Strain identifier

BacDive ID: 2760

Type strain: Yes

Species: Ruminiclostridium cellulolyticum

Strain Designation: H10

Strain history: <- ATCC; ATCC 35319 <- E. Petitdemange, Université de Nancy, France; H10

NCBI tax ID(s): 1521 (species)

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General

@ref: 2323

BacDive-ID: 2760

DSM-Number: 5812

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

description: Ruminiclostridium cellulolyticum H10 is an anaerobe, spore-forming, mesophilic bacterium that forms circular colonies and was isolated from decayed grass compost.

NCBI tax id

  • NCBI tax id: 1521
  • Matching level: species

strain history

  • @ref: 2323
  • history: <- ATCC; ATCC 35319 <- E. Petitdemange, Université de Nancy, France; H10

doi: 10.13145/bacdive2760.20230509.8.1

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 cellulolyticum
  • full scientific name: Ruminiclostridium cellulolyticum (Petitdemange et al. 1984) Zhang et al. 2018

  • synonyms

    • @ref: 20215
    • synonym: Clostridium cellulolyticum

@ref: 2323

domain: Bacteria

phylum: Firmicutes

class: Clostridia

order: Clostridiales

family: Oscillospiraceae

genus: Ruminiclostridium

species: Ruminiclostridium cellulolyticum

full scientific name: Ruminiclostridium cellulolyticum (Petitdemange et al. 1984) Zhang et al. 2018

strain designation: H10

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityflagellum arrangementconfidence
43363positive3-6 µm0.6-1 µmrod-shapedyesperitrichous
69480yes90.199
69480positive100

colony morphology

  • @ref: 43363
  • colony size: 0.5 mm
  • colony color: translucent and unpigmented
  • colony shape: circular
  • incubation period: 5-6 days
  • medium used: Cellulose agar medium

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
2323RUMINOCLOSTRIDIUM CELLULOLYTICUM (CM3) MEDIUM (DSMZ Medium 520)yeshttps://mediadive.dsmz.de/medium/520Name: RUMINOCLOSTRIDIUM CELLULOLYTICUM (CM3) MEDIUM (DSMZ Medium 520) Composition: Cellulose 9.97009 g/l (optional) Cellobiose 5.98205 g/l K2HPO4 x 3 H2O 2.89133 g/l Yeast extract 1.99402 g/l Na2CO3 1.49551 g/l KH2PO4 1.49551 g/l (NH4)2SO4 1.29611 g/l L-Cysteine HCl x H2O 0.498504 g/l MgCl2 x 6 H2O 0.199402 g/l CaCl2 x 2 H2O 0.0747757 g/l HCl 0.00249252 g/l FeCl2 x 4 H2O 0.00149551 g/l FeSO4 x 7 H2O 0.00124626 g/l Sodium resazurin 0.000498504 g/l CoCl2 x 6 H2O 0.000189432 g/l MnCl2 x 4 H2O 9.97009e-05 g/l ZnCl2 6.97906e-05 g/l Na2MoO4 x 2 H2O 3.58923e-05 g/l NiCl2 x 6 H2O 2.39282e-05 g/l H3BO3 5.98205e-06 g/l CuCl2 x 2 H2O 1.99402e-06 g/l Distilled water
43363Cellulose agar mediumyes

culture temp

@refgrowthtypetemperaturerange
2323positivegrowth35mesophilic
43363nogrowth50thermophilic
43363nogrowth20psychrophilic
43363positiveminimum25mesophilic
43363positiveoptimum32-35mesophilic
43363positivemaximum45thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
2323anaerobe
43363anaerobe
69480anaerobe99.669

spore formation

@refspore descriptiontype of sporespore formationconfidence
43363produce swollen cells, present in cultures on cellulose media 3 or more days oldsporeyes
69480yes100

compound production

  • @ref: 2323
  • compound: sugar

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
4336315963ribitol-growth
4336327613amygdalin-growth
4336322599arabinose+/-growth
43363casein-degradation
4336317057cellobiose+/-growth
4336362968cellulose+/-growth
4336324996lactate-assimilation
4336316813galactitol-growth
4336317113erythritol-growth
433634853esculin+hydrolysis
4336328757fructose+/-growth
4336328260galactose+/-growth
433635291gelatin-hydrolysis
4336317234glucose+/-growth
4336317754glycerol-growth
4336328087glycogen-growth
4336317268myo-inositol-growth
4336315443inulin-growth
4336317716lactose-growth
4336317306maltose-growth
4336329864mannitol-growth
4336337684mannose+/-growth
433636731melezitose-growth
43363milk-assimilation
4336315361pyruvate-assimilation
4336316634raffinose-growth
4336326546rhamnose-growth
4336333942ribose+/-growth
4336317814salicin-growth
4336330911sorbitol-growth
4336327922sorbose-growth
4336328017starch-hydrolysis
4336317992sucrose-growth
4336316094thiosulfate-reduction
4336327082trehalose-growth
4336318222xylose+/-growth

metabolite production

@refChebi-IDmetaboliteproduction
4336330089acetateyes
4336316526carbon dioxideyes
4336318276dihydrogenyes
4336324996DL-lactateyes
4336316236ethanolyes
4336315740formateyes
4336335581indoleno
4336316301nitriteno

enzymes

@refvalueactivityec
43363catalase-1.11.1.6
43363urease-3.5.1.5
43363lipase-
43363lecithinase-

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
2323decayed grass compostFranceFRAEurope
43363isolated in autumn from decayed grass compost packed for 3 to 4 months

isolation source categories

Cat1Cat2Cat3
#Engineered#Biodegradation#Composting
#Host#Plants#Decomposing plant
#Host#Plants#Herbaceous plants (Grass,Crops)

Safety information

risk assessment

  • @ref: 2323
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 20218
  • description: C.cellulolyticum gene for 16S ribosomal RNA
  • accession: X71847
  • length: 1642
  • database: ena
  • NCBI tax ID: 394503

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Ruminiclostridium cellulolyticum H10GCA_000022065completencbi394503
66792Clostridium cellulolyticum H10394503.7completepatric394503
66792Ruminiclostridium cellulolyticum H10643348528completeimg394503

GC content

@refGC-contentmethod
232341.0
4336341thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes87no
motileyes82.658yes
flagellatedno55.771yes
gram-positiveyes62.892no
anaerobicyes98.524no
aerobicno97.475yes
halophileno96.764no
spore-formingyes95.737no
thermophileyes86.367no
glucose-utilyes87.972no
glucose-fermentyes58.695no

External links

@ref: 2323

culture collection no.: DSM 5812, ATCC 35319, JCM 6584

straininfo link

  • @ref: 72290
  • straininfo: 40993

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Metabolism7569320The effects of tunicamycin on secretion, adhesion and activities of the cellulase complex of Clostridium cellulolyticum, ATCC 35319.Gehin A, Petitdemange HRes Microbiol10.1016/0923-2508(96)80281-61995Anti-Bacterial Agents/pharmacology, Bacterial Adhesion/*drug effects, Bacterial Proteins/chemistry/*metabolism, Cellulase/chemistry/*metabolism, Clostridium/*drug effects/enzymology/growth & development/metabolism, Electrophoresis, Polyacrylamide Gel, In Vitro Techniques, Temperature, Tunicamycin/*pharmacologyEnzymology
Metabolism8501049Adhesion and growth rate of Clostridium cellulolyticum ATCC 35319 on crystalline cellulose.Gelhaye E, Petitdemange H, Gay RJ Bacteriol10.1128/jb.175.11.3452-3458.19931993*Bacterial Adhesion, Carboxymethylcellulose Sodium/metabolism, Cellobiose/metabolism, Cellulase/analysis, Cellulose/*metabolism, Clostridium/*growth & development, Reproducibility of Results
Metabolism8636029Interaction between the endoglucanase CelA and the scaffolding protein CipC of the Clostridium cellulolyticum cellulosome.Pages S, Belaich A, Tardif C, Reverbel-Leroy C, Gaudin C, Belaich JPJ Bacteriol10.1128/jb.178.8.2279-2286.19961996Amino Acid Sequence, Bacterial Proteins/genetics/*metabolism, Base Sequence, Biosensing Techniques, Carrier Proteins/genetics/*metabolism, Cellulase/genetics/*metabolism, Cellulose/*metabolism, Cloning, Molecular, Clostridium/enzymology/genetics/*metabolism, Molecular Sequence Data, Multienzyme Complexes/genetics/*metabolism, Protein Binding, Recombinant Fusion Proteins/metabolism, Sequence Analysis, DNA, Sequence Homology, Amino AcidEnzymology
Metabolism8987692Studies of Clostridium cellulolyticum ATCC 35319 under dialysis and co-culture conditions.Gehin A, Cailliez C, Petitdemange E, Benoit LLett Appl Microbiol10.1111/j.1472-765x.1996.tb00067.x1996Cellulose/*metabolism, Clostridium/growth & development/*metabolism, Coculture Techniques, Dialysis
Metabolism10972834Spo0A directly controls the switch from acid to solvent production in solvent-forming clostridia.Ravagnani A, Jennert KC, Steiner E, Grunberg R, Jefferies JR, Wilkinson SR, Young DI, Tidswell EC, Brown DP, Youngman P, Morris JG, Young MMol Microbiol10.1046/j.1365-2958.2000.02071.x2000Acids, Bacterial Proteins/genetics/*metabolism, Base Sequence, Carboxy-Lyases/genetics, Clostridium/enzymology/genetics/*metabolism, DNA, Bacterial, Gene Expression Regulation, Bacterial, Gene Expression Regulation, Enzymologic, Genes, Bacterial, Molecular Sequence Data, Phenotype, Phosphate Acetyltransferase/genetics, Promoter Regions, Genetic, Solvents, Spores, Bacterial, Transcription Factors/genetics/*metabolismGenetics
Metabolism11101665Gene transfer to Clostridium cellulolyticum ATCC 35319.Jennert KCB, Tardif C, Young DI, Young MMicrobiology (Reading)10.1099/00221287-146-12-30712000Cellulose/metabolism, Clostridium/*genetics/growth & development/metabolism, *Conjugation, Genetic, DNA Methylation, DNA Transposable Elements, DNA, Bacterial/genetics, Deoxyribonuclease HpaII/metabolism, Electroporation/methods, Organelles/enzymology/genetics, Plasmids/genetics, *Transformation, Bacterial/geneticsEnzymology
Metabolism14756797Use of antisense RNA to modify the composition of cellulosomes produced by Clostridium cellulolyticum.Perret S, Maamar H, Belaich JP, Tardif CMol Microbiol10.1046/j.1365-2958.2003.03860.x2004Base Sequence, Binding Sites, Cellulose/*metabolism, Clostridium/*genetics/metabolism, DNA Primers, Organelles/metabolism, Phenotype, Plasmids/genetics, Polymerase Chain Reaction, RNA, Antisense/*genetics, RNA, Bacterial/genetics, RNA, Messenger/genetics, Ribosomes/metabolismPhenotype
Metabolism16102601Clostridium cellulolyticum: model organism of mesophilic cellulolytic clostridia.Desvaux MFEMS Microbiol Rev10.1016/j.femsre.2004.11.0032004Biodegradation, Environmental, Carbon/*metabolism, Cellulose/*metabolism, Clostridium cellulolyticum/enzymology/genetics/*metabolismEnzymology
16349055Colonization of Crystalline Cellulose by Clostridium cellulolyticum ATCC 35319.Gelhaye E, Gehin A, Petitdemange HAppl Environ Microbiol10.1128/aem.59.9.3154-3156.19931993
Enzymology21663329Cloning, expression, and characterization of a D-psicose 3-epimerase from Clostridium cellulolyticum H10.Mu W, Chu F, Xing Q, Yu S, Zhou L, Jiang BJ Agric Food Chem10.1021/jf201356q2011Amino Acid Sequence, Bacterial Proteins/*chemistry/*genetics/isolation & purification/metabolism, *Cloning, Molecular, Clostridium cellulolyticum/chemistry/*enzymology/genetics, Enzyme Stability, Fructose/metabolism, *Gene Expression, Kinetics, Molecular Sequence Data, Molecular Weight, Racemases and Epimerases/*chemistry/*genetics/isolation & purification/metabolism, Sequence Alignment, Substrate SpecificityMetabolism
23657055Structure and regulation of the cellulose degradome in Clostridium cellulolyticum.Xu C, Huang R, Teng L, Wang D, Hemme CL, Borovok I, He Q, Lamed R, Bayer EA, Zhou J, Xu JBiotechnol Biofuels10.1186/1754-6834-6-732013

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
2323Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 5812)https://www.dsmz.de/collection/catalogue/details/culture/DSM-5812
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
43363E. Petitdemange, F. Caillet, J. Giallo, C. Gaudin10.1099/00207713-34-2-155Clostridium cellulolyticum sp. nov., a Cellulolytic, Mesophilic: Species from Decayed GrassIJSEM 34: 155-159 1984
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)
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)
72290Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID40993.1StrainInfo: A central database for resolving microbial strain identifiers