Strain identifier
BacDive ID: 2606
Type strain: 
Species: Clostridium kluyveri
Strain Designation: K1
Strain history: <- S. Schoberth, Universität Göttingen, Germany; K1 <- G. Gottschalk <- H. A. Barker, University of California, Berkeley, USA
NCBI tax ID(s): 431943 (strain), 1534 (species)
version 9.3 (current version)
General
@ref: 276
BacDive-ID: 2606
DSM-Number: 555
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, spore-forming, mesophilic
description: Clostridium kluyveri K1 is an anaerobe, spore-forming, mesophilic bacterium that was isolated from mud.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 431943 | strain |
| 1534 | species |
strain history
- @ref: 276
- history: <- S. Schoberth, Universität Göttingen, Germany; K1 <- G. Gottschalk <- H. A. Barker, University of California, Berkeley, USA
doi: 10.13145/bacdive2606.20250331.9.3
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 kluyveri
- full scientific name: Clostridium kluyveri Barker and Taha 1942 (Approved Lists 1980)
@ref: 276
domain: Bacteria
phylum: Firmicutes
class: Clostridia
order: Clostridiales
family: Clostridiaceae
genus: Clostridium
species: Clostridium kluyveri
full scientific name: Clostridium kluyveri Barker and Taha 1942
strain designation: K1
type strain: yes
Morphology
colony morphology
- @ref: 276
- incubation period: 1-2 days
Culture and growth conditions
culture medium
- @ref: 276
- name: CLOSTRIDIUM KLUYVERI MEDIUM (DSMZ Medium 52)
- growth: yes
- link: https://mediadive.dsmz.de/medium/52
- composition: Name: CLOSTRIDIUM KLUYVERI MEDIUM (DSMZ Medium 52) Composition: K-acetate 10.0 g/l Yeast extract 1.0 g/l Na2CO3 1.0 g/l K2HPO4 0.31 g/l L-Cysteine HCl x H2O 0.25 g/l NH4Cl 0.25 g/l Na2S x 9 H2O 0.25 g/l KH2PO4 0.23 g/l MgSO4 x 7 H2O 0.2 g/l HCl 0.0025 g/l FeCl2 x 4 H2O 0.0015 g/l Sodium resazurin 0.0005 g/l NaOH 0.0005 g/l Pyridoxine hydrochloride 0.0003 g/l Thiamine-HCl x 2 H2O 0.0002 g/l Nicotinic acid 0.0002 g/l CoCl2 x 6 H2O 0.00019 g/l Calcium pantothenate 0.0001 g/l MnCl2 x 4 H2O 0.0001 g/l Vitamin B12 0.0001 g/l p-Aminobenzoic acid 8e-05 g/l ZnCl2 7e-05 g/l Na2MoO4 x 2 H2O 3.6e-05 g/l NiCl2 x 6 H2O 2.4e-05 g/l D-(+)-biotin 2e-05 g/l H3BO3 6e-06 g/l Na2WO4 x 2 H2O 4e-06 g/l Na2SeO3 x 5 H2O 3e-06 g/l CuCl2 x 2 H2O 2e-06 g/l Ethanol absolute Distilled water
culture temp
- @ref: 276
- growth: positive
- type: growth
- temperature: 37
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance | confidence |
|---|---|---|
| 276 | anaerobe | |
| 125439 | facultative anaerobe | 96.4 |
compound production
| @ref | compound |
|---|---|
| 276 | acetaldehyde dehydrogenase |
| 276 | ß hydroxybutyryl-CoA dehydrogenase |
| 276 | diaphorase |
| 276 | phosphotransacetylase |
| 276 | vinylacetyl isomerase |
| 276 | flavin nucleotides, radioactive |
| 276 | enoate reductase |
Isolation, sampling and environmental information
isolation
- @ref: 276
- sample type: mud
isolation source categories
- Cat1: #Environmental
- Cat2: #Terrestrial
- Cat3: #Mud (Sludge)
Safety information
risk assessment
- @ref: 276
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
| @ref | description | accession | length | database | NCBI tax ID |
|---|---|---|---|---|---|
| 20218 | Clostridium kluyveri strain DSM 555 16S ribosomal RNA gene, partial sequence | DQ911271 | 320 | nuccore | 431943 |
| 20218 | Clostridium kluyveri 16S ribosomal RNA | M59092 | 1460 | nuccore | 1534 |
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Clostridium kluyveri DSM 555 | GCA_000016505 | complete | ncbi | 431943 |
| 66792 | Clostridium kluyveri DSM 555 | 431943.20 | plasmid | patric | 431943 |
| 66792 | Clostridium kluyveri DSM 555 | 431943.8 | complete | patric | 431943 |
| 66792 | Clostridium kluyveri NBRC 12016 | 583346.15 | plasmid | patric | 583346 |
| 66792 | Clostridium kluyveri NBRC 12016 | 583346.6 | complete | patric | 583346 |
| 66792 | Clostridium kluyveri DSM 555 | 640753020 | complete | img | 431943 |
GC content
- @ref: 276
- GC-content: 29.8
Genome-based predictions
predictions
| @ref | model | trait | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 125438 | gram-positive | gram-positive | Positive reaction to Gram-staining | yes | 56.651 | no |
| 125438 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | yes | 87.089 | no |
| 125438 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | no | 95.011 | yes |
| 125438 | spore-forming | spore-forming | Ability to form endo- or exospores | yes | 77.594 | no |
| 125438 | thermophile | thermophilic | Ability to grow at temperatures above or equal to 45°C | no | 85.69 | yes |
| 125438 | motile2+ | flagellated | Ability to perform flagellated movement | yes | 75.066 | no |
| 125439 | BacteriaNet | spore_formation | Ability to form endo- or exospores | yes | 88.2 | |
| 125439 | BacteriaNet | motility | Ability to perform movement | yes | 82.6 | |
| 125439 | BacteriaNet | gram_stain | Reaction to gram-staining | positive | 64.1 | |
| 125439 | BacteriaNet | oxygen_tolerance | Oxygenic conditions needed for growth | facultative anaerobe | 96.4 |
External links
@ref: 276
culture collection no.: DSM 555, ATCC 12489, ATCC 8527, NCIMB 10680
straininfo link
- @ref: 72137
- straininfo: 34982
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Metabolism | 627401 | Properties of two Clostridia strains acting as catalysts for the preparative stereospecific hydrogenation of 2-enoic acids and 2-alken-1-ols with hydrogen gas. | Bader J, Gunther H, Rambeck B, Simon H | Hoppe Seylers Z Physiol Chem | 10.1515/bchm.1978.359.1.19 | 1978 | Clostridium/*isolation & purification, Fatty Acids, Unsaturated/*metabolism, Fatty Alcohols/*metabolism, Hydrogen/*pharmacology, Hydrogenation, Stereoisomerism | Enzymology |
| Metabolism | 7387331 | Utilization of (E)-2-butenoate (crotonate) by Clostridium kluyveri and some other Clostridium species. | Bader J, Gunther H, Schleicher E, Simon H, Pohl S, Mannheim W | Arch Microbiol | 10.1007/BF00403214 | 1980 | Acetates/metabolism, Butyrates/*metabolism, Carbohydrate Metabolism, Clostridium/growth & development/*metabolism, Crotonates/*metabolism, Fermentation, Glucose/metabolism, Species Specificity | Phylogeny |
| Phylogeny | 26420591 | Clostridium luticellarii sp. nov., isolated from a mud cellar used for producing strong aromatic liquors. | Wang Q, Wang CD, Li CH, Li JG, Chen Q, Li YZ | Int J Syst Evol Microbiol | 10.1099/ijsem.0.000641 | 2015 | *Alcoholic Beverages, Bacterial Typing Techniques, Base Composition, China, Clostridium/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology | Genetics |
| 32540193 | Ethanol:propionate ratio drives product selectivity in odd-chain elongation with Clostridium kluyveri and mixed communities. | Candry P, Ulcar B, Petrognani C, Rabaey K, Ganigue R | Bioresour Technol | 10.1016/j.biortech.2020.123651 | 2020 | Caproates, *Clostridium kluyveri, Ethanol, Fermentation, Propionates |
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 276 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 555) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-555 | |||
| 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 | |||
| 20218 | Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P. | 10.1016/j.syapm.2013.11.002 | StrainInfo introduces electronic passports for microorganisms. | Syst Appl Microbiol. 37: 42-50 2014 | 24321274 | |
| 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 | |
| 72137 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID34982.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
| 125438 | Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann | 10.1101/2024.08.12.607695 | Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets | |||
| 125439 | Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy | https://github.com/GenomeNet/deepG | deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 |