OTUs which showed significant differences when different extraction methods were employed.

a<p>The P value was calculated in QIIME (see methods).</p>b<p>the average percentage of reads for each primer pair (n=2) in the OTU compared to the total number of filtered reads in the samples.</p

Summary of the reads obtained under different experimental conditions.

<p>The table shows the total number of reads, the number remaining after filtering and the % of non-specific reads (those not aligning to 16S) and chimeras (see methods for chimera detection) present when different annealing temperatures, primer pairs and extraction procedures were employed. The figures show the combined results of two replications.</p>a<p>Average of the two replications.</p

OTUs which showed correlation with annealing temperature.

a<p>The P value was calculated in QIIME (see methods).</p>b<p>Pearson's r value with −1 or +1 indicating a perfect negative or positive correlation respectively and 0 indicating no correlation.</p>c<p>the average percentage of reads for each annealing temperature (n=2) in the OTU compared to the total number of filtered reads in the samples.</p

PCA visualization of the differences between the observed bacterial communities as judged by pyrosequencing generated by different experimental procedures.

<p>(a) Different primer pairs (b) Different annealing temperatures (c) Different extraction procedures.</p

Hierarchical clustering visualizing the similarity of the bacterial communities as judged by pyrosequencing using different experimental procedures.

<p>All bootstrap values greater than 90% are displayed on branch lines. (a) Different primer pairs (b) Different annealing temperatures (c) Different extraction procedures.</p

OTUs which differed significantly when different primer pairs were employed in the PCR.

a<p>The P value was calculated in QIIME (see methods).</p>b<p>values show the average percentage of reads for each primer pair (n=2) in the OTU compared to the total number of filtered reads in the sample.</p

Rarefaction curves of the 97% OTUs for the different experimental protocols.

<p>At each sampling depth, the average number of OTUs is shown (n=2) (a) Different primer pairs (b) Different annealing temperatures (c) Different extraction procedures.</p

Polysaccharide-degrading enzymes in the chicken cecal metagenome.

<p>The figure shows each class of enzyme as judged by SEED/KEGG annotation and GH (see methods) for three types of NSP. The size of pie chart reflects abundance of the enzyme class; numbers indicate quantity of genes assigned to each bacterial Taxon at the class level.</p

Gene clusters associated with polysaccharide degradation and utilization.

<p>NSP degrading genes were identified by SEED/KEGG annotation and GH domain (see methods). (A) Gene clusters encoding putative PUL systems from various <i>Bacteroidetes</i>. (B) Gene cluster encoding putative integrated polysaccharide degradation and utilization systems from various <i>Firmicutes</i>. (C) NSP degrading enzymes associated with sporulation genes * indicates predicted signal peptide.</p

Number of genes containing GH domains in different metagenomes.

<p>Data are grouped according to Allgier <i>et al</i><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0091941#pone.0091941-Allgaier1" target="_blank">[68]</a>. The numbers in parenthesis are relative to total number of GH containing genes. The data is take from ^awallaby <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0091941#pone.0091941-Pope1" target="_blank">[55]</a>^btermite <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0091941#pone.0091941-Warnecke1" target="_blank">[44]</a>, ^cpanda <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0091941#pone.0091941-Zhu2" target="_blank">[69]</a> and ^dbovine rumen <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0091941#pone.0091941-Hess1" target="_blank">[70]</a>.</p