Relative abundance of individual methanogen and Succinivibrionaceae OTUs in group R and group A.

<p>Relative abundance of OTUs identified as family Succinivibrionaceae, kingdom Archaea or class Thermoplasmata (recently reclassified as members of the order Methanomassiliicoccales) in individual liquid (L) and solid (S) rumen samples from groups R and A are shown. Different colours represent different OTU numbers. Taxonomic assignments for all OTU numbers are given in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0133234#pone.0133234.s001" target="_blank">S1 Table</a>.</p

Relative abundances of OTUs S3004, M7 and M10 and total archaea.

<p>LR = Liquid Restricted (n = 14), SR = Solid Restricted (n = 14), LA = Liquid <i>Ad lib</i> (n = 13), SA = Solid <i>Ad lib</i> (n = 13), LRA = Liquid Restricted/<i>Ad lib</i> (n = 15), SRA = Solid Restricted/<i>Ad lib</i> (n = 15), LAA = Liquid <i>Ad lib</i>/<i>Ad lib</i> (n = 13), SAA = Solid <i>Ad lib</i>/<i>Ad lib</i> (n = 13). FDR = BH-corrected P values from Wilcoxon pairwise comparisons of relative abundances between different treatment groups.</p

Correlation analysis of OTU-M7 and OTU-M10 with OTU-S3004.

<p>Scatter plot analysis of percentage relative abundances (% rel. ab.), in all liquid and solid fraction samples, of OTU-M7 (<i>Methanobrevibacter gottschalkii</i> clade) and OTU-M10 (<i>Methanobrevibacter ruminantium</i> clade) plotted against OTU-S3004. Power regression (blue dashed line) showed the highest R² values (shown on each scatter plot) in all comparisons apart from OTU-M10 (liquid) vs. OTU-S3004 (liquid) for which a polynomial regression showed the highest R² value.</p

Spearman correlation analysis between OTU M7and OTUs showing the largest (top 20) changes in relative abundance between rumen solid of group R and group A.

<p>FDR = False discovery rate of change in relative abundance between group R and group A. SR average = average % relative abundance in the solid fraction of group R. SA average = average % relative abundance in the solid fraction of group A. SR-SA = SA average subtracted from SR average. Spearman <i>ρ</i> and Spearman P with M7 = Spearman’s rank correlation coefficient with relative abundance of OTU-M7 and corresponding P value. NS = non-significant (i.e. P > 0.05).</p><p>Spearman correlation analysis between OTU M7and OTUs showing the largest (top 20) changes in relative abundance between rumen solid of group R and group A.</p

Spearman correlation analysis between OTU M7and OTUs showing the largest (top 20) changes in relative abundance between rumen liquid of group R and group A.

<p>FDR = False discovery rate of change in relative abundance between group R and group A. LR average = average % relative abundance in the liquid fraction of group R. LA average = average % relative abundance in the liquid fraction of group A. LR-LA = LA average subtracted from LR average. Spearman <i>ρ</i> and Spearman P with M7 = Spearman’s rank correlation coefficient with relative abundance of OTU-M7 and corresponding P value. NS = non-significant (i.e. P > 0.05).</p><p>Spearman correlation analysis between OTU M7and OTUs showing the largest (top 20) changes in relative abundance between rumen liquid of group R and group A.</p

Scheme of compensatory growth animal model.

<p>Scheme of compensatory growth animal model.</p

Acetate:Propionate (A:P) ratios in rumen samples from all groups.

<p>Group R (n = 14), A (n = 13), RA (n = 15) and AA (n = 13). Box and whisker plot showing median, quartiles, maximum and minimum values. FDR = BH-corrected P values derived from Wilcoxon pairwise comparisons of A:P ratios between different treatment groups.</p