Strain identifier
BacDive ID: 16356
Type strain:
Species: Streptomyces yatensis
Strain history: DSM 41771 <-- M. Goodfellow SFOCin 76.
NCBI tax ID(s): 155177 (species)
General
@ref: 10557
BacDive-ID: 16356
DSM-Number: 41771
keywords: genome sequence, 16S sequence, Bacteria, spore-forming, mesophilic
description: Streptomyces yatensis DSM 41771 is a spore-forming, mesophilic bacterium that builds an aerial mycelium and was isolated from soil.
NCBI tax id
- NCBI tax id: 155177
- Matching level: species
strain history
@ref | history |
---|---|
10557 | <- M. Goodfellow; SFOcin 76 |
67770 | DSM 41771 <-- M. Goodfellow SFOCin 76. |
doi: 10.13145/bacdive16356.20230509.8.1
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 yatensis
- full scientific name: Streptomyces yatensis Saintpierre et al. 2003
@ref: 10557
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Streptomycetaceae
genus: Streptomyces
species: Streptomyces yatensis
full scientific name: Streptomyces yatensis Saintpierre et al. 2003
type strain: yes
Morphology
cell morphology
@ref | motility | confidence | gram stain |
---|---|---|---|
69480 | no | 91.648 | |
69480 | 100 | positive |
colony morphology
@ref | colony color | medium used |
---|---|---|
69301 | Beige (1001) | ISP 7 |
69301 | Ivory (1014) | ISP 2 |
69301 | Ivory (1014) | ISP 3 |
69301 | Ivory (1014) | ISP 5 |
69301 | Ivory (1014) | ISP 6 |
69301 | Light ivory (1015) | ISP 4 |
69301 | Light ivory (1015) | suter without tyrosine |
69301 | Ochre yellow (1024) | suter with tyrosine |
multicellular morphology
@ref | forms multicellular complex | complex name | complex color | medium name |
---|---|---|---|---|
69301 | yes | Aerial mycelium | Light ivory (1015), signal black (9004) | ISP 2 |
69301 | yes | Aerial mycelium | Dusty grey (7037), signal black (9004) | ISP 3 |
69301 | yes | Aerial mycelium | Traffic white (9016) | ISP 4 |
69301 | yes | Aerial mycelium | Quarz grey (7039), signal white (9003) | ISP 5 |
69301 | no | Aerial mycelium | ISP 6 | |
69301 | yes | Aerial mycelium | Dusty grey (7037), signal white (9003) | ISP 7 |
69301 | yes | Aerial mycelium | suter with tyrosine | |
69301 | yes | Aerial mycelium | suter without tyrosine |
pigmentation
@ref | production | name | color |
---|---|---|---|
69301 | yes | Melanin | |
69301 | yes | soluble pigment | Ivory (1014), ochre yellow (1024), light ivory (1015) |
multimedia
@ref | multimedia content | caption | intellectual property rights |
---|---|---|---|
69301 | DSM_41771_image3.jpeg | Plates (65, ISP2, ISP3, ISP4, ISP5, ISP7) | Helmholtz-Zentrum für Infektionsforschung GmbH |
69301 | DSM_41771_image4.jpeg | Plates (65, ISP2, ISP3, ISP4, ISP5, ISP7) | Helmholtz-Zentrum für Infektionsforschung GmbH |
69301 | DSM_41771_image5.jpeg | (ISP6, SSM+T, SSM-T) | Helmholtz-Zentrum für Infektionsforschung GmbH |
69301 | DSM_41771_image6.jpeg | (ISP6, SSM+T, SSM-T) | Helmholtz-Zentrum für Infektionsforschung GmbH |
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
10557 | 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 |
10557 | 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 |
10557 | STARCH - MINERAL SALT - AGAR (STMS) (DSMZ Medium 252) | yes | https://mediadive.dsmz.de/medium/252 | Name: STARCH - MINERAL SALT - AGAR (STMS) (DSMZ Medium 252) Composition: Agar 14.985 g/l Starch 9.99001 g/l (NH4)2SO4 1.998 g/l CaCO3 1.998 g/l K2HPO4 0.999001 g/l MgSO4 x 7 H2O 0.999001 g/l NaCl 0.999001 g/l FeSO4 x 7 H2O 0.000999001 g/l MnCl2 x 4 H2O 0.000999001 g/l ZnSO4 x 7 H2O 0.000999001 g/l Distilled water |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
10557 | positive | growth | 28 | mesophilic |
67770 | positive | growth | 28 | mesophilic |
Physiology and metabolism
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | yes | 100 |
69480 | yes | 100 |
halophily
- @ref: 69301
- salt: NaCl
- growth: positive
- tested relation: growth
- concentration: 0 %
observation
- @ref: 67770
- observation: quinones: MK-9(H8)
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
69301 | 22599 | arabinose | +/- | growth |
69301 | 62968 | cellulose | - | growth |
69301 | 28757 | fructose | - | growth |
69301 | 17234 | glucose | + | growth |
69301 | 17268 | inositol | + | growth |
69301 | 37684 | mannose | + | growth |
69301 | 16634 | raffinose | + | growth |
69301 | 26546 | rhamnose | + | growth |
69301 | 17992 | sucrose | - | growth |
69301 | 18222 | xylose | + | growth |
68379 | 17632 | nitrate | - | reduction |
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 |
68379 | 28087 | glycogen | - | fermentation |
enzymes
@ref | value | activity | ec |
---|---|---|---|
68379 | gelatinase | + | |
68379 | urease | - | 3.5.1.5 |
68379 | N-acetyl-beta-glucosaminidase | + | 3.2.1.52 |
68379 | alpha-glucosidase | - | 3.2.1.20 |
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 | 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 | 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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
69301 | - | - | - | + | - | +/- | - | + | +/- | - | + | - | - | - | - | - | - | - | - |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
69301 | + | +/- | +/- | +/- | + | + | + | + | - | + | + | + | + | - | +/- | + | + | + | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | country | origin.country | continent | geographic location |
---|---|---|---|---|---|
10557 | soil | New Caledonia | NCL | Australia and Oceania | |
67770 | Ultramafic soil | France | FRA | Europe | Narbonne |
isolation source categories
- Cat1: #Environmental
- Cat2: #Terrestrial
- Cat3: #Soil
Safety information
risk assessment
- @ref: 10557
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Streptomyces yatensis 16S ribosomal RNA gene, partial sequence | AF336800 | 1493 | ena | 155177 |
20218 | Streptomyces yatensis gene for 16S rRNA, partial sequence, strain: NBRC 101000 | AB249962 | 1460 | ena | 155177 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Streptomyces yatensis DSM 41771 | GCA_018069625 | complete | ncbi | 155177 |
66792 | Streptomyces yatensis strain DSM 41771 | 155177.3 | complete | patric | 155177 |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | yes | 100 | no |
flagellated | no | 98.178 | no |
gram-positive | yes | 87.475 | no |
anaerobic | no | 99.321 | no |
aerobic | yes | 93.074 | no |
halophile | no | 89.273 | no |
spore-forming | yes | 94.995 | no |
thermophile | no | 98.154 | yes |
glucose-util | yes | 90.849 | no |
motile | no | 92.801 | no |
glucose-ferment | no | 90.368 | yes |
External links
@ref: 10557
culture collection no.: DSM 41771, CIP 109043, NBRC 101000, NRRL B-24116, SFOcin 76, JCM 13244, NCIMB 14454
straininfo link
- @ref: 85411
- straininfo: 87964
literature
- topic: Phylogeny
- Pubmed-ID: 28829023
- title: Streptomyces solisilvae sp. nov., isolated from tropical forest soil.
- authors: Zhou S, Yang X, Huang D, Huang X
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijsem.0.002166
- year: 2017
- mesh: Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, *Forests, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Streptomyces/*classification/genetics/isolation & purification, Tropical Climate
- topic2: Transcriptome
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
10557 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 41771) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-41771 | |||
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/ | ||||
68379 | Automatically annotated from API Coryne | |||||
68382 | Automatically annotated from API zym | |||||
69301 | Wink, J. | https://cdn.dsmz.de/wink/DSM%2041771.pdf | Compendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig | |||
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 | |||
85411 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID87964.1 | StrainInfo: A central database for resolving microbial strain identifiers |