
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent | sampling date |
|---|---|---|---|---|---|---|
| 17344 | rhizospheric soil | Hamedan Province | Iran | IRN | Asia | |
| 62934 | Soil,rhizosperic | Khuzestan province | Iran | IRN | Asia | 2008 |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Terrestrial | #Soil |
| #Host Body-Site | #Plant | #Rhizosphere |
Safety information
risk assessment
| @ref | biosafety level | biosafety level comment |
|---|---|---|
| 21431 | L1 | German classification |
| 17344 | 1 | Risk group (German classification) |
Sequence information
16S sequences
- @ref: 17344
- description: Saccharothrix ecbatanensis strain UTMC 00537 16S ribosomal RNA gene, partial sequence
- accession: JN038074
- length: 1512
- database: ena
- NCBI tax ID: 1105145
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Saccharothrix ecbatanensis DSM 45486 | GCA_014205015 | contig | ncbi | 1105145 |
| 66792 | Saccharothrix ecbatanensis strain DSM 45486 | 1105145.3 | wgs | patric | 1105145 |
| 66792 | Saccharothrix ecbatanensis DSM 45486 | 2870721527 | draft | img | 1105145 |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | yes | 100 | no |
| motile | no | 89.458 | no |
| flagellated | no | 97.035 | no |
| gram-positive | yes | 85.747 | no |
| anaerobic | no | 98.528 | no |
| aerobic | yes | 89.702 | yes |
| halophile | no | 87.639 | no |
| spore-forming | yes | 95.214 | no |
| thermophile | no | 99.551 | no |
| glucose-util | yes | 88.456 | no |
| glucose-ferment | no | 91.316 | yes |
External links
@ref: 17344
culture collection no.: DSM 45486, CCUG 63021, UTMC 537, UTMC 00537
straininfo link
- @ref: 82680
- straininfo: 400822
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 26376915 | Saccharothrix ecbatanensis sp. nov., an actinobacterium isolated from soil. | Mohammadipanah F, Hamedi J, Schumann P, Sproer C, Carmen Montero-Calasanz MD, Klenk HP | Int J Syst Evol Microbiol | 10.1099/ijsem.0.000607 | 2015 | Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Cell Wall/chemistry, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Iran, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistry | Genetics |
| Phylogeny | 27535702 | Saccharothrix isguenensis sp. nov., an actinobacterium isolated from desert soil. | Bouznada K, Bouras N, Mokrane S, Chaabane Chaouch F, Zitouni A, Potter G, Sproer C, Klenk HP, Sabaou N | Int J Syst Evol Microbiol | 10.1099/ijsem.0.001430 | 2016 | Actinomycetales/*classification/genetics/isolation & purification, Africa, Northern, Algeria, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, DNA, Bacterial/genetics, *Desert Climate, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Nucleic Acid Hybridization, Phospholipids/analysis/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistry | Transcriptome |
| Metabolism | 29275696 | Potential of rare actinomycetes in the production of metabolites against multiple oxidant agents. | Mohammadipanah F, Momenilandi M | Pharm Biol | 10.1080/13880209.2017.1417451 | 2018 | Actinobacteria/*metabolism, Animals, Antioxidants/isolation & purification/*metabolism/pharmacology, Artemia, Cell Survival/drug effects/physiology, Enzyme Inhibitors/isolation & purification/metabolism/pharmacology, Free Radical Scavengers/isolation & purification/metabolism/pharmacology, Human Umbilical Vein Endothelial Cells/drug effects/metabolism, Humans, Oxidants/*antagonists & inhibitors/*metabolism | Pathogenicity |
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 17344 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45486) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-45486 | |||
| 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 | |||
| 21431 | Wink, J. | http://www.dsmz.de/microorganisms/wink_pdf/DSM45486.pdf | Compendium of Actinobacteria . HZI-Helmholtz-Centre for Infection Research, Braunschweig | |||
| 62934 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 63021) | https://www.ccug.se/strain?id=63021 | |||
| 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) | |||
| 66793 | Mukherjee et al. | 10.1038/nbt.3886 | GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life | 35: 676-683 2017 | 28604660 | |
| 68379 | Automatically annotated from API Coryne | |||||
| 68382 | Automatically annotated from API zym | |||||
| 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 | |||
| 82680 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID400822.1 | StrainInfo: A central database for resolving microbial strain identifiers |