Multi-Omics Analysis of Gut Microbiome and Host Metabolism in Different Populations of Chinese Alligators (alligator sinensis) During Various Reintroduction Phases

Abstract

Reintroduction plays a significant role in the self-maintenance and reconstruction of wild animal populations, serving as a communication bridge between captive and wild animals. The Chinese alligator (Alligator sinensis) is a distinct and endangered reptile species found in China. The mechanisms by which artificially bred Chinese alligators adapt following their release into the wild remain poorly understood. This study aims to elucidate the alterations in gut microbiomes and metabolic phenotypes of Chinese alligators during their reintroduction. During the Chinese alligator's reintroduction, Fusobacterium and Cetobacterium became more abundant, while typical pathogens declined significantly. The gut type of the Chinese alligator changed from Acinetobacter to Cetobacterium. The construction of the gut microbial community was dominated by neutral (random) processes and shifted towards deterministic processes with the progression of reintroduction. In terms of species function, reintroduction significantly upregulated the expression of host immune-related genes and significantly decreased the expression of gut bacterial pathogenic genes and antibiotic resistance genes. Metagenomic and metabolomic KEGG enrichment analyses indicate that glucoside hydrolase families 13 and 23-alongside glycolysis and gluconeogenesis pathways-may play pivotal roles in energy metabolism, host-pathogen interactions, and homeostasis maintenance for Chinese alligators. Differential metabolite analysis identified significant upregulation of metabolites related to neuroendocrine immune modulation and significant down-regulation of anti-inflammatory metabolites during Chinese alligator reintroduction. Association analysis showed that there were significant co-metabolic effects between microorganisms and metabolites, which coordinated host adaptive interaction. This study provides insights into the synergistic mechanisms of host adaptation and wild environment adaptation for Chinese alligators.

FIGURE 1

Analysis of α diversity indices based on Tukey HSD: (a) Chao 1 index; (b) Shannon index; (c) NMDS analysis based on Bray‐Curtis distance; (d) stacked bar chestart of species composition at the TOP10 phylum level; (e) stacked bar chart of species composition at the TOP15 genus level; (f) gut microbiota type analysis.

FIGURE 2

Neutral community model (NCM) showing the predicted occurrence frequency of gut microbial communities in all (a), captive (b), training (c), and field (d) populations of Chinese alligator. The blue solid line represents the best model fit, while the blue dashed lines indicate the 95% confidence intervals around the predictions. OTUs with occurrence frequencies higher or lower than the NCM predictions are shown in green and red, respectively.

FIGURE 3

(a) Bar chart showing the number of annotated KEGG genes in all samples; (b, c) Circos diagrams displaying the distribution characteristics of the top 10 and top 15 enriched genes at level‐B (b) and pathway (c) classification levels; (d, e) functional distribution characteristics of the CAZy database: Circos diagrams showing level‐A (d) and level‐B (e).

FIGURE 4

(a) Pie chart of top 10 metabolite attribution information statistics; (b) metabolite KEGG enrichment analysis; (c) PLS‐DA score plot for discriminant analysis; (d) VIP plot showing differential metabolites (VIP value > 5, p < 0.05); (e) KEGG enrichment analysis of differential metabolites.

FIGURE 5

Network plot of differential species and differential metabolite correlation weight (Cor > 0.8, p < 0.01).