Strain identifier
BacDive ID: 16793
Type strain: 
Species: Caldanaerobacter subterraneus subsp. yonseiensis
Strain Designation: KB-1
Strain history: <- Y.-R. Pyun, Yonsei University, Seoul, Republic of Korea; KB-1 <- B.-C. Kim {1998}
NCBI tax ID(s): 111519 (subspecies)
version 8.1 (current version)
General
@ref: 5161
BacDive-ID: 16793
DSM-Number: 13777
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, thermophilic
description: Caldanaerobacter subterraneus subsp. yonseiensis KB-1 is an anaerobe, thermophilic bacterium that was isolated from mixed sample of mud and water from geothermal hot stream.
NCBI tax id
- NCBI tax id: 111519
- Matching level: subspecies
strain history
- @ref: 5161
- history: <- Y.-R. Pyun, Yonsei University, Seoul, Republic of Korea; KB-1 <- B.-C. Kim {1998}
doi: 10.13145/bacdive16793.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacillota
- domain: Bacteria
- phylum: Bacillota
- class: Clostridia
- order: Thermoanaerobacterales
- family: Thermoanaerobacteraceae
- genus: Caldanaerobacter
- species: Caldanaerobacter subterraneus subsp. yonseiensis
- full scientific name: Caldanaerobacter subterraneus subsp. yonseiensis (Kim et al. 2001) Fardeau et al. 2004
synonyms
- @ref: 20215
- synonym: Thermoanaerobacter yonseiensis
@ref: 5161
domain: Bacteria
phylum: Firmicutes
class: Clostridia
order: Thermoanaerobacterales
family: Thermoanaerobacteraceae
genus: Caldanaerobacter
species: Caldanaerobacter subterraneus subsp. yonseiensis
full scientific name: Caldanaerobacter subterraneus subsp. yonseiensis (Kim et al. 2001) Fardeau et al. 2004
strain designation: KB-1
type strain: yes
Culture and growth conditions
culture medium
- @ref: 5161
- name: RUMINOCLOSTRIDIUM CELLULOLYTICUM (CM3) MEDIUM (DSMZ Medium 520)
- growth: yes
- link: https://mediadive.dsmz.de/medium/520
- composition: Name: RUMINOCLOSTRIDIUM CELLULOLYTICUM (CM3) MEDIUM (DSMZ Medium 520) Composition: Cellulose 9.97009 g/l (optional) Cellobiose 5.98205 g/l K2HPO4 x 3 H2O 2.89133 g/l Yeast extract 1.99402 g/l Na2CO3 1.49551 g/l KH2PO4 1.49551 g/l (NH4)2SO4 1.29611 g/l L-Cysteine HCl x H2O 0.498504 g/l MgCl2 x 6 H2O 0.199402 g/l CaCl2 x 2 H2O 0.0747757 g/l HCl 0.00249252 g/l FeCl2 x 4 H2O 0.00149551 g/l FeSO4 x 7 H2O 0.00124626 g/l Sodium resazurin 0.000498504 g/l CoCl2 x 6 H2O 0.000189432 g/l MnCl2 x 4 H2O 9.97009e-05 g/l ZnCl2 6.97906e-05 g/l Na2MoO4 x 2 H2O 3.58923e-05 g/l NiCl2 x 6 H2O 2.39282e-05 g/l H3BO3 5.98205e-06 g/l CuCl2 x 2 H2O 1.99402e-06 g/l Distilled water
culture temp
- @ref: 5161
- growth: positive
- type: growth
- temperature: 75
- range: thermophilic
Physiology and metabolism
oxygen tolerance
- @ref: 5161
- oxygen tolerance: anaerobe
Isolation, sampling and environmental information
isolation
- @ref: 5161
- sample type: mixed sample of mud and water from geothermal hot stream
- geographic location: Java Island, Sileri
- country: Indonesia
- origin.country: IDN
- continent: Asia
isolation source categories
- Cat1: #Environmental
- Cat2: #Aquatic
Safety information
risk assessment
- @ref: 5161
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
| @ref | description | accession | length | database | NCBI tax ID |
|---|---|---|---|---|---|
| 5161 | Caldanaerobacter subterraneus subsp. yonseiensis partial 16S rRNA gene, type strain DSM 13777T, clone 2 | HG970170 | 1524 | ena | 111519 |
| 5161 | Caldanaerobacter subterraneus subsp. yonseiensis partial 16S rRNA gene, type strain DSM 13777T, clone 3 | HG970171 | 1587 | ena | 111519 |
| 5161 | Caldanaerobacter subterraneus subsp. yonseiensis partial 16S rRNA gene, type strain DSM 13777T, clone 1 | HG970169 | 1526 | ena | 111519 |
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Caldanaerobacter subterraneus subsp. yonseiensis KB-1 | GCA_000473865 | contig | ncbi | 1388761 |
| 66792 | Caldanaerobacter subterraneus subsp. yonseiensis KB-1 | 1388761.3 | wgs | patric | 1388761 |
GC content
- @ref: 5161
- GC-content: 37
- method: high performance liquid chromatography (HPLC)
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| motile | yes | 84.227 | no |
| gram-positive | no | 66.938 | no |
| anaerobic | yes | 99.523 | yes |
| halophile | no | 96.925 | no |
| spore-forming | yes | 91.247 | no |
| thermophile | yes | 100 | no |
| glucose-util | yes | 91.35 | no |
| aerobic | no | 98.281 | yes |
| flagellated | no | 82.629 | no |
| glucose-ferment | yes | 59.268 | no |
External links
@ref: 5161
culture collection no.: DSM 13777, KFCC 11116
straininfo link
- @ref: 85809
- straininfo: 49522
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 11491356 | Thermoanaerobacter yonseiensis sp. nov., a novel extremely thermophilic, xylose-utilizing bacterium that grows at up to 85 degrees C. | Kim BC, Grote R, Lee DW, Antranikian G, Pyun YR | Int J Syst Evol Microbiol | 10.1099/00207713-51-4-1539 | 2001 | Bacillaceae/classification/genetics/*growth & development/*isolation & purification, Base Composition, DNA, Bacterial/chemistry/genetics, Drug Resistance, Microbial, Fermentation, Fresh Water/microbiology, Hot Temperature, Japan, Lipids/analysis, Microscopy, Electron, Scanning, Molecular Sequence Data, Phylogeny | Stress |
| Enzymology | 12072959 | A novel subtilisin-like serine protease from Thermoanaerobacter yonseiensis KB-1: its cloning, expression, and biochemical properties. | Jang HJ, Kim BC, Pyun YR, Kim YS | Extremophiles | 10.1007/s00792-001-0248-1 | 2002 | Amino Acid Sequence, Base Sequence, Cloning, Molecular, Collagen/metabolism, DNA, Bacterial, Fibronectins/metabolism, Gram-Positive Bacteria/*enzymology, Molecular Sequence Data, Phylogeny, Sequence Homology, Amino Acid, Serine Endopeptidases/chemistry/*genetics/metabolism, Substrate Specificity | Metabolism |
| Phylogeny | 15023962 | Isolation from oil reservoirs of novel thermophilic anaerobes phylogenetically related to Thermoanaerobacter subterraneus: reassignment of T. subterraneus, Thermoanaerobacter yonseiensis, Thermoanaerobacter tengcongensis and Carboxydibrachium pacificum to Caldanaerobacter subterraneus gen. nov., sp. nov., comb. nov. as four novel subspecies. | Fardeau ML, Salinas MB, L'Haridon S, Jeanthon C, Verhe F, Cayol JL, Patel BKC, Garcia JL, Ollivier B | Int J Syst Evol Microbiol | 10.1099/ijs.0.02711-0 | 2004 | Anaerobiosis, Australia, Bacteria, Anaerobic/*classification/isolation & purification, Base Composition, Base Sequence, Clostridium/*classification/genetics/isolation & purification, DNA Primers, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/genetics, Fossil Fuels/*microbiology, France, Molecular Sequence Data, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics | Enzymology |
Reference
| @id | authors | catalogue | doi/url | title |
|---|---|---|---|---|
| 5161 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 13777) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-13777 | |
| 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) | |
| 85809 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID49522.1 | StrainInfo: A central database for resolving microbial strain identifiers |