Strain identifier
BacDive ID: 15216
Type strain:
Species: Streptomyces gardneri
Strain history: KCC A-0004 <-- T. Yamaguchi (IAM 0105) <-- ATCC 9604 <-- NCTC 6531.
NCBI tax ID(s): 66892 (species)
General
@ref: 9265
BacDive-ID: 15216
DSM-Number: 40064
keywords: genome sequence, 16S sequence, Bacteria, spore-forming, mesophilic, antibiotic compound production
description: Streptomyces gardneri DSM 40064 is a spore-forming, mesophilic bacterium that produces antibiotic compounds and was isolated from air contamination.
NCBI tax id
- NCBI tax id: 66892
- Matching level: species
strain history
@ref | history |
---|---|
9265 | <- E.B. Shirling, ISP <- S.A. Waksman, IMRU |
67770 | KCC A-0004 <-- T. Yamaguchi (IAM 0105) <-- ATCC 9604 <-- NCTC 6531. |
doi: 10.13145/bacdive15216.20230509.8.1
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 gardneri
- full scientific name: Streptomyces gardneri (Waksman 1942) Waksman 1961 (Approved Lists 1980)
synonyms
- @ref: 20215
- synonym: Proactinomyces gardneri
@ref: 9265
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Streptomycetaceae
genus: Streptomyces
species: Streptomyces gardneri
full scientific name: Streptomyces gardneri (Waksman 1942) Waksman 1961
type strain: yes
Morphology
cell morphology
@ref | motility | confidence | gram stain |
---|---|---|---|
69480 | no | 94.038 | |
69480 | 100 | positive |
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
9265 | 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 |
9265 | STARCH - MINERAL SALT - AGAR (STMS) (DSMZ Medium 252) | yes | https://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium252.pdf |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
18476 | positive | optimum | 28 | mesophilic |
9265 | positive | growth | 28 | mesophilic |
67770 | positive | growth | 28 | mesophilic |
Physiology and metabolism
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | yes | 98 |
69480 | yes | 100 |
compound production
@ref | compound |
---|---|
9265 | proactinomycin A, B, C |
9265 | proactinomycin B |
9265 | proactinomycin C |
9265 | proactinomycin A |
67770 | Proactinomycins A, B and C |
observation
- @ref: 67770
- observation: quinones: MK-8(H4)
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
18476 | 17234 | glucose | + | |
18476 | 22599 | arabinose | + | |
18476 | 17992 | sucrose | + | |
18476 | 18222 | xylose | - | |
18476 | 17268 | myo-inositol | - | |
18476 | 29864 | mannitol | - | |
18476 | 28757 | fructose | + | |
18476 | 26546 | rhamnose | + | |
18476 | 16634 | raffinose | + | |
18476 | 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 | 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 |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
18476 | + | + | + | + | + | + | + | + | + | + | + | + | + | - | + | + | + | + | - |
API 20E
@ref | ONPG | ADH Arg | LDC Lys | ODC | CIT | H2S | URE | TDA Trp | IND | VP | GEL |
---|---|---|---|---|---|---|---|---|---|---|---|
18476 | + | + | + | + | + | - | + | - | - | + | + |
Isolation, sampling and environmental information
isolation
@ref | sample type |
---|---|
9265 | air contamination |
67770 | Air contamination |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Engineered | #Laboratory | #Contaminant |
#Environmental | #Air |
Safety information
risk assessment
@ref | biosafety level | biosafety level comment |
---|---|---|
18476 | 1 | German classification |
9265 | 1 | Risk group (German classification) |
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Actinomyces israeli serotype 1 partial 16S rRNA | X53228 | 1386 | ena | 1659 |
20218 | Streptomyces gardneri gene for 16S rRNA, partial sequence | AB122713 | 564 | ena | 66892 |
20218 | Streptomyces gardneri gene for 16S ribosomal RNA, partial sequence, strain: JCM 4375 | D44091 | 120 | ena | 66892 |
20218 | Streptomyces gardneri gene for 16S rRNA, partial sequence, strain: NBRC 12865 | AB249908 | 1451 | ena | 66892 |
20218 | Streptomyces gardneri gene for 16S rRNA, partial sequence, strain: NBRC 3385 | AB184754 | 1470 | ena | 66892 |
20218 | Streptomyces gardneri strain NRRL B-5615T 16S ribosomal RNA gene, partial sequence | DQ442500 | 1442 | ena | 66892 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Streptomyces gardneri JCM 4375 | GCA_014655085 | contig | ncbi | 66892 |
66792 | Streptomyces gardneri strain JCM 4375 | 66892.4 | wgs | patric | 66892 |
66792 | Streptomyces gardneri strain NBRC 12865 | 66892.3 | wgs | patric | 66892 |
67770 | Streptomyces gardneri NBRC 12865 | GCA_006539185 | contig | ncbi | 66892 |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | yes | 98 | no |
gram-positive | yes | 87.627 | no |
anaerobic | no | 99.418 | no |
halophile | no | 93.656 | no |
spore-forming | yes | 94.318 | no |
glucose-util | yes | 90.227 | no |
thermophile | no | 99.158 | no |
flagellated | no | 97.335 | no |
motile | no | 94.159 | no |
aerobic | yes | 92.249 | no |
glucose-ferment | no | 84.942 | no |
External links
@ref: 9265
culture collection no.: DSM 40064, ATCC 23911, ATCC 9604, CBS 832.68, DSM 43020, ETH 28347, IFO 12865, IFO 13974, IFO 3385, IMET 7182, IMRU 3834, ISP 5064, JCM 3004, JCM 4375, KCC A-0004, KCC S-0375, NBRC 12865, NBRC 13974, NBRC 3385, RIA 1117, RIA 634, BCRC 12346, BCRC 13687, BCRC 13731, CGMCC 4.1956, NCTC 6531, NRRL B-5615, VKM Ac-1829
straininfo link
- @ref: 84314
- straininfo: 35082
literature
- Pubmed-ID: 6968019
- title: Polyclonal B cell activation by cell wall preparations of gram-positive bacteria. In vitro responses of spleen cells obtained from Balb/c, nu/nu, nu/+, C3H/He, C3H/HeJ and hybrid (DBA/N x Balb/c)F1 mice.
- authors: Saito-Taki T, Tanabe MJ, Mochizuki H, Matsumoto T, Nakano M, Takada H, Tsujimoto M, Kotani S, Kusumoto S, Shiba T, Yokogawa K, Kawata S
- journal: Microbiol Immunol
- DOI: 10.1111/j.1348-0421.1980.tb00580.x
- year: 1980
- mesh: Animals, B-Lymphocytes/*immunology, Bacteria/*immunology, Cell Wall/immunology, Female, *Lymphocyte Activation, Male, Mice, Mice, Inbred Strains/immunology, Mice, Nude/immunology, Spleen/cytology
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
9265 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 40064) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-40064 | |||
18476 | Wink, J. | http://www.dsmz.de/microorganisms/wink_pdf/DSM40064.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 | |||||
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 | |||
84314 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID35082.1 | StrainInfo: A central database for resolving microbial strain identifiers |