Strain identifier

BacDive ID: 2567

Type strain: Yes

Species: Ruminiclostridium cellobioparum

Strain Designation: Cc

Strain history: ATCC 15832 <-- L. V. Holdeman VIP 3359 <-- L. S. McClung and R. H. McBee <-- R. E. Hungate strain Cc.

NCBI tax ID(s): 29355 (species)

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General

@ref: 637

BacDive-ID: 2567

DSM-Number: 1351

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

description: Ruminiclostridium cellobioparum Cc is an anaerobe, spore-forming, mesophilic bacterium that was isolated from bovine rumen.

NCBI tax id

  • NCBI tax id: 29355
  • Matching level: species

strain history

@refhistory
637<- R. E. Hungate, University of California, Davis; Cc
67770ATCC 15832 <-- L. V. Holdeman VIP 3359 <-- L. S. McClung and R. H. McBee <-- R. E. Hungate strain Cc.

doi: 10.13145/bacdive2567.20230509.8.1

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
  • full scientific name: Ruminiclostridium cellobioparum (Hungate 1944) Zhang et al. 2018

  • synonyms

    • @ref: 20215
    • synonym: Clostridium cellobioparum

@ref: 637

domain: Bacteria

phylum: Firmicutes

class: Clostridia

order: Clostridiales

family: Oscillospiraceae

genus: Ruminiclostridium

species: Ruminiclostridium cellobioparum subsp. cellobioparum

full scientific name: Ruminiclostridium cellobioparum subsp. cellobioparum (Hungate 1944) Zhang et al. 2018

strain designation: Cc

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
66689variable1.4-3.3 µm0.5-0.6 µmrod-shapedyes
69480yes92.817
69480positive100

Culture and growth conditions

culture medium

  • @ref: 637
  • name: RUMINICLOSTRIDIUM MEDIUM (DSMZ Medium 140)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/140
  • composition: Name: RUMINICLOSTRIDIUM MEDIUM (DSMZ Medium 140) Composition: Cellobiose 5.0 g/l Na2CO3 2.5 g/l Yeast extract 1.2 g/l NaCl 1.0 g/l K2HPO4 0.5 g/l (NH4)2SO4 0.5 g/l KH2PO4 0.5 g/l L-Cysteine HCl x H2O 0.25 g/l Na2S x 9 H2O 0.25 g/l CaCl2 x 2 H2O 0.1 g/l MgSO4 x 7 H2O 0.1 g/l Sodium resazurin 0.0005 g/l Sludge Rumen fluid Distilled water

culture temp

@refgrowthtypetemperaturerange
637positivegrowth37mesophilic
66689positivegrowth25-45
66689positiveoptimum30-37mesophilic
67770positivegrowth37mesophilic

culture pH

@refabilitytypepH
66689positivegrowth5-8.2
66689positiveoptimum7-7.5

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
637anaerobe
66689obligate anaerobe
69480anaerobe98.65

spore formation

@refspore descriptiontype of sporespore formationconfidence
66689peritrichous, oval spores swelling the cell.sporeyes
69481yes100
69480yes100

observation

  • @ref: 66689
  • observation: End products of fermentation are acetate, ethanol, H2 and CO2 . No growth factors are required, but addition of rumen fluids, yeast extract, biotrypcase or vitamins stimulates growth.

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6668916634raffinose-assimilation
6668917992sucrose-assimilation
6668917057cellobiose+assimilation
6668917716lactose+assimilation
6668918222xylose+assimilation
6668928260galactose+assimilation
6668928757fructose+assimilation
6668937684mannose+assimilation
6668962968cellulose+assimilation

Isolation, sampling and environmental information

isolation

@refsample type
637bovine rumen
66689mixture of bovine rumen and human faeces
67770Bovine rumen

isolation source categories

Cat1Cat2Cat3
#Host#Mammals#Bovinae (Cow, Cattle)
#Host Body-Site#Organ#Rumen

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: X71856
  • Sequence Identity:
  • Total samples: 1202
  • soil counts: 819
  • aquatic counts: 189
  • animal counts: 126
  • plant counts: 68

Safety information

risk assessment

  • @ref: 637
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Clostridium cellobioparum gene for 16S ribosomal RNA, partial sequence, strain: JCM 1422AB6270301484ena1121303
637C.cellobioparum gene for 16S ribosomal RNAX718561510ena1121303

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792[Clostridium] cellobioparum DSM 1351 = ATCC 158321121303.3wgspatric1121303
66792Clostridium cellobioparum ATCC 158322556921656draftimg1121303
67770Ruminiclostridium cellobioparum DSM 1351 = ATCC 15832GCA_000621505scaffoldncbi1121303

GC content

@refGC-contentmethod
63741.0sequence analysis
6668941genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileyes84.936no
flagellatedyes50.823no
gram-positiveno65.854yes
anaerobicyes97.698no
aerobicno97.327no
halophileno97.503no
spore-formingyes95.368yes
thermophileno89.403yes
glucose-utilyes91.464no
glucose-fermentyes60.303no

External links

@ref: 637

culture collection no.: DSM 1351, ATCC 15832, NCIMB 10669, JCM 1422, LMG 5589, BCRC 14495, KCTC 15225, KCTC 3044, VPI 3359

straininfo link

  • @ref: 72100
  • straininfo: 1955

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
637Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 1351)https://www.dsmz.de/collection/catalogue/details/culture/DSM-1351
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
66689Xue Zhang, Bo Tu, Li-rong Dai, Paul A. Lawson, Zhen-zhen Zheng, Lai-Yan Liu, Yu Deng, Hui Zhang, Lei Cheng10.1099/ijsem.0.002966Petroclostridium xylanilyticum gen. nov., sp. nov., a xylan-degrading bacterium isolated from an oilfield, and reclassification of clostridial cluster III members into four novel genera in a new Hungateiclostridiaceae fam. nov.IJSEM 68: 3197-3211 201830124399
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)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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
72100Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID1955.1StrainInfo: A central database for resolving microbial strain identifiers