Neighbor-joining tree showing the phylogenetic relationship among the top 50 OTUs in this study (red) with known cellulose degraders (blue) and OTUs identified in the giant panda (green).

<p>Different phyla were shaded by different colors: green, Firmicutes; purple, Actinobacteria; orange, Bacteroidetes; blue, Proteobacteria. All bootstrap values > 50% were shown on the tree.</p

Characterization of the Gut Microbiota in the Red Panda (<i>Ailurus fulgens</i>)

<div><p>The red panda is the only living species of the genus <i>Ailurus</i>. Like giant pandas, red pandas are also highly specialized to feed mainly on highly fibrous bamboo. Although several studies have focused on the gut microbiota in the giant panda, little is known about the gut microbiota of the red panda. In this study, we characterized the fecal microbiota from both wild (n = 16) and captive (n = 6) red pandas using a pyrosequecing based approach targeting the V1-V3 hypervariable regions of the 16S rRNA gene. Distinct bacterial communities were observed between the two groups based on both membership and structure. Wild red pandas maintained significantly higher community diversity, richness and evenness than captive red pandas, the communities of which were skewed and dominated by taxa associated with Firmicutes. Phylogenetic analysis of the top 50 OTUs revealed that 10 of them were related to known cellulose degraders. To the best of our knowledge, this is the first study of the gut microbiota of the red panda. Our data suggest that, similar to the giant panda, the gut microbiota in the red panda might also play important roles in the digestion of bamboo.</p></div

Principal coordinate analysis of the community membership (A) and structure (B) using Jaccard and Theta YC distances, respectively.

<p>Green squares and yellow circles represent captive and wild red panda bacterial communities, respectively. Distances between symbols on the ordination plot reflect relative dissimilarities in community memberships or structures.</p

Relative abundance of OTUs at the phylum (A) and genus (B) level in the fecal microbiota from wild and captive red pandas.

<p>Relative abundance of OTUs at the phylum (A) and genus (B) level in the fecal microbiota from wild and captive red pandas.</p

Impact of DNA extraction method on measures of <i>Staphylococcus</i> relative abundance alpha diversities.

<p>(<b>A</b>) Relative abundance of <i>Staphylococcus</i> and (<b>B</b>) community diversity (Shannon index), (<b>C</b>) richness (number of observed OTUs) and (<b>D</b>) evenness (Shannon evenness) in <i>Staphylococcus</i>-rich and <i>Staphylococcus</i>-poor samples revealed by the standard lysis method (−LY, black bars) and the lysostaphin-lysozyme (+LY, white bars) method.</p

OTUs differentially represented between wild and captive red pandas identified by linear discriminant analysis coupled with effect size (LEfSe).

<p>A. Histogram showing OTUs that are more abundant in wild (green color) or captive (red color) red pandas ranked by effect size. The distribution of the most differentially distributed OTUs: OTU001 (more abundant in captive red pandas) and OTU003 (more abundant in wild red pandas) were illustrated in B and C, respectively.</p

Comparison of community alpha diversities between the wild and captive red pandas.

<p>Diversity was measured by inverse Simpson (A) and Shannon index (B); Richness (C) and evenness (D) were measured by the number of observed OTUs and Shannon Evenness index, respectively. The top and bottom boundaries of each box indicate the 75^th and 25^th quartile valudes, respectively. The black lines within each box represent the median values. Different lowercase letters above the boxplots indicate significant differences in alpha diversities between wild and captive pandas (P<0.001, Mann Whitney test).</p

Culture and pyrosequencing based measures of <i>Staphylococcus</i> abundance.

1<p>Abundance of <i>S. aureus</i> in culture (reported by clinical microbiology laboratory).</p>2<p>Relative abundance by pyrosequencing without (−LY) and with (+LY) lysostaphin-lysozyme; no. <i>Staphylococcus</i> sequence reads/no. total sequence reads.</p>3<p>Total number of OTUs observed after normalization of sequence reads to 498, the smallest number of sequences obtained among the 34 samples.</p>4<p>The rank order of the relative abundance of <i>Staphylococcus</i>.</p>5<p>With the exception of sample 16, samples with “numerous <i>S. aureus</i>” detected in culture are referred to as <i>Staphylococcus</i>-rich samples. Sample 16 and all other samples are referred to as S<i>taphylococcus</i>-poor samples.</p><p>ND: not detected.</p

Image4.PDF

<p>Bamboo-eating giant panda (Ailuropoda melanoleuca) is an enigmatic species, which possesses a carnivore-like short and simple gastrointestinal tract (GIT). Despite the remarkable studies on giant panda, its diet adaptability status continues to be a matter of debate. To resolve this puzzle, we investigated the functional potential of the giant panda gut microbiome using shotgun metagenomic sequencing of fecal samples. We also compared our data with similar data from other animal species representing herbivores, carnivores, and omnivores from current and earlier studies. We found that the giant panda hosts a bear-like gut microbiota distinct from those of herbivores indicated by the metabolic potential of the microbiome in the gut of giant pandas and other mammals. Furthermore, the relative abundance of genes involved in cellulose- and hemicellulose-digestion, and enrichment of enzymes associated with pathways of amino acid degradation and biosynthetic reactions in giant pandas echoed a carnivore-like microbiome. Most significantly, the enzyme assay of the giant panda's feces indicated the lowest cellulase and xylanase activity among major herbivores, shown by an in-vitro experimental assay of enzyme activity for cellulose and hemicellulose-degradation. All of our results consistently indicate that the giant panda is not specialized to digest cellulose and hemicellulose from its bamboo diet, making the giant panda a good mammalian model to study the unusual link between the gut microbiome and diet. The increased food intake of the giant pandas might be a strategy to compensate for the gut microbiome functions, highlighting a strong need of conservation of the native bamboo forest both in high- and low-altitude ranges to meet the great demand of bamboo diet of giant pandas.</p

Image3.PDF

<p>Bamboo-eating giant panda (Ailuropoda melanoleuca) is an enigmatic species, which possesses a carnivore-like short and simple gastrointestinal tract (GIT). Despite the remarkable studies on giant panda, its diet adaptability status continues to be a matter of debate. To resolve this puzzle, we investigated the functional potential of the giant panda gut microbiome using shotgun metagenomic sequencing of fecal samples. We also compared our data with similar data from other animal species representing herbivores, carnivores, and omnivores from current and earlier studies. We found that the giant panda hosts a bear-like gut microbiota distinct from those of herbivores indicated by the metabolic potential of the microbiome in the gut of giant pandas and other mammals. Furthermore, the relative abundance of genes involved in cellulose- and hemicellulose-digestion, and enrichment of enzymes associated with pathways of amino acid degradation and biosynthetic reactions in giant pandas echoed a carnivore-like microbiome. Most significantly, the enzyme assay of the giant panda's feces indicated the lowest cellulase and xylanase activity among major herbivores, shown by an in-vitro experimental assay of enzyme activity for cellulose and hemicellulose-degradation. All of our results consistently indicate that the giant panda is not specialized to digest cellulose and hemicellulose from its bamboo diet, making the giant panda a good mammalian model to study the unusual link between the gut microbiome and diet. The increased food intake of the giant pandas might be a strategy to compensate for the gut microbiome functions, highlighting a strong need of conservation of the native bamboo forest both in high- and low-altitude ranges to meet the great demand of bamboo diet of giant pandas.</p