Strain identifier
BacDive ID: 16460
Type strain: 
Species: Streptomyces avicenniae
Strain Designation: 9-9
Strain history: CGMCC 4.5510 <-- J. Xiao et al. MCCC 1A01535.
NCBI tax ID(s): 500153 (species)
version 9.1 (current version)
General
@ref: 15798
BacDive-ID: 16460
DSM-Number: 41943
keywords: genome sequence, 16S sequence, Bacteria, aerobe, spore-forming, Gram-positive
description: Streptomyces avicenniae 9-9 is an aerobe, spore-forming, Gram-positive bacterium that builds an aerial mycelium and was isolated from soil of mangrove plant Avicennia mariana.
NCBI tax id
- NCBI tax id: 500153
- Matching level: species
strain history
| @ref | history |
|---|---|
| 15798 | <- J. Xu; 9-9 <- J. Xu |
| 67770 | CGMCC 4.5510 <-- J. Xiao et al. MCCC 1A01535. |
doi: 10.13145/bacdive16460.20240916.9.1
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 avicenniae
- full scientific name: Streptomyces avicenniae Xiao et al. 2009
@ref: 15798
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Streptomycetaceae
genus: Streptomyces
species: Streptomyces avicenniae
full scientific name: Streptomyces avicenniae Xiao et al. 2009
strain designation: 9-9
type strain: yes
Morphology
cell morphology
| @ref | gram stain | motility | confidence |
|---|---|---|---|
| 29244 | positive | no | |
| 69480 | no | 92.5 | |
| 69480 | positive | 91.826 |
colony morphology
| @ref | colony color | incubation period | medium used |
|---|---|---|---|
| 18731 | Curry | 10-14 days | ISP 2 |
| 18731 | Curry | 10-14 days | ISP 3 |
| 18731 | Ochre yellow (1024) | 10-14 days | ISP 4 |
| 18731 | 10-14 days | ISP 7 |
multicellular morphology
| @ref | forms multicellular complex | medium name | complex name | complex color |
|---|---|---|---|---|
| 18731 | no | ISP 2 | ||
| 18731 | yes | ISP 3 | Aerial Mycelium | Pure white (9010) |
| 18731 | yes | ISP 4 | Aerial Mycelium | Light ivory (1015) |
| 18731 | no | ISP 5 | ||
| 18731 | no | ISP 6 | ||
| 18731 | no | ISP 7 |
pigmentation
- @ref: 29244
- production: yes
multimedia
| @ref | multimedia content | intellectual property rights | caption |
|---|---|---|---|
| 15798 | https://www.dsmz.de/microorganisms/photos/DSM_41943-1.jpg | © Leibniz-Institut DSMZ | |
| 15798 | https://www.dsmz.de/microorganisms/photos/DSM_41943.jpg | © Leibniz-Institut DSMZ | Medium 252 28°C |
Culture and growth conditions
culture medium
| @ref | name | growth | link | composition |
|---|---|---|---|---|
| 15798 | 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 |
| 18731 | 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 | |
| 18731 | 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: | |
| 18731 | 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 | |
| 18731 | 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 | |
| 15798 | 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 |
| 15798 | STARCH - MINERAL SALT - AGAR (STMS) (DSMZ Medium 252) | yes | https://mediadive.dsmz.de/medium/252 | Name: STARCH - MINERAL SALT - AGAR (STMS) (DSMZ Medium 252) Composition: Agar 14.985 g/l Starch 9.99001 g/l (NH4)2SO4 1.998 g/l CaCO3 1.998 g/l K2HPO4 0.999001 g/l MgSO4 x 7 H2O 0.999001 g/l NaCl 0.999001 g/l FeSO4 x 7 H2O 0.000999001 g/l MnCl2 x 4 H2O 0.000999001 g/l ZnSO4 x 7 H2O 0.000999001 g/l Distilled water |
culture temp
| @ref | growth | type | temperature |
|---|---|---|---|
| 15798 | positive | growth | 28 |
| 18731 | positive | optimum | 28 |
| 29244 | positive | growth | 15-37 |
| 29244 | positive | optimum | 28 |
| 67770 | positive | growth | 28 |
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance | confidence |
|---|---|---|
| 29244 | aerobe | |
| 69480 | aerobe | 92.563 |
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 29244 | yes | |
| 69480 | yes | 91.364 |
observation
- @ref: 67770
- observation: quinones: MK-10(H6), MK-9(H6), MK-9(H8), MK-10(H8)
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 29244 | 22599 | arabinose | + | carbon source |
| 29244 | 28260 | galactose | + | carbon source |
| 29244 | 26546 | rhamnose | + | carbon source |
| 29244 | 17992 | sucrose | + | carbon source |
| 29244 | 18222 | xylose | + | carbon source |
enzymes
| @ref | value | activity | ec |
|---|---|---|---|
| 29244 | gelatinase | + | |
| 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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 18731 | - | - | - | - | - | - | - | - | - | - | + | - | - | - | - | - | - | - | - |
Isolation, sampling and environmental information
isolation
| @ref | sample type | host species | geographic location | country | origin.country | continent |
|---|---|---|---|---|---|---|
| 15798 | soil of mangrove plant Avicennia mariana | Avicennia mariana | Fujian Province | China | CHN | Asia |
| 67770 | Rhizosphere of the mangrove plant Avicennia mariana from Fujian Province | Avicennia mariana | China | CHN | Asia |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Aquatic | #Mangrove |
| #Environmental | #Terrestrial | #Forest |
| #Environmental | #Terrestrial | #Soil |
| #Host | #Plants | #Tree |
taxonmaps
- @ref: 69479
- File name: preview.99_2737.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15;96_1457;97_1738;98_2123;99_2737&stattab=map
- Last taxonomy: Streptomyces avicenniae subclade
- 16S sequence: EU399234
- Sequence Identity:
- Total samples: 178
- soil counts: 132
- aquatic counts: 17
- animal counts: 22
- plant counts: 7
Safety information
risk assessment
- @ref: 15798
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 15798
- description: Streptomyces avicenniae strain MCCC 1A01535 16S ribosomal RNA gene, partial sequence
- accession: EU399234
- length: 1491
- database: nuccore
- NCBI tax ID: 500153
Genome sequences
- @ref: 67770
- description: Streptomyces avicenniae NRRL B-24776
- accession: GCA_000719135
- assembly level: contig
- database: ncbi
- NCBI tax ID: 500153
GC content
| @ref | GC-content | method |
|---|---|---|
| 15798 | 73.3 | high performance liquid chromatography (HPLC) |
| 29244 | 73.3 |
Genome-based predictions
predictions
| @ref | trait | model | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 69480 | gram-positive | gram-positive | Positive reaction to Gram-staining | yes | 91.826 | yes |
| 69480 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 98.392 | yes |
| 69480 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | yes | 92.563 | no |
| 69480 | spore-forming | spore-forming | Ability to form endo- or exospores | yes | 91.364 | yes |
| 69480 | thermophilic | thermophile | Ability to grow at temperatures above or equal to 45°C | no | 95.9 | no |
| 69480 | flagellated | motile2+ | Ability to perform flagellated movement | no | 92.5 | yes |
External links
@ref: 15798
culture collection no.: DSM 41943, CGMCC 4.5510, MCCC 1A01535, JCM 16801, NRRL B-24776
straininfo link
- @ref: 85496
- straininfo: 397939
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 19625443 | Streptomyces avicenniae sp. nov., a novel actinomycete isolated from the rhizosphere of the mangrove plant Avicennia mariana. | Xiao J, Wang Y, Luo Y, Xie SJ, Ruan JS, Xu J | Int J Syst Evol Microbiol | 10.1099/ijs.0.009357-0 | 2009 | Avicennia/*microbiology, China, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/chemistry/metabolism, Molecular Sequence Data, Phylogeny, Plant Roots/microbiology, RNA, Ribosomal, 16S/genetics, *Soil Microbiology, Streptomyces/chemistry/classification/genetics/*isolation & purification | Genetics |
| Phylogeny | 24243968 | Streptomyces hoynatensis sp. nov., isolated from deep marine sediment. | Veyisoglu A, Sahin N | Int J Syst Evol Microbiol | 10.1099/ijs.0.055640-0 | 2013 | Bacterial Typing Techniques, Black Sea, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/microbiology, Sequence Analysis, DNA, Streptomyces/*classification/genetics, Turkey, Vitamin K 2/chemistry, *Water Microbiology | Genetics |
| Phylogeny | 25237147 | Streptomyces burgazadensis sp. nov., isolated from soil. | Saricaoglu S, Isik K, Veyisoglu A, Saygin H, Cetin D, Guven K, Sproer C, Klenk HP, Sahin N | Int J Syst Evol Microbiol | 10.1099/ijs.0.065870-0 | 2014 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Streptomyces/*classification/genetics/isolation & purification, Turkey, Vitamin K 2/analogs & derivatives/chemistry | Genetics |
Reference
| @id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
|---|---|---|---|---|---|---|
| 15798 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 41943) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-41943 | |||
| 18731 | Wink, J. | http://www.dsmz.de/microorganisms/wink_pdf/DSM41943.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 | |||
| 29244 | 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 | 25664 | 28776041 | |
| 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) | |||
| 85496 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID397939.1 | StrainInfo: A central database for resolving microbial strain identifiers |