Strain identifier
BacDive ID: 7979
Type strain: 
Species: Micromonospora nigra
Strain history: NCIMB 2225 <-- ATCC 33088 <-- NRRL 3097 <-- A. Woyciesjes.
NCBI tax ID(s): 145857 (species)
version 8.1 (current version)
General
@ref: 11291
BacDive-ID: 7979
DSM-Number: 43818
keywords: genome sequence, 16S sequence, Bacteria, spore-forming, mesophilic, antibiotic compound production
description: Micromonospora nigra DSM 43818 is a spore-forming, mesophilic bacterium that produces antibiotic compounds and was isolated from salt pool.
NCBI tax id
- NCBI tax id: 145857
- Matching level: species
strain history
| @ref | history |
|---|---|
| 11291 | <- NRRL |
| 67770 | NCIMB 2225 <-- ATCC 33088 <-- NRRL 3097 <-- A. Woyciesjes. |
doi: 10.13145/bacdive7979.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/actinomycetota
- domain: Bacteria
- phylum: Actinomycetota
- class: Actinomycetes
- order: Micromonosporales
- family: Micromonosporaceae
- genus: Micromonospora
- species: Micromonospora nigra
- full scientific name: Micromonospora nigra (Weinstein et al. 1968) Kasai et al. 2000
synonyms
- @ref: 20215
- synonym: Micromonospora halophytica subsp. nigra
@ref: 11291
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Micromonosporaceae
genus: Micromonospora
species: Micromonospora nigra
full scientific name: Micromonospora nigra (Weinstein et al. 1968) Kasai et al. 2000
type strain: yes
Morphology
cell morphology
| @ref | motility | confidence | gram stain |
|---|---|---|---|
| 69480 | no | 95.128 | |
| 69480 | 100 | positive |
multimedia
- @ref: 11291
- multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_43818.jpg
- caption: Medium 554 28°C
- intellectual property rights: © Leibniz-Institut DSMZ
Culture and growth conditions
culture medium
| @ref | name | growth | link | composition |
|---|---|---|---|---|
| 11291 | N-Z-AMINE-MEDIUM (DSMZ Medium 554) | yes | https://mediadive.dsmz.de/medium/554 | Name: N-Z-AMINE-MEDIUM (DSMZ Medium 554) Composition: Starch 20.0 g/l Agar 20.0 g/l Glucose 10.0 g/l N-Z amine 5.0 g/l Yeast extract 5.0 g/l CaCO3 1.0 g/l Distilled water |
| 11291 | 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 |
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 11291 | positive | growth | 28 | mesophilic |
| 67770 | positive | growth | 28 | mesophilic |
Physiology and metabolism
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | yes | 98 |
| 69480 | yes | 99.446 |
compound production
| @ref | compound |
|---|---|
| 11291 | halomycin |
| 11291 | restriction endonuclease MhaI |
observation
- @ref: 67770
- observation: quinones: MK-10(H4), MK-10(H6)
metabolite production
- @ref: 67770
- metabolite: halomicin
- production: yes
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent |
|---|---|---|---|---|---|
| 11291 | salt pool | ||||
| 67770 | Mud, bottom of a salt pool | Syracuse, NY | USA | USA | North America |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Engineered | #Built environment | #Water reservoir (Aquarium/pool) |
| #Condition | #Saline |
Safety information
risk assessment
- @ref: 11291
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 11291
- description: M.halophytica 16S rRNA gene (isolate DSM 43818)
- accession: X92609
- length: 1468
- database: ena
- NCBI tax ID: 1874
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Micromonospora nigra strain DSM 43818 | 145857.5 | wgs | patric | 145857 |
| 66792 | Micromonospora nigra DSM 43818 | 2619619644 | draft | img | 145857 |
| 67770 | Micromonospora nigra DSM 43818 | GCA_900091585 | contig | ncbi | 145857 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 67770 | 71.7 | high performance liquid chromatography (HPLC) |
| 67770 | 72.6 | genome sequence analysis |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | yes | 98 | no |
| motile | no | 93.771 | no |
| gram-positive | yes | 92.424 | no |
| anaerobic | no | 99.059 | no |
| halophile | no | 93.795 | no |
| spore-forming | yes | 93.177 | no |
| thermophile | no | 98.678 | yes |
| glucose-util | yes | 86.211 | no |
| aerobic | yes | 94.527 | no |
| flagellated | no | 97.618 | no |
| glucose-ferment | no | 92.584 | no |
External links
@ref: 11291
culture collection no.: DSM 43818, ATCC 33088, NRRL 3097, JCM 8973, IFO 16103, IMSNU 22024, MTCC 1055, NBRC 16103, NCIMB 2225
straininfo link
- @ref: 77412
- straininfo: 40324
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 15653911 | Micromonospora eburnea sp. nov., isolated from a Thai peat swamp forest. | Thawai C, Tanasupawat S, Itoh T, Suwanborirux K, Suzuki KI, Kudo T | Int J Syst Evol Microbiol | 10.1099/ijs.0.63217-0 | 2005 | Bacterial Typing Techniques, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Genes, rRNA, Micromonospora/chemistry/*classification/genetics/isolation & purification, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S, Sequence Analysis, DNA, *Soil Microbiology, Thailand, *Trees | Genetics |
| Phylogeny | 22634700 | Micromonospora equina sp. nov., isolated from soil from a racecourse. | Everest GJ, Meyers PR | Int J Syst Evol Microbiol | 10.1099/ijs.0.042929-0 | 2012 | Animals, Bacterial Typing Techniques, DNA, Bacterial/genetics, Horses, Micromonospora/*classification/genetics/isolation & purification, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, South Africa | Genetics |
| Phylogeny | 23677031 | Micromonospora spongicola sp. nov., an actinomycete isolated from a marine sponge in the Gulf of Thailand. | Supong K, Suriyachadkun C, Pittayakhajonwut P, Suwanborirux K, Thawai C | J Antibiot (Tokyo) | 10.1038/ja.2013.35 | 2013 | Animals, Bacterial Typing Techniques, Base Composition, Carbohydrates/analysis, Cell Wall/chemistry, Cluster Analysis, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Diaminopimelic Acid/analysis, Micromonospora/*classification/genetics/*isolation & purification/physiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/analysis, Phylogeny, Porifera/*microbiology, RNA, Ribosomal, 16S/genetics, Seawater, Sequence Analysis, DNA, Spores, Bacterial/cytology, Thailand | Genetics |
| Phylogeny | 30810517 | Micromonospora caldifontis sp. nov., isolated from hot spring soil. | Thawai C, Tanasupawat S, Kudo T | Int J Syst Evol Microbiol | 10.1099/ijsem.0.003321 | 2019 | Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Hot Springs/*microbiology, Micromonospora/*classification/isolation & purification, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Thailand, Vitamin K 2/chemistry | Transcriptome |
| Phylogeny | 31596193 | Micromonospora deserti sp. nov., isolated from the Karakum Desert. | Saygin H, Ay H, Guven K, Cetin D, Sahin N | Int J Syst Evol Microbiol | 10.1099/ijsem.0.003752 | 2020 | Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, DNA, Bacterial/genetics, *Desert Climate, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Micromonospora/*classification/isolation & purification, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Turkmenistan | Transcriptome |
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 11291 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 43818) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-43818 | |||
| 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) | |||
| 66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | 10.1093/nar/gkaa1025 | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | Nucleic Acids Res. 49: D498-D508 2020 | 33211880 | |
| 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 | |||
| 77412 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID40324.1 | StrainInfo: A central database for resolving microbial strain identifiers |