Strain identifier

BacDive ID: 2653

Type strain: Yes

Species: Thomasclavelia ramosa

Strain Designation: 113-I

Strain history: ATCC 25582 <-- W. E. C. Moore VPI 0427 <-- A. R. Prévot 113-1 ("Ramibacterium ramosum").

NCBI tax ID(s): 445974 (strain), 1547 (species)

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General

@ref: 489

BacDive-ID: 2653

DSM-Number: 1402

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

description: Thomasclavelia ramosa 113-I is an anaerobe, mesophilic, Gram-positive bacterium of the family Coprobacillaceae.

NCBI tax id

NCBI tax idMatching level
1547species
445974strain

strain history

@refhistory
489<- ATCC <- W.E.C. Moore, VPI 0427 <- A.R. Prévot, 113-I (Ramibacterium ramosum)
67770ATCC 25582 <-- W. E. C. Moore VPI 0427 <-- A. R. Prévot 113-1 ("Ramibacterium ramosum").

doi: 10.13145/bacdive2653.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Erysipelotrichia
  • order: Erysipelotrichales
  • family: Coprobacillaceae
  • genus: Thomasclavelia
  • species: Thomasclavelia ramosa
  • full scientific name: Thomasclavelia ramosa (Veillon and Zuber 1898) Lawson et al. 2023

  • synonyms

    @refsynonym
    20215Erysipelatoclostridium ramosum
    20215Bacillus ramosus
    20215Clostridium ramosum

@ref: 489

domain: Bacteria

phylum: Firmicutes

class: Clostridia

order: Clostridiales

family: Clostridiaceae

genus: Clostridium

species: Clostridium ramosum

full scientific name: Clostridium ramosum (Veillon and Zuber 1898) Holdeman et al. 1971

strain designation: 113-I

type strain: yes

Morphology

cell morphology

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

Culture and growth conditions

culture medium

@refnamegrowthlink
489COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium693.pdf
489FASTIDIOUS ANAEROBE BROTH (DSMZ Medium 1203a)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium1203a.pdf

culture temp

@refgrowthtypetemperaturerange
489positivegrowth37mesophilic
47909positivegrowth37mesophilic
67770positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
489anaerobe
47909anaerobe
69480anaerobe100

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 99.289

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6836727082trehalose+builds acid from
6836762345L-rhamnose-builds acid from
6836730911sorbitol-builds acid from
6836716634raffinose+builds acid from
683676731melezitose-builds acid from
6836716024D-mannose+builds acid from
6836717057cellobiose+builds acid from
6836717754glycerol-builds acid from
683674853esculin+hydrolysis
683675291gelatin-hydrolysis
6836730849L-arabinose-builds acid from
6836765327D-xylose-builds acid from
6836717814salicin+builds acid from
6836717306maltose+builds acid from
6836717992sucrose+builds acid from
6836717716lactose+builds acid from
6836716899D-mannitol+builds acid from
6836717634D-glucose+builds acid from
6836716199urea-hydrolysis
6836727897tryptophan-energy source

metabolite production

  • @ref: 68367
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 68367
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
68367beta-glucosidase+3.2.1.21
68367gelatinase-
68367urease-3.5.1.5

API 20A

@refINDUREGLUMANLACSACMALSALXYLARAGELESCGLYCELMNEMLZRAFSORRHATRE
489--++++++---+-++-+--+

Isolation, sampling and environmental information

taxonmaps

  • @ref: 69479
  • File name: preview.99_1031.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15821;96_590;97_691;98_806;99_1031&stattab=map
  • Last taxonomy: Erysipelatoclostridium ramosum subclade
  • 16S sequence: AB595128
  • Sequence Identity:
  • Total samples: 106958
  • soil counts: 626
  • aquatic counts: 2108
  • animal counts: 103847
  • plant counts: 377

Safety information

risk assessment

  • @ref: 489
  • biosafety level: 2
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218C.ramosum 16S ribosomal RNA small subunitM237311530ena1547
20218Clostridium ramosum DSM 1402 16S ribosomal RNA gene, partial sequenceHM245949829ena445974
20218Clostridium ramosum strain DSM 1402 16S ribosomal RNA gene, partial sequenceHQ012012927ena445974
20218Clostridium ramosum 16S rRNA gene, strain DSM 1402X734401526ena445974
489Clostridium ramosum gene for 16S ribosomal RNA, partial sequence, strain: JCM 1298AB5951281488ena1547

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Thomasclavelia ramosa DSM 1402GCA_014131695completencbi445974
66792Clostridium ramosum DSM 1402445974.6wgspatric445974
66792Erysipelatoclostridium ramosum DSM 1402445974.19completepatric445974
66792Erysipelatoclostridium ramosum strain FDAARGOS_9061547.129completepatric1547
66792Erysipelatoclostridium ramosum DSM 1402641736198draftimg445974
67770Thomasclavelia ramosa DSM 1402GCA_000154485scaffoldncbi445974

GC content

@refGC-contentmethod
48931.4sequence analysis
6777026thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno58no
motileno90.161no
flagellatedno91.849no
gram-positiveyes95.359no
anaerobicyes97.739no
aerobicno98.507no
halophileno78.78no
spore-formingno66.639no
glucose-utilyes85.881no
thermophileno97.928yes
glucose-fermentyes71.364no

External links

@ref: 489

culture collection no.: CCUG 24038, DSM 1402, ATCC 25582, NCIB 10673, VPI 0427, JCM 1298, BCRC 14518, KCTC 3323, NCIMB 10673, NCTC 11812

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny7574587Bacteriostatic effect of orally administered bovine lactoferrin on proliferation of Clostridium species in the gut of mice fed bovine milk.Teraguchi S, Shin K, Ozawa K, Nakamura S, Fukuwatari Y, Tsuyuki S, Namihira H, Shimamura SAppl Environ Microbiol10.1128/aem.61.2.501-506.19951995Administration, Oral, Animals, Cattle, Clostridium/*drug effects/growth & development, Colony Count, Microbial, Diet, Feces/microbiology, Female, Hydrolysis, Intestines/*microbiology, Lactoferrin/administration & dosage/isolation & purification/*pharmacology, Mice, Mice, Inbred BALB C, Milk/*chemistry, Species SpecificityPathogenicity
Phylogeny35536223Tannockella kyphosi gen. nov., sp. nov., a member of the family Erysipelotrichaceae, isolated from the hindgut of the marine herbivorous fish Kyphosus sydneyanus.Pardesi B, Roberton AM, Wollmuth EM, Angert ER, Rosendale DI, White WL, Clements KDInt J Syst Evol Microbiol10.1099/ijsem.0.0053742022Animals, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Firmicutes, Gram-Positive Rods/genetics, *Kyphosis, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Tenericutes/geneticsTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
489Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 1402)https://www.dsmz.de/collection/catalogue/details/culture/DSM-1402
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
47909Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 24038)https://www.ccug.se/strain?id=24038
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/
68367Automatically annotated from API 20A
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)