Strain identifier
BacDive ID: 23443
Type strain:
Species: Caldicoprobacter guelmensis
Strain Designation: D2C22
Strain history: M.-L. Fardeau D2C22.
NCBI tax ID(s): 1170224 (species)
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
@ref | history |
---|---|
19337 | <- M. L. Fardeau, Lab. Microbiol. de l'IRD/ESIL, Univ. de Provence et de la Méditerranée, Marseille, France; D2C22 <- A. Bouanane {2010} |
67770 | M.-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
@ref | gram stain | cell length | cell width | cell shape | motility | confidence |
---|---|---|---|---|---|---|
30742 | positive | 8.5 µm | 0.35 µm | rod-shaped | no | |
69480 | positive | 99.998 |
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
@ref | growth | type | temperature | range | confidence |
---|---|---|---|---|---|
19337 | positive | growth | 65 | thermophilic | |
30742 | positive | growth | 45-85 | hyperthermophilic | |
30742 | positive | optimum | 65 | thermophilic | |
67770 | positive | growth | 70 | thermophilic | |
69480 | thermophilic | 100 |
culture pH
@ref | ability | type | pH | PH range |
---|---|---|---|---|
30742 | positive | growth | 05-09 | alkaliphile |
30742 | positive | optimum | 6.8 |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance | confidence |
---|---|---|
19337 | anaerobe | |
30742 | anaerobe | |
69480 | anaerobe | 99.998 |
spore formation
@ref | spore formation | confidence |
---|---|---|
30742 | no | |
69481 | yes | 100 |
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
30742 | NaCl | positive | growth | 0-2 % |
30742 | NaCl | positive | optimum | 0.1 % |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
30742 | 22599 | arabinose | + | carbon source |
30742 | 17057 | cellobiose | + | carbon source |
30742 | 28757 | fructose | + | carbon source |
30742 | 28260 | galactose | + | carbon source |
30742 | 17234 | glucose | + | carbon source |
30742 | 17716 | lactose | + | carbon source |
30742 | 17306 | maltose | + | carbon source |
30742 | 37684 | mannose | + | carbon source |
30742 | 28053 | melibiose | + | carbon source |
30742 | 15361 | pyruvate | + | carbon source |
30742 | 33942 | ribose | + | carbon source |
30742 | 17992 | sucrose | + | carbon source |
30742 | 18222 | xylose | + | carbon source |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent | latitude | longitude |
---|---|---|---|---|---|---|---|
19337 | water from a terrestrial hot spring | near Guelma | Algeria | DZA | Africa | 36.47 | 7.43 |
67770 | Hydrothermal hot spring of Guelma in north-east Algeria |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#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
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Caldicoprobacter guelmensis DSM 24605 | GCA_016908415 | contig | ncbi | 1170224 |
66792 | Caldicoprobacter guelmensis strain DSM 24605 | 1170224.4 | wgs | patric | 1170224 |
66792 | Caldicoprobacter guelmensis DSM 24605 | 2901129015 | draft | img | 1170224 |
GC content
@ref | GC-content | method |
---|---|---|
19337 | 41.6 | high performance liquid chromatography (HPLC) |
30742 | 41.6 |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | yes | 100 | no |
motile | yes | 51.78 | yes |
gram-positive | yes | 84.264 | yes |
anaerobic | yes | 98.796 | no |
aerobic | no | 97.791 | yes |
halophile | no | 94.043 | yes |
spore-forming | yes | 52.806 | yes |
flagellated | no | 91.749 | no |
thermophile | yes | 100 | yes |
glucose-util | yes | 89.976 | yes |
glucose-ferment | yes | 56.073 | no |
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
@id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
---|---|---|---|---|---|---|
19337 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 24605) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-24605 | |||
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 | |||
30742 | 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 | 27073 | 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 | |||
87595 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID400115.1 | StrainInfo: A central database for resolving microbial strain identifiers |