Unexpected Microbial and Genetic Diversity in the Gut of Chinese Giant Salamander

The gut microbiome is crucial for animal health, yet the diversity of the critically endangered Chinese giant salamander's gut microbiota remains largely uncharacterized. In this study, we first conducted a comprehensive landscape survey of the gut microbiome of the Chinese giant salamander using 16S rRNA sequencing across a wide geographic range, identifying a distinct microbial cluster within its habitat. Subsequently, using shotgun metagenomes, we recovered 1518 metagenome-assembled genomes. Notably, 85% of the newly identified genomes could not be assigned to any known bacterial species, indicating a significant presence of novel taxa in Chinese giant salamander intestines. We observed substantial species-level variations in the gut microbiome across different age groups, with some novel species uniquely enriched in specific age populations. From the gut symbionts, we established a gene catalog comprising 3 278 107 non-redundant protein-coding genes, of which 7733 were annotated into recognized KEGG orthology groups. Additionally, we found that the gut microbiota of the Chinese giant salamander exhibits enhanced functional capacities explicitly in lipid metabolism and assimilatory sulfate reduction. Significant variations in the abundance of related enzyme-encoding genes across age groups suggest the unique roles of microbial metabolism in salamander health. By identifying microbial genomes and constructing an integrated gene catalog from metagenomic data, we significantly expand the resources available for research on the gut microbiome of the Chinese giant salamander, paving the way for further investigations into its ecological and health-related implications.