Strain identifier

BacDive ID: 2841

Type strain: Yes

Species: Clostridium phytofermentans

Strain Designation: ISDg

Strain history: <- T. Warnick, University of Massachusetts, Department of Microbiology, USA; ISDg

NCBI tax ID(s): 66219 (species)

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General

@ref: 7715

BacDive-ID: 2841

DSM-Number: 18823

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

description: Clostridium phytofermentans ISDg is an anaerobe, spore-forming, mesophilic bacterium that forms circular colonies and was isolated from forest soil.

NCBI tax id

  • NCBI tax id: 66219
  • Matching level: species

strain history

  • @ref: 7715
  • history: <- T. Warnick, University of Massachusetts, Department of Microbiology, USA; ISDg

doi: 10.13145/bacdive2841.20230509.8.1

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 phytofermentans
  • full scientific name: Clostridium phytofermentans Warnick et al. 2002

  • synonyms

    • @ref: 20215
    • synonym: Lachnoclostridium phytofermentans

@ref: 7715

domain: Bacteria

phylum: Firmicutes

class: Clostridia

order: Clostridiales

family: Clostridiaceae

genus: Clostridium

species: Clostridium phytofermentans

full scientific name: Clostridium phytofermentans Warnick et al. 2002

strain designation: ISDg

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
43383negative3-15 µm0.5-0.8 µmrod-shapedyes
69480yes92.823
69480positive100

colony morphology

  • @ref: 43383
  • colony size: 2-5 mm
  • colony color: translucent
  • colony shape: circular
  • incubation period: 7 days
  • medium used: GS-2CB agar medium

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7715RUMINOCLOSTRIDIUM 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
43383GS-2CB agar mediumyes

culture temp

@refgrowthtypetemperaturerange
7715positivegrowth30mesophilic
43383positiveoptimum37mesophilic
43383nogrowth45thermophilic
43383nogrowth5psychrophilic
43383positivegrowth42thermophilic
43383positivegrowth15psychrophilic

culture pH

@refabilitytypepHPH range
43383positivegrowth6-9alkaliphile
43383nogrowth5.5
43383positiveoptimum8-8.5

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
7715anaerobe
43383obligate anaerobe
69480anaerobe99.999

spore formation

@refspore descriptiontype of sporespore formationconfidence
43383round, terminal, caused swelling of the cellendosporeyes
69481yes100
69480yes99.447

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
4338322599arabinose+fermentation
4338317057cellobiose+fermentation
4338362968cellulose+fermentation
433834853esculin-hydrolysis
4338328757fructose+fermentation
4338328260galactose+fermentation
4338328066gentiobiose+fermentation
4338317234glucose+fermentation
4338317716lactose+fermentation
4338317306maltose+fermentation
4338337684mannose+fermentation
4338317632nitrate-reduction
4338317309pectin+fermentation
4338362969polygalacturonic acid+fermentation
4338333942ribose+fermentation
4338328017starch+fermentation
4338316189sulfate-reduction
4338337166xylan+fermentation
4338318222xylose+fermentation

antibiotic resistance

@refChEBImetaboliteis antibioticis resistant
433836104kanamycinyesyes
4338317076streptomycinyesyes

enzymes

  • @ref: 43383
  • value: urease
  • activity: +/-
  • ec: 3.5.1.5

Isolation, sampling and environmental information

isolation

  • @ref: 7715
  • sample type: forest soil
  • geographic location: Massachusetts, near Quabin Reservoir
  • country: USA
  • origin.country: USA
  • continent: North America

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Forest
#Environmental#Terrestrial#Soil

Safety information

risk assessment

  • @ref: 7715
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 7715
  • description: Clostridium phytofermentans strain ISDg 16S ribosomal RNA gene, partial sequence
  • accession: AF020431
  • length: 1371
  • database: ena
  • NCBI tax ID: 357809

Genome sequences

  • @ref: 66792
  • description: Clostridium phytofermentans ISDg
  • accession: 357809.8
  • assembly level: complete
  • database: patric
  • NCBI tax ID: 357809

GC content

  • @ref: 7715
  • GC-content: 35.9
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
gram-positiveyes51.37yes
anaerobicyes97.442yes
halophileno89.473no
spore-formingyes95.394yes
glucose-utilyes89.523no
motileyes85.32yes
flagellatedno59.609no
thermophileno97.902no
aerobicno97.664yes
glucose-fermentyes66.884no

External links

@ref: 7715

culture collection no.: DSM 18823, ATCC 700394

straininfo link

  • @ref: 72365
  • straininfo: 87699

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny12148621Clostridium phytofermentans sp. nov., a cellulolytic mesophile from forest soil.Warnick TA, Methe BA, Leschine SBInt J Syst Evol Microbiol10.1099/00207713-52-4-11552002Bacterial Typing Techniques, Cellulose/*metabolism, Clostridium/*classification/genetics/metabolism/physiology, DNA, Ribosomal/analysis, Ethanol/metabolism, Fermentation, Genotype, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, *TreesGenetics
Metabolism21280028Consolidated bioprocessing (CBP) performance of Clostridium phytofermentans on AFEX-treated corn stover for ethanol production.Jin M, Balan V, Gunawan C, Dale BEBiotechnol Bioeng10.1002/bit.230592011Clostridium/*metabolism, Ethanol/*metabolism, Fermentation, Glucans/metabolism, Hydrolysis, Industrial Microbiology/*methods, Saccharomyces cerevisiae/metabolism, Zea mays/*metabolismBiotechnology
Metabolism22359098Consolidated bioprocessing (CBP) of AFEX-pretreated corn stover for ethanol production using Clostridium phytofermentans at a high solids loading.Jin M, Gunawan C, Balan V, Dale BEBiotechnol Bioeng10.1002/bit.244582012Acetates/metabolism, Biotechnology/*methods, Clostridium/*growth & development/*metabolism, Ethanol/*metabolism, Fermentation, Glucans/metabolism, Zea mays/*metabolismBiotechnology
Metabolism26637592Direct Image-Based Enumeration of Clostridium phytofermentans Cells on Insoluble Plant Biomass Growth Substrates.Alvelo-Maurosa JG, Lee SJ, Hazen SP, Leschine SBAppl Environ Microbiol10.1128/AEM.03119-152015Benzenesulfonates, Biomass, Clostridium/*growth & development/*metabolism, Colony Count, Microbial/instrumentation/methods, Edible Grain/metabolism, Ethanol/metabolism, Fermentation, Fluorescent Dyes, Image Processing, Computer-Assisted/*methods, Lignin/metabolism, Mutation, Plant Development, Sorghum/genetics/metabolism

Reference

@idauthorscataloguedoi/urltitlejournal
7715Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18823)https://www.dsmz.de/collection/catalogue/details/culture/DSM-18823
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
43383Thomas A. Warnick, Barbara A. Methe, Susan B. Leschine10.1099/ijs.0.02125-0Clostridium phytofermentans sp. nov., a cellulolytic mesophile from forest soilIJSEM 52: 1155-1160 2002
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)
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
72365Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID87699.1StrainInfo: A central database for resolving microbial strain identifiers