Strain identifier

BacDive ID: 2807

Type strain: Yes

Species: Clostridium laramiense

Strain Designation: NK1

Strain history: <- ATCC <- B. Ray, University of Wyoming, Laramie, USA; NK1 <- N. Kalchayanand {1989}

NCBI tax ID(s): 205326 (subspecies)

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

@ref: 5584

BacDive-ID: 2807

DSM-Number: 14864

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, spore-forming, psychrophilic, motile

description: Clostridium laramiense NK1 is an anaerobe, spore-forming, psychrophilic bacterium that was isolated from spoiled umcooked beef.

NCBI tax id

  • NCBI tax id: 205326
  • Matching level: subspecies

strain history

  • @ref: 5584
  • history: <- ATCC <- B. Ray, University of Wyoming, Laramie, USA; NK1 <- N. Kalchayanand {1989}

doi: 10.13145/bacdive2807.20230509.8.1

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 laramiense
  • full scientific name: Clostridium laramiense corrig. Kalchayanand et al. 1993
  • synonyms

    @refsynonym
    20215Clostridium laramie
    20215Clostridium estertheticum subsp. laramiense

@ref: 5584

domain: Bacteria

phylum: Firmicutes

class: Clostridia

order: Clostridiales

family: Clostridiaceae

genus: Clostridium

species: Clostridium estertheticum subsp. laramiense

full scientific name: Clostridium estertheticum subsp. laramiense (Kalchayanand et al. 1993) Spring et al. 2003

strain designation: NK1

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram stain
69480yes93.092
69480100positive

colony morphology

  • @ref: 5584
  • incubation period: >14 days

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
5584WILKINS-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
5584CHOPPED 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

culture temp

  • @ref: 5584
  • growth: positive
  • type: growth
  • temperature: 10
  • range: psychrophilic

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
5584anaerobe
69480anaerobe99.491

spore formation

@refspore formationconfidence
69481yes100
69480yes100

Isolation, sampling and environmental information

isolation

  • @ref: 5584
  • sample type: spoiled umcooked beef
  • country: USA
  • origin.country: USA
  • continent: North America

isolation source categories

Cat1Cat2Cat3
#Engineered#Food production#Meat
#Host#Other#Decomposing animal

taxonmaps

  • @ref: 69479
  • File name: preview.99_505.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_34;96_327;97_364;98_413;99_505&stattab=map
  • Last taxonomy: Clostridium
  • 16S sequence: AJ506115
  • Sequence Identity:
  • Total samples: 18467
  • soil counts: 9246
  • aquatic counts: 5428
  • animal counts: 1548
  • plant counts: 2245

Safety information

risk assessment

  • @ref: 5584
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Clostridium estertheticum subsp. laramiense strain DSM 14864 16S ribosomal RNA gene, partial sequenceDQ911251327ena205326
5584Clostridium estertheticum subsp. laramiense 16S rRNA gene, strain DSM 14864AJ5061151473ena205326

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Clostridium estertheticum subsp. laramiense DSM 14864GCA_008933175contigncbi205326
66792Clostridium estertheticum subsp. laramiense strain DSM 14864205326.4wgspatric205326
66792Clostridium estertheticum laramiense DSM 148642860493848draftimg205326

GC content

@refGC-contentmethod
558432high performance liquid chromatography (HPLC)
558426thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileyes81.979no
gram-positiveyes69.701no
anaerobicyes95.946no
aerobicno96.585yes
halophileno96.821no
spore-formingyes94.251no
glucose-utilyes91.943no
flagellatedyes58.507no
thermophileno98.847yes
glucose-fermentyes66.958no

External links

@ref: 5584

culture collection no.: DSM 14864, ATCC 51254

straininfo link

  • @ref: 72333
  • straininfo: 265711

literature

  • topic: Phylogeny
  • Pubmed-ID: 12892121
  • title: Characterization of novel psychrophilic clostridia from an Antarctic microbial mat: description of Clostridium frigoris sp. nov., Clostridium lacusfryxellense sp. nov., Clostridium bowmanii sp. nov. and Clostridium psychrophilum sp. nov. and reclassification of Clostridium laramiense as Clostridium estertheticum subsp. laramiense subsp. nov.
  • authors: Spring S, Merkhoffer B, Weiss N, Kroppenstedt RM, Hippe H, Stackebrandt E
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.02554-0
  • year: 2003
  • mesh: Antarctic Regions, Clostridium/*classification/genetics/isolation & purification/metabolism, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fresh Water/microbiology, Genotype, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Species Specificity, Terminology as Topic
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
5584Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 14864)https://www.dsmz.de/collection/catalogue/details/culture/DSM-14864
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
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)
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
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
72333Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID265711.1StrainInfo: A central database for resolving microbial strain identifiers