Strain identifier
BacDive ID: 2518
Type strain: 
Species: Clostridium fervidum
Strain Designation: Rt4-B1
Strain history: <- DSM <- ATCC <- BKC Patel, Rt4-B1
NCBI tax ID(s): 1121261 (strain), 29344 (species)
version 8.1 (current version)
General
@ref: 2174
BacDive-ID: 2518
DSM-Number: 5463
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, spore-forming, thermophilic, rod-shaped
description: Clostridium fervidum Rt4-B1 is an anaerobe, spore-forming, thermophilic bacterium that was isolated from hot spring.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 29344 | species |
| 1121261 | strain |
strain history
| @ref | history |
|---|---|
| 2174 | <- ATCC <- B.K.C. Patel, Rt4-B1 |
| 67771 | <- DSM <- ATCC <- BKC Patel, Rt4-B1 |
doi: 10.13145/bacdive2518.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacillota
- domain: Bacteria
- phylum: Bacillota
- class: Clostridia
- order: Eubacteriales
- family: Clostridiaceae
- genus: Clostridium
- species: Clostridium fervidum
- full scientific name: Clostridium fervidum corrig. Patel et al. 1987
synonyms
@ref synonym 20215 Clostridium fervidus 20215 Caloramator fervidus
@ref: 2174
domain: Bacteria
phylum: Firmicutes
class: Clostridia
order: Clostridiales
family: Clostridiaceae
genus: Caloramator
species: Caloramator fervidus
full scientific name: Caloramator fervidus (Patel et al. 1987) Collins et al. 1994 emend. Ogg and Patel 2011
strain designation: Rt4-B1
type strain: yes
Morphology
cell morphology
| @ref | cell shape | gram stain | motility | confidence |
|---|---|---|---|---|
| 67771 | rod-shaped | |||
| 67771 | negative | |||
| 69480 | yes | 91.097 | ||
| 69480 | positive | 100 |
Culture and growth conditions
culture medium
- @ref: 2174
- name: THERMOANAEROBACTER BROCKII MEDIUM (DSMZ Medium 144)
- growth: yes
- link: https://mediadive.dsmz.de/medium/144
- composition: Name: THERMOANAEROBACTER BROCKII MEDIUM (DSMZ Medium 144) Composition: Trypticase peptone 10.0 g/l D-Glucose 5.0 g/l Yeast extract 3.0 g/l K2HPO4 1.5 g/l Na2S x 9 H2O 1.0 g/l NH4Cl 0.9 g/l KH2PO4 0.75 g/l MgCl2 x 6 H2O 0.4 g/l Nitrilotriacetic acid 0.1152 g/l NaCl 0.009 g/l FeSO4 x 7 H2O 0.003 g/l FeCl2 x 4 H2O 0.0018 g/l CoCl2 x 6 H2O 0.00153 g/l MnCl2 x 4 H2O 0.0009 g/l CaCl2 x 2 H2O 0.0009 g/l ZnCl2 0.0009 g/l Sodium resazurin 0.0005 g/l NiCl2 x 6 H2O 0.00027 g/l Na2SeO3 x 5 H2O 0.00027 g/l CuCl2 0.00018 g/l H3BO3 9e-05 g/l Na2MoO4 x 2 H2O 9e-05 g/l Pyridoxine hydrochloride 5e-05 g/l p-Aminobenzoic acid 2.5e-05 g/l (DL)-alpha-Lipoic acid 2.5e-05 g/l Riboflavin 2.5e-05 g/l Calcium D-(+)-pantothenate 2.5e-05 g/l Thiamine HCl 2.5e-05 g/l Nicotinic acid 2.5e-05 g/l Biotin 1e-05 g/l Folic acid 1e-05 g/l Vitamin B12 5e-07 g/l Distilled water
culture temp
| @ref | growth | type | temperature | range | confidence |
|---|---|---|---|---|---|
| 2174 | positive | growth | 65 | thermophilic | |
| 67771 | positive | growth | 65 | thermophilic | |
| 69480 | thermophilic | 100 |
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance | confidence |
|---|---|---|
| 2174 | anaerobe | |
| 67771 | anaerobe | |
| 69480 | anaerobe | 99.999 |
spore formation
- @ref: 69480
- spore formation: yes
- confidence: 96.192
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent |
|---|---|---|---|---|---|
| 2174 | hot spring | Kuiran Park | New Zealand | NZL | Australia and Oceania |
| 67771 | From hot spring | Kuiran Park | New Zealand | NZL | Australia and Oceania |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Aquatic | #Thermal spring |
| #Condition | #Thermophilic (>45°C) |
Safety information
risk assessment
- @ref: 2174
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
| @ref | description | accession | length | database | NCBI tax ID |
|---|---|---|---|---|---|
| 2174 | Clostridium fervidus (ATCC 43204) 16S ribosomal RNA (16S rRNA) gene | L09187 | 1519 | ena | 1121261 |
| 67771 | Caloramator fervidus strain RT4. B1 16S ribosomal RNA, partial sequence | NR_025899 | 1519 | nuccore | 29344 |
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Caloramator fervidus DSM 5463 | GCA_900108045 | contig | ncbi | 29344 |
| 66792 | Caloramator fervidus strain DSM 5463 | 29344.3 | wgs | patric | 29344 |
| 66792 | Caloramator fervidus DSM 5463 | 2599185232 | draft | img | 29344 |
GC content
- @ref: 2174
- GC-content: 39.0
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | yes | 87 | no |
| gram-positive | no | 52.033 | yes |
| anaerobic | yes | 99.032 | yes |
| halophile | no | 78.074 | no |
| spore-forming | yes | 57.079 | no |
| glucose-util | yes | 90.171 | no |
| motile | yes | 83.57 | no |
| flagellated | no | 80.386 | no |
| aerobic | no | 98.26 | yes |
| thermophile | yes | 100 | yes |
| glucose-ferment | yes | 64.428 | no |
External links
@ref: 2174
culture collection no.: DSM 5463, ATCC 43204, KCTC 15126
straininfo link
- @ref: 72053
- straininfo: 41707
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 2174 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 5463) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-5463 | |||
| 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 | |||
| 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) | |||
| 66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | 10.1093/nar/gkaa1025 | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | Nucleic Acids Res. 49: D498-D508 2020 | 33211880 | |
| 67771 | Curators of the KCTC | https://kctc.kribb.re.kr/En/Kctc | ||||
| 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) | |||
| 72053 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID41707.1 | StrainInfo: A central database for resolving microbial strain identifiers |