Strain identifier

BacDive ID: 2524

Type strain: Yes

Species: Caloramator mitchellensis

Strain Designation: VF08

Strain history: <- CD Ogg and BKC Patel, Griffith Univ., Brisbane, Australia, VF08

NCBI tax ID(s): 908809 (species)

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General

@ref: 14356

BacDive-ID: 2524

DSM-Number: 25793

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, thermophilic, Gram-negative, motile, rod-shaped

description: Caloramator mitchellensis VF08 is an anaerobe, thermophilic, Gram-negative bacterium that was isolated from geothermal waters.

NCBI tax id

  • NCBI tax id: 908809
  • Matching level: species

strain history

@refhistory
14356<- T. Itoh, JCM <- C. Ogg and B. K. C. Patel, Griffith Univ., Brisbane, Australia; VF08
67770C. D. Ogg and B. K. C. Patel VF08.
67771<- CD Ogg and BKC Patel, Griffith Univ., Brisbane, Australia, VF08

doi: 10.13145/bacdive2524.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Clostridia
  • order: Eubacteriales
  • family: Clostridiaceae
  • genus: Caloramator
  • species: Caloramator mitchellensis
  • full scientific name: Caloramator mitchellensis Ogg and Patel 2011

@ref: 14356

domain: Bacteria

phylum: Firmicutes

class: Clostridia

order: Clostridiales

family: Clostridiaceae

genus: Caloramator

species: Caloramator mitchellensis

full scientific name: Caloramator mitchellensis Ogg and Patel 2011

strain designation: VF08

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityflagellum arrangement
29876negative2 µm0.6 µmrod-shapedyes
67771rod-shapedyesperitrichous
67771curved-shaped
67771negative

Culture and growth conditions

culture medium

  • @ref: 14356
  • name: PY + X MEDIUM (DSMZ Medium 104b)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/104b
  • composition: Name: PY + X MEDIUM (DSMZ Medium 104b) Composition: Yeast extract 10.0 g/l D-Glucose 5.0 g/l Trypticase peptone 5.0 g/l Meat peptone 5.0 g/l L-Cysteine HCl x H2O 0.5 g/l NaHCO3 0.4 g/l NaCl 0.08 g/l KH2PO4 0.04 g/l K2HPO4 0.04 g/l MgSO4 x 7 H2O 0.02 g/l CaCl2 x 2 H2O 0.01 g/l Sodium resazurin 0.0005 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
14356positivegrowth50thermophilic
29876positivegrowth37-60
29876positiveoptimum55thermophilic
67770positivegrowth50thermophilic
67771positivegrowth55thermophilic

culture pH

@refabilitytypepHPH range
29876positivegrowth06-09alkaliphile
29876positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
14356anaerobe
29876anaerobe
67771anaerobe

spore formation

@refspore formation
29876no
67771no

halophily

  • @ref: 29876
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-2 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2987617057cellobiose+carbon source
2987628757fructose+carbon source
2987617234glucose+carbon source
2987617306maltose+carbon source
2987615361pyruvate+carbon source
2987616634raffinose+carbon source
2987633942ribose+carbon source
2987617822serine+carbon source
2987617992sucrose+carbon source
2987618222xylose+carbon source
2987617632nitrate+reduction

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
14356geothermal watersQueensland, Mitchell, Great Artesian Basin boreAustraliaAUSAustralia and Oceania
67771From water sample collected from a Great Artesian Basin boreAustraliaAUSAustralia and Oceania
67770Great Artesian Basin boreMitchell, QueenslandAustraliaAUSAustralia and Oceania

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Aquatic

taxonmaps

  • @ref: 69479
  • File name: preview.99_174574.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_285;96_64959;97_84281;98_114282;99_174574&stattab=map
  • Last taxonomy: Caloramator mitchellensis subclade
  • 16S sequence: GU723692
  • Sequence Identity:
  • Total samples: 661
  • soil counts: 284
  • aquatic counts: 271
  • animal counts: 93
  • plant counts: 13

Safety information

risk assessment

  • @ref: 14356
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 14356
  • description: Caloramator mitchellensis 16S ribosomal RNA gene, partial sequence
  • accession: GU723692
  • length: 1605
  • database: ena
  • NCBI tax ID: 908809

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Caloramator mitchellensis VF082833544911draftimg908809
67771Caloramator mitchellensis VF08GCA_001440545contigncbi908809

GC content

@refGC-contentmethod
1435638.4thermal denaturation, midpoint method (Tm)
2987638.4

External links

@ref: 14356

culture collection no.: DSM 25793, JCM 15828, KCTC 5735

straininfo link

  • @ref: 72058
  • straininfo: 407020

literature

  • topic: Phylogeny
  • Pubmed-ID: 20400665
  • title: Caloramator mitchellensis sp. nov., a thermoanaerobe isolated from the geothermal waters of the Great Artesian Basin of Australia, and emended description of the genus Caloramator.
  • authors: Ogg CD, Patel BKC
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.023655-0
  • year: 2010
  • mesh: Anti-Bacterial Agents/pharmacology, Australia, Base Composition, Cluster Analysis, Culture Media/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fermentation, Glucose/metabolism, Gram-Positive Bacteria/*classification/genetics/*isolation & purification/physiology, Hot Springs/*microbiology, Microbial Sensitivity Tests, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
14356Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 25793)https://www.dsmz.de/collection/catalogue/details/culture/DSM-25793
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
29876Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2625028776041
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updates33211880Nucleic Acids Res. 49: D498-D508 2020
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
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
72058Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID407020.1StrainInfo: A central database for resolving microbial strain identifiers