Strain identifier
BacDive ID: 16624
Type strain: 
Species: Sphaerisporangium melleum
Strain Designation: 3-28(8)
Strain history: I. Ara 3-28(8).
NCBI tax ID(s): 321316 (species)
version 9.1 (current version)
General
@ref: 12207
BacDive-ID: 16624
DSM-Number: 44954
keywords: genome sequence, 16S sequence, Bacteria, spore-forming
description: Sphaerisporangium melleum 3-28 is a spore-forming bacterium that was isolated from sandy soil.
NCBI tax id
- NCBI tax id: 321316
- Matching level: species
strain history
| @ref | history |
|---|---|
| 12207 | <- T. Kudo (Sphaerosporangium melleum) <- I. Ara; 3-28(8) |
| 67770 | I. Ara 3-28(8). |
doi: 10.13145/bacdive16624.20240916.9.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/actinomycetota
- domain: Bacteria
- phylum: Actinomycetota
- class: Actinomycetes
- order: Streptosporangiales
- family: Streptosporangiaceae
- genus: Sphaerisporangium
- species: Sphaerisporangium melleum
- full scientific name: Sphaerisporangium melleum corrig. Ara and Kudo 2007
synonyms
- @ref: 20215
- synonym: Sphaerosporangium melleum
@ref: 12207
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Streptosporangiaceae
genus: Sphaerisporangium
species: Sphaerisporangium melleum
full scientific name: Sphaerisporangium melleum Ara and Kudo 2007
strain designation: 3-28(8)
type strain: yes
Culture and growth conditions
culture medium
| @ref | name | growth | link | composition |
|---|---|---|---|---|
| 12207 | 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 |
| 12207 | ROLLED OATS MINERAL MEDIUM (DSMZ Medium 84) | yes | https://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium84.pdf |
culture temp
| @ref | growth | type | temperature |
|---|---|---|---|
| 12207 | positive | growth | 28 |
| 67770 | positive | growth | 28 |
Physiology and metabolism
spore formation
- @ref: 69481
- spore formation: yes
- confidence: 100
observation
- @ref: 67770
- observation: quinones: MK-9(III,VIII-H4), MK-9(H6)
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent |
|---|---|---|---|---|---|
| 12207 | sandy soil | Chokoria | Bangladesh | BGD | Asia |
| 67770 | Sandy soil at a forest-side waterfall | Chokoria, Cox's Bazar | Bangladesh | BGD | Asia |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Terrestrial | #Sandy |
| #Environmental | #Terrestrial | #Soil |
Safety information
risk assessment
- @ref: 12207
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 12207
- description: Sphaerisporangium melleum gene for 16S rRNA, partial sequence, strain: 3-28(8)
- accession: AB208714
- length: 1503
- database: nuccore
- NCBI tax ID: 321316
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Sphaerisporangium melleum NBRC 107356 | GCA_016863375 | contig | ncbi | 321316 |
| 66792 | Sphaerisporangium melleum JCM 13064 | GCA_014646695 | scaffold | ncbi | 321316 |
| 66792 | Sphaerisporangium melleum strain JCM 13064 | 321316.3 | wgs | patric | 321316 |
| 66792 | Sphaerisporangium melleum strain NBRC 107356 | 321316.4 | wgs | patric | 321316 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 12207 | 71 | |
| 67770 | 71 | high performance liquid chromatography (HPLC) |
Genome-based predictions
predictions
| @ref | trait | model | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 69481 | spore-forming | spore-forming | Ability to form endo- or exospores | yes | 100 | no |
| 69480 | gram-positive | gram-positive | Positive reaction to Gram-staining | yes | 88.004 | no |
| 69480 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 87.534 | no |
| 69480 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | yes | 87.032 | no |
| 69480 | spore-forming | spore-forming | Ability to form endo- or exospores | yes | 87.056 | no |
| 69480 | thermophilic | thermophile | Ability to grow at temperatures above or equal to 45°C | no | 95.5 | yes |
| 69480 | flagellated | motile2+ | Ability to perform flagellated movement | no | 84 | no |
External links
@ref: 12207
culture collection no.: DSM 44954, JCM 13064, NBRC 107356, BCC 36478, CGMCC 4.5528
straininfo link
- @ref: 85645
- straininfo: 297460
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 25294725 | Sphaerisporangium dianthi sp. nov., an endophytic actinomycete isolated from a root of Dianthus chinensis L. | Xing J, Liu C, Zhang Y, He H, Zhou Y, Li L, Zhao J, Liu S, Wang X, Xiang W | Antonie Van Leeuwenhoek | 10.1007/s10482-014-0298-x | 2014 | Actinobacteria/*classification/genetics/*isolation & purification, Bacterial Typing Techniques, Carbohydrates/analysis, Cell Wall/chemistry, Cluster Analysis, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Dianthus/*microbiology, Endophytes/*classification/genetics/*isolation & purification, Fatty Acids/analysis, Locomotion, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/analysis, Phylogeny, Plant Roots/microbiology, Plants, Medicinal/microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analysis | Enzymology |
| Phylogeny | 25963939 | Sphaerisporangium corydalis sp. nov., isolated from the root of Corydalis yanhusuo L. | Wang X, Liu C, Cheng J, Zhang Y, Ma Z, Li L, Wang X, Xiang W | Antonie Van Leeuwenhoek | 10.1007/s10482-015-0471-x | 2015 | Actinobacteria/*classification/genetics/*isolation & purification/physiology, Aerobiosis, Cell Wall/chemistry, China, Cluster Analysis, Corydalis/*microbiology, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Diaminopimelic Acid/analysis, Fatty Acids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/analysis, Phospholipids/analysis, Phylogeny, Plant Roots/microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analysis | Genetics |
Reference
| @id | authors | catalogue | doi/url | title |
|---|---|---|---|---|
| 12207 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44954) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-44954 | |
| 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 | |
| 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/ | ||
| 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 | |
| 85645 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID297460.1 | StrainInfo: A central database for resolving microbial strain identifiers |