Strain identifier
BacDive ID: 13260
Type strain:
Species: Amycolatopsis saalfeldensis
Strain Designation: 2406-001
Strain history: DSM 44993 <-- I. Groth HKI 0457 <-- Ch. Weigel.
NCBI tax ID(s): 394193 (species)
General
@ref: 12225
BacDive-ID: 13260
DSM-Number: 44993
keywords: genome sequence, 16S sequence, Bacteria, aerobe, spore-forming, mesophilic, Gram-positive, rod-shaped
description: Amycolatopsis saalfeldensis 2406-001 is an aerobe, spore-forming, mesophilic bacterium that builds an aerial mycelium and was isolated from Feengrotten, rock wall centralgrotta, 2nd floor.
NCBI tax id
- NCBI tax id: 394193
- Matching level: species
strain history
@ref | history |
---|---|
12225 | <- I. Groth; HKI 0457 <- Ch. Weigel |
67770 | DSM 44993 <-- I. Groth HKI 0457 <-- Ch. Weigel. |
doi: 10.13145/bacdive13260.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/actinomycetota
- domain: Bacteria
- phylum: Actinomycetota
- class: Actinomycetes
- order: Pseudonocardiales
- family: Pseudonocardiaceae
- genus: Amycolatopsis
- species: Amycolatopsis saalfeldensis
- full scientific name: Amycolatopsis saalfeldensis Carlsohn et al. 2007
@ref: 12225
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Pseudonocardiaceae
genus: Amycolatopsis
species: Amycolatopsis saalfeldensis
full scientific name: Amycolatopsis saalfeldensis Carlsohn et al. 2007 emend. Nouioui et al. 2018
strain designation: 2406-001
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell shape | motility | confidence |
---|---|---|---|---|
32064 | positive | rod-shaped | no | |
69480 | no | 94.101 | ||
69480 | positive | 100 |
colony morphology
@ref | colony color | incubation period | medium used |
---|---|---|---|
20154 | Beige (1001) | 10-14 days | ISP 2 |
20154 | Beige (1001) | 10-14 days | ISP 3 |
20154 | Beige (1001) | 10-14 days | ISP 4 |
20154 | Beige (1001) | 10-14 days | ISP 5 |
20154 | Beige (1001) | 10-14 days | ISP 6 |
20154 | Beige (1001) | 10-14 days | ISP 7 |
multicellular morphology
@ref | forms multicellular complex | complex name | complex color | medium name |
---|---|---|---|---|
20154 | yes | Aerial Mycelium | Cream | ISP 2 |
20154 | yes | Aerial Mycelium | Cream | ISP 3 |
20154 | yes | Aerial Mycelium | Cream | ISP 4 |
20154 | no | ISP 5 | ||
20154 | no | ISP 6 | ||
20154 | yes | Aerial Mycelium | Cream | ISP 7 |
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
12225 | 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 |
20154 | 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 | |
20154 | 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: | |
20154 | 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 | |
20154 | 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 | |
20154 | 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 | |
20154 | 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 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
12225 | positive | growth | 28 | mesophilic |
20154 | positive | optimum | 28 | mesophilic |
32064 | positive | growth | 10-42 | |
32064 | positive | optimum | 27.5 | mesophilic |
67770 | positive | growth | 28 | mesophilic |
culture pH
@ref | ability | type | pH |
---|---|---|---|
32064 | positive | growth | 4.5-8.0 |
32064 | positive | optimum | 6.25 |
Physiology and metabolism
oxygen tolerance
- @ref: 32064
- oxygen tolerance: aerobe
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | yes | 100 |
69480 | yes | 99.447 |
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
32064 | NaCl | positive | growth | 0.0-2.0 % |
32064 | NaCl | positive | optimum | 2 % |
observation
- @ref: 67770
- observation: quinones: MK-9(H4)
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
32064 | 30089 | acetate | + | carbon source |
32064 | 22599 | arabinose | + | carbon source |
32064 | 16947 | citrate | + | carbon source |
32064 | 28757 | fructose | + | carbon source |
32064 | 17234 | glucose | + | carbon source |
32064 | 25115 | malate | + | carbon source |
32064 | 29864 | mannitol | + | carbon source |
32064 | 506227 | N-acetylglucosamine | + | carbon source |
32064 | 26546 | rhamnose | + | carbon source |
32064 | 30031 | succinate | + | carbon source |
32064 | 17992 | sucrose | + | carbon source |
32064 | 53426 | tween 80 | + | carbon source |
32064 | 18222 | xylose | + | carbon source |
32064 | 4853 | esculin | + | hydrolysis |
68369 | 25115 | malate | - | assimilation |
68369 | 17128 | adipate | - | assimilation |
68369 | 27689 | decanoate | - | assimilation |
68369 | 24265 | gluconate | - | assimilation |
68369 | 17306 | maltose | - | assimilation |
68369 | 59640 | N-acetylglucosamine | - | assimilation |
68369 | 16899 | D-mannitol | - | assimilation |
68369 | 16024 | D-mannose | - | assimilation |
68369 | 30849 | L-arabinose | - | assimilation |
68369 | 17634 | D-glucose | - | assimilation |
68369 | 5291 | gelatin | - | hydrolysis |
68369 | 16199 | urea | - | hydrolysis |
68369 | 29016 | arginine | - | hydrolysis |
68369 | 17634 | D-glucose | - | fermentation |
68369 | 27897 | tryptophan | - | energy source |
68369 | 17632 | nitrate | - | reduction |
metabolite production
@ref | Chebi-ID | metabolite | production |
---|---|---|---|
32064 | 16136 | hydrogen sulfide | yes |
68369 | 35581 | indole | no |
metabolite tests
- @ref: 68369
- Chebi-ID: 35581
- metabolite: indole
- indole test: -
enzymes
@ref | value | activity | ec |
---|---|---|---|
32064 | acid phosphatase | + | 3.1.3.2 |
32064 | alkaline phosphatase | + | 3.1.3.1 |
32064 | gelatinase | + | |
32064 | cytochrome oxidase | + | 1.9.3.1 |
32064 | urease | + | 3.5.1.5 |
68369 | gelatinase | - | |
68369 | urease | - | 3.5.1.5 |
68369 | arginine dihydrolase | - | 3.5.3.6 |
68382 | alkaline phosphatase | + | 3.1.3.1 |
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 | alpha-galactosidase | - | 3.2.1.22 |
68382 | beta-galactosidase | - | 3.2.1.23 |
68382 | beta-glucuronidase | - | 3.2.1.31 |
68382 | N-acetyl-beta-glucosaminidase | + | 3.2.1.52 |
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 | Control |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
20154 | + | + | + | - | + | - | - | - | - | + | + | - | - | - | + | + | + | - | - | |
12225 | + | - | - | - | + | - | - | - | - | +/- | +/- | - | - | - | - | - | + | +/- | - | - |
API 20NE
@ref | NO3 | TRP | GLU_ Ferm | ADH Arg | URE | ESC | GEL | PNPG | GLU_ Assim | ARA | MNE | MAN | NAG | MAL | GNT | CAP | ADI | MLT | CIT | PAC |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
12225 | - | - | - | - | - | +/- | - | - | - | - | - | - | - | - | - | - | - | - | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent |
---|---|---|---|---|---|
12225 | Feengrotten, rock wall centralgrotta, 2nd floor | Thuringia, Saalfeld | Germany | DEU | Europe |
67770 | Acidic and heavy-metal-containing rocks in the central grotto of the medieval alum slate mine Feengrotten | Saalfeld, Thuringia | Germany | DEU | Europe |
isolation source categories
- Cat1: #Environmental
- Cat2: #Terrestrial
- Cat3: #Geologic
Safety information
risk assessment
@ref | biosafety level | biosafety level comment |
---|---|---|
12225 | 1 | Risk group (German classification) |
20154 | 1 |
Sequence information
16S sequences
- @ref: 12225
- description: Amycolatopsis saalfeldensis strain 2406-001 16S ribosomal RNA gene, partial sequence
- accession: DQ792500
- length: 1448
- database: ena
- NCBI tax ID: 394193
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Amycolatopsis saalfeldensis strain DSM 44993 | 394193.4 | wgs | patric | 394193 |
66792 | Amycolatopsis saalfeldensis DSM 44993 | 2634166333 | draft | img | 394193 |
67770 | Amycolatopsis saalfeldensis DSM 44993 | GCA_900110575 | scaffold | ncbi | 394193 |
GC content
- @ref: 67770
- GC-content: 71
- method: genome sequence analysis
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | yes | 100 | no |
gram-positive | yes | 85.047 | yes |
anaerobic | no | 99.03 | no |
halophile | no | 92.659 | no |
spore-forming | yes | 88.864 | no |
glucose-util | yes | 89.972 | no |
aerobic | yes | 89.531 | yes |
motile | no | 94.429 | yes |
flagellated | no | 97.439 | no |
thermophile | no | 98.081 | no |
glucose-ferment | no | 91.858 | no |
External links
@ref: 12225
culture collection no.: DSM 44993, JCM 14909, NRRL B-24474, HKI 0457
straininfo link
- @ref: 82464
- straininfo: 297474
literature
- topic: Phylogeny
- Pubmed-ID: 17625209
- title: Amycolatopsis saalfeldensis sp. nov., a novel actinomycete isolated from a medieval alum slate mine.
- authors: Carlsohn MR, Groth I, Tan GYA, Schutze B, Saluz HP, Munder T, Yang J, Wink J, Goodfellow M
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.64903-0
- year: 2007
- mesh: Actinobacteria/chemistry/*classification/genetics/*isolation & purification, Bacterial Typing Techniques, Cluster Analysis, DNA Fingerprinting, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Genes, rRNA, Genotype, Germany, Molecular Sequence Data, Phylogeny, Polymerase Chain Reaction/methods, Quinones/analysis, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, *Soil Microbiology
- topic2: Genetics
Reference
@id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed | journal |
---|---|---|---|---|---|---|---|
12225 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44993) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-44993 | ||||
20154 | Wink, J. | http://www.dsmz.de/microorganisms/wink_pdf/DSM44993.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 | ||||
32064 | 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 | 28311 | 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) | ||||
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 | 33211880 | Nucleic Acids Res. 49: D498-D508 2020 | ||
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | |||||
68369 | Automatically annotated from API 20NE | ||||||
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 | ||||
82464 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID297474.1 | StrainInfo: A central database for resolving microbial strain identifiers |