Vaibhav Upadhyay

Vaibhav Upadhyay, MD, PhD is an Assistant Professor in the Department of Medicine at UCSF's School of Medicine. As a physician-scientist, he leads research on gut microbiome impacts on human health with clinical focus in pulmonary medicine. His laboratory investigates microbial influences on acute lung injury and chronic diseases using multi-omic approaches.

Education includes:

• BS in Biochemistry from Duke University (2007)
• PhD in Immunology from University of Chicago (2013)
• MD from University of Chicago (2015)
• Internal Medicine Residency at UCSF (2018)
• Pulmonary and Critical Care Fellowship at UCSF (2021)
• Chief Fellowship in Pulmonary and Critical Care at UCSF (2021)

Research focuses on gut-lung axis interactions, particularly how gut microbial metabolites influence pulmonary inflammation and injury. His work bridges immunology, microbiome science, and pulmonary medicine to develop novel therapeutic approaches for acute lung injury and interstitial lung diseases. Current projects examine bacterial lactate effects on lung epithelial mitochondria and microbial contributions to drug response variability.

Publications consistently explore microbiome-host interactions across disease contexts, with recent emphasis on COVID-19 impacts on microbiota stability, microbial influences on cancer therapy toxicity, and diet-microbiome-immune system crosstalk. Research employs cutting-edge techniques including phage immunoprecipitation sequencing, single-nucleus RNA-seq, and multi-omics integration.

Awards and honors:

• ATS RCMB Abstract Scholarship (2022)
• Jeffrey Golden Outstanding Clinical Fellow Award (2021)
• Two Pulmonary Division Clinical Fellow Awards (2019, 2020)
• UCSF Fellows Leadership Cohort (2020)
• Alpha Omega Alpha Honor Society (2014)
• Best Dissertation Award, University of Chicago (2013)
• Summa Cum Laude, Duke University (2007)

Research funding includes an NIH/NHLBI K08 award (2023-2028) studying gut bacterial metabolites in acute lung injury, a Benioff Center grant examining SARS-CoV-2 microbiome interactions, and a CTSI grant exploring autoantigens in interstitial lung disease. Leads a research team collaborating with multiple UCSF laboratories including the Turnbaugh Lab.