Strain identifier

BacDive ID: 2568

Type strain: Yes

Species: Clostridium cellulovorans

Strain Designation: 743B

Strain history: <- R. A. Mah, University of California, School of Public Health, Los Angeles, USA; 743B

NCBI tax ID(s): 1493 (species)

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General

@ref: 1287

BacDive-ID: 2568

DSM-Number: 3052

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, spore-forming, mesophilic, Gram-negative, other, colony-forming

description: Clostridium cellulovorans 743B is an anaerobe, spore-forming, mesophilic bacterium that forms rhizoid colonies and was isolated from methanogenic fermentation of hybrid poplar wood.

NCBI tax id

  • NCBI tax id: 1493
  • Matching level: species

strain history

  • @ref: 1287
  • history: <- R. A. Mah, University of California, School of Public Health, Los Angeles, USA; 743B

doi: 10.13145/bacdive2568.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Clostridia
  • order: Eubacteriales
  • family: Clostridiaceae
  • genus: Clostridium
  • species: Clostridium cellulovorans
  • full scientific name: Clostridium cellulovorans Sleat et al. 1985

@ref: 1287

domain: Bacteria

phylum: Firmicutes

class: Clostridia

order: Clostridiales

family: Clostridiaceae

genus: Clostridium

species: Clostridium cellulovorans

full scientific name: Clostridium cellulovorans Sleat et al. 1985

strain designation: 743B

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityflagellum arrangementconfidence
43428negative2.5-3.5 µm0.7-0.9 µmothernoperitrichous
43428negative4-7 µm1.5-2 µmothernoperitrichous
69480positive99.999

colony morphology

  • @ref: 43428
  • colony size: 1-2 mm
  • colony color: creamy-white and opaque
  • colony shape: rhizoid
  • incubation period: 2 days
  • medium used: Cellobiose agar

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
1287RUMINOCLOSTRIDIUM 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
1287CLOSTRIDIUM CELLULOVORANS MEDIUM (DSMZ Medium 320)yeshttps://mediadive.dsmz.de/medium/320Name: CLOSTRIDIUM CELLULOVORANS MEDIUM (DSMZ Medium 320) Composition: Cellobiose 5.0 g/l K2HPO4 x 3 H2O 1.0 g/l NH4Cl 1.0 g/l Na2CO3 1.0 g/l KCl 0.5 g/l MgSO4 x 7 H2O 0.5 g/l Trypticase peptone 0.5 g/l L-Cysteine HCl x H2O 0.15 g/l Na2S x 9 H2O 0.15 g/l Yeast extract 0.08 g/l HCl 0.0025 g/l FeCl2 x 4 H2O 0.0015 g/l Sodium resazurin 0.0005 g/l CoCl2 x 6 H2O 0.00019 g/l MnCl2 x 4 H2O 0.0001 g/l ZnCl2 7e-05 g/l Na2MoO4 x 2 H2O 3.6e-05 g/l NiCl2 x 6 H2O 2.4e-05 g/l H3BO3 6e-06 g/l CuCl2 x 2 H2O 2e-06 g/l Sludge Rumen fluid Distilled water
43428Cellobiose agaryes

culture temp

@refgrowthtypetemperaturerange
1287positivegrowth37mesophilic
43428positivegrowth20-40
43404positiveoptimum37mesophilic

culture pH

@refabilitytypepH
43428positivegrowth6.4-7.8
43428positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
1287anaerobe
43428obligate anaerobe
69480anaerobe99.617

spore formation

@refspore formationspore descriptionconfidence
43428yes
43404yeslocated either centrally or subterminally
69481yes93
69480yes100

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
4342822599arabinose-fermentation
4342822605arabinitol-fermentation
43428casein-hydrolysis
4340417057cellobiose+carbon source
4342817057cellobiose+fermentation
4340462968cellulose+carbon source
4342862968cellulose+fermentation
4342818276dihydrogen+fermentation
4342824996lactate-fermentation
4342824996lactate+fermentation
4342817113erythritol-fermentation
4340428757fructose+carbon source
4342828757fructose+fermentation
4340428260galactose+carbon source
4342828260galactose+fermentation
434285291gelatin-hydrolysis
4340417234glucose+carbon source
4342817234glucose+fermentation
4342817754glycerol-fermentation
4342817716lactose+fermentation
4342817306maltose+fermentation
4340437684mannose+carbon source
4342837684mannose+fermentation
434286731melezitose-fermentation
4340417309pectin+carbon source
4342817309pectin+fermentation
4342815361pyruvate-fermentation
4342826546rhamnose-fermentation
4342830911sorbitol-fermentation
4342828017starch-hydrolysis
4342817992sucrose+fermentation
4342816189sulfate-reduction
4342827082trehalose-fermentation
4340437166xylan+carbon source
4342837166xylan+fermentation
4342818222xylose-fermentation
43428yeast extract+required for growth

metabolite production

@refChebi-IDmetaboliteproduction
4342830089acetateyes
4342817968butyrateyes
4342816526carbon dioxideyes
4342818276dihydrogenyes
4342824996DL-lactateyes
4342816236ethanolyes
4342815740formateyes

enzymes

  • @ref: 43428
  • value: catalase
  • activity: -
  • ec: 1.11.1.6

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
1287methanogenic fermentation of hybrid poplar wood
43428a batch methanogenic fermentation of finely divided hybrid poplar woodInstitute of Gas Technology, ChicagoUSAUSANorth America

isolation source categories

Cat1Cat2Cat3
#Condition#Anoxic (anaerobic)
#Host#Plants
#Host Body Product#Plant#Timber

taxonmaps

  • @ref: 69479
  • File name: preview.99_83.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_34;96_68;97_71;98_76;99_83&stattab=map
  • Last taxonomy: Clostridium cellulovorans subclade
  • 16S sequence: X71849
  • Sequence Identity:
  • Total samples: 6435
  • soil counts: 3150
  • aquatic counts: 1721
  • animal counts: 1021
  • plant counts: 543

Safety information

risk assessment

  • @ref: 1287
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Corynebacterium matruchotii clone OCM003 16S ribosomal RNA gene, partial sequenceGU420836443ena43768
20218Clostridium cellulovorans 16S rRNA gene, strain DSM 3052X734381513ena573061
1287C.cellulovorans gene for 16S ribosomal RNAX718491506ena573061

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Clostridium cellulovorans 743BGCA_000145275completencbi573061
66792Clostridium cellulovorans 743BGCA_000180115scaffoldncbi573061
66792Clostridium cellulovorans 743B573061.5completepatric573061
66792Clostridium cellulovorans 743B (Prj:52819)573061.4wgspatric573061
66792Clostridium cellulovorans 743B, ATCC 35296648276630draftimg573061
66792Clostridium cellulovorans 743B, ATCC 35296648028016completeimg573061

GC content

@refGC-contentmethod
128726.0-27.0
4342826-27Buoyant density centrifugation (BD)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes93no
motileyes75.17yes
flagellatedyes88.574yes
gram-positiveyes76.606no
anaerobicyes96.287yes
aerobicno93.942yes
halophileno96.699no
spore-formingyes95.715yes
thermophileno97.261yes
glucose-utilyes89.067yes
glucose-fermentyes78.932yes

External links

@ref: 1287

culture collection no.: DSM 3052, ATCC 35296, OCM 3

straininfo link

  • @ref: 72101
  • straininfo: 40980

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Enzymology8982083Characterization of engF, a gene for a non-cellulosomal Clostridium cellulovorans endoglucanase.Sheweita SA, Ichi-ishi A, Park JS, Liu C, Malburg LM Jr, Doi RHGene10.1016/s0378-1119(96)00544-61996Amino Acid Sequence, Base Sequence, Binding Sites, Calcium/pharmacology, Cellulase/*chemistry, Cellulose/metabolism, Cloning, Molecular, Clostridium/*enzymology, Electrophoresis, Polyacrylamide Gel, Escherichia coli/genetics, Gene Expression/genetics, Genes, Bacterial/genetics, Molecular Sequence Data, Molecular Weight, Protein Sorting Signals/chemistry/genetics, Recombinant Proteins/chemistry/genetics/isolation & purification, Sequence Analysis, Sequence Homology, Substrate SpecificityGenetics
Phylogeny16346602Isolation and Characterization of an Anaerobic, Cellulolytic Bacterium, Clostridium cellulovorans sp. nov.Sleat R, Mah RA, Robinson RAppl Environ Microbiol10.1128/aem.48.1.88-93.19841984
Phylogeny30358527Clostridium composti sp. nov., a new anaerobic bacteria isolated from compost.Shin Y, Paek J, Son AY, Kim H, Kook JK, Paek WK, Chang YHInt J Syst Evol Microbiol10.1099/ijsem.0.0030742018Bacterial Typing Techniques, Base Composition, Clostridium/*classification/genetics/isolation & purification, *Composting, DNA, Bacterial/genetics, Fatty Acids/chemistry, Fermentation, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil MicrobiologyTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
1287Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 3052)https://www.dsmz.de/collection/catalogue/details/culture/DSM-3052
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
43404Yutaka Tamaru, Hideo Miyake, Kouichi Kuroda, Akihito Nakanishi, Yujiro Kawade, Kousuke Yamamoto, Masaaki Uemura, Yasuhiro Fujita, Roy H. Doi, Mitsuyoshi Ueda10.1128/JB.01450-09Genome Sequence of the Cellulosome-Producing Mesophilic Organism Clostridium cellulovorans 743BJ. Bacteriol. 192: 901-902 201019948806
43428Robert Sleat, Robert A. Mah, Ralph Robinsonhttp://aem.asm.org/content/48/1/88.short Isolation and Characterization of an Anaerobic, Cellulolytic Bacterium, Clostridium cellulovorans sp. nov.Appl. Environ. Microbiol. 48: 88-93 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)
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)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
72101Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID40980.1StrainInfo: A central database for resolving microbial strain identifiers