Strain identifier
BacDive ID: 15055
Type strain:
Species: Streptomyces bottropensis
Strain history: CIP <- 1997, IFO <- 1969, SAJ <- OWU: strain ISP 5262
NCBI tax ID(s): 1054862 (strain), 42235 (species)
General
@ref: 9416
BacDive-ID: 15055
DSM-Number: 40262
keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, spore-forming, mesophilic, antibiotic compound production
description: Streptomyces bottropensis DSM 40262 is an obligate aerobe, spore-forming, mesophilic bacterium that produces antibiotic compounds and was isolated from soil.
NCBI tax id
NCBI tax id | Matching level |
---|---|
1054862 | strain |
42235 | species |
strain history
@ref | history |
---|---|
9416 | <- E.B. Shirling, ISP <- J.C. Hoogerheide B-35 |
67770 | KCC S-0459 <-- IFO 13023 <-- SAJ <-- ISP 5262 <-- J. C. Hoogerheide B-25. |
116900 | CIP <- 1997, IFO <- 1969, SAJ <- OWU: strain ISP 5262 |
doi: 10.13145/bacdive15055.20230509.8.1
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 bottropensis
- full scientific name: Streptomyces bottropensis Waksman 1961 (Approved Lists 1980)
synonyms
- @ref: 20215
- synonym: Streptomyces stelliscabiei
@ref: 9416
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Streptomycetaceae
genus: Streptomyces
species: Streptomyces bottropensis
full scientific name: Streptomyces bottropensis Waksman 1961 emend. Nouioui et al. 2018
type strain: yes
Morphology
cell morphology
@ref | motility | confidence | gram stain | cell shape |
---|---|---|---|---|
69480 | no | 90.344 | ||
69480 | 100 | positive | ||
116900 | no | positive | rod-shaped |
colony morphology
- @ref: 116900
multimedia
@ref | multimedia content | intellectual property rights | caption |
---|---|---|---|
9416 | https://www.dsmz.de/microorganisms/photos/DSM_40262-1.JPG | © Leibniz-Institut DSMZ | |
9416 | https://www.dsmz.de/microorganisms/photos/DSM_40262.jpg | © Leibniz-Institut DSMZ | Medium 65 28°C |
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
9416 | 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 |
39250 | MEDIUM 57 - for Streptomyces, Nocardioides, Lentzea albidocapillata and Streptoverticillium reticulum | yes | Distilled water make up to (1000.000 ml);Agar (15.000 g);Glucose (4.000g);Yeast extract (4.000 g);Malt extract (10.000 g);Calcium carbonate (2.000 g) | |
9416 | STARCH - MINERAL SALT - AGAR (STMS) (DSMZ Medium 252) | yes | https://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium252.pdf | |
116900 | CIP Medium 236 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=236 | |
116900 | CIP Medium 57 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=57 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
18574 | positive | optimum | 28 | mesophilic |
9416 | positive | growth | 28 | mesophilic |
39250 | positive | growth | 30 | mesophilic |
67770 | positive | growth | 28 | mesophilic |
116900 | positive | growth | 25-37 | mesophilic |
116900 | no | growth | 10 | psychrophilic |
116900 | no | growth | 41 | thermophilic |
116900 | no | growth | 45 | thermophilic |
Physiology and metabolism
oxygen tolerance
- @ref: 116900
- oxygen tolerance: obligate aerobe
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | yes | 100 |
69480 | yes | 100 |
compound production
- @ref: 9416
- compound: bottromycin
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
116900 | NaCl | positive | growth | 0-2 % |
116900 | NaCl | no | growth | 4 % |
116900 | NaCl | no | growth | 6 % |
116900 | NaCl | no | growth | 8 % |
116900 | NaCl | no | growth | 10 % |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
18574 | 17234 | glucose | + | |
18574 | 22599 | arabinose | + | |
18574 | 17992 | sucrose | + | |
18574 | 18222 | xylose | - | |
18574 | 17268 | myo-inositol | + | |
18574 | 29864 | mannitol | + | |
18574 | 28757 | fructose | - | |
18574 | 26546 | rhamnose | + | |
18574 | 16634 | raffinose | + | |
18574 | 62968 | cellulose | + | |
68371 | Potassium 5-ketogluconate | - | builds acid from | |
68371 | Potassium 2-ketogluconate | - | builds acid from | |
68371 | 24265 | gluconate | - | builds acid from |
68371 | 18403 | L-arabitol | - | builds acid from |
68371 | 18333 | D-arabitol | - | builds acid from |
68371 | 28847 | D-fucose | - | builds acid from |
68371 | 16443 | D-tagatose | - | builds acid from |
68371 | 62318 | D-lyxose | - | builds acid from |
68371 | 32528 | turanose | - | builds acid from |
68371 | 28066 | gentiobiose | - | builds acid from |
68371 | 17151 | xylitol | - | builds acid from |
68371 | 28017 | starch | - | builds acid from |
68371 | 16634 | raffinose | - | builds acid from |
68371 | 6731 | melezitose | - | builds acid from |
68371 | 15443 | inulin | - | builds acid from |
68371 | 28053 | melibiose | - | builds acid from |
68371 | 17716 | lactose | - | builds acid from |
68371 | 17306 | maltose | - | builds acid from |
68371 | 17814 | salicin | - | builds acid from |
68371 | 4853 | esculin | - | builds acid from |
68371 | 18305 | arbutin | - | builds acid from |
68371 | 27613 | amygdalin | - | builds acid from |
68371 | 320061 | methyl alpha-D-glucopyranoside | - | builds acid from |
68371 | 43943 | methyl alpha-D-mannoside | - | builds acid from |
68371 | 17924 | D-sorbitol | - | builds acid from |
68371 | 16899 | D-mannitol | - | builds acid from |
68371 | 17268 | myo-inositol | - | builds acid from |
68371 | 16813 | galactitol | - | builds acid from |
68371 | 17266 | L-sorbose | - | builds acid from |
68371 | 12936 | D-galactose | - | builds acid from |
68371 | 74863 | methyl beta-D-xylopyranoside | - | builds acid from |
68371 | 15963 | ribitol | - | builds acid from |
68371 | 65328 | L-xylose | - | builds acid from |
68371 | 65327 | D-xylose | - | builds acid from |
68371 | 16988 | D-ribose | + | builds acid from |
68371 | 17108 | D-arabinose | - | builds acid from |
68371 | 17113 | erythritol | - | builds acid from |
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 |
116900 | 4853 | esculin | - | hydrolysis |
116900 | 606565 | hippurate | - | hydrolysis |
116900 | 17632 | nitrate | - | reduction |
116900 | 16301 | nitrite | - | reduction |
116900 | 17632 | nitrate | - | respiration |
metabolite production
@ref | metabolite | production | Chebi-ID |
---|---|---|---|
67770 | bottromycin | yes | |
68368 | acetoin | yes | 15688 |
68368 | indole | no | 35581 |
68368 | hydrogen sulfide | no | 16136 |
116900 | indole | no | 35581 |
metabolite tests
@ref | Chebi-ID | metabolite | voges-proskauer-test | indole test | methylred-test |
---|---|---|---|---|---|
68368 | 15688 | acetoin | + | ||
68368 | 35581 | indole | - | ||
116900 | 15688 | acetoin | - | ||
116900 | 17234 | glucose | - |
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 |
116900 | oxidase | - | |
116900 | beta-galactosidase | + | 3.2.1.23 |
116900 | alcohol dehydrogenase | - | 1.1.1.1 |
116900 | gelatinase | - | |
116900 | amylase | - | |
116900 | DNase | - | |
116900 | caseinase | - | 3.4.21.50 |
116900 | catalase | + | 1.11.1.6 |
116900 | tween esterase | - | |
116900 | gamma-glutamyltransferase | - | 2.3.2.2 |
116900 | lecithinase | - | |
116900 | lipase | - | |
116900 | lysine decarboxylase | - | 4.1.1.18 |
116900 | ornithine decarboxylase | - | 4.1.1.17 |
116900 | phenylalanine ammonia-lyase | - | 4.3.1.24 |
116900 | tryptophan deaminase | - | |
116900 | urease | - | 3.5.1.5 |
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 | 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 | 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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
18574 | + | + | + | - | + | + | - | - | - | + | + | + | + | - | + | + | + | + | - | |
116900 | + | + | + | - | + | - | - | - | - | + | + | - | - | - | - | - | + | - | - | - |
API 20E
@ref | ONPG | ADH Arg | LDC Lys | ODC | CIT | H2S | URE | TDA Trp | IND | VP | GEL |
---|---|---|---|---|---|---|---|---|---|---|---|
18574 | + | + | + | - | + | - | + | - | - | + | + |
API 50CHac
@ref | GLY | ERY | DARA | LARA | RIB | DXYL | LXYL | ADO | MDX | GAL | GLU | FRU | MNE | SBE | RHA | DUL | INO | MAN | SOR | MDM | MDG | NAG | AMY | ARB | ESC | SAL | CEL | MAL | LAC | MEL | SAC | TRE | INU | MLZ | RAF | AMD | GLYG | XLT | GEN | TUR | LYX | TAG | DFUC | LFUC | DARL | LARL | GNT | 2KG | 5KG |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
116900 | +/- | - | - | +/- | + | - | - | - | - | - | +/- | +/- | +/- | - | +/- | - | - | - | - | - | - | +/- | - | - | - | - | +/- | - | - | - | +/- | +/- | - | - | - | - | +/- | - | - | - | - | - | - | +/- | - | - | - | - | - |
API biotype100
@ref | GLU | FRU | GAL | TRE | MNE | SBE | MEL | SAC | RAF | MTE | MAL | LAC | LTE | MbGa | MaGa | CEL | GEN | MbGu | ESC | RIB | ARA | XYL | PLE | RHA | FUC | MLZ | DARL | LARL | XLT | DUL | TAG | GLY | INO | MAN | MTL | TUR | SOR | ADO | HBG | LYX | ERY | MDG | 3MDG | SAT | MUC | LTAT | DTAT | MTAT | DMLT | LMLT | CATE | TATE | TTE | CIT | GRT | GAT | 2KG | 5KG | TRY | NAG | GNT | PAC | PAT | pOBE | QAT | GTE | mOBE | BAT | PPAT | CMT | TGE | BET | PCE | ABT | HIN | LAT | CAP | CYT | HIS | SUC | FUM | GRE | GYT | AVT | ETN | TTN | GLN | ITA | 3OBU | APT | GTT | PRO | DALA | LALA | SER | MNT | PROP | TYR | 2KT |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
116900 | + | + | + | - | + | - | + | + | - | + | + | + | + | + | - | + | - | - | + | + | + | + | - | + | + | - | + | - | - | - | - | + | - | + | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | + | + | - | - | + | - | - | - | - | - | + | + | - | - | - | - | - | - | - | - | + | + | - | + | + | - | - | - | - | + | + | + | - | - | - | - | - | + | - | - | + | + | + | - | + | + | - | - | + | - |
Isolation, sampling and environmental information
isolation
@ref | sample type |
---|---|
9416 | soil |
116900 | Environment, Soil |
isolation source categories
- Cat1: #Environmental
- Cat2: #Terrestrial
- Cat3: #Soil
taxonmaps
- @ref: 69479
- File name: preview.99_1896.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15;96_102;97_135;98_1456;99_1896&stattab=map
- Last taxonomy: Streptomyces bottropensis
- 16S sequence: AB184262
- Sequence Identity:
- Total samples: 153
- soil counts: 120
- aquatic counts: 1
- animal counts: 7
- plant counts: 25
Safety information
risk assessment
@ref | biosafety level | biosafety level comment |
---|---|---|
9416 | 1 | Risk group (German classification) |
18574 | 1 | German classification |
116900 | 1 | Risk group (French classification) |
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Streptomyces bottropensis gene for 16S ribosomal RNA, 23S ribosomal RNA, complete and partial sequence, strain:ATCC 25435 | AB026217 | 1857 | ena | 1054862 |
20218 | Streptomyces bottropensis strain DSM40262 16S-23S intergenic spacer region, partial sequence | AF363493 | 306 | ena | 1054862 |
20218 | Streptomyces bottropensis gene for 16S ribosomal RNA, complete sequence | D63868 | 1531 | ena | 1054862 |
20218 | Streptomyces bottropensis ATCC 25435 strain DSM 40262 clone ITS 16S-23S ribosomal RNA intergenic spacer, partial sequence | AY296951 | 283 | ena | 1054862 |
20218 | Streptomyces bottropensis ATCC 25435 strain DSM 40262 clone ITS11 16S-23S ribosomal RNA intergenic spacer, partial sequence | AY296952 | 273 | ena | 1054862 |
20218 | Streptomyces bottropensis ATCC 25435 strain DSM 40262 clone ITS29 16S-23S ribosomal RNA intergenic spacer, partial sequence | AY296954 | 274 | ena | 1054862 |
20218 | Streptomyces bottropensis ATCC 25435 strain DSM 40262 clone ITS3 16S-23S ribosomal RNA intergenic spacer, partial sequence | AY296955 | 285 | ena | 1054862 |
20218 | Streptomyces bottropensis gene for 16S ribosomal RNA, partial sequence, strain: JCM 4459 | D44156 | 121 | ena | 1054862 |
20218 | Streptomyces bottropensis gene for 16S rRNA, partial sequence, strain: NBRC 13023 | AB184262 | 1476 | ena | 42235 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Streptomyces bottropensis ATCC 25435 | 1054862.3 | wgs | patric | 1054862 |
66792 | Streptomyces bottropensis ATCC 25435 | 1054862.11 | complete | patric | 1054862 |
66792 | Streptomyces bottropensis DSM40262. | 2582581526 | draft | img | 42235 |
66792 | Streptomyces bottropensis ATCC 25435 | 2517572239 | draft | img | 1054862 |
66792 | Streptomyces bottropensis ATCC 25435 | 2551306667 | draft | img | 1054862 |
67770 | Streptomyces bottropensis ATCC 25435 | GCA_000340335 | scaffold | ncbi | 1054862 |
67770 | Streptomyces bottropensis ATCC 25435 | GCA_000383595 | scaffold | ncbi | 1054862 |
GC content
- @ref: 67770
- GC-content: 71.2
- method: genome sequence analysis
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | yes | 100 | no |
motile | no | 94.686 | no |
flagellated | no | 96.995 | no |
gram-positive | yes | 86.194 | no |
anaerobic | no | 99.018 | no |
aerobic | yes | 92.307 | no |
halophile | no | 94.236 | no |
spore-forming | yes | 95.149 | no |
thermophile | no | 98.329 | no |
glucose-util | yes | 89.992 | no |
glucose-ferment | no | 88.49 | no |
External links
@ref: 9416
culture collection no.: DSM 40262, ATCC 25435, CBS 163.64, CBS 667.69, ETH 23899, IFO 13023, ISP 5262, JCM 4459, NBRC 13023, RIA 1215, BCRC 12063, CGMCC 4.1669, CIP 105278, KACC 20131, MTCC 4729, NRRL ISP-5262, VKM Ac-1755
straininfo link
- @ref: 84161
- straininfo: 45754
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Genetics | 23516178 | Draft Genome Sequence of Streptomyces bottropensis ATCC 25435, a Bottromycin-Producing Actinomycete. | Zhang H, Zhou W, Zhuang Y, Liang X, Liu T | Genome Announc | 10.1128/genomeA.00019-13 | 2013 | ||
Phylogeny | 33871674 | Streptomyces adelaidensis sp. nov., an actinobacterium isolated from the root of Callitris preissii with potential for plant growth-promoting properties. | Kaewkla O, Suriyachadkun C, Franco CMM | Arch Microbiol | 10.1007/s00203-021-02308-4 | 2021 | Cupressaceae/*microbiology, Fatty Acids/analysis, Genome, Bacterial, Genotype, Phylogeny, Plant Development, Plant Roots/microbiology, Streptomyces/chemistry/classification/genetics/*isolation & purification | Genetics |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
9416 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 40262) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-40262 | |||
18574 | Wink, J. | http://www.dsmz.de/microorganisms/wink_pdf/DSM40262.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 | |
39250 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/17280 | ||||
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 | |||||
68371 | Automatically annotated from API 50CH acid | |||||
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 | |||
84161 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID45754.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
116900 | Curators of the CIP | Collection of Institut Pasteur (CIP 105278) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105278 |