Strain identifier
BacDive ID: 132174
Type strain: 
Species: Caldimonas caldifontis
Strain history: W.-J. Li YIM 78140.
NCBI tax ID(s): 1452508 (species)
version 8.1 (current version)
General
@ref: 23963
BacDive-ID: 132174
DSM-Number: 27262
keywords: genome sequence, 16S sequence, Bacteria, thermophilic, motile
description: Caldimonas caldifontis DSM 27262 is a thermophilic, motile bacterium that was isolated from hot spring water.
NCBI tax id
- NCBI tax id: 1452508
- Matching level: species
strain history
| @ref | history |
|---|---|
| 23963 | <- W.-J. Li, YIM; YIM 78140 <- L. Dong, YIM |
| 67770 | W.-J. Li YIM 78140. |
doi: 10.13145/bacdive132174.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Betaproteobacteria
- order: Burkholderiales
- family: Comamonadaceae
- genus: Caldimonas
- species: Caldimonas caldifontis
- full scientific name: Caldimonas caldifontis (Dong et al. 2014) Liu et al. 2023
synonyms
- @ref: 20215
- synonym: Zhizhongheella caldifontis
@ref: 23963
domain: Bacteria
phylum: Proteobacteria
class: Betaproteobacteria
order: Burkholderiales
family: Comamonadaceae
genus: Zhizhongheella
species: Zhizhongheella caldifontis
full scientific name: Zhizhongheella caldifontis Dong et al. 2014
type strain: yes
Morphology
cell morphology
| @ref | motility | confidence | gram stain |
|---|---|---|---|
| 69480 | yes | 96.791 | |
| 69480 | 99.999 | negative |
Culture and growth conditions
culture medium
- @ref: 23963
- name: MODIFIED T5 (DSMZ Medium 1335)
- growth: yes
- link: https://mediadive.dsmz.de/medium/1335
- composition: Name: MODIFIED T5 MEDIUM (DSMZ Medium 1335) Composition: Agar 20.0 g/l Yeast extract 2.0 g/l CaCl2 x 2 H2O 1.0 g/l Starch 1.0 g/l Glucose 1.0 g/l Tryptone 0.5 g/l Distilled water
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 23963 | positive | growth | 40 | thermophilic |
| 67770 | positive | growth | 40 | thermophilic |
Physiology and metabolism
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | no | 100 |
| 69480 | no | 99.991 |
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent |
|---|---|---|---|---|---|
| 23963 | hot spring water | Yunnan province, Tengchong, Hehua hot spring | China | CHN | Asia |
| 67770 | Hot spring water from Hehua hot spring | Tengchong, Yunnan Province, south-west China | China | CHN | Asia |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Aquatic | #Thermal spring |
| #Condition | #Thermophilic (>45°C) |
taxonmaps
- @ref: 69479
- File name: preview.99_46900.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_1;96_3153;97_3862;98_33865;99_46900&stattab=map
- Last taxonomy: Comamonadaceae
- 16S sequence: KF771277
- Sequence Identity:
- Total samples: 231
- soil counts: 53
- aquatic counts: 97
- animal counts: 35
- plant counts: 46
Safety information
risk assessment
- @ref: 23963
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 23963
- description: Zhizhongheella caldifontis strain YIM 78140 16S ribosomal RNA gene, partial sequence
- accession: KF771277
- length: 1548
- database: ena
- NCBI tax ID: 1452508
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Zhizhongheella caldifontis strain BCRC 80649 | 1452508.3 | wgs | patric | 1452508 |
| 66792 | Zhizhongheella caldifontis BCRC 80649 | 2831908861 | draft | img | 1452508 |
| 67770 | Caldimonas caldifontis BCRC 80649 | GCA_002930615 | contig | ncbi | 1452508 |
GC content
- @ref: 23963
- GC-content: 70.8
- method: high performance liquid chromatography (HPLC)
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| motile | yes | 85.748 | no |
| gram-positive | no | 99.224 | no |
| anaerobic | no | 98.235 | no |
| halophile | no | 88.155 | no |
| spore-forming | no | 95.853 | no |
| thermophile | yes | 63.795 | yes |
| glucose-util | no | 61.402 | no |
| aerobic | yes | 91.679 | no |
| flagellated | yes | 74.651 | no |
| glucose-ferment | no | 88.204 | no |
External links
@ref: 23963
culture collection no.: DSM 27262, BCRC 80649, KCTC 32557, YIM 78140, JCM 19651
straininfo link
- @ref: 90529
- straininfo: 400064
literature
- topic: Phylogeny
- Pubmed-ID: 24515725
- title: Zhizhongheella caldifontis gen. nov., sp. nov., a novel member of the family Comamonadaceae.
- authors: Dong L, Ming H, Liu L, Zhou EM, Yin YR, Duan YY, Nie GX, Feng HG, Li WJ
- journal: Antonie Van Leeuwenhoek
- DOI: 10.1007/s10482-014-0131-6
- year: 2014
- mesh: Bacterial Typing Techniques, Base Composition, China, Cluster Analysis, Comamonadaceae/*classification/genetics/growth & development/*isolation & purification, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Hot Springs/microbiology, Molecular Sequence Data, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA
- topic2: Genetics
Reference
| @id | authors | title | doi/url | catalogue | journal | pubmed |
|---|---|---|---|---|---|---|
| 20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | 10.1099/ijsem.0.004332 | |||
| 23963 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-27262 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 27262) | |||
| 66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | |||
| 66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | 10.1093/nar/gkaa1025 | Nucleic Acids Res. 49: D498-D508 2020 | 33211880 | |
| 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. | MicrobeAtlas 1.0 beta | https://microbeatlas.org/ | |||
| 69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | |||
| 69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | Predictions based on the model GenomeNet Sporulation v. 1 | 10.21203/rs.3.rs-2527258/v1 | |||
| 90529 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | StrainInfo: A central database for resolving microbial strain identifiers | 10.60712/SI-ID400064.1 |