Strain identifier
BacDive ID: 15291
Type strain:
Species: Streptomyces helvaticus
Strain history: KCC S-0768 <-- IFO 13382 <-- SAJ <-- ISP 5431 <-- INMI 1013-B.
NCBI tax ID(s): 68186 (species)
General
@ref: 9539
BacDive-ID: 15291
DSM-Number: 40431
keywords: genome sequence, 16S sequence, Bacteria, spore-forming, mesophilic
description: Streptomyces helvaticus DSM 40431 is a spore-forming, mesophilic bacterium that was isolated from Soil.
NCBI tax id
- NCBI tax id: 68186
- Matching level: species
strain history
@ref | history |
---|---|
9539 | <- E.B. Shirling, ISP <- N.A. Krassilnikov, INMI |
67770 | KCC S-0768 <-- IFO 13382 <-- SAJ <-- ISP 5431 <-- INMI 1013-B. |
doi: 10.13145/bacdive15291.20230509.8.1
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 helvaticus
- full scientific name: Streptomyces helvaticus (Krassilnikov et al. 1965) Pridham 1970 (Approved Lists 1980)
synonyms
- @ref: 20215
- synonym: Actinomyces helvaticus
@ref: 9539
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Streptomycetaceae
genus: Streptomyces
species: Streptomyces helvaticus
full scientific name: Streptomyces helvaticus (Krassilnikov et al. 1965) Pridham 1970
type strain: yes
Morphology
cell morphology
@ref | motility | confidence | gram stain |
---|---|---|---|
69480 | no | 92.637 | |
69480 | 100 | positive |
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
9539 | 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 |
9539 | ROLLED OATS MINERAL MEDIUM (DSMZ Medium 84) | yes | https://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium84.pdf |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
18590 | positive | optimum | 28 | mesophilic |
9539 | positive | growth | 28 | mesophilic |
67770 | positive | growth | 28 | mesophilic |
Physiology and metabolism
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | yes | 100 |
69480 | yes | 100 |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
18590 | 17234 | glucose | + | |
18590 | 22599 | arabinose | + | |
18590 | 17992 | sucrose | - | |
18590 | 18222 | xylose | - | |
18590 | 17268 | myo-inositol | + | |
18590 | 29864 | mannitol | - | |
18590 | 28757 | fructose | - | |
18590 | 26546 | rhamnose | - | |
18590 | 16634 | raffinose | - | |
18590 | 62968 | cellulose | - | |
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 |
metabolite production
@ref | Chebi-ID | metabolite | production |
---|---|---|---|
68368 | 15688 | acetoin | no |
68368 | 35581 | indole | no |
68368 | 16136 | hydrogen sulfide | no |
metabolite tests
@ref | Chebi-ID | metabolite | voges-proskauer-test | indole test |
---|---|---|---|---|
68368 | 15688 | acetoin | - | |
68368 | 35581 | indole | - |
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 |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
18590 | + | + | + | - | + | + | + | + | + | + | + | - | + | - | + | + | + | - | - |
API 20E
@ref | ONPG | ADH Arg | LDC Lys | ODC | CIT | H2S | URE | TDA Trp | IND | VP | GEL |
---|---|---|---|---|---|---|---|---|---|---|---|
18590 | - | + | + | + | - | - | + | - | - | - | - |
Isolation, sampling and environmental information
isolation
- @ref: 67770
- sample type: Soil
taxonmaps
- @ref: 69479
- File name: preview.99_834.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15;96_102;97_109;98_662;99_834&stattab=map
- Last taxonomy: Streptomyces
- 16S sequence: AB184367
- Sequence Identity:
- Total samples: 1611
- soil counts: 953
- aquatic counts: 126
- animal counts: 103
- plant counts: 429
Safety information
risk assessment
@ref | biosafety level | biosafety level comment |
---|---|---|
18590 | 1 | German classification |
9539 | 1 | Risk group (German classification) |
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Streptomyces helvaticus gene for 16S ribosomal RNA, partial sequence, strain: JCM 4768 | D44346 | 120 | ena | 68216 |
20218 | Streptomyces helvaticus gene for 16S rRNA, partial sequence, strain: NBRC 13382 | AB184367 | 1477 | ena | 68216 |
20218 | Streptomyces helvaticus strain NRRL B-12365T 16S ribosomal RNA gene, partial sequence | DQ442504 | 1453 | ena | 68216 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Streptomyces chryseus JCM 4768 | GCA_014650855 | scaffold | ncbi | 68186 |
66792 | Streptomyces chryseus strain JCM 4768 | 68186.6 | wgs | patric | 68186 |
66792 | Streptomyces helvaticus strain DSM 40431 | 68216.4 | wgs | patric | 68186 |
67770 | Streptomyces chryseus DSM 40431 | GCA_005981965 | contig | ncbi | 68186 |
GC content
- @ref: 67770
- GC-content: 76.9
- method: thermal denaturation, midpoint method (Tm)
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | yes | 100 | no |
flagellated | no | 98.585 | no |
gram-positive | yes | 88.261 | no |
anaerobic | no | 98.709 | no |
aerobic | yes | 89.665 | no |
halophile | no | 95.331 | no |
spore-forming | yes | 93.87 | no |
thermophile | no | 96.884 | yes |
glucose-util | yes | 90.365 | no |
motile | no | 94.847 | no |
glucose-ferment | no | 88.77 | no |
External links
@ref: 9539
culture collection no.: DSM 40431, ATCC 19841, CBS 683.72, IFO 13382, INMI 1013B, ISP 5431, NBRC 13382, RIA 1343, JCM 4768, BCRC 16245, CGMCC 4.1911, INMI 1013-B, NRRL B-12365, VKM Ac-192
straininfo link
- @ref: 84385
- straininfo: 389276
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 19567563 | Streptomyces hypolithicus sp. nov., isolated from an Antarctic hypolith community. | Le Roes-Hill M, Rohland J, Meyers PR, Cowan DA, Burton SG | Int J Syst Evol Microbiol | 10.1099/ijs.0.007971-0 | 2009 | Antarctic Regions, Bacterial Typing Techniques, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Microscopy, Electron, Scanning, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Streptomyces/*classification/genetics/*isolation & purification/physiology | Genetics |
Phylogeny | 31204968 | Streptomyces altiplanensis sp. nov., an alkalitolerant species isolated from Chilean Altiplano soil, and emended description of Streptomyces chryseus (Krasil'nikov et al. 1965) Pridham 1970. | Cortes-Albayay C, Dorador C, Schumann P, Schniete JK, Herron P, Andrews B, Asenjo J, Nouioui I | Int J Syst Evol Microbiol | 10.1099/ijsem.0.003525 | 2019 | Alkalies, Altitude, Bacterial Typing Techniques, Base Composition, Chile, DNA, Bacterial/genetics, *Desert Climate, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Hydrogen-Ion Concentration, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Streptomyces/*classification/isolation & purification | Transcriptome |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
9539 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 40431) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-40431 | |||
18590 | Wink, J. | http://www.dsmz.de/microorganisms/wink_pdf/DSM40431.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 | |
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 | |||||
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 | |||
84385 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID389276.1 | StrainInfo: A central database for resolving microbial strain identifiers |