Strain identifier

BacDive ID: 23443

Type strain: Yes

Species: Caldicoprobacter guelmensis

Strain Designation: D2C22

Strain history: M.-L. Fardeau D2C22.

NCBI tax ID(s): 1170224 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 19337

BacDive-ID: 23443

DSM-Number: 24605

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

description: Caldicoprobacter guelmensis D2C22 is an anaerobe, thermophilic, Gram-positive bacterium that was isolated from water from a terrestrial hot spring.

NCBI tax id

  • NCBI tax id: 1170224
  • Matching level: species

strain history

@refhistory
19337<- M. L. Fardeau, Lab. Microbiol. de l'IRD/ESIL, Univ. de Provence et de la Méditerranée, Marseille, France; D2C22 <- A. Bouanane {2010}
67770M.-L. Fardeau D2C22.

doi: 10.13145/bacdive23443.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Clostridia
  • order: Eubacteriales
  • family: Caldicoprobacteraceae
  • genus: Caldicoprobacter
  • species: Caldicoprobacter guelmensis
  • full scientific name: Caldicoprobacter guelmensis Bouanane-Darenfed et al. 2013

@ref: 19337

domain: Bacteria

phylum: Firmicutes

class: Clostridia

order: Clostridiales

family: Caldicoprobacteraceae

genus: Caldicoprobacter

species: Caldicoprobacter guelmensis

full scientific name: Caldicoprobacter guelmensis Bouanane-Darenfed et al. 2013

strain designation: D2C22

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
30742positive8.5 µm0.35 µmrod-shapedno
69480positive99.998

Culture and growth conditions

culture medium

  • @ref: 19337
  • name: PY + X MEDIUM (N2/CO2) (DSMZ Medium 104c)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/104c
  • composition: Name: PY + X MEDIUM (N2/CO2) (DSMZ Medium 104c) 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 Na2CO3 1.0 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

@refgrowthtypetemperaturerangeconfidence
19337positivegrowth65thermophilic
30742positivegrowth45-85hyperthermophilic
30742positiveoptimum65thermophilic
67770positivegrowth70thermophilic
69480thermophilic100

culture pH

@refabilitytypepHPH range
30742positivegrowth05-09alkaliphile
30742positiveoptimum6.8

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
19337anaerobe
30742anaerobe
69480anaerobe99.998

spore formation

@refspore formationconfidence
30742no
69481yes100

halophily

@refsaltgrowthtested relationconcentration
30742NaClpositivegrowth0-2 %
30742NaClpositiveoptimum0.1 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3074222599arabinose+carbon source
3074217057cellobiose+carbon source
3074228757fructose+carbon source
3074228260galactose+carbon source
3074217234glucose+carbon source
3074217716lactose+carbon source
3074217306maltose+carbon source
3074237684mannose+carbon source
3074228053melibiose+carbon source
3074215361pyruvate+carbon source
3074233942ribose+carbon source
3074217992sucrose+carbon source
3074218222xylose+carbon source

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitude
19337water from a terrestrial hot springnear GuelmaAlgeriaDZAAfrica36.477.43
67770Hydrothermal hot spring of Guelma in north-east Algeria

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_112215.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_3079;96_14245;97_49476;98_76086;99_112215&stattab=map
  • Last taxonomy: Caldicoprobacter guelmensis subclade
  • 16S sequence: JQ707908
  • Sequence Identity:
  • Total samples: 24
  • soil counts: 3
  • aquatic counts: 20
  • plant counts: 1

Safety information

risk assessment

  • @ref: 19337
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 19337
  • description: Caldicoprobacter guelmensis strain D2C22 16S ribosomal RNA gene, partial sequence
  • accession: JQ707908
  • length: 1531
  • database: ena
  • NCBI tax ID: 1170224

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Caldicoprobacter guelmensis DSM 24605GCA_016908415contigncbi1170224
66792Caldicoprobacter guelmensis strain DSM 246051170224.4wgspatric1170224
66792Caldicoprobacter guelmensis DSM 246052901129015draftimg1170224

GC content

@refGC-contentmethod
1933741.6high performance liquid chromatography (HPLC)
3074241.6

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileyes51.78yes
gram-positiveyes84.264yes
anaerobicyes98.796no
aerobicno97.791yes
halophileno94.043yes
spore-formingyes52.806yes
flagellatedno91.749no
thermophileyes100yes
glucose-utilyes89.976yes
glucose-fermentyes56.073no

External links

@ref: 19337

culture collection no.: DSM 24605, JCM 17646

straininfo link

  • @ref: 87595
  • straininfo: 400115

literature

  • topic: Phylogeny
  • Pubmed-ID: 23041645
  • title: Caldicoprobacter guelmensis sp. nov., a thermophilic, anaerobic, xylanolytic bacterium isolated from a hot spring.
  • authors: Bouanane-Darenfed A, Ben Hania W, Hacene H, Cayol JL, Ollivier B, Fardeau ML
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.043497-0
  • year: 2012
  • mesh: Algeria, Bacteria, Anaerobic/classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Fermentation, Gram-Positive Bacteria/*classification/genetics/isolation & purification, Hot Springs/*microbiology, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Xylans/metabolism
  • topic2: Enzymology

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
19337Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 24605)https://www.dsmz.de/collection/catalogue/details/culture/DSM-24605
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
30742Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2707328776041
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
87595Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID400115.1StrainInfo: A central database for resolving microbial strain identifiers