All roads lead to Rome: the plasticity of gut microbiome drives the extensive adaptation of the Yarkand toad-headed agama (Phrynocephalus axillaris) to different altitudes

Abstract

The gut microbiome was involved in a variety of physiological processes and played a key role in host environmental adaptation. However, the mechanisms of their response to altitudinal environmental changes remain unclear. In this study, we used 16S rRNA sequencing and LC-MS metabolomics to investigate the changes in the gut microbiome and metabolism of the Yarkand toad-headed agama (Phrynocephalus axillaris) at different altitudes (-80 m to 2000 m). The results demonstrated that Firmicutes, Bacteroidetes, and Proteobacteria were the dominant phylum, Lachnospiraceae and Oscillospiraceae were the most abundant family, and the low-altitude populations had higher richness than high-altitude populations; Akkermansiaceae appeared to be enriched in high-altitude populations and the relative abundance tended to increase with altitude. The gut microbiome of three populations of P. axillaris at different altitudes was clustered into two different enterotypes, low-altitude populations and high-altitude populations shared an enterotype dominated by Akkermansia, Kineothrix, Phocaeicola; intermediate-altitude populations had an enterotype dominated by Mesorhizobium, Bradyrhizobium. Metabolites involved in amino acid and lipid metabolism differed significantly at different altitudes. The above results suggest that gut microbiome plasticity drives the extensive adaptation of P. axillaris to multi-stress caused by different altitudes. With global warming, recognizing the adaptive capacity of wide-ranging species to altitude can help plan future conservation strategies.

Keywords: 16S rRNA; LC-MS metabolomics; Phrynocephalus axillaris; altitude gradients; gut microbiome; plasticity.

FIGURE 1

The relative abundance of the gut microbiome at the phylum (A), family (B), and genus (C) levels in three populations of Phrynocephalus axillaris at different altitudes. Different colors in the figures indicate the different microbes composition, and details are shown on the right sides of each figure, respectively.

FIGURE 2

Boxplots of phylum level gut microbiome alpha-diversity of the three populations of Phrynocephalus axillaris at different altitudes. (A) Chao1 index; (B) ACE index; (C) Shannon index; (D) Simpson index (P < 0.05 indicated by*, P < 0.01 indicated by**).

FIGURE 3

Differences in the relative abundance of microbiome at phyla (A), family (B), and genus (C) levels in three populations of Phrynocephalus axillaris at different altitudes. P < 0.05 indicated by*, P < 0.01 indicated by**.

FIGURE 4

Differences in gut microbiome taxonomic composition among three elevation populations of Phrynocephalus axillaris at different altitudes. (A) Differences in gut microbiome determined by linear discriminate analysis of effect size (LEfSe) among three populations of P. axillaris at different altitudes. (B) Gut microbiome enterotype associated with elevation using Bray-Curtis dissimilarity of P. axillaris. The highlighted taxa were significantly enriched in the group that corresponds to each color (P < 0.05). Linear discriminatory analysis (LDA) scores >3.5.

FIGURE 5

Different functions of gut microbiome of three populations of Phrynocephalus axillaris at different altitudes. The microbial functions were predicted using PICRUSt2 at the first (A) and the second (B) level of the KEGG pathway and were expressed as relative abundances. P < 0.05 indicated by*, P < 0.01 indicated by**.

FIGURE 6

Principal coordinate analysis (PCA) (A) and PLS-DA analysis diagram (B) based on metabolomics of the three populations of Phrynocephalus axillaris at different altitudes. Metabolites variable importance of projection (VIP) analysis (C) and ANOVA test of metabolites (VIP > 1) (D) in fecal sample from three populations of P. axillaris at different altitudes, metabolites above the solid line had significant differences.