Strain identifier

BacDive ID: 2619

Type strain: Yes

Species: Clostridium nexile

Strain history: DSM 1787 <-- E. P. Cato <-- L. V. Holdeman and W. E. C. Moore; VPI C48-37.

NCBI tax ID(s): 500632 (strain), 29361 (species)

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General

@ref: 654

BacDive-ID: 2619

DSM-Number: 1787

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, Gram-positive

description: Clostridium nexile DSM 1787 is an anaerobe, mesophilic, Gram-positive bacterium that was isolated from human faeces.

NCBI tax id

NCBI tax idMatching level
500632strain
29361species

strain history

@refhistory
654<- E. P. Cato, Virginia Polytechnical Institute and State University, Blacksburg, V., USA <- L. V. Holdeman and W. E. C. Moore
67770DSM 1787 <-- E. P. Cato <-- L. V. Holdeman and W. E. C. Moore; VPI C48-37.

doi: 10.13145/bacdive2619.20230509.8.1

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 nexile
  • full scientific name: Clostridium nexile Holdeman and Moore 1974 (Approved Lists 1980)

  • synonyms

    • @ref: 20215
    • synonym: Tyzzerella nexilis

@ref: 654

domain: Bacteria

phylum: Firmicutes

class: Clostridia

order: Clostridiales

family: Clostridiaceae

genus: Clostridium

species: Clostridium nexile

full scientific name: Clostridium nexile Holdeman and Moore 1974

type strain: yes

Morphology

cell morphology

  • @ref: 69480
  • gram stain: positive
  • confidence: 100

Culture and growth conditions

culture medium

  • @ref: 654
  • name: CHOPPED MEAT MEDIUM WITH CARBOHYDRATES (DSMZ Medium 110)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/110
  • composition: Name: 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

@refgrowthtypetemperaturerange
654positivegrowth37mesophilic
67770positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
654anaerobe
69480anaerobe99.486

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 99.61

Isolation, sampling and environmental information

isolation

@refsample type
654human faeces
67770Human feces

isolation source categories

Cat1Cat2Cat3
#Host#Human
#Host Body Product#Gastrointestinal tract#Feces (Stool)

Safety information

risk assessment

  • @ref: 654
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
654Clostridium nexile 16S rRNA gene, strain DSM 1787X734431524ena500632
67770Tyzzerella nexilis JCM 31500 gene for 16S rRNA, partial sequenceLC5198561471ena29361

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Clostridium nexile DSM 1787500632.7wgspatric500632
66792Tyzzerella nexilis DSM 1787642979369draftimg500632
67770[Clostridium] nexile DSM 1787GCA_000156035scaffoldncbi500632

GC content

@refGC-contentmethod
65440.1sequence analysis
6777040thermal denaturation, midpoint method (Tm)
6777044.4high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes67no
gram-positiveyes95.549no
anaerobicyes99.721yes
halophileno82.055no
spore-formingno71.185no
glucose-utilyes88.221no
aerobicno98.738yes
thermophileno98.146yes
motileno89.799no
flagellatedno92.445no
glucose-fermentyes78.481no

External links

@ref: 654

culture collection no.: DSM 1787, ATCC 27757, JCM 31500, VPI C48-37, BCRC 14523, VTT E-021854

straininfo link

  • @ref: 72150
  • straininfo: 39160

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny26637816Sellimonas intestinalis gen. nov., sp. nov., isolated from human faeces.Seo B, Yoo JE, Lee YM, Ko GInt J Syst Evol Microbiol10.1099/ijsem.0.0008172015
Phylogeny28556772Faecalimonas umbilicata gen. nov., sp. nov., isolated from human faeces, and reclassification of Eubacterium contortum, Eubacterium fissicatena and Clostridium oroticum as Faecalicatena contorta gen. nov., comb. nov., Faecalicatena fissicatena comb. nov. and Faecalicatena orotica comb. nov.Sakamoto M, Iino T, Ohkuma MInt J Syst Evol Microbiol10.1099/ijsem.0.0017902017Bacterial Typing Techniques, Base Composition, Clostridiales/*classification/genetics/isolation & purification, Clostridium/classification, DNA, Bacterial/genetics, Eubacterium/classification, Fatty Acids/chemistry, Feces/*microbiology, Genes, Bacterial, Humans, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAPathogenicity
Phylogeny29204666Glucerabacter canisensis gen. nov., sp. nov., isolated from dog feces and its effect on the hydrolysis of plant glucosylceramide in the intestine of dogs.Kawata M, Tsukamoto A, Isozaki R, Nobukawa S, Kawahara N, Akutsu S, Suzuki M, Asanuma NArch Microbiol10.1007/s00203-017-1463-12017Animals, Base Composition, Clostridium/*genetics/isolation & purification/metabolism, DNA, Bacterial/genetics, Dogs, Fatty Acids/analysis/chemistry, Feces/microbiology, Female, Glucosylceramides/*metabolism, Hydrolysis, Intestines/microbiology, Molecular Typing, Phylogeny, Plant Extracts/metabolism, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAMetabolism
Phylogeny32100703Blautia faecicola sp. nov., isolated from faeces from a healthy human.Kim JS, Park JE, Lee KC, Choi SH, Oh BS, Yu SY, Eom MK, Kang SW, Han KI, Suh MK, Lee DH, Yoon H, Kim BY, Yang SJ, Lee JH, Lee JS, Park SHInt J Syst Evol Microbiol10.1099/ijsem.0.0040152020Acetic Acid/metabolism, Bacterial Typing Techniques, Base Composition, Clostridiales/*classification/isolation & purification, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Feces/*microbiology, Fermentation, Humans, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNAPathogenicity

Reference

@idauthorscataloguedoi/urltitle
654Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 1787)https://www.dsmz.de/collection/catalogue/details/culture/DSM-1787
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
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/
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)
72150Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID39160.1StrainInfo: A central database for resolving microbial strain identifiers