Strain identifier
BacDive ID: 8013
Type strain:
Species: Micromonospora pattaloongensis
Strain Designation: TJ2-2
Strain history: C. Thawai TJ2-2.
NCBI tax ID(s): 405436 (species)
General
@ref: 15929
BacDive-ID: 8013
DSM-Number: 45245
keywords: genome sequence, 16S sequence, Bacteria, spore-forming, mesophilic, Gram-positive
description: Micromonospora pattaloongensis TJ2-2 is a spore-forming, mesophilic, Gram-positive bacterium that was isolated from Thai mangrove forest.
NCBI tax id
- NCBI tax id: 405436
- Matching level: species
strain history
@ref | history |
---|---|
15929 | <- JCM/RIKEN; JCM 12833 <- C. Thawai; TJ2-2 |
67770 | C. Thawai TJ2-2. |
doi: 10.13145/bacdive8013.20230509.8.1
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 pattaloongensis
- full scientific name: Micromonospora pattaloongensis Thawai et al. 2008
@ref: 15929
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Micromonosporaceae
genus: Micromonospora
species: Micromonospora pattaloongensis
full scientific name: Micromonospora pattaloongensis Thawai et al. 2008
strain designation: TJ2-2
type strain: yes
Morphology
cell morphology
@ref | gram stain | motility | confidence |
---|---|---|---|
32385 | positive | no | |
69480 | positive | 100 |
pigmentation
- @ref: 32385
- production: yes
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
15929 | TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) | yes | https://mediadive.dsmz.de/medium/535 | Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water |
15929 | 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 |
15929 | NUTRIENT AGAR (DSMZ Medium 1) | yes | https://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium1.pdf |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
15929 | positive | growth | 28 | mesophilic |
32385 | positive | growth | 25-40 | |
32385 | positive | optimum | 27.5 | mesophilic |
67770 | positive | growth | 28 | mesophilic |
Physiology and metabolism
spore formation
@ref | spore formation | confidence |
---|---|---|
32385 | yes | |
69481 | yes | 100 |
69480 | yes | 99.447 |
halophily
- @ref: 32385
- salt: NaCl
- growth: positive
- tested relation: growth
- concentration: <3 %
observation
- @ref: 67770
- observation: quinones: MK-10(H4), MK-10(H6), MK-10(H8)
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
32385 | 22599 | arabinose | + | carbon source |
32385 | 17057 | cellobiose | + | carbon source |
32385 | 28757 | fructose | + | carbon source |
32385 | 28260 | galactose | + | carbon source |
32385 | 17234 | glucose | + | carbon source |
32385 | 17716 | lactose | + | carbon source |
32385 | 33942 | ribose | + | carbon source |
32385 | 17814 | salicin | + | carbon source |
32385 | 18222 | xylose | + | carbon source |
32385 | 17632 | nitrate | + | reduction |
enzymes
- @ref: 32385
- value: gelatinase
- activity: +
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent |
---|---|---|---|---|---|
15929 | Thai mangrove forest | Pattaloong Province | Thailand | THA | Asia |
67770 | Soil from mangrove forest | Pattaloong Province | Thailand | THA | Asia |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Environmental | #Aquatic | #Mangrove |
#Environmental | #Terrestrial | #Forest |
Safety information
risk assessment
- @ref: 15929
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 15929
- description: Micromonospora pattaloongensis gene for 16S ribosomal RNA, partial sequence
- accession: AB275607
- length: 1511
- database: ena
- NCBI tax ID: 405436
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Micromonospora pattaloongensis strain DSM 45245 | 405436.4 | wgs | patric | 405436 |
66792 | Micromonospora pattaloongensis DSM 45245 | 2693429860 | draft | img | 405436 |
67770 | Micromonospora pattaloongensis DSM 45245 | GCA_900107255 | contig | ncbi | 405436 |
GC content
@ref | GC-content | method |
---|---|---|
15929 | 71.5 | |
67770 | 71.5 | high performance liquid chromatography (HPLC) |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | yes | 100 | no |
gram-positive | yes | 88.216 | yes |
anaerobic | no | 98.622 | no |
halophile | no | 92.803 | no |
spore-forming | yes | 91.125 | yes |
glucose-util | yes | 90.255 | yes |
aerobic | yes | 94.375 | no |
flagellated | no | 91.856 | yes |
motile | yes | 58.076 | no |
thermophile | no | 91.764 | yes |
glucose-ferment | no | 92.058 | no |
External links
@ref: 15929
culture collection no.: DSM 45245, JCM 12833, TISTR 1559, NRRL B-24764
straininfo link
- @ref: 77443
- straininfo: 396994
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 18599686 | Micromonospora pattaloongensis sp. nov., isolated from a Thai mangrove forest. | Thawai C, Tanasupawat S, Kudo T | Int J Syst Evol Microbiol | 10.1099/ijs.0.65410-0 | 2008 | Fatty Acids/metabolism, Micromonospora/chemistry/*classification/genetics/ultrastructure, Microscopy, Electron, Scanning, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Soil Microbiology, Species Specificity, Thailand, Trees/*microbiology, Verbenaceae | Genetics |
Phylogeny | 19651739 | Micromonospora pisi sp. nov., isolated from root nodules of Pisum sativum. | C Garcia L, Martinez-Molina E, Trujillo ME | Int J Syst Evol Microbiol | 10.1099/ijs.0.012708-0 | 2009 | Bacterial Proteins/genetics, Base Sequence, DNA Gyrase/genetics, Micromonospora/*classification/genetics/physiology, Molecular Sequence Data, Peas/*microbiology, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Root Nodules, Plant/*microbiology, Sequence Analysis, RNA, Spain | Genetics |
Phylogeny | 20305066 | Micromonospora rhizosphaerae sp. nov., isolated from mangrove rhizosphere soil. | Wang C, Xu XX, Qu Z, Wang HL, Lin HP, Xie QY, Ruan JS, Hong K | Int J Syst Evol Microbiol | 10.1099/ijs.0.020461-0 | 2010 | Bacterial Typing Techniques, Base Composition, Carbohydrates/analysis, China, DNA, Bacterial/genetics, Euphorbiaceae/*microbiology, Fatty Acids/analysis, Micromonospora/*classification/genetics/isolation & purification, Molecular Sequence Data, Phospholipids/analysis, Phylogeny, *Rhizosphere, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analysis | Genetics |
Phylogeny | 23178729 | Micromonospora sonneratiae sp. nov., isolated from a root of Sonneratia apetala. | Li L, Tang YL, Wei B, Xie QY, Deng Z, Hong K | Int J Syst Evol Microbiol | 10.1099/ijs.0.043570-0 | 2012 | Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Endophytes/classification/genetics/isolation & purification, Fatty Acids/analysis, Genes, Bacterial, Lythraceae/*microbiology, Micromonospora/*classification/genetics/isolation & purification, Molecular Sequence Data, *Phylogeny, Plant Roots/microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Soil Microbiology, Vitamin K 2/analysis | Enzymology |
Phylogeny | 24108323 | Micromonospora polyrhachis sp. nov., an actinomycete isolated from edible Chinese black ant (Polyrhachis vicina Roger). | Xiang W, Yu C, Liu C, Zhao J, Yang L, Xie B, Li L, Hong K, Wang X | Int J Syst Evol Microbiol | 10.1099/ijs.0.055863-0 | 2013 | Animals, Ants/*microbiology, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Genes, Bacterial, Micromonospora/*classification/genetics/isolation & purification, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/chemistry | Genetics |
Phylogeny | 26446196 | Micromonospora zhanjiangensis sp. nov., isolated from mangrove forest soil. | Zhang L, Li L, Deng Z, Hong K | Int J Syst Evol Microbiol | 10.1099/ijsem.0.000667 | 2015 | Avicennia, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Micromonospora/*classification/genetics/isolation & purification, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Ubiquinone/chemistry, *Wetlands | Genetics |
Phylogeny | 26620702 | Micromonospora ovatispora sp. nov. isolated from mangrove soil. | Li L, Hong K | Int J Syst Evol Microbiol | 10.1099/ijsem.0.000808 | 2015 |
Reference
@id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed | journal |
---|---|---|---|---|---|---|---|
15929 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45245) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-45245 | ||||
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 | ||||
32385 | 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 | 28610 | 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) | ||||
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 | 33211880 | Nucleic Acids Res. 49: D498-D508 2020 | ||
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 | ||||
77443 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID396994.1 | StrainInfo: A central database for resolving microbial strain identifiers |