Strain identifier

BacDive ID: 2846

Type strain: Yes

Species: Clostridium aestuarii

Strain Designation: HY-45-18

Strain history: <- J Chun, SNU, HY-45-18

NCBI tax ID(s): 338193 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 8.1 (current version)

General

@ref: 8147

BacDive-ID: 2846

DSM-Number: 19521

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, spore-forming, mesophilic, Gram-negative, motile, rod-shaped

description: Clostridium aestuarii HY-45-18 is an anaerobe, spore-forming, mesophilic bacterium that was isolated from tidal flat sediment.

NCBI tax id

  • NCBI tax id: 338193
  • Matching level: species

strain history

@refhistory
8147<- JCM <- J. Chun; HY-45-18
67770J. Chun HY-45-18.
67771<- J Chun, SNU, HY-45-18

doi: 10.13145/bacdive2846.20230509.8.1

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 aestuarii
  • full scientific name: Clostridium aestuarii Kim et al. 2007

@ref: 8147

domain: Bacteria

phylum: Firmicutes

class: Clostridia

order: Clostridiales

family: Clostridiaceae

genus: Clostridium

species: Clostridium aestuarii

full scientific name: Clostridium aestuarii Kim et al. 2007

strain designation: HY-45-18

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityflagellum arrangement
31822negative02-04 µm0.7-0.8 µmrod-shapedyes
67771rod-shapedyesperitrichous
67771negative

pigmentation

  • @ref: 31822
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 8147
  • 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
8147positivegrowth30mesophilic
31822positivegrowth15-30
31822positiveoptimum30mesophilic
67770positivegrowth30mesophilic
67771positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
31822positivegrowth5.5-8.5alkaliphile
31822positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
8147anaerobe
31822anaerobe
67771anaerobe

spore formation

@refspore formationtype of spore
31822yes
67771yesendospore

halophily

@refsaltgrowthtested relationconcentration
31822NaClpositivegrowth01-10 %
31822NaClpositiveoptimum4 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3182217234glucose+carbon source
3182217306maltose+carbon source
3182217992sucrose+carbon source

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitude
8147tidal flat sedimentGanghwa IslandRepublic of KoreaKORAsia37.5833126.45
67770Tidal flat on Ganghwa IslandRepublic of KoreaKORAsia
67771From sedimen, tidal flatGanghwa IslandRepublic of KoreaKORAsia37.5922126.457

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Tidal flat
#Environmental#Terrestrial#Sediment

taxonmaps

  • @ref: 69479
  • File name: preview.99_89664.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_34;96_5006;97_47195;98_61886;99_89664&stattab=map
  • Last taxonomy: Clostridium aestuarii subclade
  • 16S sequence: DQ126679
  • Sequence Identity:
  • Total samples: 254
  • soil counts: 4
  • aquatic counts: 233
  • animal counts: 13
  • plant counts: 4

Safety information

risk assessment

  • @ref: 8147
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 8147
  • description: Clostridium aestuarii strain HY-45-18 16S ribosomal RNA gene, partial sequence
  • accession: DQ126679
  • length: 1433
  • database: ena
  • NCBI tax ID: 338193

Genome sequences

  • @ref: 66792
  • description: Clostridium aestuarii HY-45-18
  • accession: GCA_026735135
  • assembly level: scaffold
  • database: ncbi
  • NCBI tax ID: 338193

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileyes87.26yes
flagellatedyes69.037yes
gram-positiveno70.132yes
anaerobicyes99.124yes
aerobicno98.727yes
halophileno82.898no
spore-formingyes95.433yes
glucose-fermentno50.849no
thermophileno92.143no
glucose-utilyes87.133yes

External links

@ref: 8147

culture collection no.: DSM 19521, IMSNU 40129, JCM 13194, KCTC 5147

straininfo link

  • @ref: 72370
  • straininfo: 232205

literature

  • topic: Phylogeny
  • Pubmed-ID: 17551049
  • title: Clostridium aestuarii sp. nov., from tidal flat sediment.
  • authors: Kim S, Jeong H, Chun J
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.64428-0
  • year: 2007
  • mesh: 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
  • topic2: Metabolism

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
8147Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19521)https://www.dsmz.de/collection/catalogue/details/culture/DSM-19521
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
31822Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2808828776041
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
72370Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID232205.1StrainInfo: A central database for resolving microbial strain identifiers