Strain identifier
BacDive ID: 16530
Type strain: 
Species: Microbispora hainanensis
Strain Designation: 211020
Strain history: CGMCC 4.5595 <-- X. X. Xu et al. 211020.
NCBI tax ID(s): 568844 (species)
version 8.1 (current version)
General
@ref: 16789
BacDive-ID: 16530
DSM-Number: 45428
keywords: genome sequence, 16S sequence, Bacteria, aerobe, spore-forming, mesophilic, Gram-positive
description: Microbispora hainanensis 211020 is an aerobe, spore-forming, mesophilic bacterium that was isolated from rhizosphere soil of Excoecaria agallocha.
NCBI tax id
- NCBI tax id: 568844
- Matching level: species
strain history
| @ref | history |
|---|---|
| 16789 | <- K. Hong, Institute of Tropical Bioscience and Biotechnology, Haikou, China; 211020 <- X. Xu |
| 67770 | CGMCC 4.5595 <-- X. X. Xu et al. 211020. |
doi: 10.13145/bacdive16530.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/actinomycetota
- domain: Bacteria
- phylum: Actinomycetota
- class: Actinomycetes
- order: Streptosporangiales
- family: Streptosporangiaceae
- genus: Microbispora
- species: Microbispora hainanensis
- full scientific name: Microbispora hainanensis Xu et al. 2012
@ref: 16789
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Streptosporangiaceae
genus: Microbispora
species: Microbispora hainanensis
full scientific name: Microbispora hainanensis Xu et al. 2012
strain designation: 211020
type strain: yes
Morphology
cell morphology
| @ref | gram stain | motility | confidence |
|---|---|---|---|
| 30491 | positive | no | |
| 69480 | positive | 100 |
Culture and growth conditions
culture medium
| @ref | name | growth | link | composition |
|---|---|---|---|---|
| 16789 | 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 |
| 16789 | 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 |
| 16789 | 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 |
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 16789 | positive | growth | 28 | mesophilic |
| 30491 | positive | growth | 20-50 | |
| 67770 | positive | growth | 28 | mesophilic |
culture pH
- @ref: 30491
- ability: positive
- type: growth
- pH: 05-08
Physiology and metabolism
oxygen tolerance
- @ref: 30491
- oxygen tolerance: aerobe
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 30491 | yes | |
| 69481 | yes | 100 |
| 69480 | yes | 100 |
halophily
- @ref: 30491
- salt: NaCl
- growth: positive
- tested relation: growth
- concentration: 0-1 %
observation
- @ref: 67770
- observation: quinones: MK- 9(H4), MK-9(H2), MK-9(H0)
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 30491 | 17057 | cellobiose | + | carbon source |
| 30491 | 23652 | dextrin | + | carbon source |
| 30491 | 28260 | galactose | + | carbon source |
| 30491 | 17234 | glucose | + | carbon source |
| 30491 | 17306 | maltose | + | carbon source |
| 30491 | 29864 | mannitol | + | carbon source |
| 30491 | 37684 | mannose | + | carbon source |
| 30491 | 28053 | melibiose | + | carbon source |
| 30491 | 26546 | rhamnose | + | carbon source |
| 30491 | 30911 | sorbitol | + | carbon source |
| 30491 | 17632 | nitrate | + | reduction |
Isolation, sampling and environmental information
isolation
| @ref | sample type | host species | geographic location | country | origin.country | continent |
|---|---|---|---|---|---|---|
| 16789 | rhizosphere soil of Excoecaria agallocha | Excoecaria agallocha | Hainan Province, Wenchang | China | CHN | Asia |
| 67770 | Rhizosphere soil of Excoecaria agallocha in a mangrove | Excoecaria agallocha | Hainan Province | China | CHN | Asia |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Terrestrial | #Soil |
| #Host | #Plants | #Tree |
| #Host Body-Site | #Plant | #Rhizosphere |
Safety information
risk assessment
- @ref: 16789
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 16789
- description: Microbispora hainanensis strain 211020 16S ribosomal RNA gene, partial sequence
- accession: FJ261972
- length: 1480
- database: ena
- NCBI tax ID: 568844
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Microbispora hainanensis strain DSM 45428 | 568844.3 | wgs | patric | 568844 |
| 67770 | Microbispora hainanensis DSM 45428 | GCA_006874475 | contig | ncbi | 568844 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 16789 | 70.8 | high performance liquid chromatography (HPLC) |
| 30491 | 70.8 |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | yes | 100 | no |
| gram-positive | yes | 88.65 | no |
| anaerobic | no | 98.845 | yes |
| halophile | no | 92.704 | yes |
| spore-forming | yes | 95.75 | no |
| glucose-util | yes | 90.008 | yes |
| thermophile | no | 98.21 | yes |
| flagellated | no | 97.894 | no |
| motile | no | 92.705 | yes |
| aerobic | yes | 89.051 | yes |
| glucose-ferment | no | 91.83 | no |
External links
@ref: 16789
culture collection no.: DSM 45428, CGMCC 4.5595, JCM 19666
straininfo link
- @ref: 85561
- straininfo: 401891
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 22140174 | Microbispora hainanensis sp. nov., isolated from rhizosphere soil of Excoecaria agallocha in a mangrove. | Xu XX, Wang HL, Lin HP, Wang C, Qu Z, Xie QY, Ruan JS, Hong K | Int J Syst Evol Microbiol | 10.1099/ijs.0.037267-0 | 2011 | Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Diaminopimelic Acid/analysis, Euphorbiaceae/*microbiology, Fatty Acids/analysis, Molecular Sequence Data, Phospholipids/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, *Rhizosphere, Sequence Analysis, DNA, *Soil Microbiology | Genetics |
| Phylogeny | 30247118 | Microbispora triticiradicis sp. nov., a novel actinomycete isolated from the root of wheat (Triticum aestivum L.). | Han C, Tian Y, Zhao J, Yu Z, Jiang S, Guo X, Xiang W, Wang X | Int J Syst Evol Microbiol | 10.1099/ijsem.0.003040 | 2018 | Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, Plant Roots/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Triticum/*microbiology, Vitamin K 2/analogs & derivatives/chemistry | Transcriptome |
| Phylogeny | 30325294 | Microbispora soli sp. nov., isolated from soil of a hot spring. | Kittisrisopit S, Pittayakhajonwut P, Tadtong S, Thawai C | Int J Syst Evol Microbiol | 10.1099/ijsem.0.003075 | 2018 | Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Hot Springs/*microbiology, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Thailand, Vitamin K 2/analogs & derivatives/chemistry | Transcriptome |
| Phylogeny | 30739286 | Microbispora tritici sp. nov., a novel actinomycete isolated from a root of wheat (Triticum aestivum L.). | Han C, Zhao J, Yu B, Shi H, Zhang C, Guo X, Xiang W, Wang X | Antonie Van Leeuwenhoek | 10.1007/s10482-019-01246-y | 2019 | Actinobacteria/*classification/genetics/*isolation & purification/physiology, Bacterial Typing Techniques, Cell Wall/chemistry, Cluster Analysis, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Diaminopimelic Acid/analysis, Fatty Acids/analysis, Glycolipids/analysis, Nucleic Acid Hybridization, Phospholipids/analysis, Phylogeny, Plant Roots/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Triticum/*microbiology, Vitamin K 2/analysis | Transcriptome |
| Phylogeny | 32632152 | A novel diterpene agent isolated from Microbispora hainanensis strain CSR-4 and its in vitro and in silico inhibition effects on acetylcholine esterase enzyme. | Thawai C, Bunbamrung N, Pittayakhajonwut P, Chongruchiroj S, Pratuangdejkul J, He YW, Tadtong S, Sareedenchai V, Prombutara P, Qian Y | Sci Rep | 10.1038/s41598-020-68009-y | 2020 | Acetylcholinesterase/chemistry/drug effects, Actinobacteria/*chemistry/classification/genetics, Animals, Antioxidants/chemistry/isolation & purification/pharmacology, Catalytic Domain, Chlorocebus aethiops, Cholinesterase Inhibitors/chemistry/isolation & purification/*pharmacology, Computer Simulation, Diterpenes/chemistry/isolation & purification/*pharmacology, Humans, In Vitro Techniques, Mice, Molecular Dynamics Simulation, Molecular Structure, Neuroprotective Agents/chemistry/isolation & purification/pharmacology, Phylogeny, RNA, Ribosomal, 16S/genetics, Recombinant Proteins/chemistry/drug effects, Vero Cells | Enzymology |
Reference
| @id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
|---|---|---|---|---|---|---|
| 16789 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45428) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-45428 | |||
| 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 | |||
| 30491 | 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 | 26824 | 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/ | ||||
| 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 | |||
| 85561 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID401891.1 | StrainInfo: A central database for resolving microbial strain identifiers |