Strain identifier
BacDive ID: 16752
Type strain:
Species: Planifilum fimeticola
Strain Designation: H0165
Strain history: A. Nakamura H0165.
NCBI tax ID(s): 201975 (species)
General
@ref: 12110
BacDive-ID: 16752
DSM-Number: 44946
keywords: genome sequence, 16S sequence, Bacteria, aerobe, spore-forming, thermophilic, Gram-positive
description: Planifilum fimeticola H0165 is an aerobe, spore-forming, thermophilic bacterium that was isolated from a hyperthermal compost.
NCBI tax id
- NCBI tax id: 201975
- Matching level: species
strain history
@ref | history |
---|---|
12110 | <- A. Nakamura <- K. Hatayama; H0165 |
67770 | A. Nakamura H0165. |
doi: 10.13145/bacdive16752.20230509.8.1
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 fimeticola
- full scientific name: Planifilum fimeticola Hatayama et al. 2005
@ref: 12110
domain: Bacteria
phylum: Firmicutes
class: Bacilli
order: Bacillales
family: Thermoactinomycetaceae
genus: Planifilum
species: Planifilum fimeticola
full scientific name: Planifilum fimeticola Hatayama et al. 2005
strain designation: H0165
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 |
---|---|---|---|---|
12110 | 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 |
12110 | 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 |
---|---|---|---|---|---|
12110 | positive | growth | 60 | thermophilic | |
31346 | positive | growth | 50-65 | thermophilic | |
31346 | positive | optimum | 59 | thermophilic | |
67770 | positive | growth | 55 | thermophilic | |
69480 | thermophilic | 99.486 |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
12110 | 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 |
---|---|---|---|---|---|
12110 | 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_59948.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_358;96_16384;97_20105;98_42596;99_59948&stattab=map
- Last taxonomy: Planifilum fimeticola subclade
- 16S sequence: AB088364
- Sequence Identity:
- Total samples: 4691
- soil counts: 2431
- aquatic counts: 628
- animal counts: 933
- plant counts: 699
Safety information
risk assessment
- @ref: 12110
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 12110
- description: Planifilum fimeticola gene for 16S rRNA, partial sequence, strain:H0165
- accession: AB088364
- length: 1510
- database: ena
- NCBI tax ID: 201975
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Planifilum fimeticola strain DSM 44946 | 201975.3 | wgs | patric | 201975 |
66792 | Planifilum fimeticola DSM 44946 | 2728369512 | draft | img | 201975 |
67770 | Planifilum fimeticola DSM 44946 | GCA_003001905 | scaffold | ncbi | 201975 |
GC content
@ref | GC-content | method |
---|---|---|
12110 | 60.3 | high performance liquid chromatography (HPLC) |
31346 | 60.3 |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | yes | 100 | no |
motile | no | 79.804 | no |
gram-positive | yes | 89.675 | yes |
anaerobic | no | 97.941 | yes |
aerobic | yes | 93.777 | yes |
halophile | no | 75.821 | no |
spore-forming | yes | 92.091 | yes |
glucose-util | yes | 91.518 | no |
flagellated | no | 91.124 | no |
thermophile | yes | 99.746 | no |
glucose-ferment | no | 93.29 | no |
External links
@ref: 12110
culture collection no.: DSM 44946, ATCC BAA 969, JCM 12507, BCRC 16827
straininfo link
- @ref: 85770
- straininfo: 265620
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 |
---|---|---|---|---|---|---|
12110 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44946) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-44946 | |||
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) | |||
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 | |||
85770 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID265620.1 | StrainInfo: A central database for resolving microbial strain identifiers |