High-yield and phylogenetically robust methods of DNA recovery for analysis of microbial biofilms adherent to plant biomass in the herbivore gut

Rosewarne, Carly P., Pope, Phillip B., Denman, Stuart E., McSweeney, Christopher S., O'Cuiv, Paraic and Morrison, Mark (2011) High-yield and phylogenetically robust methods of DNA recovery for analysis of microbial biofilms adherent to plant biomass in the herbivore gut. Microbial Ecology, 61 2: 448-454. doi:10.1007/s00248-010-9745-z


Author Rosewarne, Carly P.
Pope, Phillip B.
Denman, Stuart E.
McSweeney, Christopher S.
O'Cuiv, Paraic
Morrison, Mark
Title High-yield and phylogenetically robust methods of DNA recovery for analysis of microbial biofilms adherent to plant biomass in the herbivore gut
Journal name Microbial Ecology   Check publisher's open access policy
ISSN 0095-3628
1432-184X
Publication date 2011-02-01
Sub-type Article (original research)
DOI 10.1007/s00248-010-9745-z
Volume 61
Issue 2
Start page 448
End page 454
Total pages 7
Place of publication New York, United States
Publisher Springer
Language eng
Formatted abstract
Recent studies have shown the microbial biofilms adherent to plant biomass in the gastrointestinal tracts of humans and other herbivores are quite different to planktonic populations. If these biofilm communities are to be properly characterized by metagenomics methods, then the microbial desorption methods used must ensure the phylogenetic diversity and genetic potential recovered is biologically valid. To that end, we describe here two different methods for desorbing microbes tightly adherent to plant biomass; and used PCR-DGGE analyses of the Bacteria and Archaea rrs genes to show both these desorption methods were effective in recovering the adherent microbial biofilm with no apparent biases in microbe recovery. We also present a derivation of the "repeated bead beating and column (RBB+C) purification" method of DNA extraction that results in the recovery of high molecular weight DNA. These DNA samples can be fragmented and size fractionated by sucrose density gradient centrifugation, bypassing the use of gel-plug lysis and pulsed-field gel electrophoresis separation of DNA for metagenomic library constructions.
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status Non-UQ

Document type: Journal Article
Sub-type: Article (original research)
Collection: UQ Diamantina Institute Publications
 
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