Wild and Captive Environments Drive the Convergence of Gut Microbiota and Impact Health in Threatened Equids

Abstract

To explore how the living environment influences the establishment of gut microbiota in different species, as well as the extent to which changes in the living environment caused by captive breeding affect wildlife's gut microbiota and health, we used 16S rRNA gene amplicon sequencing and shotgun metagenomic sequencing to compare the gut microbiome of two species of threatened equids, the Przewalski's Horse and the Asian wild ass, in the wild and captivity. The results revealed that different species of Equidae living in the same environment showed remarkable convergence of gut microflora. At the same time, captive populations exhibited significantly "unhealthy" microbiota, such as low Alpha diversity, high levels of potentially pathogenic bacteria and biomarkers of physical or psychological disease, and enrichment of microbial functions associated with exogenous exposure and susceptibility, implying that the artificial environment created by captivity may adversely impact the health of wildlife to some extent. Our findings demonstrate the importance of the environmental factors for the establishment of gut microbiota and host health and provide new insights into the conservation of wildlife in captivity from the perspective of the microbiome.

Keywords: equid; gut microbiota; health; microbiome convergence; sympatry; wild and captive.

Figure 1

Shannon index’s Alpha diversity rarefaction curves on the OTU level. The abscissa represents the number of reads selected randomly; the ordinate represents the Alpha diversity measured.

Figure 2

Wilcoxon rank-sum test for differences in Alpha diversity (Shannon index) between groups on the OTU level. ^**p < 0.01 and ^***p < 0.001.

Figure 3

Non-metric multidimensional scaling (NMDS) plot of the gut microbiota in equids on the OTU level. The closer the points, the more similar of microbial community composition.

Figure 4

Fecal microbial community composition on the Phylum (A) and family (B) level in equids in the wild and captivity and values are averaged within groups.

Figure 5

Linear discriminant analysis (LDA) effect size (LEfSe) analyses (LDA score threshold >4.0) on fecal microbial communities between wild PHs and AWAs (A), captive PHs and AWAs (B), wild and captive PHs (C), and wild and captive AWAs (D).

Figure 6

Linear discriminant analysis (LDA) effect size (LEfSe) analyses (LDA score threshold >2.0) of KEGG functional pathways for the microbial metagenome of the wild and captive equids.