The microbial community in the feces of the white rhinoceros (Ceratotherium simum) as determined by barcoded pyrosequencing analysis

Abstract

As a non-ruminant herbivore, the white rhinoceros has the ability to utilize fibrous plant matter through microbial fermentation in the hindgut. So far, there has been no report using molecular techniques to study the gut microbiota of the white rhinoceros. We used barcoded pyrosequencing to characterize 105,651 sequences of 16S rRNA genes obtained from fecal samples from five white rhinoceroses. Results showed that Firmicutes and Bacteroidetes were the predominant phyla in the samples, which were comprised largely of unclassified bacteria. The microbiota of one animal treated with drug therapy differed from those in other healthy animals, and was dominated by Aerococcus -related bacteria. The core microbiota in the healthy rhinoceros were dominated by phyla Firmicutes and Bacteroidetes, represented by the Ruminococcaceae, Lachnospiraceae, Rikenellaceae and Prevotellaceae families. The present work provides a phylogenetic framework for understanding the complex microbial community of the rhinoceros; however, further studies are required to link the distinctive microbiota with their digestive role in the hindgut of the white rhinoceros.

Figure 1. Rarefaction curves.

Rarefaction curves comparing the number of reads with the number of phylotypes found in the DNA in the feces of five rhinoceroses.

Figure 2. Fecal bacterial community at the phylum level.

Relative abundance of bacterial groups (phylum level) in the feces of five white rhinoceroses.

Figure 3. Fecal bacterial community at the family level.

Relative abundance of bacterial groups (family level) in the feces of five white rhimoceroses.

Figure 4. Fecal bacterial community at the genus level.

Relative abundance of bacterial groups (genus level) in the feces of five white rhinoceroses.

Figure 5. Bacterial distribution among the five samples.

Double dendrogram showing the bacterial distribution among the fecal samples of five rhinoceroses. The bacterial phylogenetic tree was calculated using the neighbor-joining method, and the relationship among samples was determined using Bray distance and the complete clustering method. Total 50 genera with the abundance higher than 0.1% within total bacteria were sorted for the analysis. The heatmap plot depicts the relative percentage of each bacterial genus (variables clustering on the Y-axis) within each sample (X-axis clustering). The relative values for the bacterial genus are depicted by color intensity in the legend indicated at the top of the figure. Clusters based on the distance of the five samples along the X-axis and the bacterial genera along the Y-axis are indicated at the top and bottom of the figure, respectively.