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 Kopecny, Kevin J. Shingfield, Frederic Boyer, Eric Coissac, Pierre Taberlet, R. John Wallace

*Corresponding author for this work

Research output: Contribution to journalArticle

37 Citations (Scopus)

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 degrees 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 <0.01) in eDNA samples. The qPCR indicated significantly higher amount of Firmicutes in iDNA sample frozen with glycerol (P <0.01). Deep sequencing analysis of iDNA samples revealed the prevalence of Bacteroidetes and similarity of samples frozen with and without cryoprotectants, which differed from sample stored with ethanol at room temperature. Centrifugation and consequent filtration of rumen fluid subjected to the eDNA isolation procedure considerably changed the ratio of molecular operational taxonomic units (MOTUs) of Bacteroidetes and Firmicutes. Intracellular DNA extraction using bead-beating method from cheesecloth sieved rumen content mixed with PBS-glycerol and stored at -80 degrees C was found as the optimal method to study ruminal bacterial profile. (C) 2013 Elsevier Ltd. All rights reserved.

Original languageEnglish
Pages (from-to)80-84
Number of pages5
JournalAnaerobe
Volume29
Early online date12 Oct 2013
DOIs
Publication statusPublished - Oct 2014

Keywords

  • intracellular DNA
  • extracellular DNA
  • storage conditions
  • rumen fluid
  • bacterial diversity
  • firmicutes
  • bacteroidetes
  • PCR-DGGE
  • Q-PCR
  • metabarcoding
  • microbial communities
  • nuclease activities
  • digesta
  • cryopreservation
  • diversity
  • inoculum
  • freeze
  • RNA

Cite this

Effect of DNA extraction and sample preservation method on rumen bacterial population. / Fliegerova, Katerina; Tapio, Ilma; Bonin, Aurelie; Mrazek, Jakub; Callegari, Maria Luisa; Bani, Paolo; Bayat, Alireza; Vilkki, Johanna; Kopecny, Jan; Shingfield, Kevin J.; Boyer, Frederic; Coissac, Eric; Taberlet, Pierre; Wallace, R. John.

In: Anaerobe, Vol. 29, 10.2014, p. 80-84.

Research output: Contribution to journalArticle

Fliegerova, K, Tapio, I, Bonin, A, Mrazek, J, Callegari, ML, Bani, P, Bayat, A, Vilkki, J, Kopecny, J, Shingfield, KJ, Boyer, F, Coissac, E, Taberlet, P & Wallace, RJ 2014, 'Effect of DNA extraction and sample preservation method on rumen bacterial population', Anaerobe, vol. 29, pp. 80-84. https://doi.org/10.1016/j.anaerobe.2013.09.015
Fliegerova K, Tapio I, Bonin A, Mrazek J, Callegari ML, Bani P et al. Effect of DNA extraction and sample preservation method on rumen bacterial population. Anaerobe. 2014 Oct;29:80-84. https://doi.org/10.1016/j.anaerobe.2013.09.015
Fliegerova, Katerina ; Tapio, Ilma ; Bonin, Aurelie ; Mrazek, Jakub ; Callegari, Maria Luisa ; Bani, Paolo ; Bayat, Alireza ; Vilkki, Johanna ; Kopecny, Jan ; Shingfield, Kevin J. ; Boyer, Frederic ; Coissac, Eric ; Taberlet, Pierre ; Wallace, R. John. / Effect of DNA extraction and sample preservation method on rumen bacterial population. In: Anaerobe. 2014 ; Vol. 29. pp. 80-84.
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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 degrees 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 <0.01) in eDNA samples. The qPCR indicated significantly higher amount of Firmicutes in iDNA sample frozen with glycerol (P <0.01). Deep sequencing analysis of iDNA samples revealed the prevalence of Bacteroidetes and similarity of samples frozen with and without cryoprotectants, which differed from sample stored with ethanol at room temperature. Centrifugation and consequent filtration of rumen fluid subjected to the eDNA isolation procedure considerably changed the ratio of molecular operational taxonomic units (MOTUs) of Bacteroidetes and Firmicutes. Intracellular DNA extraction using bead-beating method from cheesecloth sieved rumen content mixed with PBS-glycerol and stored at -80 degrees C was found as the optimal method to study ruminal bacterial profile. (C) 2013 Elsevier Ltd. All rights reserved.",
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AU - Fliegerova, Katerina

AU - Tapio, Ilma

AU - Bonin, Aurelie

AU - Mrazek, Jakub

AU - Callegari, Maria Luisa

AU - Bani, Paolo

AU - Bayat, Alireza

AU - Vilkki, Johanna

AU - Kopecny, Jan

AU - Shingfield, Kevin J.

AU - Boyer, Frederic

AU - Coissac, Eric

AU - Taberlet, Pierre

AU - Wallace, R. John

N1 - This work was supported by Ruminomics (project no. 289319 of EC's 7th Framework Programme: Food, Agriculture, Fisheries and Biotechnology)

PY - 2014/10

Y1 - 2014/10

N2 - 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 degrees 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 <0.01) in eDNA samples. The qPCR indicated significantly higher amount of Firmicutes in iDNA sample frozen with glycerol (P <0.01). Deep sequencing analysis of iDNA samples revealed the prevalence of Bacteroidetes and similarity of samples frozen with and without cryoprotectants, which differed from sample stored with ethanol at room temperature. Centrifugation and consequent filtration of rumen fluid subjected to the eDNA isolation procedure considerably changed the ratio of molecular operational taxonomic units (MOTUs) of Bacteroidetes and Firmicutes. Intracellular DNA extraction using bead-beating method from cheesecloth sieved rumen content mixed with PBS-glycerol and stored at -80 degrees C was found as the optimal method to study ruminal bacterial profile. (C) 2013 Elsevier Ltd. All rights reserved.

AB - 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 degrees 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 <0.01) in eDNA samples. The qPCR indicated significantly higher amount of Firmicutes in iDNA sample frozen with glycerol (P <0.01). Deep sequencing analysis of iDNA samples revealed the prevalence of Bacteroidetes and similarity of samples frozen with and without cryoprotectants, which differed from sample stored with ethanol at room temperature. Centrifugation and consequent filtration of rumen fluid subjected to the eDNA isolation procedure considerably changed the ratio of molecular operational taxonomic units (MOTUs) of Bacteroidetes and Firmicutes. Intracellular DNA extraction using bead-beating method from cheesecloth sieved rumen content mixed with PBS-glycerol and stored at -80 degrees C was found as the optimal method to study ruminal bacterial profile. (C) 2013 Elsevier Ltd. All rights reserved.

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KW - extracellular DNA

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KW - bacterial diversity

KW - firmicutes

KW - bacteroidetes

KW - PCR-DGGE

KW - Q-PCR

KW - metabarcoding

KW - microbial communities

KW - nuclease activities

KW - digesta

KW - cryopreservation

KW - diversity

KW - inoculum

KW - freeze

KW - RNA

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M3 - Article

VL - 29

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EP - 84

JO - Anaerobe

JF - Anaerobe

SN - 1075-9964

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