Figure 1.
Rarefaction analysis for the assessment of OTU coverage.
(A) Sample-based rarefaction curve showing the increase in OTU numbers as a function of the number of individuals sampled. Each added sample adds OTUs to the plot which has not yet been seen in previous samples. The curve becomes asymptotic as the OTU number saturates, and each sample adds an increasingly smaller number of new OTUs, indicating adequate coverage for the environment being tested. (B) Individual rarefaction curves for each rumen sample taken.
Figure 2.
Composition and abundance of bacterial taxa, as determined by pyrosequencing of the 16 S rDNA gene.
(A) Pie chart showing the average distribution of the phyla across all ruminal samples. (B) Box plot showing the relative abundance of each phylum, represented as percentage on the Y-axis. The boxes represent the interquartile range (IQR) between the first and third quartiles (25th and 75th percentiles, respectively) and the vertical line inside the box defines the median. Whiskers represent the lowest and highest values within 1.5 times the IQR from the first and third quartiles, respectively. Samples with a relative abundance of a given phylum exceeding those values are represented as points beside the boxes (color-coded).
Figure 3.
OTU occurrence across samples.
Different OTUs were summed into categories according to their frequency of occurrence across different ruminal samples and binned accordingly, from OTUs shared by up to 10% of the samples to those shared by all samples. The X-axis represents the percentage of cows sharing a specific OTU. The Y-axis represents the percentage of OTUs found in each category.
Figure 4.
Shared genera and abundance across samples.
Box plot showing the relative abundance of the bacterial genera shared by all samples, represented as log percentage on the X-axis. The boxes represent the interquartile range (IQR) between the first and third quartiles (25th and 75th percentiles, respectively) and the vertical line inside the box defines the median. Whiskers represent the lowest and highest values within 1.5 times the IQR from the first and third quartiles, respectively. Samples with a relative abundance of a given taxon exceeding those values are represented as points beside the boxes. The box color denotes the phylum of the genera: Bacteroidetes (blue), Firmicutes (red), Proteobacteria (green), Tenericutes (light blue), Cyanobacteria (orange), TM7 (gray), Actinobacteria (purple). Taxa not indentified at the genus level are identified by an asterisk and their highest taxonomic identification.
Figure 5.
Pairwise similarity calculation.
The average of pairwise comparisons of each sample to all others was calculated. The QIIME pipeline was used to compute the Bray-Curtis metric (gray bars) and the weighted UniFrac metric (black bars). The X-axis denotes the serial number of the cow from which the rumen sample was taken, and the Y-axis represents the degree of similarity: the closer the similarity to 1, the more similar the samples. At the bottom, average and standard deviation of each similarity metric calculated across all cow pairs are shown.