Strain identifier
BacDive ID: 16751
Type strain:
Species: Planifilum fulgidum
Strain Designation: 500275
Strain history: A. Nakamura 500275.
NCBI tax ID(s): 201973 (species)
General
@ref: 12109
BacDive-ID: 16751
DSM-Number: 44945
keywords: genome sequence, 16S sequence, Bacteria, aerobe, spore-forming, thermophilic, Gram-positive
description: Planifilum fulgidum 500275 is an aerobe, spore-forming, thermophilic bacterium that was isolated from a hyperthermal compost.
NCBI tax id
- NCBI tax id: 201973
- Matching level: species
strain history
@ref | history |
---|---|
12109 | <- A. Nakamura <- K. Hatayama; 500275 |
67770 | A. Nakamura 500275. |
doi: 10.13145/bacdive16751.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacillota
- domain: Bacteria
- phylum: Bacillota
- class: Bacilli
- order: Caryophanales
- family: Thermoactinomycetaceae
- genus: Planifilum
- species: Planifilum fulgidum
- full scientific name: Planifilum fulgidum Hatayama et al. 2005
@ref: 12109
domain: Bacteria
phylum: Firmicutes
class: Bacilli
order: Bacillales
family: Thermoactinomycetaceae
genus: Planifilum
species: Planifilum fulgidum
full scientific name: Planifilum fulgidum Hatayama et al. 2005
strain designation: 500275
type strain: yes
Morphology
cell morphology
@ref | gram stain | confidence |
---|---|---|
31346 | positive | |
69480 | positive | 100 |
pigmentation
- @ref: 31346
- production: yes
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
12109 | LB (Luria-Bertani) MEDIUM (DSMZ Medium 381) | yes | https://mediadive.dsmz.de/medium/381 | Name: LB (Luria-Bertani) MEDIUM (DSMZ Medium 381) Composition: Agar 20.0 g/l NaCl 10.0 g/l Tryptone 10.0 g/l Yeast extract 5.0 g/l Distilled water |
12109 | CZAPEK PEPTONE AGAR (DSMZ Medium 83) | yes | https://mediadive.dsmz.de/medium/83 | Name: CZAPEK PEPTONE AGAR (DSMZ Medium 83) Composition: Sucrose 30.0 g/l Agar 20.0 g/l Peptone 5.0 g/l NaNO3 3.0 g/l Yeast extract 2.0 g/l K2HPO4 1.0 g/l MgSO4 x 7 H2O 0.5 g/l KCl 0.5 g/l FeSO4 x 7 H2O 0.01 g/l Distilled water |
culture temp
@ref | growth | type | temperature | range | confidence |
---|---|---|---|---|---|
12109 | positive | growth | 60 | thermophilic | |
31346 | positive | growth | 50-67 | thermophilic | |
31346 | positive | optimum | 62.5 | thermophilic | |
67770 | positive | growth | 60 | thermophilic | |
69480 | thermophilic | 100 |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
12109 | aerobe |
31346 | aerobe |
spore formation
@ref | spore formation | confidence |
---|---|---|
31346 | yes | |
69481 | yes | 100 |
69480 | yes | 100 |
observation
- @ref: 67770
- observation: quinones: MK-7
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent |
---|---|---|---|---|---|
12109 | a hyperthermal compost | Motobu, Okinawa prefecture | Japan | JPN | Asia |
67770 | Hyperthermal compost | Motobu, Okinawa | Japan | JPN | Asia |
isolation source categories
- Cat1: #Engineered
- Cat2: #Biodegradation
- Cat3: #Composting
taxonmaps
- @ref: 69479
- File name: preview.99_56804.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_358;96_16384;97_20105;98_25119;99_56804&stattab=map
- Last taxonomy: Planifilum
- 16S sequence: AB088362
- Sequence Identity:
- Total samples: 8368
- soil counts: 4724
- aquatic counts: 744
- animal counts: 1352
- plant counts: 1548
Safety information
risk assessment
- @ref: 12109
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 12109
- description: Planifilum fulgidum gene for 16S rRNA, partial sequence, strain:500275
- accession: AB088362
- length: 1516
- database: ena
- NCBI tax ID: 201973
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Planifilum fulgidum strain DSM 44945 | 201973.5 | wgs | patric | 201973 |
66792 | Planifilum fulgidum DSM 44945 | 2615840724 | draft | img | 201973 |
67770 | Planifilum fulgidum DSM 44945 | GCA_900113175 | scaffold | ncbi | 201973 |
GC content
@ref | GC-content | method |
---|---|---|
12109 | 58.7 | |
31346 | 59.35 | |
67770 | 60 | high performance liquid chromatography (HPLC) |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | yes | 100 | no |
motile | no | 78.979 | no |
gram-positive | yes | 87.493 | yes |
anaerobic | no | 95.45 | no |
aerobic | yes | 89.897 | yes |
halophile | no | 82.322 | no |
spore-forming | yes | 92.055 | yes |
glucose-util | yes | 89.273 | no |
flagellated | no | 92.089 | no |
thermophile | yes | 100 | yes |
glucose-ferment | no | 93.01 | no |
External links
@ref: 12109
culture collection no.: DSM 44945, ATCC BAA 970, JCM 12508, BCRC 16828
straininfo link
- @ref: 85769
- straininfo: 265621
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 16166716 | Planifilum fimeticola gen. nov., sp. nov. and Planifilum fulgidum sp. nov., novel members of the family 'Thermoactinomycetaceae' isolated from compost. | Hatayama K, Shoun H, Ueda Y, Nakamura A | Int J Syst Evol Microbiol | 10.1099/ijs.0.63367-0 | 2005 | Bacterial Typing Techniques, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Genes, rRNA, Gram-Positive Endospore-Forming Bacteria/*classification/genetics/isolation & purification/physiology, Hot Temperature, Japan, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Refuse Disposal/*methods, Sequence Analysis, DNA, *Soil Microbiology | Stress |
Phylogeny | 17684270 | Planifilum yunnanense sp. nov., a thermophilic thermoactinomycete isolated from a hot spring. | Zhang YX, Dong C, Biao S | Int J Syst Evol Microbiol | 10.1099/ijs.0.64646-0 | 2007 | Actinomycetales/chemistry/*classification/*isolation & purification/physiology, China, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/analysis, Hot Springs/*microbiology, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Vitamin K 2/analysis | Genetics |
Phylogeny | 23024147 | Polycladomyces abyssicola gen. nov., sp. nov., a thermophilic filamentous bacterium isolated from hemipelagic sediment. | Tsubouchi T, Shimane Y, Mori K, Usui K, Hiraki T, Tame A, Uematsu K, Maruyama T, Hatada Y | Int J Syst Evol Microbiol | 10.1099/ijs.0.043596-0 | 2012 | Bacillales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Geologic Sediments/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Pacific Ocean, Peptidoglycan/analysis, Phospholipids/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/analysis | Genetics |
Reference
@id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed | journal |
---|---|---|---|---|---|---|---|
12109 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44945) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-44945 | ||||
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 | ||||
31346 | 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 | 27660 | 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/ | |||||
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) | ||||
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 | ||||
85769 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID265621.1 | StrainInfo: A central database for resolving microbial strain identifiers |