Strain identifier

BacDive ID: 6375

Type strain: Yes

Species: Cellulosilyticum lentocellum

Strain Designation: RHM5

Strain history: <- DSM <- NCIMB <- RH Madden, RHM5

NCBI tax ID(s): 642492 (strain), 29360 (species)

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General

@ref: 2163

BacDive-ID: 6375

DSM-Number: 5427

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

description: Cellulosilyticum lentocellum RHM5 is an anaerobe, spore-forming, mesophilic bacterium that was isolated from river sediment with paper mill waste.

NCBI tax id

NCBI tax idMatching level
29360species
642492strain

strain history

@refhistory
2163<- NCIMB <- R.H. Madden, RHM5
67771<- DSM <- NCIMB <- RH Madden, RHM5

doi: 10.13145/bacdive6375.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Clostridia
  • order: Eubacteriales
  • family: Lachnospiraceae
  • genus: Cellulosilyticum
  • species: Cellulosilyticum lentocellum
  • full scientific name: Cellulosilyticum lentocellum (Murray et al. 1987) Cai and Dong 2010

  • synonyms

    • @ref: 20215
    • synonym: Clostridium lentocellum

@ref: 2163

domain: Bacteria

phylum: Firmicutes

class: Clostridia

order: Clostridiales

family: Lachnospiraceae

genus: Cellulosilyticum

species: Cellulosilyticum lentocellum

full scientific name: Cellulosilyticum lentocellum (Murray et al. 1987) Cai and Dong 2010

strain designation: RHM5

type strain: yes

Morphology

cell morphology

@refcell shapemotilitygram stainconfidence
67771rod-shapedyes
67771curved-shaped
67771negative
69480positive100

Culture and growth conditions

culture medium

  • @ref: 2163
  • name: RUMINOCLOSTRIDIUM CELLULOLYTICUM (CM3) MEDIUM (DSMZ Medium 520)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/520
  • composition: Name: 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

culture temp

@refgrowthtypetemperaturerange
2163positivegrowth30mesophilic
67771positivegrowth25mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
2163anaerobe
67771anaerobe
69480anaerobe99.596

spore formation

@reftype of sporespore formationconfidence
67771sporeyes
69480yes95.634

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
2163river sediment with paper mill wasteScotland, Aberdeen, River DonUnited KingdomGBREurope
67771From river sediment with paper mill wasteRiver Don, Aberdeen, ScotlandUnited KingdomGBREurope

isolation source categories

Cat1Cat2Cat3
#Engineered#Industrial
#Engineered#Waste
#Environmental#Aquatic#River (Creek)
#Environmental#Aquatic#Sediment

Safety information

risk assessment

  • @ref: 2163
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218C.lentocellum gene for 16S ribosomal RNAX718511508ena642492
20218Clostridium lentocellum 16S rRNA gene, strain DSM 5427X761621459ena642492

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Cellulosilyticum lentocellum DSM 5427GCA_000178835completencbi642492
66792Clostridium lentocellum DSM 5427642492.3wgspatric642492
66792Cellulosilyticum lentocellum RHM5, DSM 5427650716026completeimg642492

GC content

@refGC-contentmethod
216334.0sequence analysis
6777136.0genome sequence analysis
6777134.0

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes85no
motileyes84.636yes
flagellatedyes70.51no
gram-positiveyes53.182yes
anaerobicyes97.32yes
aerobicno97.257yes
halophileno86.989no
spore-formingyes96.37yes
thermophileno99.313yes
glucose-utilyes84.208no
glucose-fermentyes70.868no

External links

@ref: 2163

culture collection no.: DSM 5427, ATCC 49066, KCTC 15127, NCIMB 11756, NCIB 11756

straininfo link

  • @ref: 75848
  • straininfo: 46088

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19661493Cellulosilyticum ruminicola gen. nov., sp. nov., isolated from the rumen of yak, and reclassification of Clostridium lentocellum as Cellulosilyticum lentocellum comb. nov.Cai S, Dong XInt J Syst Evol Microbiol10.1099/ijs.0.014712-02009Animals, Bacterial Typing Techniques, Base Composition, Cattle/*microbiology, Cellulose/metabolism, Clostridium/*classification/genetics/physiology, DNA, Ribosomal/analysis/genetics, Fatty Acids/analysis, Genes, rRNA, Genotype, Gram-Negative Bacteria/*classification/genetics/*isolation & purification/physiology, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Rumen/*microbiology, Sequence Analysis, DNA, Species SpecificityGenetics
Genetics21398547Complete genome sequence of the cellulose-degrading bacterium Cellulosilyticum lentocellum.Miller DA, Suen G, Bruce D, Copeland A, Cheng JF, Detter C, Goodwin LA, Han CS, Hauser LJ, Land ML, Lapidus A, Lucas S, Meincke L, Pitluck S, Tapia R, Teshima H, Woyke T, Fox BG, Angert ER, Currie CRJ Bacteriol10.1128/JB.00239-112011Cellulose/chemistry/*metabolism, *Genome, Bacterial, Geologic Sediments/microbiology, Gram-Positive Endospore-Forming Rods/*classification/*genetics, Industrial Waste, Molecular Sequence Annotation, Molecular Sequence Data, Paper, RNA, Bacterial/genetics, Rivers, Waste Disposal, Fluid, Water Pollutants, ChemicalMetabolism

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
2163Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 5427)https://www.dsmz.de/collection/catalogue/details/culture/DSM-5427
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
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
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)
75848Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID46088.1StrainInfo: A central database for resolving microbial strain identifiers