Strain identifier

BacDive ID: 2842

Type strain: Yes

Species: Clostridium ganghwense

Strain Designation: HY-42-06

Strain history: <- J Chun, SNU, HY-42-06

NCBI tax ID(s): 312089 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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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

@refhistory
7688<- JCM; JCM 13193 <- J. Chun, Seoul Natl. Univ., Republic of Korea; HY-42-06
67770J. 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

@refgram staincell lengthcell widthcell shapemotilityflagellum arrangement
31550negative04-08 µm0.7-0.8 µmrod-shapedyes
67771rod-shapedyesperitrichous
67771negative

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

@refgrowthtypetemperaturerange
7688positivegrowth35mesophilic
31550positivegrowth15-40
31550positiveoptimum35mesophilic
67770positivegrowth35mesophilic
67771positivegrowth35mesophilic

culture pH

@refabilitytypepHPH range
31550positivegrowth5.5-10alkaliphile
31550positiveoptimum7.5

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
7688anaerobe
31550anaerobe
67771anaerobe

spore formation

  • @ref: 31550
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
31550NaClpositivegrowth0-5 %
31550NaClpositiveoptimum0-5 %

observation

  • @ref: 31550
  • observation: aggregates in chains

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3155017057cellobiose+carbon source
3155017234glucose+carbon source
3155017306maltose+carbon source
3155037684mannose+carbon source
3155017814salicin+carbon source
315504853esculin+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

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitude
7688tidal flat sedimentGanghwa IslandRepublic of KoreaKORAsia37.5833126.45
67770Tidal flat sediment from Ganghwa IslandRepublic of KoreaKORAsia
67771From tidal flat sedimentGanghwa IslandRepublic of KoreaKORAsia37.5886126.454

isolation source categories

Cat1Cat2Cat3
#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

traitpredictionconfidencetraining_data
motileyes86.687yes
flagellatedyes73.744yes
gram-positiveno52.534no
anaerobicyes98.703no
aerobicno98.714no
halophileno83.266no
spore-formingyes92.515yes
glucose-fermentno55.682no
thermophileno95.176yes
glucose-utilyes88.163no

External links

@ref: 7688

culture collection no.: DSM 18771, IMSNU 40127, JCM 13193, KCTC 5146

straininfo link

  • @ref: 72366
  • straininfo: 232204

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny16585678Clostridium ganghwense sp. nov., isolated from tidal flat sediment.Kim S, Jeong H, Kim S, Chun JInt J Syst Evol Microbiol10.1099/ijs.0.63791-02006Clostridium/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 MicrobiologyEnzymology
Phylogeny17551049Clostridium aestuarii sp. nov., from tidal flat sediment.Kim S, Jeong H, Chun JInt J Syst Evol Microbiol10.1099/ijs.0.64428-02007Anaerobiosis, 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 MicrobiologyMetabolism
Metabolism21357455Description 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 YInt J Syst Evol Microbiol10.1099/ijs.0.026989-02011Acetic 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/metabolismPhylogeny

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
7688Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18771)https://www.dsmz.de/collection/catalogue/details/culture/DSM-18771
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
31550Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2784128776041
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
69479João 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
72366Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID232204.1StrainInfo: A central database for resolving microbial strain identifiers