Strain identifier

BacDive ID: 2624

Type strain: Yes

Species: Clostridium paraputrificum

Strain history: ATCC 25780 <-- L. DS. Smith VPI 1584.

NCBI tax ID(s): 29363 (species)

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

@ref: 1176

BacDive-ID: 2624

DSM-Number: 2630

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic

description: Clostridium paraputrificum DSM 2630 is an anaerobe, mesophilic bacterium of the family Clostridiaceae.

NCBI tax id

  • NCBI tax id: 29363
  • Matching level: species

strain history

@refhistory
1176<- ATCC <- L.DS. Smith, VPI 1584
67770ATCC 25780 <-- L. DS. Smith VPI 1584.

doi: 10.13145/bacdive2624.20230509.8.1

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 paraputrificum
  • full scientific name: Clostridium paraputrificum (Bienstock 1906) Snyder 1936 (Approved Lists 1980)
  • synonyms

    • @ref: 20215
    • synonym: Bacillus paraputrificus

@ref: 1176

domain: Bacteria

phylum: Firmicutes

class: Clostridia

order: Clostridiales

family: Clostridiaceae

genus: Clostridium

species: Clostridium paraputrificum

full scientific name: Clostridium paraputrificum (Bienstock 1906) Snyder 1936

type strain: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
1176CHOPPED 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
1176CHOPPED MEAT MEDIUM (DSMZ Medium 78)yeshttps://mediadive.dsmz.de/medium/78Name: CHOPPED MEAT MEDIUM (DSMZ Medium 78) Composition: Ground beef 500.0 g/l Casitone 30.0 g/l Agar 15.0 g/l Ethanol 9.5 g/l (optional) K2HPO4 5.0 g/l Yeast extract 5.0 g/l L-Cysteine HCl 0.5 g/l Haemin 0.005 g/l (optional) Resazurin 0.001 g/l Vitamin K3 0.0005 g/l (optional) Vitamin K1 (optional) NaOH (optional) Distilled water

culture temp

@refgrowthtypetemperaturerange
1176positivegrowth37mesophilic
51161positivegrowth37mesophilic
67770positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
1176anaerobe
51161anaerobe

Isolation, sampling and environmental information

taxonmaps

  • @ref: 69479
  • File name: preview.99_3373.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_34;96_1253;97_2106;98_2586;99_3373&stattab=map
  • Last taxonomy: Clostridium paraputrificum subclade
  • 16S sequence: AB536771
  • Sequence Identity:
  • Total samples: 61941
  • soil counts: 2219
  • aquatic counts: 4616
  • animal counts: 54761
  • plant counts: 345

Safety information

risk assessment

  • @ref: 1176
  • biosafety level: 2
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Clostridium paraputrificum strain DSM 2630 16S ribosomal RNA gene, partial sequenceHM245948836ena29363
20218Clostridium paraputrificum 16S rRNA gene, strain DSM 2630X734451511ena29363
20218Clostridium paraputrificum gene for 16S ribosomal RNA, partial sequence, strain: JCM 1293AB5367711476ena29363
1176C.paraputrificum 16S rRNA geneX759071467ena29363

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Clostridium paraputrificum strain NCTC1183329363.20wgspatric29363
67770Clostridium paraputrificum NCTC11833GCA_900447045contigncbi29363

GC content

@refGC-contentmethod
117627.0
6777027thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
gram-positiveyes81.675no
anaerobicyes98.399yes
halophileno84.564no
spore-formingyes93.606no
glucose-utilyes88.506no
motileyes81.069no
flagellatedyes60.005no
aerobicno98.435yes
thermophileno95.024no
glucose-fermentyes63.563no

External links

@ref: 1176

culture collection no.: DSM 2630, ATCC 25780, NCIB 10671, CCUG 32755, NCTC 11833, VPI 1584, JCM 1293, BCRC 14550, NCIMB 10671

straininfo link

  • @ref: 72155
  • straininfo: 265463

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Pathogenicity24083511Growth-Inhibiting and morphostructural effects of constituents identified in Asarum heterotropoides root on human intestinal bacteria.Perumalsamy H, Jung MY, Hong SM, Ahn YJBMC Complement Altern Med10.1186/1472-6882-13-2452013Asarum/*chemistry, Bacteria/*drug effects, Cell Shape/drug effects, Gastrointestinal Tract/drug effects/*microbiology, Humans, Microbial Sensitivity Tests, Microbiota/*drug effects, Plant Extracts/chemistry/*pharmacology, Plant Roots/chemistry
Metabolism33938389Completion of the gut microbial epi-bile acid pathway.Doden HL, Wolf PG, Gaskins HR, Anantharaman K, Alves JMP, Ridlon JMGut Microbes10.1080/19490976.2021.19072712021Actinobacteria/genetics, Bacterial Proteins/genetics/metabolism, Bile Acids and Salts/*metabolism, Clostridium/*enzymology/*genetics/*metabolism, Clostridium Infections/microbiology, DNA, Bacterial, Gastrointestinal Microbiome, Humans, Hydroxysteroid Dehydrogenases/*genetics/*metabolism, Lithocholic Acid/metabolism, NADP/metabolism, Phylogeny, Recombinant Proteins/genetics/metabolismEnzymology

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
1176Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 2630)https://www.dsmz.de/collection/catalogue/details/culture/DSM-2630
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
51161Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 32755)https://www.ccug.se/strain?id=32755
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
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
72155Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID265463.1StrainInfo: A central database for resolving microbial strain identifiers