Microbial genomics is transforming our understanding of infectious disease, immunity, and human health. Researchers in the Department of Genetics and Genomic Sciences (GGS) at the Icahn School of Medicine at Mount Sinai are using cutting-edge genomic tools to track pathogens, study host-microbe interactions, and develop microbial-based therapies. From emerging infections to the microbiome’s role in chronic disease, this work supports global public health and opens new frontiers in precision medicine.
The Pathogen Surveillance Program (PSP) brings together experts in infectious disease, genomics, epidemiology, and computational modeling to monitor and characterize viral and bacterial threats - most recently SARS-CoV-2 during the COVID-19 pandemic. These pathogens pose significant risks across communities and healthcare settings, and surveillance is essential to mitigate their spread and impact.
Using advanced whole-genome sequencing and bioinformatics, PSP researchers study the evolution, transmission, and host interactions of infectious agents. This includes identifying emerging pathogens and genetic variants with the potential to drive outbreaks. A deeper understanding of pathogen genetic diversity is expected to enhance risk assessments, inform public health responses, and improve patient outcomes.
Beyond pathogens, commensal microbes - the human microbiome - also play a central role in health and disease. GGS scientists use both experimental and computational approaches to study how microbial communities influence inflammatory bowel disease (IBD), allergies, COVID-19, influenza, cancer, and other conditions. Their work has led to innovative treatment strategies, including microbiota transplants. Mount Sinai researchers currently lead two clinical trials investigating microbial therapies for IBD and food allergies.
Active research is also focused on how commensal microbes interact with the immune system and influence disease risk. Developing models to study these interactions will advance the design of next-generation microbial therapeutics.
A growing concern is the emergence of antibiotic resistance and the rise of opportunistic infections. Mount Sinai researchers have shown that viral infections like influenza can indirectly influence antibiotic resistance gene expression by altering the respiratory microbiome. Other studies have identified links between oral commensals and severe COVID-19 outcomes. To address these questions, GGS teams are developing specialized tools for analyzing challenging tissue types such as the lung and expanding their focus to include the often-overlooked co-microbiome—bacteria, fungi, and viruses that coexist in complex communities.