Composition and similarity of bovine rumen microbiota across individual animals

Abstract

The bovine rumen houses a complex microbiota which is responsible for cattle's remarkable ability to convert indigestible plant mass into food products. Despite this ecosystem's enormous significance for humans, the composition and similarity of bacterial communities across different animals and the possible presence of some bacterial taxa in all animals' rumens have yet to be determined. We characterized the rumen bacterial populations of 16 individual lactating cows using tag amplicon pyrosequencing. Our data showed 51% similarity in bacterial taxa across samples when abundance and occurrence were analyzed using the Bray-Curtis metric. By adding taxon phylogeny to the analysis using a weighted UniFrac metric, the similarity increased to 82%. We also counted 32 genera that are shared by all samples, exhibiting high variability in abundance across samples. Taken together, our results suggest a core microbiome in the bovine rumen. Furthermore, although the bacterial taxa may vary considerably between cow rumens, they appear to be phylogenetically related. This suggests that the functional requirement imposed by the rumen ecological niche selects taxa that potentially share similar genetic features.

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 (25^th and 75^th 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 (25^th and 75^th 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.