Strain identifier

BacDive ID: 16708

Type strain: Yes

Species: Meiothermus rufus

Strain Designation: CAL-4

Strain history: <- M. da Costa, Univ. Coimbra, Portugal <- L. Albuquerque; CAL-4

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General

@ref: 16217

BacDive-ID: 16708

DSM-Number: 22234

keywords: genome sequence, 16S sequence, Bacteria, thermophilic, Gram-negative

description: Meiothermus rufus CAL-4 is a thermophilic, Gram-negative bacterium that was isolated from water from a hot spring.

NCBI tax id

NCBI tax idMatching level
604331strain
604332species

strain history

  • @ref: 16217
  • history: <- M. da Costa, Univ. Coimbra, Portugal <- L. Albuquerque; CAL-4

doi: 10.13145/bacdive16708.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/deinococcota
  • domain: Bacteria
  • phylum: Deinococcota
  • class: Deinococci
  • order: Thermales
  • family: Thermaceae
  • genus: Meiothermus
  • species: Meiothermus rufus
  • full scientific name: Meiothermus rufus Albuquerque et al. 2010

@ref: 16217

domain: Bacteria

phylum: Deinococcus-Thermus

class: Deinococci

order: Thermales

family: Thermaceae

genus: Meiothermus

species: Meiothermus rufus

full scientific name: Meiothermus rufus Albuquerque et al. 2010

strain designation: CAL-4

type strain: yes

Morphology

cell morphology

  • @ref: 69480
  • gram stain: negative
  • confidence: 99.777

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
16217MODIFIED THERMUS 162 MEDIUM (DSMZ Medium 630)yeshttps://mediadive.dsmz.de/medium/630Name: MODIFIED THERMUS 162 MEDIUM (DSMZ Medium 630) Composition: Agar 28.0 g/l Na2HPO4 x 12 H2O 4.3 g/l Yeast extract 2.5 g/l Tryptone 2.5 g/l KH2PO4 0.544 g/l MgCl2 x 6 H2O 0.2 g/l CaSO4 x 2 H2O 0.04 g/l Nitrilotriacetic acid 0.0064 g/l Fe(III) citrate 0.00122472 g/l FeCl2 x 4 H2O 0.0005 g/l MnCl2 x 4 H2O 0.00025 g/l CoCl2 x 4 H2O 0.00015 g/l CuCl2 x 2 H2O 2.5e-05 g/l Na2MoO4 x 2 H2O 2.5e-05 g/l H3BO3 1e-05 g/l NiCl2 x 6 H2O 1e-05 g/l Distilled water
16217THERMUS 162 MEDIUM (DSMZ Medium 878)yeshttps://mediadive.dsmz.de/medium/878Name: THERMUS 162 MEDIUM (DSMZ Medium 878) Composition: Agar 28.0 g/l Na2HPO4 x 12 H2O 4.3 g/l Yeast extract 1.0 g/l Tryptone 1.0 g/l KH2PO4 0.544 g/l MgCl2 x 6 H2O 0.2 g/l Nitrilotriacetic acid 0.1 g/l CaSO4 x 2 H2O 0.04 g/l Fe(III) citrate 0.00122472 g/l MnSO4 x H2O 0.00114 g/l ZnSO4 x 7 H2O 0.00025 g/l H3BO3 0.00025 g/l CoCl2 x 6 H2O 2.25e-05 g/l CuSO4 x 5 H2O 1.25e-05 g/l Na2MoO4 x 2 H2O 1.25e-05 g/l H2SO4 Distilled water

culture temp

@refgrowthtypetemperaturerangeconfidence
16217positivegrowth55thermophilic
69480thermophilic99.605

Physiology and metabolism

spore formation

@refspore formationconfidence
69481no100
69480no99.986

Isolation, sampling and environmental information

isolation

  • @ref: 16217
  • sample type: water from a hot spring
  • geographic location: Auvergne, Chaudes-Aigues hydrothermal area, Lavoire fountain
  • country: France
  • origin.country: FRA
  • continent: Europe

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Thermal spring
#Condition#Thermophilic (>45°C)

taxonmaps

  • @ref: 69479
  • File name: preview.99_8314.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_137;96_3814;97_4704;98_6050;99_8314&stattab=map
  • Last taxonomy: Meiothermus rufus subclade
  • 16S sequence: FN178496
  • Sequence Identity:
  • Total samples: 105
  • soil counts: 7
  • aquatic counts: 92
  • animal counts: 5
  • plant counts: 1

Safety information

risk assessment

  • @ref: 16217
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 16217
  • description: Meiothermus rufus DSM 22234 partial 16S rRNA gene, strain CAL-4
  • accession: FN178496
  • length: 1487
  • database: ena
  • NCBI tax ID: 604331

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Meiothermus rufus DSM 22234GCA_000423425scaffoldncbi604331
66792Meiothermus rufus DSM 22234604331.3wgspatric604331
66792Meiothermus rufus DSM 222342522572180draftimg604331

GC content

  • @ref: 16217
  • GC-content: 64.1±0.4
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno86.994no
flagellatedno96.191no
gram-positiveno93.24no
anaerobicno96.416no
aerobicyes88.11no
halophileno86.456no
spore-formingno95.801no
thermophileyes100no
glucose-utilyes84.212no
glucose-fermentno89.038no

External links

@ref: 16217

culture collection no.: DSM 22234, LMG 24878

straininfo link

  • @ref: 85727
  • straininfo: 360702

literature

  • topic: Phylogeny
  • Pubmed-ID: 19577874
  • title: Meiothermus rufus sp. nov., a new slightly thermophilic red-pigmented species and emended description of the genus Meiothermus.
  • authors: Albuquerque L, Ferreira C, Tomaz D, Tiago I, Verissimo A, da Costa MS, Nobre MF
  • journal: Syst Appl Microbiol
  • DOI: 10.1016/j.syapm.2009.05.002
  • year: 2009
  • mesh: Bacteria/chemistry/*classification/growth & development/*isolation & purification, Bacterial Physiological Phenomena, Bacterial Typing Techniques, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, France, Glycolipids/analysis, Hot Springs/*microbiology, Hydrogen-Ion Concentration, Molecular Sequence Data, Phylogeny, Pigments, Biological/biosynthesis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Temperature
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitle
16217Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 22234)https://www.dsmz.de/collection/catalogue/details/culture/DSM-22234
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
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)
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
85727Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID360702.1StrainInfo: A central database for resolving microbial strain identifiers