Strain identifier

BacDive ID: 5434

Type strain: Yes

Species: Clostridium moniliforme

Strain Designation: 2055

Strain history: STAFF 1029 <-- ATCC 25546 <-- L. V. Holdeman VPI 0142B <-- A. Prévot 2055.

NCBI tax ID(s): 39489 (species)

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General

@ref: 1542

BacDive-ID: 5434

DSM-Number: 3984

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

description: Clostridium moniliforme 2055 is an anaerobe, spore-forming, mesophilic bacterium that forms circular colonies and was isolated from infected wound.

NCBI tax id

  • NCBI tax id: 39489
  • Matching level: species

strain history

@refhistory
1542<- ATCC <- L.V. Holdeman, VPI 0142B <- A. Prévot, 2055
67770STAFF 1029 <-- ATCC 25546 <-- L. V. Holdeman VPI 0142B <-- A. Prévot 2055.

doi: 10.13145/bacdive5434.20230509.8.1

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 moniliforme
  • full scientific name: Clostridium moniliforme (Repaci 1910) Lawson and Rainey 2016

  • synonyms

    @refsynonym
    20215Bacillus moniliforme
    20215Eubacterium moniliforme

@ref: 1542

domain: Bacteria

phylum: Firmicutes

class: Clostridia

order: Clostridiales

family: Clostridiaceae

genus: Clostridium

species: Clostridium moniliforme

full scientific name: Clostridium moniliforme (Repaci 1910) Lawson and Rainey 2016

strain designation: 2055

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityflagellum arrangementconfidence
43779positive1.7-9.4 µm0.6-0.9 µmrod-shapedyesperitrichous
69480positive100

colony morphology

@refcolony sizecolony colorcolony shapeincubation periodmedium used
437792-8 mmOpaquecircular2 daysHorse blood agar
490912 days

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
1542AMB MEDIUM (DSMZ Medium 455)yeshttps://mediadive.dsmz.de/medium/455Name: AMB MEDIUM (DSMZ Medium 455) Composition: Meat infusion 25.0 g/l K2HPO4 15.0 g/l Glucose 5.0 g/l Yeast extract 5.0 g/l Trypticase peptone 4.0 g/l Starch 1.0 g/l Cysteine 1.0 g/l (NH4)2SO4 1.0 g/l MgSO4 0.2 g/l CaCl2 0.01 g/l Distilled water
43779Horse blood agaryes

culture temp

@refgrowthtypetemperaturerange
1542positivegrowth37mesophilic
49091positivegrowth37mesophilic
67770positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
1542anaerobe
49091anaerobe
69480anaerobe98.649

spore formation

@refspore formationconfidence
69481yes100
69480yes98.397

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
4377924996lactate-assimilation
4377915963ribitol-builds acid from
4377923652dextrin-builds acid from
4377916813galactitol-builds acid from
4377915978glycerol 3-phosphate-builds acid from
4377915443inulin-builds acid from
4377927922sorbose-builds acid from
43779606565hippurate-hydrolysis
4377928260galactose+fermentation

metabolite production

  • @ref: 43779
  • Chebi-ID: 18276
  • metabolite: dihydrogen
  • production: yes

Isolation, sampling and environmental information

isolation

@refsample type
1542infected wound
43779Blood, various kinds of human clinical infections, intestinal tract, soil
49091Human infected wound
67770Infected wound

isolation source categories

Cat1Cat2Cat3
#Host Body-Site#Other#Wound
#Host#Human
#Host Body Product#Fluids#Blood
#Host Body-Site#Gastrointestinal tract
#Infection#Disease

taxonmaps

  • @ref: 69479
  • File name: preview.99_26521.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_34;96_1766;97_2114;98_4240;99_26521&stattab=map
  • Last taxonomy: Clostridium moniliforme
  • 16S sequence: NR_104892
  • Sequence Identity:
  • Total samples: 502
  • soil counts: 3
  • aquatic counts: 9
  • animal counts: 486
  • plant counts: 4

Safety information

risk assessment

  • @ref: 1542
  • biosafety level: 2
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Eubacterium moniliforme partial 16S rRNA gene, strain 2055HF5583731488ena39489
20218Eubacterium moniliforme gene for 16S ribosomal RNA, partial sequence, strain: JCM 9990AB5409851476ena39489
1542Eubacterium moniliforme 16S ribosomal RNAL346221463ena39489
1542Clostridium moniliforme strain 2055 16S ribosomal RNA, partial sequenceNR_1048921488nuccore39489

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Clostridium moniliforme DSM 3984GCA_017873235contigncbi39489
66792Clostridium moniliforme strain DSM 398439489.3wgspatric39489
66792Eubacterium moniliforme DSM 39842913335541draftimg39489

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
gram-positiveyes89.184no
anaerobicyes99.11yes
halophileno73.791no
spore-formingyes94.004no
glucose-utilyes90.801no
aerobicno98.406yes
motileyes83.236yes
flagellatedyes64.167yes
thermophileno93.525yes
glucose-fermentyes74.186no

External links

@ref: 1542

culture collection no.: DSM 3984, ATCC 25546, CCUG 28088, JCM 9990, VPI 0142B

straininfo link

  • @ref: 74922
  • straininfo: 38589

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
1542Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 3984)https://www.dsmz.de/collection/catalogue/details/culture/DSM-3984
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
43779Paul A. Lawson, Fred A. Rainey10.1099/ijsem.0.000824Proposal to restrict the genus Clostridium Prazmowski to Clostridium butyricum and related speciesIJSEM 66: 1009-1016 201626643615
49091Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 28088)https://www.ccug.se/strain?id=28088
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/
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
74922Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID38589.1StrainInfo: A central database for resolving microbial strain identifiers