Strain identifier
BacDive ID: 7797
Type strain:
Species: Actinocatenispora rupis
Strain Designation: CS5-AC17
Strain history: DSM 45178 <-- S. D. Lee CS5-AC17.
NCBI tax ID(s): 519421 (species)
General
@ref: 15642
BacDive-ID: 7797
DSM-Number: 45178
keywords: genome sequence, 16S sequence, Bacteria, aerobe, spore-forming, mesophilic, Gram-positive
description: Actinocatenispora rupis CS5-AC17 is an aerobe, spore-forming, mesophilic bacterium that was isolated from soil of cliff.
NCBI tax id
- NCBI tax id: 519421
- Matching level: species
strain history
@ref | history |
---|---|
15642 | <- S. D. Lee; CS5-AC17 |
67770 | DSM 45178 <-- S. D. Lee CS5-AC17. |
doi: 10.13145/bacdive7797.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/actinomycetota
- domain: Bacteria
- phylum: Actinomycetota
- class: Actinomycetes
- order: Micromonosporales
- family: Micromonosporaceae
- genus: Actinocatenispora
- species: Actinocatenispora rupis
- full scientific name: Actinocatenispora rupis Seo and Lee 2009
@ref: 15642
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Micromonosporaceae
genus: Actinocatenispora
species: Actinocatenispora rupis
full scientific name: Actinocatenispora rupis Seo and Lee 2009
strain designation: CS5-AC17
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell length | cell width | motility | confidence |
---|---|---|---|---|---|
29428 | positive | 1.25 µm | 0.45 µm | ||
69480 | no | 92.449 | |||
69480 | positive | 100 |
colony morphology
@ref | colony color | incubation period | medium used |
---|---|---|---|
20175 | Light ivory (1015) | 10-14 days | ISP 2 |
20175 | Cream (9001) | 10-14 days | ISP 3 |
20175 | Light ivory (1015) | 10-14 days | ISP 4 |
20175 | Light ivory (1015) | 10-14 days | ISP 5 |
20175 | Ivory (1014) | 10-14 days | ISP 6 |
20175 | Cream (9001) | 10-14 days | ISP 7 |
multicellular morphology
@ref | forms multicellular complex | medium name |
---|---|---|
20175 | no | ISP 2 |
20175 | no | ISP 3 |
20175 | no | ISP 4 |
20175 | no | ISP 5 |
20175 | no | ISP 6 |
20175 | no | ISP 7 |
pigmentation
- @ref: 29428
- production: no
multimedia
- @ref: 15642
- multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_45178.jpg
- caption: Medium 65 28°C
- intellectual property rights: © Leibniz-Institut DSMZ
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
15642 | ROLLED OATS MINERAL MEDIUM (DSMZ Medium 84) | yes | https://mediadive.dsmz.de/medium/84 | Name: ROLLED OATS MINERAL MEDIUM (DSMZ Medium 84) Composition: Agar 20.0 g/l Rolled oats 20.0 g/l ZnSO4 x 7 H2O 0.001 g/l MnCl2 x 4 H2O 0.001 g/l FeSO4 x 7 H2O 0.001 g/l Distilled water |
15642 | 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 |
20175 | 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 | |
20175 | 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: | |
20175 | 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 | |
20175 | 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 | |
20175 | 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 | |
20175 | 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 | |
15642 | GPHF-MEDIUM (DSMZ Medium 553) | yes | https://mediadive.dsmz.de/medium/553 | Name: GPHF-MEDIUM (DSMZ Medium 553) Composition: Agar 20.0 g/l Glucose 10.0 g/l Beef extract 5.0 g/l Yeast extract 5.0 g/l Casein peptone 5.0 g/l CaCl2 x 2 H2O 0.74 g/l Distilled water |
15642 | ISP2 MEDIUM (DSMZ Medium 987) | yes | https://mediadive.dsmz.de/medium/987 | Name: ISP 2 MEDIUM (DSMZ Medium 987) Composition: Agar 20.0 g/l Malt extract 10.0 g/l Dextrose 4.0 g/l Yeast extract 4.0 g/l Distilled water |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
15642 | positive | growth | 28 | mesophilic |
20175 | positive | optimum | 28 | mesophilic |
29428 | positive | growth | 25-42 | |
29428 | positive | optimum | 37 | mesophilic |
67770 | positive | growth | 28 | mesophilic |
culture pH
@ref | ability | type | pH | PH range |
---|---|---|---|---|
29428 | positive | growth | 5.1-12.1 | alkaliphile |
29428 | positive | optimum | 7.1 |
Physiology and metabolism
oxygen tolerance
- @ref: 29428
- oxygen tolerance: aerobe
spore formation
@ref | spore formation | confidence |
---|---|---|
29428 | yes | |
69481 | yes | 100 |
69480 | yes | 100 |
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
29428 | NaCl | positive | growth | 0-4 % |
29428 | NaCl | positive | optimum | 7.1 % |
observation
@ref | observation |
---|---|
29428 | aggregates in clumps |
67770 | quinones: MK-9(H4), MK-9(H6), MK-9(H8) |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
20175 | 17234 | glucose | + | |
20175 | 22599 | arabinose | +/- | |
20175 | 17992 | sucrose | + | |
20175 | 18222 | xylose | +/- | |
20175 | 17268 | myo-inositol | +/- | |
20175 | 29864 | mannitol | + | |
20175 | 28757 | fructose | + | |
20175 | 26546 | rhamnose | +/- | |
20175 | 16634 | raffinose | - | |
20175 | 62968 | cellulose | - | |
29428 | 15963 | ribitol | + | carbon source |
29428 | 22599 | arabinose | + | carbon source |
29428 | 17057 | cellobiose | + | carbon source |
29428 | 16947 | citrate | + | carbon source |
29428 | 28260 | galactose | + | carbon source |
29428 | 17754 | glycerol | + | carbon source |
29428 | 17716 | lactose | + | carbon source |
29428 | 17306 | maltose | + | carbon source |
29428 | 29864 | mannitol | + | carbon source |
29428 | 37684 | mannose | + | carbon source |
29428 | 26546 | rhamnose | + | carbon source |
29428 | 30911 | sorbitol | + | carbon source |
29428 | 17992 | sucrose | + | carbon source |
29428 | 27082 | trehalose | + | carbon source |
29428 | 53426 | tween 80 | + | carbon source |
29428 | 4853 | esculin | + | hydrolysis |
enzymes
@ref | value | activity | ec |
---|---|---|---|
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
20175 | + | + | + | - | + | + | - | + | - | + | + | + | + | + | + | + | + | + | + |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent |
---|---|---|---|---|---|
15642 | soil of cliff | Jeju, Mara Island | Republic of Korea | KOR | Asia |
67770 | Soil from a cliff on Mara Island | Jeju | Republic of Korea | KOR | Asia |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Environmental | #Terrestrial | #Geologic |
#Environmental | #Terrestrial | #Soil |
taxonmaps
- @ref: 69479
- File name: preview.99_119412.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_94;96_2691;97_3305;98_80504;99_119412&stattab=map
- Last taxonomy: Actinocatenispora rupis subclade
- 16S sequence: AM980986
- Sequence Identity:
- Total samples: 2865
- soil counts: 2086
- aquatic counts: 83
- animal counts: 242
- plant counts: 454
Safety information
risk assessment
- @ref: 15642
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 15642
- description: Actinocatenispora rupis partial 16S rRNA gene, type strain CS5-AC17T
- accession: AM980986
- length: 1408
- database: ena
- NCBI tax ID: 519421
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Actinocatenispora rupis NBRC 107355 | GCA_016861975 | contig | ncbi | 519421 |
66792 | Actinocatenispora rupis strain NBRC 107355 | 519421.3 | wgs | patric | 519421 |
GC content
@ref | GC-content | method |
---|---|---|
15642 | 74.3 | high performance liquid chromatography (HPLC) |
29428 | 74.3 |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | yes | 100 | no |
gram-positive | yes | 90.109 | yes |
anaerobic | no | 99.008 | yes |
halophile | no | 86.052 | no |
spore-forming | yes | 91.186 | yes |
glucose-util | yes | 90.007 | no |
aerobic | yes | 91.885 | yes |
thermophile | no | 96.584 | no |
flagellated | no | 98.515 | no |
motile | no | 91.232 | no |
glucose-ferment | no | 90.62 | no |
External links
@ref: 15642
culture collection no.: DSM 45178, JCM 16894, NBRC 107355, NRRL B-24660
straininfo link
- @ref: 77239
- straininfo: 403338
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 19643893 | Actinocatenispora rupis sp. nov., isolated from cliff soil, and emended description of the genus Actinocatenispora. | Seo SH, Lee SD | Int J Syst Evol Microbiol | 10.1099/ijs.0.012922-0 | 2009 | DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Micromonosporaceae/*classification/genetics/*isolation & purification, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, *Soil Microbiology | Genetics |
Phylogeny | 34242158 | Actinocatenispora comari sp. nov., an endophytic actinomycete isolated from aerial parts of Comarum salesowianum. | Oyunbileg N, Iizaka Y, Hamada M, Davaapurev BO, Fukumoto A, Tsetseg B, Kato F, Tamura T, Batkhuu J, Anzai Y | Int J Syst Evol Microbiol | 10.1099/ijsem.0.004861 | 2021 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Endophytes/classification/isolation & purification, Fatty Acids/chemistry, Micromonosporaceae/*classification/isolation & purification, Mongolia, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, Plant Components, Aerial/*microbiology, RNA, Ribosomal, 16S/genetics, Rosacea/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry | Enzymology |
Reference
@id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
---|---|---|---|---|---|---|
15642 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45178) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-45178 | |||
20175 | Wink, J. | http://www.dsmz.de/microorganisms/wink_pdf/DSM45178.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 | |||
29428 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | 10.1128/mSphere.00237-17 | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 25834 | 28776041 | |
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/ | ||||
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 | |||
77239 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID403338.1 | StrainInfo: A central database for resolving microbial strain identifiers |