Strain identifier
BacDive ID: 16582
Type strain:
Species: Planotetraspora silvatica
Strain Designation: TT 00-51
Strain history: NBRC 100141 <-- T. Tamura TT 00-51.
NCBI tax ID(s): 234614 (species)
General
@ref: 12055
BacDive-ID: 16582
DSM-Number: 44746
keywords: genome sequence, 16S sequence, Bacteria, aerobe, spore-forming, mesophilic, Gram-positive
description: Planotetraspora silvatica TT 00-51 is an aerobe, spore-forming, mesophilic bacterium that was isolated from forest soil.
NCBI tax id
- NCBI tax id: 234614
- Matching level: species
strain history
@ref | history |
---|---|
12055 | <- T. Tamura; TT 00-51 |
67770 | NBRC 100141 <-- T. Tamura TT 00-51. |
doi: 10.13145/bacdive16582.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/actinomycetota
- domain: Bacteria
- phylum: Actinomycetota
- class: Actinomycetes
- order: Streptosporangiales
- family: Streptosporangiaceae
- genus: Planotetraspora
- species: Planotetraspora silvatica
- full scientific name: Planotetraspora silvatica Tamura and Sakane 2004
@ref: 12055
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Streptosporangiaceae
genus: Planotetraspora
species: Planotetraspora silvatica
full scientific name: Planotetraspora silvatica Tamura and Sakane 2004
strain designation: TT 00-51
type strain: yes
Morphology
cell morphology
@ref | gram stain | motility | confidence |
---|---|---|---|
30134 | positive | ||
69480 | no | 94.308 | |
69480 | positive | 100 |
colony morphology
@ref | colony color | incubation period | medium used |
---|---|---|---|
20110 | Grey brown (8019) | 10-14 days | ISP 2 |
20110 | Grey brown (8019) | 10-14 days | ISP 3 |
20110 | Beige (1001) | 10-14 days | ISP 4 |
20110 | Beige (1001) | 10-14 days | ISP 5 |
20110 | Golden yellow (1004) | 10-14 days | ISP 6 |
20110 | Beige (1001) | 10-14 days | ISP 7 |
multicellular morphology
@ref | forms multicellular complex | medium name |
---|---|---|
20110 | no | ISP 2 |
20110 | no | ISP 3 |
20110 | no | ISP 4 |
20110 | no | ISP 5 |
20110 | no | ISP 6 |
20110 | no | ISP 7 |
pigmentation
- @ref: 30134
- production: yes
Culture and growth conditions
culture medium
@ref | name | growth | composition | link |
---|---|---|---|---|
20110 | 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 | |
20110 | 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: | |
20110 | 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 | |
20110 | 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 | |
20110 | 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 | |
20110 | 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 | |
12055 | GPHF-MEDIUM (DSMZ Medium 553) | yes | Name: GPHF-MEDIUM (DSMZ Medium 553) Composition: Agar 20.0 g/l Glucose 10.0 g/l Beef extract 5.0 g/l Yeast extract 5.0 g/l Casein peptone 5.0 g/l CaCl2 x 2 H2O 0.74 g/l Distilled water | https://mediadive.dsmz.de/medium/553 |
12055 | TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) | yes | Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water | https://mediadive.dsmz.de/medium/535 |
12055 | N-Z-AMINE-MEDIUM (DSMZ Medium 554) | yes | Name: N-Z-AMINE-MEDIUM (DSMZ Medium 554) Composition: Starch 20.0 g/l Agar 20.0 g/l Glucose 10.0 g/l N-Z amine 5.0 g/l Yeast extract 5.0 g/l CaCO3 1.0 g/l Distilled water | https://mediadive.dsmz.de/medium/554 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
20110 | positive | optimum | 28 | mesophilic |
30134 | positive | growth | 25-30 | mesophilic |
30134 | positive | optimum | 27.5 | mesophilic |
67770 | positive | growth | 28 | mesophilic |
12055 | positive | growth | 28 | mesophilic |
Physiology and metabolism
oxygen tolerance
- @ref: 30134
- oxygen tolerance: aerobe
spore formation
@ref | spore formation | confidence |
---|---|---|
30134 | yes | |
69481 | yes | 92 |
69480 | yes | 100 |
observation
- @ref: 67770
- observation: quinones: MK-9(H4), MK-9(H2), MK-9
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
20110 | 17234 | glucose | + | |
20110 | 22599 | arabinose | + | |
20110 | 17992 | sucrose | + | |
20110 | 18222 | xylose | - | |
20110 | 17268 | myo-inositol | + | |
20110 | 29864 | mannitol | + | |
20110 | 28757 | fructose | + | |
20110 | 26546 | rhamnose | + | |
20110 | 16634 | raffinose | + | |
20110 | 62968 | cellulose | + | |
30134 | 28260 | galactose | + | carbon source |
30134 | 17234 | glucose | + | carbon source |
30134 | 17716 | lactose | + | carbon source |
30134 | 17306 | maltose | + | carbon source |
30134 | 29864 | mannitol | + | carbon source |
30134 | 28053 | melibiose | + | carbon source |
30134 | 16634 | raffinose | + | carbon source |
30134 | 26546 | rhamnose | + | carbon source |
enzymes
@ref | value | activity | ec |
---|---|---|---|
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
20110 | + | + | + | - | + | + | + | + | - | + | + | + | + | - | + | + | + | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent |
---|---|---|---|---|---|
12055 | forest soil | Amami-island, Kagoshima pref. | Japan | JPN | Asia |
67770 | Forest soil | Amami Island, Kagoshima Pref. | Japan | JPN | Asia |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Environmental | #Terrestrial | #Forest |
#Environmental | #Terrestrial | #Soil |
Safety information
risk assessment
@ref | biosafety level | biosafety level comment |
---|---|---|
12055 | 1 | Risk group (German classification) |
20110 | 1 | German classification |
Sequence information
16S sequences
- @ref: 12055
- description: Planotetraspora silvatica gene for 16S ribosomal RNA, partial sequence
- accession: AB112082
- length: 1472
- database: ena
- NCBI tax ID: 234614
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Planotetraspora silvatica NBRC 100141 | GCA_016863315 | contig | ncbi | 234614 |
66792 | Planotetraspora silvatica strain NBRC 100141 | 234614.3 | wgs | patric | 234614 |
GC content
@ref | GC-content | method |
---|---|---|
30134 | 71 | |
67770 | 70-71 | high performance liquid chromatography (HPLC) |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | yes | 92 | no |
motile | no | 93.47 | no |
gram-positive | yes | 87.434 | yes |
anaerobic | no | 98.83 | yes |
aerobic | yes | 93.522 | yes |
halophile | no | 94.183 | no |
spore-forming | yes | 92.995 | yes |
glucose-util | yes | 90.683 | no |
flagellated | no | 98.187 | no |
thermophile | no | 97.878 | yes |
glucose-ferment | no | 92.244 | no |
External links
@ref: 12055
culture collection no.: DSM 44746, NBRC 100141, JCM 12867, BCRC 16800, CGMCC 4.5632
straininfo link
- @ref: 85609
- straininfo: 134454
literature
- topic: Phylogeny
- Pubmed-ID: 15545433
- title: Planotetraspora silvatica sp. nov. and emended description of the genus Planotetraspora.
- authors: Tamura T, Sakane T
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.02981-0
- year: 2004
- mesh: Actinomycetales/chemistry/*classification/cytology/*isolation & purification, Alanine/isolation & purification, Bacterial Typing Techniques, Cell Wall/chemistry, DNA, Bacterial/chemistry/isolation & purification, DNA, Ribosomal/chemistry/isolation & purification, Diaminopimelic Acid/isolation & purification, Genes, rRNA, Glutamic Acid/isolation & purification, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Spores, Bacterial/cytology, Vitamin K 2/*analogs & derivatives/isolation & purification
- topic2: Enzymology
Reference
@id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
---|---|---|---|---|---|---|
12055 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44746) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-44746 | |||
20110 | Wink, J. | http://www.dsmz.de/microorganisms/wink_pdf/DSM44746.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 | |||
30134 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | 10.1128/mSphere.00237-17 | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 26485 | 28776041 | |
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/ | ||||
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 | |||
85609 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID134454.1 | StrainInfo: A central database for resolving microbial strain identifiers |