Strain identifier

BacDive ID: 130927

Type strain: No

Species: Thomasclavelia ramosa

Strain Designation: SRB509-5-F-B

Strain history: <- T. Clavel, TU Munich, Freising-Weihenstephan, Germany; SRB509-5-F-B

NCBI tax ID(s): 1547 (species)

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General

@ref: 22219

BacDive-ID: 130927

DSM-Number: 29357

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

description: Thomasclavelia ramosa SRB509-5-F-B is an anaerobe, mesophilic bacterium that was isolated from ileal mucosa; TNFdeltaARE/+ C57BL/6 mouse.

NCBI tax id

  • NCBI tax id: 1547
  • Matching level: species

strain history

  • @ref: 22219
  • history: <- T. Clavel, TU Munich, Freising-Weihenstephan, Germany; SRB509-5-F-B

doi: 10.13145/bacdive130927.20230509.8.1

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: 22219

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: SRB509-5-F-B

type strain: no

Morphology

colony morphology

  • @ref: 22219
  • incubation period: 2-3 days

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
22219PYG 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
22219FASTIDIOUS ANAEROBE AGAR (DSMZ Medium 1203)yeshttps://mediadive.dsmz.de/medium/1203Name: FASTIDIOUS ANAEROBE AGAR (DSMZ Medium 1203) Composition: Horse blood 100.0 g/l Fastidious Anaerobe Agar 45.7 g/l Distilled water
22219CHOPPED 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

  • @ref: 22219
  • growth: positive
  • type: growth
  • temperature: 37
  • range: mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 22219
  • oxygen tolerance: anaerobe

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6838016199urea-hydrolysis
6838029016arginine-hydrolysis
6838016024D-mannose+fermentation
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-
68380proline-arylamidase-3.4.11.5
68380L-arginine arylamidase-
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
68380arginine dihydrolase-3.5.3.6
68380urease-3.5.1.5

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
22219--+/-++++--+++----+--+---------
22219---++++--+++-----------------
22219---++++--+++-----------------

Isolation, sampling and environmental information

isolation

  • @ref: 22219
  • sample type: ileal mucosa; 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#Small intestine

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: KR364754
  • Sequence Identity:
  • Total samples: 106958
  • soil counts: 626
  • aquatic counts: 2108
  • animal counts: 103847
  • plant counts: 377

Safety information

risk assessment

  • @ref: 22219
  • biosafety level: 2
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 22219
  • description: Erysipelatoclostridium ramosum strain SRB509-5-F-B 16S ribosomal RNA gene, partial sequence
  • accession: KR364754
  • length: 1417
  • database: ena
  • NCBI tax ID: 1547

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Erysipelatoclostridium ramosum strain FDAARGOS_11061547.131completepatric1547
66792Thomasclavelia ramosa DSM 29357GCA_024622805contigncbi1547

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno88.812no
gram-positiveyes94.715no
anaerobicyes98.191no
aerobicno98.904yes
halophileno77.023no
spore-formingno64.345no
thermophileno97.591no
glucose-utilyes87.191no
flagellatedno92.867no
glucose-fermentyes70.969no

External links

@ref: 22219

culture collection no.: DSM 29357

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
22219Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-29357Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 29357)
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/