Wastewater based surveillance revealed temporal dynamics of gut microbiota and virome during the COVID-19 pandemic

Wastewater microbiome surveillance was used to characterize the temporal dynamics of the gut microbiota during the COVID-19 pandemic. The virome, dominated by temperate bacteriophages, showed high sensitivity to SARS-CoV-2, whereas the bacterial community exhibited greater adaptability and stability. The abundance of antimicrobial resistance genes (ARGs) was significantly and positively correlated with SARS-CoV-2 concentrations. These findings reveal, for the first time, the interaction network among gut bacteria, viruses, and ARGs, underscoring the unique value of wastewater microbiome surveillance in reflecting population health status.