Age-Based Variations in the Gut Microbiome of the Shennongjia (Hubei) Golden Snub-Nosed Monkey (Rhinopithecus roxellana hubeiensis)

Abstract

The gut microbiota represents a source of genetic and metabolic diversity of a complex polymicrobial ecosystem within its host. To investigate age-based variations of the gut microbiota among Shennongjia golden snub-nosed monkeys (Rhinopithecus roxellana hubeiensis), we characterized the microbial species in fecal samples from 18 Shennongjia golden snub-nosed monkeys evenly pooled into 3 aged groups (Group 1, 1-3 years; Group 2, 5-8 years; Group 3, above 12 years) in Shennongjia, Hubei Province, China. Genomic DNA was extracted from fecal samples, and the 16S rRNA gene V4 region was sequenced using the Illumina high-throughput MiSeq platform PE250. A total of 28 microbial phyla were identified in the gut microbiome of these monkeys with the ten most abundant phyla (i.e., Firmicutes, Bacteroidetes, Verrucomicrobia, Spirochaetes, Tenericutes, Proteobacteria, Planctomycetes, Fibrobacteres, Cyanobacteria, and Euryarchaeota). A total of 1,469 (of 16 phyla and 166 genera), 1,381 (of 16 phyla and 157 genera), and 1,931 (of 19 phyla and 190 genera) operational taxonomic units (OTUs) were revealed in Groups 1, 2, and 3, respectively, with Group 3 containing the most diverse groups of OTUs as revealed by the species relative abundance clustering analysis. These results suggest that the gut microbiota in these monkeys maintain a dynamic status, starting from the early developmental stages of life with the species relative abundance increasing with age. This is the first study to comprehensively characterize the gut microbiota and provide valuable information for monitoring the health and nutritional needs of this endangered primate at different ages.

Figure 1

The alpha diversity indices including observed species index (a), Shannon's diversity index (b), Simpson's diversity index (c), chao1 diversity index (d), and ACE diversity index (e), presented in box plots of 18 fecal samples in three groups of Shennongjia golden snub-nosed monkeys.

Figure 2

Relative abundance of the top 10 most abundant microbial phyla (a) and genera (b) identified in the fecal samples of three different aged groups of Shennongjia golden snub-nosed monkeys.

Figure 3

The relative abundance of top 35 most abundant microbial genera in the 18 fecal samples (a) of three groups (b) of Shennongjia golden snub-nosed monkeys based on the species relative abundance clustering and presented in heatmaps. Scaled bar represents log-transformed relative abundance.

Figure 4

The relative abundance of a total of 28 microbial phyla identified in three aged groups of Shennongjia golden snub-nosed monkeys presented in a heatmap. Scaled bar represents log-transformed relative abundance.

Figure 5

Venn map showing the distributions of common and unique operational taxonomic units (OTUs) among three aged groups of Shennongjia golden snub-nosed monkeys.

Figure 6

The UPGMA clustering of the microbial phyla derived from 18 individual samples (a) and three aged groups (b) of Shennongjia golden snub-nosed monkeys at phylum level based on weighted UniFrac distances.

Figure 7

The principal coordinate analysis (PCoA) showing the PCoA plot (a) and the box plot (b) of three aged groups of Shennongjia golden snub-nosed monkeys based on weighted UniFrac distances.