Microbiome Research


Jack A Gilbert Lab

University of California San Diego

Pediatrics & Scripps Institution of Oceanography

A highly interdisciplinary group leading research in medical and environmental microbiology, microbial ecology, and biotechnology development. 

Our work transcends microbiome studies across environmental and human health, with marine model organisms and ecosystems informing studies in human infectious disease, diet, and cardiometabolic, immune and mental health.


In the Gilbert Lab, we value the participation of every member of our community and want to ensure everyone has an enjoyable and fulfilling experience, both professionally and personally. To ensure that everyone in the lab knows the expectations and enjoys their time in the lab, we have created a Code of Conduct that helps every member understand expectations, how to handle conflict resolution, and how to engage in creating a supportive ecosystem for all. 


SARS-CoV-2 detection status associates with bacterial community composition in patients and the hospital environment

C. Marotz, P. Belda-Ferre, F. Ali, P. Das, S. Huang, K. Cantrell, L. Jiang, C. Martino, R.E. Diner, G. Rahman, D. McDonald, G. Armstrong, S. Kodera, S. Donato, G. Ecklu-Mensah, N. Gottel, M.C. Salas Garcia, L.Y. Chiang, R.A. Salido, J.P. Shaffer, K. Sanders, G. Humphrey, G. Ackermann, N. Haimeinen, K.L. Beck, H. Kim, A.P. Carrieri, L. Parida, Y. Vazquez Baeza, F.J. Torriani, R. Knight, J.A. Gilbert, D.A. Sweeney, S.M. Allard.
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Microbiome response in an urban river system is dominated by seasonality over wastewater treatment upgrades

S. Kodera, A. Sharma, C. Martino, M. Dsouza, M. Grippo, H.L. Lutz, R. Knight, J.A. Gilbert, C. Negri, S.M. Allard.
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UC San Diego Receives $14M to Drive Precision Nutrition with Gut Microbiome Data

National Institutes of Health establishes Microbiome and Metagenomics Center at UC San Diego, part of new effort to predict individual responses to food and inform personalized nutrition recommendations

Leads: Jack Gilbert and Rob Knight
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