Supported by the National Natural Science Foundation of China (Grant No. T2525019) and other funding sources, a research team led by Professor Su Shuo from the School of Public Health at Fudan University and the Shanghai Institute of Major Infectious Diseases and Biosecurity, in collaboration with the Institute of Microbiology, Chinese Academy of Sciences, and other institutions, has made significant progress in studying mammalian microbiomes and cross-species transmission of antibiotic resistance genes. The related findings, titled “Extensive cross-species transmission of pathogens and antibiotic resistance genes in mammals neglected by public health surveillance”, were published online in Cell on August 26, 2025 (https://doi.org/10.1016/j.cell.2025.08.016).

A systematic characterization of microbial pathogens and antibiotic resistance genes (ARGs) in mammals, as well as their mechanisms of cross-species transmission, has long been hindered by methodological bottlenecks, including insufficient sensitivity for detecting low-abundance microorganisms, limited taxonomic resolution, and incomplete understanding of the coupling between ARGs and mobile genetic elements (MGEs).

To overcome these challenges, the research team established a high-resolution, multi-omics framework for microbiome analysis, which enabled precise identification of low-abundance and previously uncharacterized microorganisms. In addition, a high-accuracy ARG–MGE annotation system was developed, allowing the construction of multidimensional cross-species networks for clinically important ARGs.

Through the analysis of nearly 30,000 mammalian microbial genomes, the study identified 128 viral species, more than 10,000 bacterial taxa, over 200 fungal species, and multiple parasites, among which over 7,000 bacterial taxa were previously undescribed, highlighting the extensive microbial “dark matter.” Moreover, a total of 157 clinically prioritized ARGs in mammalian microbiomes showed over 99% identity to ARGs from human microbiomes and were frequently associated with MGEs, indicating potential implications for clinical efficacy.

This study fills gaps in mammalian microbiome research, reveals networks of cross-species transmission of pathogens and ARGs, expands human understanding of microbial diversity and potential ecological risks, and provides both theoretical foundations and technical support for the precise prediction of emerging pathogens and antibiotic resistance surveillance.

Figure: High-resolution mammalian microbiome atlas integrating multi-omics approaches