Effect of DNA extraction and sample preservation method on rumen bacterial population

Katerina Fliegerova, Ilma Tapio, Aurelie Bonin, Jakub Mrazek, Maria Luisa Callegari, Paolo Bani, Alireza Bayat, Johanna Vilkki, Jan Kopečný, Kevin J Shingfield, Frederic Boyer, Eric Coissac, Pierre Taberlet, R. John Wallace

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61 Citations (SciVal)
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Abstract

The comparison of the bacterial profile of intracellular (iDNA) and extracellular DNA (eDNA) isolated from cow rumen content stored under different conditions was conducted. The influence of rumen fluid treatment (cheesecloth squeezed, centrifuged, filtered), storage temperature (RT, -80 °C) and cryoprotectants (PBS-glycerol, ethanol) on quality and quantity parameters of extracted DNA was evaluated by bacterial DGGE analysis, real-time PCR quantification and metabarcoding approach using high-throughput sequencing. Samples clustered according to the type of extracted DNA due to considerable differences between iDNA and eDNA bacterial profiles, while storage temperature and cryoprotectants additives had little effect on sample clustering. The numbers of Firmicutes and Bacteroidetes were lower (P 
Original languageEnglish
Pages (from-to)80-84
Number of pages5
JournalAnaerobe
Volume29
DOIs
Publication statusPublished - 12 Oct 2013
Event8th International Symposium on Anaerobic Microbiology (ISAM 8): No oxygen - still vigorous - Innsbruck, Austria
Duration: 12 Jun 201315 Jun 2013

Keywords

  • Intracellular DNA
  • Extracellular DNA
  • Storage conditions
  • Rumen fluid
  • Bacterial diversity
  • Firmicutes
  • Bacteroidetes
  • PCR-DGGE
  • Q-PCR
  • Metabarcoding

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