Interactions Between Humans and Microbiomes in Hospital Environments

Background Microorganisms constantly circulate among humans, animals, plants, and the environments they inhabit. Hospital settings represent particularly complex microbial ecosystems because they are influenced by intensive sanitation practices, continuous patient turnover, and high human activity. These conditions create selective pressures that shape a distinctive and constantly evolving microbiome. Hospitals can therefore be considered important microbial reservoirs where interactions between people and surfaces occur continuously. This study aimed firstly to investigate how the hospital microbiome develops and changes over time in newly opened wards. Secondly, it explored whether even short hospital stays may promote microbial transfer between patients and the surrounding clinical environment. Methods The research was conducted within the ANTHEM project (AdvaNced Technologies for Human-centrEd Medicine), funded through the Italian National Complementary Investment Plan linked to the PNRR. Two sampling campaigns were carried out at the Fondazione IRCCS San Gerardo dei Tintori Hospital in Monza, Italy. The first campaign consisted of a one-year longitudinal study focused on monitoring microbial changes after the opening of three hospital wards. The second campaign examined short patient stays by collecting environmental samples from pre-admission areas and skin samples from patients’ dominant hands before and after their visits. More than 130 adult outpatients participated. Overall, 1,300 environmental samples and 260 skin samples were analyzed through sequencing of the V3–V4 region of the 16S rRNA gene. Diversity analyses, differential abundance testing, and core microbiome identification were performed, together with source–sink and microbial overlap analyses. Results and Conclusion Hospital surfaces were mainly dominated by skin-associated bacterial genera, including Staphylococcus, Corynebacterium, Cutibacterium, and Finegoldia. Short-term exposure also promoted bidirectional microbial exchange between patients and hospital environments. These findings highlight hospitals as dynamic microbial ecosystems and underline the importance of understanding these interactions to improve infection prevention strategies.