Diet and environment drive the convergence of gut microbiome in wild-released giant pandas and forest musk deer

Abstract

Reintroduction is important for recovering endangered species, and gut microbiome is crucial for successful wildlife reintroduction. This study utilized 16S rRNA high-throughput sequencing of 791 fecal samples to examine the gut microbial changes in giant pandas (Ailuropoda melanoleuca) and forest musk deer (Moschus berezovskii) across captivity, semi-release, and release stages. Our results revealed a similar transitional pattern in the gut microbiome of both species, with semi-release stage displaying an intermediate state between captive and wild microbiome. We also observed that both species are enriched in Pseudomonas and functional pathways related to amino acid metabolism, ATP-binding cassette transporters, and acetyl-CoA/propionyl-CoA carboxylase. Furthermore, the SourceTracker analysis indicated putative contributions of plant and soil microbiome to the gut microbiome of forest musk deer. These findings suggest that similar herbivorous diets and same environment may contribute to the convergence of gut microbiome. In conclusion, our study provides valuable insights for reintroducing endangered wildlife.

Keywords: Microbiology; Nature conservation; Zoology.

Graphical abstract

Figure 1

Transitional changes in the gut microbiome of giant pandas and forest musk deer from captivity to release N represents the number of samples at each stage (A and B) Relative abundances of the predominant bacterial phyla (A) and genera (B) in the gut microbiome of giant pandas at different stages. (C and D) Relative abundances of the predominant bacterial phyla (C) and genera (D) in the gut microbiome of forest musk deer at different stages. (E) Relative abundance of Pseudomonas across different groups at each stage, highlighting its enrichment in the release stage. Wilcoxon rank-sum test, ∗p < 0.05, ∗∗p < 0 0.01, and ∗∗∗∗p < 0.0001. (F) Principal coordinate analysis (PCoA) based on weighted UniFrac distances showing clustering patterns of gut microbiome in giant pandas across the three stages. Permutational multivariate analysis of variance (PERMANOVA) statistical analyses were conducted with 999 permutations using the function Adonis. (G) PCoA based on weighted UniFrac distances showing clustering patterns of gut microbiome in forest musk deer across the three stages. PERMANOVA statistical analyses were conducted with 999 permutations using the function Adonis. (H and I) Co-occurrence network analyses highlighting the connections of gut microbiome in giant pandas (H) and forest musk deer (I) at different stages, with major bacterial families and their phyla indicated.

Figure 2

Microbial and functional convergence in the gut microbiome of giant pandas and forest musk deer N represents the number of samples at each stage. (A) Principal coordinate analysis (PCoA) based on unweighted UniFrac distances, illustrating gut microbiome composition across different groups. PERMANOVA statistical analyses were conducted with 999 permutations using the function Adonis. (B) Boxplot showing unweighted UniFrac distances to compare the gut microbiome composition between giant pandas (GP) and forest musk deer (MD) at captive, semi-release, and release stages. Student’s t test, ∗∗∗p < 0.001. (C) PCoA based on Bray-Curtis distances, illustrating functional differences at the COG (cluster of orthologous groups) level across groups. PERMANOVA statistical analyses were conducted with 999 permutations using the function Adonis. (D) Boxplot comparing Bray-Curtis distances of functional differences between giant pandas and forest musk deer across the three stages. Student’s t test, ∗∗∗p < 0.001.

Figure 3

Shared OTUs analysis between released giant pandas and forest musk deer (A) Venn diagram illustrating the number of operational taxonomic units (OTUs) shared between the gut microbiome of released giant pandas (GP-Release) and forest musk deer (MD-Release). (B) TOP 20 genera of shared OTUs between released giant pandas and forest musk deer. (C) Classification of shared OTUs at the phylum level, with different colors representing microbial taxa and bubble size indicating relative abundance. (D) Classification of shared OTUs at the genus level, with different colors representing microbial taxa and bubble size indicating relative abundance.

Figure 4

COG and KEGG enrichment analysis of functional features in giant pandas and forest musk deer Data are presented as the median value, lower quartile, and upper quartile, dots indicate discrete points. (A–C) Giant pandas and forest musk deer convergent function at the COG function level. (D) Giant pandas and forest musk deer convergent function at the KEGG enzyme function level. (E–H) Giant pandas and forest musk deer convergent function at the KEGG orthology function level.

Figure 5

The SourceTracker analysis of gut microbiome in forest musk deer (A) Genera with top 10 abundance in plants. (B) Genera with top 10 abundance in soil. (C) SourceTracker analysis of gut microbiome in the semi-release forest musk deer and the percent of bacteria originating from plant and soil at the semi-release stage. (D) SourceTracker analysis of gut microbiome in released forest musk deer and the percent of bacteria originating from plant and soil at the released stage.