Strain identifier
BacDive ID: 2842
Type strain:
Species: Clostridium ganghwense
Strain Designation: HY-42-06
Strain history: <- J Chun, SNU, HY-42-06
NCBI tax ID(s): 312089 (species)
General
@ref: 7688
BacDive-ID: 2842
DSM-Number: 18771
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, Gram-negative, motile, rod-shaped
description: Clostridium ganghwense HY-42-06 is an anaerobe, mesophilic, Gram-negative bacterium that was isolated from tidal flat sediment.
NCBI tax id
- NCBI tax id: 312089
- Matching level: species
strain history
@ref | history |
---|---|
7688 | <- JCM; JCM 13193 <- J. Chun, Seoul Natl. Univ., Republic of Korea; HY-42-06 |
67770 | J. Chun HY-42-06. |
67771 | <- J Chun, SNU, HY-42-06 |
doi: 10.13145/bacdive2842.20230509.8.1
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 ganghwense
- full scientific name: Clostridium ganghwense Kim et al. 2006
@ref: 7688
domain: Bacteria
phylum: Firmicutes
class: Clostridia
order: Clostridiales
family: Clostridiaceae
genus: Clostridium
species: Clostridium ganghwense
full scientific name: Clostridium ganghwense Kim et al. 2006
strain designation: HY-42-06
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell length | cell width | cell shape | motility | flagellum arrangement |
---|---|---|---|---|---|---|
31550 | negative | 04-08 µm | 0.7-0.8 µm | rod-shaped | yes | |
67771 | rod-shaped | yes | peritrichous | |||
67771 | negative |
pigmentation
- @ref: 31550
- production: yes
Culture and growth conditions
culture medium
- @ref: 7688
- name: RCM MEDIUM (WITH SEA SALTS) (DSMZ Medium 634b)
- growth: yes
- link: https://mediadive.dsmz.de/medium/634b
- composition: Name: RCM MEDIUM (with Sea Salts) (DSMZ Medium 634b) Composition: dehydrated RCM medium 38.0 g/l Sea salts 30.0 g/l Sodium resazurin 0.0005 g/l Distilled water
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
7688 | positive | growth | 35 | mesophilic |
31550 | positive | growth | 15-40 | |
31550 | positive | optimum | 35 | mesophilic |
67770 | positive | growth | 35 | mesophilic |
67771 | positive | growth | 35 | mesophilic |
culture pH
@ref | ability | type | pH | PH range |
---|---|---|---|---|
31550 | positive | growth | 5.5-10 | alkaliphile |
31550 | positive | optimum | 7.5 |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
7688 | anaerobe |
31550 | anaerobe |
67771 | anaerobe |
spore formation
- @ref: 31550
- spore formation: no
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
31550 | NaCl | positive | growth | 0-5 % |
31550 | NaCl | positive | optimum | 0-5 % |
observation
- @ref: 31550
- observation: aggregates in chains
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
31550 | 17057 | cellobiose | + | carbon source |
31550 | 17234 | glucose | + | carbon source |
31550 | 17306 | maltose | + | carbon source |
31550 | 37684 | mannose | + | carbon source |
31550 | 17814 | salicin | + | carbon source |
31550 | 4853 | esculin | + | hydrolysis |
metabolite production
- @ref: 31550
- Chebi-ID: 35581
- metabolite: indole
- production: yes
metabolite tests
- @ref: 31550
- Chebi-ID: 35581
- metabolite: indole
- indole test: +
enzymes
- @ref: 31550
- value: gelatinase
- activity: +
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent | latitude | longitude |
---|---|---|---|---|---|---|---|
7688 | tidal flat sediment | Ganghwa Island | Republic of Korea | KOR | Asia | 37.5833 | 126.45 |
67770 | Tidal flat sediment from Ganghwa Island | Republic of Korea | KOR | Asia | |||
67771 | From tidal flat sediment | Ganghwa Island | Republic of Korea | KOR | Asia | 37.5886 | 126.454 |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Environmental | #Terrestrial | #Tidal flat |
#Environmental | #Terrestrial | #Sediment |
taxonmaps
- @ref: 69479
- File name: preview.99_95763.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_34;96_5006;97_6059;98_65698;99_95763&stattab=map
- Last taxonomy: Clostridium ganghwense subclade
- 16S sequence: AY903294
- Sequence Identity:
- Total samples: 157
- soil counts: 3
- aquatic counts: 120
- animal counts: 34
Safety information
risk assessment
- @ref: 7688
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 7688
- description: Clostridium ganghwense strain HY-42-06 16S ribosomal RNA gene, partial sequence
- accession: AY903294
- length: 1433
- database: ena
- NCBI tax ID: 312089
Genome sequences
- @ref: 66792
- description: Clostridium ganghwense HY-42-06
- accession: GCA_026735165
- assembly level: scaffold
- database: ncbi
- NCBI tax ID: 312089
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
motile | yes | 86.687 | yes |
flagellated | yes | 73.744 | yes |
gram-positive | no | 52.534 | no |
anaerobic | yes | 98.703 | no |
aerobic | no | 98.714 | no |
halophile | no | 83.266 | no |
spore-forming | yes | 92.515 | yes |
glucose-ferment | no | 55.682 | no |
thermophile | no | 95.176 | yes |
glucose-util | yes | 88.163 | no |
External links
@ref: 7688
culture collection no.: DSM 18771, IMSNU 40127, JCM 13193, KCTC 5146
straininfo link
- @ref: 72366
- straininfo: 232204
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 16585678 | Clostridium ganghwense sp. nov., isolated from tidal flat sediment. | Kim S, Jeong H, Kim S, Chun J | Int J Syst Evol Microbiol | 10.1099/ijs.0.63791-0 | 2006 | Clostridium/classification/cytology/*isolation & purification/physiology, DNA, Bacterial/chemistry/isolation & purification, DNA, Ribosomal/chemistry/isolation & purification, Geologic Sediments/*microbiology, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/analysis/genetics, Spores, Bacterial/cytology, *Water Microbiology | Enzymology |
Phylogeny | 17551049 | Clostridium aestuarii sp. nov., from tidal flat sediment. | Kim S, Jeong H, Chun J | Int J Syst Evol Microbiol | 10.1099/ijs.0.64428-0 | 2007 | Anaerobiosis, Bacterial Typing Techniques, Butyric Acid/metabolism, Clostridium/*classification/genetics/*isolation & purification/metabolism, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fermentation, Genes, rRNA, Geologic Sediments/*microbiology, Glucose/metabolism, Glycerol/metabolism, Korea, Locomotion, Molecular Sequence Data, Phylogeny, Propionates/metabolism, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Sodium Chloride/metabolism, Spores, Bacterial, Water Microbiology | Metabolism |
Metabolism | 21357455 | Description of Christensenella minuta gen. nov., sp. nov., isolated from human faeces, which forms a distinct branch in the order Clostridiales, and proposal of Christensenellaceae fam. nov. | Morotomi M, Nagai F, Watanabe Y | Int J Syst Evol Microbiol | 10.1099/ijs.0.026989-0 | 2011 | Acetic Acid/metabolism, Anaerobiosis, Bacterial Typing Techniques, Base Composition, Butyrates/metabolism, Carbohydrates/analysis, Catalase/metabolism, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/metabolism, Feces/*microbiology, Fermentation, Glucose/metabolism, Gram-Positive Bacteria/*classification/genetics/*isolation & purification/physiology, Humans, Molecular Sequence Data, Oxidoreductases/metabolism, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sucrose/metabolism, Urease/metabolism | Phylogeny |
Reference
@id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
---|---|---|---|---|---|---|
7688 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18771) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-18771 | |||
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 | |||
31550 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | 10.1128/mSphere.00237-17 | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 27841 | 28776041 | |
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) | |||
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
67771 | Curators of the KCTC | https://kctc.kribb.re.kr/En/Kctc | ||||
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. | https://microbeatlas.org/ | MicrobeAtlas 1.0 beta | |||
72366 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID232204.1 | StrainInfo: A central database for resolving microbial strain identifiers |