Strain identifier

BacDive ID: 2767

Type strain: Yes

Species: Ruminiclostridium cellobioparum subsp. termitidis

Strain Designation: CT1112

Strain history: <- J. L. Garcia, Université de Provence, Marseille, France; CT1112 <- P. Hethener and A. Brauman

NCBI tax ID(s): 29371 (subspecies)

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

@ref: 2158

BacDive-ID: 2767

DSM-Number: 5398

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

description: Ruminiclostridium cellobioparum subsp. termitidis CT1112 is an anaerobe, mesophilic bacterium that was isolated from hindgut, termite Nasutitermes lujae.

NCBI tax id

  • NCBI tax id: 29371
  • Matching level: subspecies

strain history

  • @ref: 2158
  • history: <- J. L. Garcia, Université de Provence, Marseille, France; CT1112 <- P. Hethener and A. Brauman

doi: 10.13145/bacdive2767.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Clostridia
  • order: Eubacteriales
  • family: Oscillospiraceae
  • genus: Ruminiclostridium
  • species: Ruminiclostridium cellobioparum subsp. termitidis
  • full scientific name: Ruminiclostridium cellobioparum subsp. termitidis (Hethener et al. 1992) Zhang et al. 2018
  • synonyms

    @refsynonym
    20215Ruminiclostridium termitidis
    20215Clostridium termitidis

@ref: 2158

domain: Bacteria

phylum: Firmicutes

class: Clostridia

order: Clostridiales

family: Oscillospiraceae

genus: Ruminiclostridium

species: Ruminiclostridium cellobioparum subsp. termitidis

full scientific name: Ruminiclostridium cellobioparum subsp. termitidis (Hethener et al. 1992) Zhang et al. 2018

strain designation: CT1112

type strain: yes

Culture and growth conditions

culture medium

  • @ref: 2158
  • name: RUMINICLOSTRIDIUM CELLOBIOPARUM MEDIUM (DSMZ Medium 539)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/539
  • composition: Name: RUMINICLOSTRIDIUM CELLOBIOPARUM MEDIUM (DSMZ Medium 539) Composition: Cellulose 4.99501 g/l (optional) Cellobiose 4.99501 g/l NaCl 0.999001 g/l Na2CO3 0.999001 g/l Yeast extract 0.499501 g/l KCl 0.499501 g/l Na2S x 9 H2O 0.3996 g/l MgCl2 x 6 H2O 0.3996 g/l NH4Cl 0.2997 g/l KH2PO4 0.1998 g/l CaCl2 x 2 H2O 0.14985 g/l HCl 0.0024975 g/l FeCl2 x 4 H2O 0.0014985 g/l Sodium resazurin 0.0004995 g/l CoCl2 x 6 H2O 0.00018981 g/l MnCl2 x 4 H2O 9.99001e-05 g/l ZnCl2 6.99301e-05 g/l Na2MoO4 x 2 H2O 3.5964e-05 g/l NiCl2 x 6 H2O 2.3976e-05 g/l H3BO3 5.99401e-06 g/l CuCl2 x 2 H2O 1.998e-06 g/l Distilled water

culture temp

  • @ref: 2158
  • growth: positive
  • type: growth
  • temperature: 37
  • range: mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 2158
  • oxygen tolerance: anaerobe

Isolation, sampling and environmental information

isolation

  • @ref: 2158
  • sample type: hindgut, termite Nasutitermes lujae
  • host species: Nasutitermes lujae
  • country: Republic of the Congo
  • origin.country: COG
  • continent: Africa

isolation source categories

Cat1Cat2Cat3
#Host#Arthropoda#Insecta
#Host Body-Site#Gastrointestinal tract

taxonmaps

  • @ref: 69479
  • File name: preview.99_7333.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_196;96_1460;97_1742;98_5377;99_7333&stattab=map
  • Last taxonomy: Ruminiclostridium cellobioparum subclade
  • 16S sequence: FR733680
  • Sequence Identity:
  • Total samples: 1202
  • soil counts: 819
  • aquatic counts: 189
  • animal counts: 126
  • plant counts: 68

Safety information

risk assessment

  • @ref: 2158
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 2158
  • description: Clostridium termitidis partial 16S rRNA gene, type strain DSM5398T
  • accession: FR733680
  • length: 1512
  • database: ena
  • NCBI tax ID: 29371

Genome sequences

  • @ref: 66792
  • description: Ruminiclostridium cellobioparum subsp. termitidis CT1112
  • accession: GCA_000350485
  • assembly level: contig
  • database: ncbi
  • NCBI tax ID: 1195236

GC content

@refGC-contentmethod
215841.2sequence analysis
215839.2

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileyes86.104no
flagellatedyes56.606no
gram-positiveno63.267no
anaerobicyes97.82yes
aerobicno96.741yes
halophileno97.275no
spore-formingyes96.2no
glucose-utilyes91.278no
thermophileno89.966yes
glucose-fermentyes55.311no

External links

@ref: 2158

culture collection no.: DSM 5398, ATCC 51846

straininfo link

  • @ref: 72297
  • straininfo: 43211

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Metabolism11760953Metabolism of cinnamic acids by some Clostridiales and emendation of the descriptions of Clostridium aerotolerans, Clostridium celerecrescens and Clostridium xylanolyticum.Chamkha M, Garcia JL, Labat MInt J Syst Evol Microbiol10.1099/00207713-51-6-21052001Bacterial Typing Techniques, Cinnamates/*metabolism, Clostridium/*classification/growth & development/*metabolism, Culture Media, Glucose/metabolismCultivation
Genetics23704187Draft Genome Sequence of the Cellulolytic, Mesophilic, Anaerobic Bacterium Clostridium termitidis Strain CT1112 (DSM 5398).Lal S, Ramachandran U, Zhang X, Munir R, Sparling R, Levin DBGenome Announc10.1128/genomeA.00281-132013
Metabolism25101643Comparative analysis of carbohydrate active enzymes in Clostridium termitidis CT1112 reveals complex carbohydrate degradation ability.Munir RI, Schellenberg J, Henrissat B, Verbeke TJ, Sparling R, Levin DBPLoS One10.1371/journal.pone.01042602014Animals, Carbohydrate Metabolism/*physiology, Cellobiose/*metabolism, Clostridium/*enzymology, Ethanol/metabolism, Glycoside Hydrolases/*metabolism, Hydrogen/metabolism, Isoptera/microbiology, Monosaccharides/*metabolism, Species SpecificityEnzymology
Pathogenicity25957533Quantitative proteomic analysis of the cellulolytic system of Clostridium termitidis CT1112 reveals distinct protein expression profiles upon growth on alpha-cellulose and cellobiose.Munir RI, Spicer V, Shamshurin D, Krokhin OV, Wilkins J, Ramachandran U, Sparling R, Levin DBJ Proteomics10.1016/j.jprot.2015.04.0262015Bacterial Proteins/*biosynthesis, Cellobiose/chemistry/*pharmacology, Cellulose/chemistry/*pharmacology, Clostridium/*growth & development, Gene Expression Regulation/*drug effects, Proteomics
Phylogeny26907553Comparative Genomics of Core Metabolism Genes of Cellulolytic and Non-cellulolytic Clostridium Species.Lal S, Levin DBAdv Biochem Eng Biotechnol10.1007/10_2015_50072016Bacteria, Anaerobic/classification/genetics, Bacterial Proteins/*genetics, Biofuels/*microbiology, Cellulose, Chromosome Mapping, Clostridium/*classification/*genetics, Energy Metabolism/genetics, Gene Expression Regulation, Bacterial/*genetics, Genome, Bacterial/*genetics, Signal Transduction/genetics, Species SpecificityGenetics
Metabolism27215540Transcriptomic and proteomic analyses of core metabolism in Clostridium termitidis CT1112 during growth on alpha-cellulose, xylan, cellobiose and xylose.Munir RI, Spicer V, Krokhin OV, Shamshurin D, Zhang X, Taillefer M, Blunt W, Cicek N, Sparling R, Levin DBBMC Microbiol10.1186/s12866-016-0711-x2016Bacterial Proteins/genetics/metabolism, Cellobiose/metabolism, Cellulose/metabolism, Clostridium/genetics/*growth & development/metabolism, Fermentation, Gene Expression Profiling/*methods, Gene Expression Regulation, Bacterial, Lignin/*metabolism, Metabolic Networks and Pathways, Proteomics/*methods, Sequence Analysis, RNA/*methods, Xylans/metabolism, Xylose/metabolismTranscriptome

Reference

@idauthorscataloguedoi/urltitle
2158Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 5398)https://www.dsmz.de/collection/catalogue/details/culture/DSM-5398
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
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)
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
72297Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID43211.1StrainInfo: A central database for resolving microbial strain identifiers