Microbial communities on station and train surfaces in Chennai Metro: Insights into urban transit microbiome

Urban public transport systems, particularly metro networks, serve as key hubs for microbial transmission, yet the urban microbiome in densely populated regions like India remains poorly characterized. These environments harbor diverse microbial communities, including both beneficial and pathogenic species, which can influence public health. The COVID-19 pandemic has further highlighted the need to monitor microbial ecosystems, particularly with respect to antimicrobial resistance (AMR) genes that may have escalated due to increased antibiotic use during health crises. In a first-of-its-kind study in India, we comprehensively characterized microbial communities and the prevalence of AMR genes in the Chennai Metro system. Of the 96 surface swab samples collected from 12 stations across two metro lines, 47 samples passed quality control and were subsequently analyzed using whole genome metagenomic sequencing. Comparative analysis with global urban microbiome datasets revealed distinct microbial profiles, including eight core species unique to Chennai. Surface type significantly influenced microbial diversity, with kiosks displaying the highest diversity levels. While AMR gene presence was minimal overall, genes associated with Sulfonamide and Rifamycin resistance were detected. These findings highlight unique microbial signatures and emphasize the need for ongoing surveillance and targeted interventions to mitigate microbial transmission risks in densely populated urban areas.