Strain identifier
BacDive ID: 16929
Type strain:
Species: Actinomadura kijaniata
Strain Designation: SSC 1256, 13-363
Strain history: KCC A-0306 <-- MS 2153 <-- ATCC 31588 <-- Schering Corp.; SCC 1256.
NCBI tax ID(s): 1220561 (strain), 46161 (species)
General
@ref: 11052
BacDive-ID: 16929
DSM-Number: 43764
keywords: genome sequence, 16S sequence, Bacteria, aerobe, spore-forming, mesophilic, Gram-positive, antibiotic compound production
description: Actinomadura kijaniata SSC 1256 is an aerobe, spore-forming, mesophilic bacterium that builds an aerial mycelium and produces antibiotic compounds.
NCBI tax id
NCBI tax id | Matching level |
---|---|
1220561 | strain |
46161 | species |
strain history
@ref | history |
---|---|
11052 | <- N.S. Agre, VKM <- Schering Corp., SSC 1256 |
67771 | <- JCM <- KCC <- MS2153 <- ATCC <- Schering Corp.SCC1256 |
67770 | KCC A-0306 <-- MS 2153 <-- ATCC 31588 <-- Schering Corp.; SCC 1256. |
doi: 10.13145/bacdive16929.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/actinomycetota
- domain: Bacteria
- phylum: Actinomycetota
- class: Actinomycetes
- order: Streptosporangiales
- family: Thermomonosporaceae
- genus: Actinomadura
- species: Actinomadura kijaniata
- full scientific name: Actinomadura kijaniata Horan and Brodsky 1982
@ref: 11052
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Thermomonosporaceae
genus: Actinomadura
species: Actinomadura kijaniata
full scientific name: Actinomadura kijaniata Horan and Brodsky 1982 emend. Nouioui et al. 2018
strain designation: SSC 1256, 13-363
type strain: yes
Morphology
cell morphology
@ref | gram stain | confidence |
---|---|---|
67771 | positive | |
69480 | positive | 100 |
colony morphology
@ref | colony color | incubation period | medium used |
---|---|---|---|
19586 | Dark green | 10-14 days | ISP 2 |
19586 | Dark green | 10-14 days | ISP 3 |
19586 | Dark green | 10-14 days | ISP 4 |
19586 | Dark green | 10-14 days | ISP 5 |
19586 | Bright green | 10-14 days | ISP 6 |
19586 | Bright green | 10-14 days | ISP 7 |
multicellular morphology
@ref | forms multicellular complex | complex name | complex color | medium name |
---|---|---|---|---|
19586 | yes | Aerial Mycelium | White | ISP 2 |
19586 | yes | Aerial Mycelium | White | ISP 3 |
19586 | no | ISP 4 | ||
19586 | no | ISP 5 | ||
19586 | no | ISP 6 | ||
19586 | no | ISP 7 |
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
11052 | GPHF-MEDIUM (DSMZ Medium 553) | yes | https://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium553.pdf | |
19586 | 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 | |
19586 | 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: | |
19586 | 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 | |
19586 | 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 | |
19586 | 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 | |
19586 | 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 | |
11052 | 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 |
11052 | 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 |
---|---|---|---|---|
19586 | positive | optimum | 28 | mesophilic |
11052 | positive | growth | 28 | mesophilic |
67770 | positive | growth | 28 | mesophilic |
67771 | positive | growth | 28 | mesophilic |
Physiology and metabolism
oxygen tolerance
- @ref: 67771
- oxygen tolerance: aerobe
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | yes | 100 |
69480 | yes | 100 |
compound production
@ref | compound |
---|---|
11052 | kijanimycin |
20216 | Kijanimicin |
halophily
- @ref: 19586
- salt: NaCl
- growth: positive
- tested relation: maximum
- concentration: 2.5 %
observation
@ref | observation |
---|---|
67770 | quinones: MK-9(H4), MK-9(H2), MK-9(H6), MK-9(H4), MK-9(H8) |
67771 | quinones: MK-9(H_4_), MK-9(H_2_) |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
19586 | 17234 | glucose | + | |
19586 | 22599 | arabinose | + | |
19586 | 17992 | sucrose | + | |
19586 | 18222 | xylose | - | |
19586 | 17268 | myo-inositol | + | |
19586 | 29864 | mannitol | - | |
19586 | 28757 | fructose | + | |
19586 | 26546 | rhamnose | +/- | |
19586 | 16634 | raffinose | - | |
19586 | 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 | metabolite | production | Chebi-ID |
---|---|---|---|
67770 | kijanimicin | yes | |
68368 | acetoin | yes | 15688 |
68368 | indole | no | 35581 |
68368 | hydrogen sulfide | no | 16136 |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
19586 | + | + | + | + | + | + | + | + | + | + | + | - | + | - | + | + | + | - | - |
API 20E
@ref | ONPG | ADH Arg | LDC Lys | ODC | CIT | H2S | URE | TDA Trp | IND | VP | GEL |
---|---|---|---|---|---|---|---|---|---|---|---|
19586 | + | + | + | + | + | - | + | - | - | + | + |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent |
---|---|---|---|---|---|
11052 | soil | Kenya | Kenya | KEN | Africa |
67770 | Soil | Kenya | KEN | Africa | |
67771 | From soil | Kenya | KEN | Africa |
isolation source categories
- Cat1: #Environmental
- Cat2: #Terrestrial
- Cat3: #Soil
Safety information
risk assessment
@ref | biosafety level | biosafety level comment |
---|---|---|
11052 | 1 | Risk group (German classification) |
19586 | 1 | Risk group (German classification) |
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | A.kijaniata 16S rRNA gene | X97890 | 1448 | ena | 46161 |
20218 | Actinomadura kijaniata 16S rRNA gene | U49006 | 1409 | ena | 46161 |
20218 | Actinomadura kijaniata 16S-23S ribosomal RNA intergenic spacer region, partial sequence | AF134099 | 462 | ena | 46161 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Actinomadura kijaniata NBRC 14229 | 1220561.3 | wgs | patric | 1220561 |
66792 | Actinomadura kijaniata NBRC 14229 | 2731957573 | draft | img | 1220561 |
66792 | Actinomadura kijaniata ATCC 31588 | 651717042 | draft | img | 46161 |
67770 | Actinomadura kijaniata NBRC 14229 | GCA_001552175 | contig | ncbi | 1220561 |
GC content
@ref | GC-content | method |
---|---|---|
67771 | 69.7 | thermal denaturation, midpoint method (Tm) |
67770 | 73.2 | genome sequence analysis |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | yes | 100 | no |
motile | no | 89.686 | no |
gram-positive | yes | 87.549 | yes |
anaerobic | no | 98.947 | yes |
aerobic | yes | 90.231 | yes |
halophile | no | 92.453 | no |
spore-forming | yes | 94.968 | no |
glucose-util | yes | 89.965 | yes |
flagellated | no | 97.603 | no |
thermophile | no | 95.213 | yes |
glucose-ferment | no | 90.815 | no |
External links
@ref: 11052
culture collection no.: DSM 43764, ATCC 31588, CCRC 13146, IFO 14229, IMET 9741, JCM 3306, KCTC 9129, NBRC 14229, NCIMB 13755, NRRL 12069, NRRL B-16121, VKM Ac-874, BCRC 13416, CGMCC 4.2099, IMSNU 20006, MTCC 707, NRRL B-16261, BCRC 13146, IFO (now NBRC) 14229, SCC 1256
straininfo link
- @ref: 85934
- straininfo: 38247
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 7328052 | Kijanimicin (Sch 25663), a novel antibiotic produced by Actinomadura kijaniata SCC 1256. Fermentation, isolation, characterization and biological properties. | Waitz JA, Horan AC, Kalyanpur M, Lee BK, Loebenberg D, Marquez JA, Miller G, Patel MG | J Antibiot (Tokyo) | 10.7164/antibiotics.34.1101 | 1981 | *Aminoglycosides, Anti-Bacterial Agents/*isolation & purification/pharmacology, Bacteria/drug effects, Chemical Phenomena, Chemistry, Fermentation, Glycosides/isolation & purification/pharmacology, Nocardiaceae/*analysis | Enzymology |
Phylogeny | 12807192 | Actinomadura namibiensis sp. nov. | Wink J, Kroppenstedt RM, Seibert G, Stackebrandt E | Int J Syst Evol Microbiol | 10.1099/ijs.0.02286-0 | 2003 | Actinomycetales/chemistry/*classification/genetics/physiology, Bacterial Typing Techniques, DNA, Ribosomal, *Desert Climate, Microscopy, Electron, Scanning, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S, Sequence Analysis, DNA, *Soil Microbiology, Spores, Bacterial | Genetics |
Phylogeny | 35816443 | Actinomadura parmotrematis sp. nov., isolated from the foliose lichen, Parmotrema praesorediosum (Nyl.) Hale. | Somphong A, Poengsungnoen V, Buaruang K, Suriyachadkun C, Sripreechasak P, Tanasupawat S, Phongsopitanun W | Int J Syst Evol Microbiol | 10.1099/ijsem.0.005447 | 2022 | Actinomadura, *Actinomycetales, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Lichens, Parmeliaceae, Phospholipids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Soil Microbiology, Vitamin K 2 | Transcriptome |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
11052 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 43764) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-43764 | |||
19586 | Wink, J. | http://www.dsmz.de/microorganisms/wink_pdf/DSM43764.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/ | ||||
67771 | Curators of the KCTC | https://kctc.kribb.re.kr/En/Kctc | ||||
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 | |||
85934 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID38247.1 | StrainInfo: A central database for resolving microbial strain identifiers |