Strain identifier

BacDive ID: 16752

Type strain: Yes

Species: Planifilum fimeticola

Strain Designation: H0165

Strain history: A. Nakamura H0165.

NCBI tax ID(s): 201975 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 8.1 (current version)

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

@refhistory
12110<- A. Nakamura <- K. Hatayama; H0165
67770A. 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

@refgram stainconfidence
31346positive
69480positive100

pigmentation

  • @ref: 31346
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
12110LB (Luria-Bertani) MEDIUM (DSMZ Medium 381)yeshttps://mediadive.dsmz.de/medium/381Name: 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
12110CZAPEK PEPTONE AGAR (DSMZ Medium 83)yeshttps://mediadive.dsmz.de/medium/83Name: 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

@refgrowthtypetemperaturerangeconfidence
12110positivegrowth60thermophilic
31346positivegrowth50-65thermophilic
31346positiveoptimum59thermophilic
67770positivegrowth55thermophilic
69480thermophilic99.486

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
12110aerobe
31346aerobe

spore formation

@refspore formationconfidence
31346yes
69481yes100
69480yes100

observation

  • @ref: 67770
  • observation: quinones: MK-7

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
12110a hyperthermal compostMotobu, Okinawa prefectureJapanJPNAsia
67770Hyperthermal compostMotobu, OkinawaJapanJPNAsia

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

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Planifilum fimeticola strain DSM 44946201975.3wgspatric201975
66792Planifilum fimeticola DSM 449462728369512draftimg201975
67770Planifilum fimeticola DSM 44946GCA_003001905scaffoldncbi201975

GC content

@refGC-contentmethod
1211060.3high performance liquid chromatography (HPLC)
3134660.3

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileno79.804no
gram-positiveyes89.675yes
anaerobicno97.941yes
aerobicyes93.777yes
halophileno75.821no
spore-formingyes92.091yes
glucose-utilyes91.518no
flagellatedno91.124no
thermophileyes99.746no
glucose-fermentno93.29no

External links

@ref: 12110

culture collection no.: DSM 44946, ATCC BAA 969, JCM 12507, BCRC 16827

straininfo link

  • @ref: 85770
  • straininfo: 265620

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny16166716Planifilum 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 AInt J Syst Evol Microbiol10.1099/ijs.0.63367-02005Bacterial 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 MicrobiologyStress
Phylogeny17684270Planifilum yunnanense sp. nov., a thermophilic thermoactinomycete isolated from a hot spring.Zhang YX, Dong C, Biao SInt J Syst Evol Microbiol10.1099/ijs.0.64646-02007Actinomycetales/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/analysisGenetics
Phylogeny23024147Polycladomyces 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 YInt J Syst Evol Microbiol10.1099/ijs.0.043596-02012Bacillales/*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/analysisGenetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
12110Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44946)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44946
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
31346Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2766028776041
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
69479João 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
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
85770Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID265620.1StrainInfo: A central database for resolving microbial strain identifiers