Strain identifier

BacDive ID: 2620

Type strain: Yes

Species: Clostridium oceanicum

Strain history: ATCC 25647 <-- L. DS. Smith VPI 3082.

NCBI tax ID(s): 1543 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 9 (current version):
version 8.1:
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 9 (current version)

General

@ref: 610

BacDive-ID: 2620

DSM-Number: 1290

keywords: 16S sequence, Bacteria, anaerobe

description: Clostridium oceanicum DSM 1290 is an anaerobe bacterium that was isolated from marine sediment.

NCBI tax id

  • NCBI tax id: 1543
  • Matching level: species

strain history

@refhistory
610<- ATCC <- L. DS. Smith, Virginia Polytechnical Institute and State University, Blacksburg, V., USA; VPI 3082
67770ATCC 25647 <-- L. DS. Smith VPI 3082.

doi: 10.13145/bacdive2620.20240510.9

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 oceanicum
  • full scientific name: Clostridium oceanicum Smith 1970 (Approved Lists 1980)

@ref: 610

domain: Bacteria

phylum: Firmicutes

class: Clostridia

order: Clostridiales

family: Clostridiaceae

genus: Clostridium

species: Clostridium oceanicum

full scientific name: Clostridium oceanicum Smith 1970

type strain: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
610CHOPPED MEAT MEDIUM WITH CARBOHYDRATES (DSMZ Medium 110)yeshttps://mediadive.dsmz.de/medium/110Name: CHOPPED MEAT MEDIUM WITH CARBOHYDRATES (DSMZ Medium 110) Composition: Ground beef 500.0 g/l Casitone 30.0 g/l Agar 15.0 g/l K2HPO4 5.0 g/l Yeast extract 5.0 g/l D-Glucose 4.0 g/l Starch 1.0 g/l Maltose 1.0 g/l Cellobiose 1.0 g/l L-Cysteine HCl 0.5 g/l Ethanol 0.19 g/l Vitamin K3 0.05 g/l Hemin 0.005 g/l Sodium resazurin 0.0005 g/l Vitamin K1 NaOH Distilled water
610WILKINS-CHALGREN ANAEROBE BROTH (DSMZ Medium 339)yeshttps://mediadive.dsmz.de/medium/339Name: WILKINS-CHALGREN ANAEROBE BROTH (DSMZ Medium 339) Composition: dehydrated Wilkins-Chalgren medium 33.0 g/l L-Cysteine HCl 0.3 g/l Sodium resazurin 0.0005 g/l Distilled water

culture temp

@refgrowthtypetemperature
610positivegrowth37
67770positivegrowth37

Physiology and metabolism

oxygen tolerance

  • @ref: 610
  • oxygen tolerance: anaerobe

Isolation, sampling and environmental information

isolation

@refsample typegeographic location
610marine sedimentAtlantic Ocean
67770Marine sediment

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Marine
#Environmental#Aquatic#Sediment

taxonmaps

  • @ref: 69479
  • File name: preview.99_136121.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_34;96_52639;97_67856;98_90783;99_136121&stattab=map
  • Last taxonomy: Clostridium oceanicum subclade
  • 16S sequence: LC007108
  • Sequence Identity:
  • Total samples: 2762
  • soil counts: 156
  • aquatic counts: 1897
  • animal counts: 648
  • plant counts: 61

Safety information

risk assessment

  • @ref: 610
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Clostridium oceanicum strain ATCC 25647 16S ribosomal RNA gene, partial sequenceDQ911254318nuccore1543
20218Clostridium oceanicum 16S ribosomal RNAM591011460nuccore1543
610Clostridium oceanicum partial 16S rRNA gene, type strain DSM 1290T, clone 1FR7499231560nuccore1543
610Clostridium oceanicum partial 16S rRNA gene, type strain DSM 1290T, clone 2FR7499241560nuccore1543
610Clostridium oceanicum partial 16S rRNA gene, type strain DSM 1290T, clone 3FR7499251620nuccore1543
610Clostridium oceanicum partial 16S rRNA gene, type strain DSM 1290T, clone 4FR7499261597nuccore1543
610Clostridium oceanicum partial 16S rRNA gene, type strain DSM 1290T, clone 5FR7499271560nuccore1543
67770Clostridium oceanicum gene for 16S ribosomal RNA, partial sequence, strain: JCM 1407LC0071081473nuccore1543
124043Clostridium oceanicum DSM 1290 gene for 16S rRNA, partial sequence.LC752427563nuccore1543

GC content

@refGC-contentmethod
61023.0
6777023thermal denaturation, midpoint method (Tm)

External links

@ref: 610

culture collection no.: DSM 1290, ATCC 25647, NCIMB 10625, VPI 3082, JCM 1407, BCRC 14482, LMG 3287

straininfo link

  • @ref: 72151
  • straininfo: 1957

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
610Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 1290)https://www.dsmz.de/collection/catalogue/details/culture/DSM-1290
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
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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
72151Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID1957.1StrainInfo: A central database for resolving microbial strain identifiers
124043Dr. Isabel Schober, Dr. Julia KoblitzData extracted from sequence databases, automatically matched based on designation and taxonomy