Consensus dendrogram illustrating the similarity of microbial communities obtained using different DNA extraction methods.

<p>For each rumen sample and microbial group, a matrix of pair-wise Pearson similarities was constructed, tabulating the similarity of the community structure determined using each different DNA extraction method with the structure determined using DNA from every other method. These matrices were converted to distances to produce six matrices (bacterial genera [sheep and cow], archaeal mixed taxonomic ranks [sheep and cow], ciliate protozoal genera [cow only], and fungal subgenera [cow only]), which were used to generate six trees using the UPGMA algorithm [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0074787#B23" target="_blank">23</a>], from which a consensus tree was formed using the CONSENSE program in PHYLIP [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0074787#B23" target="_blank">23</a>]. The scale bar represents 1% community difference.