Comparative Analysis of Gut Microbiome Community Structures in Different Populations of Asian Elephants in China and Their Correlation with Diet

Abstract

Background: The interaction and co-evolution between the gut microbiome and the host play important roles in the host's physiology, nutrition, and health. Diet is considered an important driver of differences in the gut microbiota; however, research on the relationship between the gut microbiota and diet in Asian elephants remains limited.

Methods: In this study, we explored the gut microbiota structure and its relationship with diet in different populations of Asian elephants through metagenomic sequencing, combined with previously published dietary data.

Results: This study found that the dominant gut microbiota of Asian elephants includes the phyla Bacillota (29.85% in BP, 22.79% in RC, 21.89% in SM, 31.67% in ML, and 33.00% in NGH), Bacteroidota (25.25% in BP, 31.44% in RC, 16.44% in SM, 25.73% in ML, and 23.74% in NGH), and Spirochaetota (3.49% in BP, 6.18% in RC, 1.71% in SM, 2.69% in ML, and 3.52% in NGH), with significant differences in the gut microbiota among different populations. Correlation analysis between the gut microbiota and diet revealed that dietary diversity did not directly affect the alpha diversity of the gut microbiota. However, specific food types might play a key role in shaping the gut microbiota structure by regulating the abundance of certain microbiota.

Conclusions: This study reveals significant differences in the gut microbiota structure among different populations of Asian elephants and explores the impact of diet on the structure. The results provide foundational data for a deeper understanding of the gut microbiota structure of Asian elephants and offer important references for the scientific conservation and precise management strategies of this species.

Keywords: Asian elephant; diet–gut microbiome interaction; gut microbiome; metagenomic sequencing; microbial diversity.

Figure 1

The locations of Asian elephant fecal sample collection in Yunnan Province, China. The five-pointed star marker represents the Xishuangbanna Asian Elephant Rescue and Breeding Center population (RC, n = 11). The areas marked with different colors indicate the distribution ranges of various wild populations. BP: Banna–Pu’er population (n = 60); SM: Shangyong–Mengla population (n = 8); ML: Menghai–Lancang population (n = 9); NGH: Nangunhe population (n = 19).

Figure 2

Gut microbiome composition of Asian elephant across different populations in China. (a) The stacked bar plot shows the relative abundance of the main gut microbiota at the phylum level within each group. Different colors represent different phyla, and lower-abundance taxa are grouped together as “Others”. (b) The stacked bar plot shows the relative abundance of the main gut microbiota at the class level within each group. Different colors represent different classes, and lower-abundance taxa are grouped together as “Others”. (c) The Chord diagram displays the relative abundance of the main gut microbiota at the order level within each group. The width of the connecting bars indicates the relative abundance of the microbiota at the order level across different groups, with lower-abundance taxa grouped as “Others”. (d) The Chord diagram displays the relative abundance of the main gut microbiota at the family level within each group. The width of the connecting bars indicates the relative abundance of the microbiota at the family level across different groups, with lower-abundance taxa grouped as “Others”.

Figure 3

Gut microbiome diversity of Asian elephant across different populations in China. (a–c) Box plots display the comparison of alpha diversity differences in the gut microbiota composition across different populations, with (a) showing the Shannon index, (b) showing the Simpson index, and (c) showing the Chao1 index. Significant differences detected by the Kruskal–Wallis H test; “*” indicates significant difference between two groups; * p < 0.05, ** p < 0.01, and *** p < 0.001. (d) Principal Coordinate Analysis (PCoA) of the beta diversity in the gut microbiota composition across different populations based on the Bray–Curtis distance. (e) Nonmetric Multidimensional Scaling (NMDS) analysis of the beta diversity in the gut microbiota composition across different populations based on the Bray–Curtis distance.

Figure 4

Mapping interaction based on the relative abundance of gut microbiota. (a) Gut microbiota interaction network at the family level. Nodes represent different bacterial families, with size indicating relative abundance, color-coded by order. Edge width represents interaction strength, with purple indicating positive correlations and blue-green indicating negative correlations. (b) Gut microbiota interaction network at the genus level. Nodes represent different bacterial genera, with size indicating relative abundance, color-coded by family. Edge width represents interaction strength, with purple indicating positive correlations and blue-green indicating negative correlations.

Figure 5

The relationship between gut microbiota diversity and dietary diversity. (a–c) The relationship between dietary alpha diversity and gut microbiome alpha diversity, with (a–c) representing the relationships of the Shannon index, Simpson index, and Chao1 index, respectively. Each point represents an individual sample, with different colors corresponding to different groups. The solid line represents the fitted regression line, and the gray shaded area indicates the 95% confidence interval. The marginal density plots display the distribution of dietary and microbiome diversity along the X-axis and Y-axis, respectively. (d,e) Procrustes analysis of the correlation between diet and gut microbiota communities, with (d) representing the order level and (e) representing the genus level of the gut microbiota. Triangles represent the gut microbiota, circles represent diet, and different colors correspond to different groups.

Figure 6

Correlation analysis between gut microbiota and forage plants. (a,b) Heatmap of Mantel test correlations between the family (a) and genus (b) levels of the top 16 forage plants and the phylum level of gut microbiota. (c,d) Pearson correlation analysis of the gut microbiome dataset with the dietary dataset at the family (c) and genus (d) levels. The color gradient in the heatmap represents the Pearson correlation coefficients between the microbial abundance and dietary data, with blue indicating positive correlations and red indicating negative correlations. Significant differences detected by the Pearson correlation test; “*” indicates significant correlation; * p < 0.05, ** p < 0.01, and *** p < 0.001.