Strain identifier

BacDive ID: 2817

Type strain: Yes

Species: Clostridium carboxidivorans

Strain Designation: P7

Strain history: <- R. S. Tanner, Department of Botany and Microbiology, University of Oklahoma, Norman, USA; P7 <- R. Laopaiboon {1999}

NCBI tax ID(s): 217159 (species)

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General

@ref: 17478

BacDive-ID: 2817

DSM-Number: 15243

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

description: Clostridium carboxidivorans P7 is an anaerobe, spore-forming, mesophilic bacterium that was isolated from agricultural lagoon.

NCBI tax id

  • NCBI tax id: 217159
  • Matching level: species

strain history

  • @ref: 17478
  • history: <- R. S. Tanner, Department of Botany and Microbiology, University of Oklahoma, Norman, USA; P7 <- R. Laopaiboon {1999}

doi: 10.13145/bacdive2817.20230509.8.1

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 carboxidivorans
  • full scientific name: Clostridium carboxidivorans Liou et al. 2005

@ref: 17478

domain: Bacteria

phylum: Firmicutes

class: Clostridia

order: Clostridiales

family: Clostridiaceae

genus: Clostridium

species: Clostridium carboxidivorans

full scientific name: Clostridium carboxidivorans Liou et al. 2005

strain designation: P7

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityflagellum arrangementconfidence
43392positive3 µm0.5 µmrod-shapedyesperitrichous
69480yes93.646
69480positive99.998

colony morphology

  • @ref: 43392
  • colony size: 2-4 mm
  • colony color: white and opaque
  • incubation period: 7-14 days
  • medium used: Acetogen medium

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
17478PY + X MEDIUM (N2/CO2) (DSMZ Medium 104c)yeshttps://mediadive.dsmz.de/medium/104cName: PY + X MEDIUM (N2/CO2) (DSMZ Medium 104c) Composition: Yeast extract 10.0 g/l D-Glucose 5.0 g/l Trypticase peptone 5.0 g/l Meat peptone 5.0 g/l Na2CO3 1.0 g/l L-Cysteine HCl x H2O 0.5 g/l NaHCO3 0.4 g/l NaCl 0.08 g/l KH2PO4 0.04 g/l K2HPO4 0.04 g/l MgSO4 x 7 H2O 0.02 g/l CaCl2 x 2 H2O 0.01 g/l Sodium resazurin 0.0005 g/l Distilled water
43392Acetogen mediumyes

culture temp

@refgrowthtypetemperaturerange
17478positivegrowth35mesophilic
43392positiveoptimum38mesophilic

culture pH

  • @ref: 43392
  • ability: positive
  • type: optimum
  • pH: 6.2

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
17478anaerobe
43392anaerobe
69480anaerobe99.444

spore formation

@refspore descriptiontype of sporespore formationconfidence
43392subterminal or terminal with light cell swellingsporeyes
69481yes100
69480yes100

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
4339216449alanine+growth
4339227613amygdalin-growth
4339229016arginine-growth
4339222653asparagine+growth
4339235391aspartate+growth
4339217750betaine+growth
4339228885butanol+growth
4339216526carbon dioxide+growth
4339217245carbon monoxide+growth
43392casamino acids+growth
4339217057cellobiose+growth
4339262968cellulose+growth
4339215354choline+growth
4339216947citrate+growth
4339217108D-arabinose-growth
4339218276dihydrogen+growth
4339224996lactate-growth
4339225115malate-growth
433924853esculin-hydrolysis
4339216236ethanol+growth
4339228757fructose+growth
4339233984fucose-growth
4339228260galactose+growth
433925291gelatin-hydrolysis
4339224265gluconate-growth
4339217234glucose+growth
4339229987glutamate+growth
4339217754glycerol+growth
4339227570histidine+growth
4339217268myo-inositol+growth
4339230849L-arabinose+growth
4339217716lactose-growth
4339217306maltose-growth
4339229864mannitol+growth
4339237684mannose+growth
433926731melezitose+growth
4339228053melibiose-growth
4339217790methanol-growth
4339217632nitrate-reduction
4339217309pectin+growth
4339228831propanol+growth
4339216634raffinose-growth
4339226546rhamnose+growth
4339233942ribose+growth
4339217822serine+growth
4339230911sorbitol-growth
4339228017starch+growth
4339230031succinate-growth
4339217992sucrose+growth
43392132111syringate+growth
4339227082trehalose+growth
4339218222xylose+growth

metabolite production

@refChebi-IDmetaboliteproduction
4339230089acetateyes
4339228885butanolyes
4339217968butyrateyes
4339216236ethanolyes
4339235581indoleno

enzymes

@refvalueactivityec
43392catalase-1.11.1.6
43392cytochrome oxidase-1.9.3.1
43392urease-3.5.1.5

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
17478agricultural lagoonOklahomaUSAUSANorth America
43392an agricultural settling lagoonOklahomaUSAUSANorth America

isolation source categories

Cat1Cat2
#Environmental#Aquatic
#Engineered#Agriculture

taxonmaps

  • @ref: 69479
  • File name: preview.99_3450.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_34;96_1801;97_2159;98_2649;99_3450&stattab=map
  • Last taxonomy: Clostridium
  • 16S sequence: FR733710
  • Sequence Identity:
  • Total samples: 12042
  • soil counts: 5169
  • aquatic counts: 4051
  • animal counts: 2029
  • plant counts: 793

Safety information

risk assessment

  • @ref: 17478
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessiondatabaselengthNCBI tax ID
4339216S rRNA gene sequenceAY170379nuccore
17478Clostridium carboxidivorans partial 16S rRNA gene, type strain DSM15243TFR733710ena1499217159

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Clostridium carboxidivorans P7GCA_001038625completencbi536227
66792Clostridium carboxidivorans P7GCA_000175595contigncbi536227
66792Clostridium carboxidivorans P7GCA_000163855scaffoldncbi536227
66792Clostridium carboxidivorans P7536227.3wgspatric536227
66792Clostridium carboxidivorans P7536227.16plasmidpatric536227
66792Clostridium carboxidivorans P7536227.17plasmidpatric536227
66792Clostridium carboxidivorans P7536227.13completepatric536227
66792Clostridium carboxidivorans P7645058736draftimg536227
66792Clostridium carboxidivorans P7647533125draftimg536227
66792Clostridium carboxidivorans P72654588030completeimg536227

GC content

  • @ref: 17478
  • GC-content: 31-32
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileyes85.144yes
flagellatedyes52.164no
gram-positiveno50.735no
anaerobicyes97.654yes
aerobicno98.033yes
halophileno96.887no
spore-formingyes95.886yes
glucose-utilyes90.437yes
thermophileno97.432yes
glucose-fermentyes65.515no

External links

@ref: 17478

culture collection no.: DSM 15243, ATCC BAA 624, KCTC 15178

straininfo link

  • @ref: 72342
  • straininfo: 265596

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny16166714Clostridium carboxidivorans sp. nov., a solvent-producing clostridium isolated from an agricultural settling lagoon, and reclassification of the acetogen Clostridium scatologenes strain SL1 as Clostridium drakei sp. nov.Liou JS, Balkwill DL, Drake GR, Tanner RSInt J Syst Evol Microbiol10.1099/ijs.0.63482-02005Acetic Acid/*metabolism, *Agriculture, Bacterial Typing Techniques, Carbon Monoxide/*metabolism, Clostridium/*classification/genetics/growth & development/isolation & purification, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Genes, rRNA, Geologic Sediments/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Solvents/*metabolism, *Water MicrobiologyMetabolism
Phylogeny35353674Clostridium muellerianum sp. nov., a carbon monoxide-oxidizing acetogen isolated from old hay.Doyle DA, Smith PR, Lawson PA, Tanner RSInt J Syst Evol Microbiol10.1099/ijsem.0.0052972022Bacterial Typing Techniques, Base Composition, *Carbon Monoxide, Clostridium, DNA, Bacterial/genetics, *Fatty Acids/chemistry, Oxidation-Reduction, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNATranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
17478Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15243)https://www.dsmz.de/collection/catalogue/details/culture/DSM-15243
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
43392Jack S.-C. Liou, David L. Balkwill, Gwendolyn R. Drake, Ralph S. Tanner10.1099/ijs.0.63482-0Clostridium carboxidivorans sp. nov., a solvent-producing clostridium isolated from an agricultural settling lagoon, and reclassification of the acetogen Clostridium scatologenes strain SL1 as Clostridium drakei sp. nov.IJSEM 55: 2085-2091 200516166714
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
72342Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID265596.1StrainInfo: A central database for resolving microbial strain identifiers