Strain identifier

BacDive ID: 130926

Type strain: No

Species: Thomasclavelia ramosa

Strain Designation: PG-426-CC.8.1

Strain history: <- T. Clavel, TU Munich, Freising-Weihenstephan, Germany; PG-426-CC.8.1

NCBI tax ID(s): 1547 (species)

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General

@ref: 22218

BacDive-ID: 130926

DSM-Number: 29355

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

description: Thomasclavelia ramosa PG-426-CC.8.1 is an anaerobe, mesophilic bacterium that was isolated from caecal content; TNFdeltaARE/+ C57BL/6 mouse.

NCBI tax id

  • NCBI tax id: 1547
  • Matching level: species

strain history

  • @ref: 22218
  • history: <- T. Clavel, TU Munich, Freising-Weihenstephan, Germany; PG-426-CC.8.1

doi: 10.13145/bacdive130926.20230509.8.1

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: 22218

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: PG-426-CC.8.1

type strain: no

Morphology

colony morphology

  • @ref: 22218
  • incubation period: 1-2 days

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
22218PYG MEDIUM (MODIFIED) (DSMZ Medium 104)yeshttps://mediadive.dsmz.de/medium/104Name: PYG MEDIUM (modified) (DSMZ Medium 104) Composition: Yeast extract 10.0 g/l Peptone 5.0 g/l Trypticase peptone 5.0 g/l Beef extract 5.0 g/l Glucose 5.0 g/l L-Cysteine HCl x H2O 0.5 g/l NaHCO3 0.4 g/l NaCl 0.08 g/l K2HPO4 0.04 g/l KH2PO4 0.04 g/l MgSO4 x 7 H2O 0.02 g/l CaCl2 x 2 H2O 0.01 g/l Hemin 0.005 g/l Ethanol 0.0038 g/l Resazurin 0.001 g/l Tween 80 Vitamin K1 NaOH Distilled water
22218CHOPPED 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
22218CHOPPED 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: 22218
  • growth: positive
  • type: growth
  • temperature: 37
  • range: mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 22218
  • oxygen tolerance: anaerobe

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6838016199urea-hydrolysis
6838029016arginine-hydrolysis
6838016634raffinose-fermentation
6838029985L-glutamate-degradation
6838017632nitrate-reduction
6838027897tryptophan-energy source

metabolite production

  • @ref: 68380
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 68380
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
68380serine arylamidase-
68380glutamyl-glutamate arylamidase-
68380histidine arylamidase-
68380glycin arylamidase-
68380alanine arylamidase-3.4.11.2
68380tyrosine arylamidase-
68380pyrrolidonyl arylamidase-3.4.19.3
68380leucine arylamidase-3.4.11.1
68380phenylalanine arylamidase-
68380leucyl glycin arylamidase-3.4.11.1
68380proline-arylamidase-3.4.11.5
68380L-arginine arylamidase-
68380alkaline phosphatase-3.1.3.1
68380tryptophan deaminase-4.1.99.1
68380alpha-fucosidase-3.2.1.51
68380glutamate decarboxylase-4.1.1.15
68380N-acetyl-beta-glucosaminidase+3.2.1.52
68380beta-glucuronidase-3.2.1.31
68380alpha-arabinosidase-3.2.1.55
68380beta-glucosidase+3.2.1.21
68380alpha-glucosidase+3.2.1.20
68380beta-Galactosidase 6-phosphate+
68380beta-galactosidase+3.2.1.23
68380alpha-galactosidase-3.2.1.22
68380arginine dihydrolase-3.5.3.6
68380urease-3.5.1.5

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
22218---++++--+-------------------
22218---++++--++---------------
22218---++++--++---------------

Isolation, sampling and environmental information

isolation

  • @ref: 22218
  • sample type: caecal content; TNFdeltaARE/+ C57BL/6 mouse
  • geographic location: Freising
  • country: Germany
  • origin.country: DEU
  • continent: Europe

isolation source categories

Cat1Cat2Cat3
#Host#Mammals#Muridae (Mouse/Rat)
#Host Body-Site#Gastrointestinal tract#Large intestine
#Host Body Product#Gastrointestinal tract#Caecal content

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: KU196082
  • Sequence Identity:
  • Total samples: 106958
  • soil counts: 626
  • aquatic counts: 2108
  • animal counts: 103847
  • plant counts: 377

Safety information

risk assessment

  • @ref: 22218
  • biosafety level: 2
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 22218
  • description: Erysipelatoclostridium ramosum strain DSM 29355 16S ribosomal RNA gene, partial sequence
  • accession: KU196082
  • length: 1393
  • database: ena
  • NCBI tax ID: 1547

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Erysipelatoclostridium ramosum strain FDAARGOS_11051547.130completepatric1547
66792Thomasclavelia ramosa DSM 29355GCA_024622785contigncbi1547

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno89.413no
gram-positiveyes95.167no
anaerobicyes98.16yes
aerobicno98.805no
halophileno77.684no
spore-formingno58.691no
thermophileno98.217yes
glucose-utilyes86.05no
flagellatedno93.35no
glucose-fermentyes69.347no

External links

@ref: 22218

culture collection no.: DSM 29355

Reference

@idauthorstitledoi/urlcatalogue
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
22218Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-29355Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 29355)
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
68380Automatically annotated from API rID32A
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/