Strain identifier
BacDive ID: 2577
Type strain:
Species: Clostridium cylindrosporum
Strain Designation: HC-1
Strain history: <- Institut für Mikrobiologie, Universität Göttingen (IMG), Germany; IMG 1641 <- G. Gottschalk <- H. A. Barker and J. V. Beck, University of California, Berkeley, USA; HC-1
NCBI tax ID(s): 1121307 (strain), 1495 (species)
General
@ref: 317
BacDive-ID: 2577
DSM-Number: 605
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, spore-forming, mesophilic, motile
description: Clostridium cylindrosporum HC-1 is an anaerobe, spore-forming, mesophilic bacterium that was isolated from soil.
NCBI tax id
NCBI tax id | Matching level |
---|---|
1121307 | strain |
1495 | species |
strain history
- @ref: 317
- history: <- Institut für Mikrobiologie, Universität Göttingen (IMG), Germany; IMG 1641 <- G. Gottschalk <- H. A. Barker and J. V. Beck, University of California, Berkeley, USA; HC-1
doi: 10.13145/bacdive2577.20230509.8.1
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 cylindrosporum
- full scientific name: Clostridium cylindrosporum (ex Barker and Beck 1942) Andreesen et al. 1985
@ref: 317
domain: Bacteria
phylum: Firmicutes
class: Clostridia
order: Clostridiales
family: Clostridiaceae
genus: Clostridium
species: Clostridium cylindrosporum
full scientific name: Clostridium cylindrosporum (ex Barker and Beck 1942) Andreesen et al. 1985
strain designation: HC-1
type strain: yes
Morphology
cell morphology
@ref | motility | confidence | gram stain |
---|---|---|---|
69480 | yes | 93.729 | |
69480 | 100 | positive |
Culture and growth conditions
culture medium
- @ref: 317
- name: GOTTSCHALKIA MEDIUM (DSMZ Medium 76)
- growth: yes
- link: https://mediadive.dsmz.de/medium/76
- composition: Name: GOTTSCHALKIA MEDIUM (DSMZ Medium 76) Composition: Uric acid 2.0 g/l Na2CO3 1.5 g/l Yeast extract 1.0 g/l K2HPO4 0.91 g/l KOH 0.67 g/l Na-thioglycolate 0.5 g/l MgSO4 x 7 H2O 0.25 g/l CaCl2 x 2 H2O 0.015 g/l FeSO4 x 7 H2O 0.006 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 CoCl2 x 6 H2O 0.00019 g/l MnCl2 x 4 H2O 0.0001 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 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 Distilled water
culture temp
- @ref: 317
- growth: positive
- type: growth
- temperature: 37
- range: mesophilic
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance | confidence |
---|---|---|
317 | anaerobe | |
69480 | anaerobe | 99.71 |
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | yes | 100 |
69480 | yes | 98.169 |
compound production
- @ref: 317
- compound: xanthine dehydrogenase
Isolation, sampling and environmental information
isolation
- @ref: 317
- sample type: soil
- geographic location: California
- country: USA
- origin.country: USA
- continent: North America
isolation source categories
- Cat1: #Environmental
- Cat2: #Terrestrial
- Cat3: #Soil
Safety information
risk assessment
- @ref: 317
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 317
- description: Clostridium cylindrosporum 16S rRNA gene, partial, strain DSM 605
- accession: Y18179
- length: 1479
- database: ena
- NCBI tax ID: 1495
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Clostridium cylindrosporum DSM 605 | GCA_001047375 | contig | ncbi | 1121307 |
66792 | Clostridium cylindrosporum DSM 605 | 1121307.3 | wgs | patric | 1121307 |
66792 | Clostridium cylindrosporum DSM 605 | 2630968942 | draft | img | 1121307 |
GC content
- @ref: 317
- GC-content: 27.9
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | yes | 100 | no |
motile | yes | 86.581 | no |
flagellated | no | 57.905 | no |
gram-positive | yes | 79.682 | no |
anaerobic | yes | 98.307 | yes |
aerobic | no | 95.811 | yes |
halophile | no | 94.838 | no |
spore-forming | yes | 92.463 | no |
thermophile | no | 97.504 | yes |
glucose-util | yes | 60.243 | no |
glucose-ferment | no | 54.76 | no |
External links
@ref: 317
culture collection no.: DSM 605, ATCC 7905, IMG 1641
straininfo link
- @ref: 72110
- straininfo: 34889
literature
Pubmed-ID | title | authors | journal | DOI | year | topic |
---|---|---|---|---|---|---|
16347398 | Sporulation of Clostridium cylindrosporum on a Defined, Low-Manganese Medium. | Sacks LE, Smith MR | Appl Environ Microbiol | 10.1128/aem.53.7.1696-1698.1987 | 1987 | |
26272578 | Draft Genome Sequence of Purine-Degrading Clostridium cylindrosporum HC-1 (DSM 605). | Poehlein A, Montoya Solano JD, Bengelsdorf FR, Schiel-Bengelsdorf B, Daniel R, Durre P | Genome Announc | 10.1128/genomeA.00917-15 | 2015 | Genetics |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
317 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 605) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-605 | |||
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 | |
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 | |||
72110 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID34889.1 | StrainInfo: A central database for resolving microbial strain identifiers |