Strain identifier
BacDive ID: 15492
Type strain:
Species: Streptomyces californicus
Strain history: KCC S-0015 <-- T. Yamaguchi (IAM 0003) <-- ATCC 3312 <-- IMRU 3312.
NCBI tax ID(s): 67351 (species)
General
@ref: 9241
BacDive-ID: 15492
DSM-Number: 40058
keywords: genome sequence, 16S sequence, Bacteria, spore-forming, mesophilic, antibiotic compound production
description: Streptomyces californicus DSM 40058 is a spore-forming, mesophilic bacterium that builds an aerial mycelium and produces antibiotic compounds.
NCBI tax id
- NCBI tax id: 67351
- Matching level: species
strain history
@ref | history |
---|---|
9241 | <- E.B. Shirling, ISP <- S.A. Waksman, IMRU |
67770 | KCC S-0015 <-- T. Yamaguchi (IAM 0003) <-- ATCC 3312 <-- IMRU 3312. |
doi: 10.13145/bacdive15492.20230509.8.1
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 californicus
- full scientific name: Streptomyces californicus (Waksman and Curtis 1916) Waksman and Henrici 1948 (Approved Lists 1980)
synonyms
@ref synonym 20215 Actinomyces californicus 20215 Streptomyces floridae
@ref: 9241
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Streptomycetaceae
genus: Streptomyces
species: Streptomyces puniceus
full scientific name: Streptomyces puniceus Patelski 1951
type strain: no
Morphology
cell morphology
@ref | motility | confidence | gram stain |
---|---|---|---|
69480 | no | 92.84 | |
69480 | 100 | positive |
multicellular morphology
@ref | forms multicellular complex | complex name | complex color | medium name |
---|---|---|---|---|
19804 | yes | Aerial Mycelium | Grey | ISP 2 |
19804 | yes | Aerial Mycelium | Grey | ISP 3 |
19804 | yes | Aerial Mycelium | Grey | ISP 4 |
19804 | yes | Aerial Mycelium | Grey | ISP 5 |
19804 | yes | Aerial Mycelium | Grey | ISP 6 |
19804 | yes | Aerial Mycelium | Grey | ISP 7 |
Culture and growth conditions
culture medium
- @ref: 9241
- name: GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)
- growth: yes
- link: https://mediadive.dsmz.de/medium/65
- composition: 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
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
19804 | positive | optimum | 28 | mesophilic |
9241 | positive | growth | 28 | mesophilic |
67770 | positive | growth | 28 | mesophilic |
Physiology and metabolism
spore formation
@ref | spore description | spore formation | confidence |
---|---|---|---|
19804 | Formation of spore chains: rectiflixibilis, spore surface: smooth | yes | |
69481 | yes | 100 | |
69480 | yes | 100 |
compound production
@ref | compound |
---|---|
9241 | viomycin |
20216 | Griseorhodin |
20216 | Sideromycin |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
19804 | 62968 | cellulose | - | |
19804 | 16634 | raffinose | - | |
19804 | 26546 | rhamnose | - | |
19804 | 28757 | fructose | + | |
19804 | 29864 | mannitol | + | |
19804 | 17268 | myo-inositol | - | |
19804 | 18222 | xylose | + | |
19804 | 17992 | sucrose | - | |
19804 | 22599 | arabinose | + | |
19804 | 17234 | glucose | + | |
68368 | 17634 | D-glucose | + | fermentation |
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 | yes |
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 |
API 20E
@ref | ONPG | ADH Arg | LDC Lys | ODC | CIT | H2S | URE | TDA Trp | IND | VP | GEL | GLU |
---|---|---|---|---|---|---|---|---|---|---|---|---|
19804 | + | + | + | - | - | - | + | + | - | + | + | + |
Isolation, sampling and environmental information
isolation
- @ref: 9241
- sample type: soil
isolation source categories
- Cat1: #Environmental
- Cat2: #Terrestrial
- Cat3: #Soil
taxonmaps
- @ref: 69479
- File name: preview.99_135.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15;96_102;97_109;98_120;99_135&stattab=map
- Last taxonomy: Streptomyces
- 16S sequence: AB184755
- Sequence Identity:
- Total samples: 4030
- soil counts: 2441
- aquatic counts: 286
- animal counts: 1009
- plant counts: 294
Safety information
risk assessment
@ref | biosafety level | biosafety level comment |
---|---|---|
9241 | 1 | Risk group (German classification) |
19804 | 1 | Risk group (German classification) |
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Streptomyces californicus gene for 16S rRNA, partial sequence, strain: NBRC 12750 | AB184116 | 1480 | ena | 67281 |
20218 | Streptomyces californicus gene for 16S rRNA, partial sequence, strain: NBRC 3386 | AB184755 | 1477 | ena | 67281 |
20218 | Streptomyces californicus strain IFO 12750 16S ribosomal RNA gene, partial sequence | AY999837 | 1419 | ena | 67281 |
20218 | Streptomyces californicus strain DSM 40058 16S ribosomal RNA gene, partial sequence | AY999845 | 1420 | ena | 67281 |
20218 | Streptomyces californicus gene for 16S ribosomal RNA, partial sequence, strain: JCM 4567 | D44236 | 120 | ena | 67281 |
20218 | Streptomyces californicus strain DSM 40058 16S ribosomal RNA gene, partial sequence | GU383162 | 779 | ena | 67281 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Streptomyces californicus strain FDAARGOS_1209 | 67351.14 | complete | patric | 67351 |
67770 | Streptomyces californicus NRRL B-1221 | GCA_000715715 | scaffold | ncbi | 67351 |
67770 | Streptomyces californicus NRRL B-2098 | GCA_000717645 | contig | ncbi | 67351 |
67770 | Streptomyces californicus NRRL ISP-5058 | GCA_000716065 | scaffold | ncbi | 67351 |
GC content
@ref | GC-content | method |
---|---|---|
67770 | 70 | fluorimetric |
67770 | 72.7 | genome sequence analysis |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | yes | 100 | no |
gram-positive | yes | 92.835 | no |
anaerobic | no | 99.046 | no |
halophile | no | 93.853 | no |
spore-forming | yes | 94.516 | yes |
glucose-util | yes | 88.292 | no |
thermophile | no | 98.67 | no |
flagellated | no | 98.049 | no |
motile | no | 94.27 | no |
aerobic | yes | 93.559 | no |
glucose-ferment | no | 85.047 | yes |
External links
@ref: 9241
culture collection no.: DSM 40058, ATCC 11896, ATCC 19734, ATCC 3312, CBS 125.20, CBS 354.53, CBS 473.68, ETH 10212, IFO 12750, IFO 3386, IMET 40261, IMRU 3312, IMRU 3313, ISP 5058, JCM 4015, JCM 4567, KCC S-0015, KCC S-0567, NBRC 12750, NBRC 3386, NRRL B-1221, NRRL B-2098, RIA 1015, RIA 63, BCRC 13688, CCM 3016, CGMCC 4.0570, HUT 6049, IFM 1070, KCTC 19939, KCTC 19957, LMG 19309, NBIMCC 1036, NCAIM B.01475, NRRL ISP-5058, VKM Ac-575, VTT E-991421
straininfo link
- @ref: 84579
- straininfo: 38299
literature
- topic: Phylogeny
- Pubmed-ID: 21148669
- title: Streptomyces sundarbansensis sp. nov., an actinomycete that produces 2-allyloxyphenol.
- authors: Arumugam M, Mitra A, Pramanik A, Saha M, Gachhui R, Mukherjee J
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.028258-0
- year: 2010
- mesh: Base Composition, DNA, Bacterial/genetics, Fatty Acids/metabolism, Geologic Sediments/*microbiology, India, Molecular Sequence Data, Phenols/*metabolism, Phylogeny, RNA, Ribosomal, 16S/genetics, Streptomyces/*classification/genetics/*isolation & purification/metabolism
- topic2: Metabolism
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
9241 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 40058) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-40058 | |||
19804 | Wink, J. | http://www.dsmz.de/microorganisms/wink_pdf/DSM40058.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 | |||
20216 | Curators of the HKI | http://www.leibniz-hki.de/de/ | Collection Description Leibniz-Institut für Naturstoff-Forschung und Infektionsbiologie e. V. Hans-Knöll-Institut (HKI) | |||
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 | |||||
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 | |||
84579 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID38299.1 | StrainInfo: A central database for resolving microbial strain identifiers |