The pandemic has highlighted the need to consider animal health and the health of natural environments, both of which have proven to have a bidirectional relationship with human health. Special Issue "One Health meets Omics: The way forward to investigate zoonosis" The review provides a detailed overview of the reptile gut microbiome, highlighting the importance of omics, and in particular culture-independent methods, such as shotgun metagenomics, in the study of animals. [Extracted from the article]