The Gut Microbiome of the Asiatic Toad (Bufo gargarizans) Reflects Environmental Changes and Human Activities

Amphibians are extremely sensitive to environmental changes, and their gut microbiome may have different responses to environmental changes. Here, metagenomic sequencing was used to investigate the intestinal microbiota of the Asiatic toad (Bufo gargarizans) from three different habitats (city areas, transition areas, and wild areas) of Sichuan Province, China. The results showed that Proteobacteria, Firmicutes, and Fusobacteria were the main bacteria in the gut of B. gargarizans. There were significant differences in the composition and function of the gut microbiome among the samples from the three different habitats. Enterobacteriaceae showed significant changes in the three habitats and occupied a high relative abundance in the city areas, especially for Citrobacter. Especially, antibiotic resistance genes (ARGs) and virulence factors (VFs) were significantly increased in city areas. We performed de novo assembly of the metagenome-assembled genomes (MAGs). In total, 322 nonredundant MAGs were reconstructed, 304 of which might be potential novel genomes. Among the 13 species-level genome bins (SGBs) belonging to Enterobacteriaceae, the one belonging to Citrobacter portucalensis annotated the most types of ARGs and VFs. Phylogenetic and functional analyses of the assembled C. portucalensis MAG and public genome data were carried out, suggesting that it may play a potential role in intestinal diseases in amphibians. Our study revealed the differences in the gut microbiome of B. gargarizans across different habitats and suggests that amphibian intestinal microbiota could serve as environmental indicators to reflect environmental changes and human activities. The reconstructed MAGs expanded our understanding of the gut microbiota in amphibians, which may serve as a substantial reservoir for microbiome resources.