Human conservation efforts have pros and cons for endangered animals. Metagenomic analysis of the gut microbiome provides valuable insights and tools for wildlife conservation. However, most studies only focus on changes in microbial species and potential functional genes, leaving out the assembly mechanisms and metabolic activities of wildlife gut microbiome. Herein, we investigated the gut microbiome of golden snub-nosed monkeys under varied conservation strategies (wild, captive, and food provision) using metagenome and metabolome analysis. We found that the conserved monkeys had more non-redundant genes, distinct community diversities, and less stable gut microbiota. Source-tracking analysis showed captive group has fewer wild-sourced microbes than food provision group. The captive group had more habitat specialists with narrower niche breadth compared to the provision/wild counterparts. Besides, captive group’s microbiota governed by deterministic processes more than provisioned/wild groups. Procrustes analysis revealed changes in antibiotic resistance genes and virulence factors linked to mobile genetic elements in conserved monkeys. Notably, gut microbiota and metabolomic dataset had significant co-variation and clear separation among the wild, captive and food provision groups. Weighted correlation network analysis identified co-varying modules of microbiota and metabolites with opposite variation trends between the wild and conserved animals, specifically linked to co-metabolism pathways associated with essential amino acids. This study provides new insights into the structural features, assembly mechanisms, community functions, and microbiota-metabolome associations of wildlife gut microbiome under different conservation strategies and have significant implications for advancing sustainable conservation practices.

Soil microbial diversity distribution patterns and their ecological linkage with aboveground plant diversity are essential for both theoretical and applied ecology. However, a number of studies have shown soil microbial distribution patterns along different environmental gradients are inconsistent and their ecological linkages with plant diversity haven’t been well clarified. In this study, the plant and soil microbial diversity was simultaneously surveyed in 30 natural broadleaved forest sites along a 2500 km latitudinal gradient (18°–40°N) in China. The soil bacterial and fungal diversity was detected using the Illumina sequencing technique. The results showed soil bacterial and fungal community structure differed significantly among different sites and their alpha -diversity significantly increased as latitudinal increased (P < 0.001), and the plant and soil microbial beta-diversity was significantly linkages (P < 0.001). Based on the partial Mantel test, boosted regression tree and structural equation model analysis, we found plant alpha-diversity had no positive correlation with soil microbial alpha-diversity, and soil pH and climate condition (including mean annual precipitation and mean annual temperature) were the most important factors affecting soil microbial community structure. However, soil microbial heterogeneity might significantly affect aboveground plant community structure. Our analysis indicated that the plant beta-diversity could predict soil microbial beta-diversity at regional forest system, and soil pH plays higher roles than plant diversity in affecting soil microbial community at regional scale. This study provides new insights into the soil microbial diversity distribution patterns and ecological linkage between plant diversity and soil microbial diversity in natural forest ecosystem at the regional scale.