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Renowned UC San Diego Microbiome Pioneer Rob Knight Elected to the National Academy of Engineering

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Rob Knight, a University of California San Diego professor and international leader in the study of the roles microbes play in human health and disease and the functioning of ecosystems, has been elected to the National Academy of Engineering–the highest professional recognition afforded to engineers and computer scientists. On Feb. 6, 2024, the National Academy of Engineering recognized Knight for his pioneering leadership and “for understanding microbiomes and their application to healthcare and sustainability.”

Knight has dedicated his career to the study of microbiomes–the microorganisms that live in the environment and the human body. His research is relevant for a wide range of practical applications, and his affiliations on campus reflect the deep interdisciplinary nature of his work. Knight is a professor in the Department of Pediatrics in the UC San Diego School of Medicine; and a professor in the Shu Chien-Gene Lay Department of Bioengineering and the Department of Computer Science and Engineering at the UC San Diego Jacobs School of Engineering, where he is also the founding director of the UC San Diego Center for Microbiome Innovation. Also at UC San Diego, Knight is affiliated with the Halıcıoğlu Data Science Institute (HDSI) and the Institute for Engineering in Medicine (IEM). 

During the COVID-19 pandemic, Knight’s team played a key role in building a wastewater surveillance system for the SARS-CoV2 virus, which helped the UC San Diego campus to successfully and safely reopen in mid-2020. The system was adopted by the San Diego region at large in 2021.

At Rady Children’s Hospital San Diego, Knight holds The Wolfe Family Endowed Chair in Microbiome Research where he has investigated the role of the microbiome in pediatric patients with cystic fibrosis and chronic airway disease. 

“We are pleased that Professor Knight’s groundbreaking work has been recognized with his induction into the prestigious National Academy of Engineering,” said UC San Diego Chancellor Pradeep K. Khosla, who is also an elected member of the National Academy of Engineering. “Professor Knight’s dedication to understanding the fundamental evolution of biomolecules, genomes and communities among ecosystems and commitment to develop and share innovative tools and techniques with scientists worldwide to promote further research underscores the quality of faculty at UC San Diego – and their ongoing impact on the world.”  

portrait of Rob Knight
Rob Knight, a professor at the University of Calfornia San Diego, was elected to the National Academy of Engineering. 

Groundbreaking microbiome research

Knight, a leader in the scientific study of microbiomes, is focused on understanding the multitude of ways in which these microbes affect our daily lives, from their presence in and on our bodies, to how they are involved with disease, and how they play roles in diverse ecosystems around the world. 

His work bridges microbiology sampling methods, with bioinformatics and big data. Knight has helped uncover connections between changes in the human gut microbiome and allergies, inflammatory bowel disease, obesity and many other conditions. Growing evidence suggests gut microbes also influence the brain, potentially affecting mood, behavior and psychiatric illnesses. Knight’s team has also enhanced our understanding of microbes in environments ranging from the oceans to the tundra, and made high-throughput sequencing techniques accessible to thousands of researchers around the world. 

At the UC San Diego Center for Microbiome Innovation, the Knight Lab uses advanced DNA sequencing and computational techniques to analyze and understand microbial communities, and their work has produced many of the initial software tools and laboratory techniques that enabled microbiome science.

“This is an unexpected and remarkable honor, and demonstrates the excitement and potential in the microbiome space, which intersects biology, medicine and engineering,” Knight said. “At the Center for Microbiome Innovation, we are focused on harnessing this potential in ways that are useful for both academia and industry, and on engineering new user interfaces that make microbiome data useful and accessible to researchers, clinicians and patients.”  

Knight is also the co-founder of the American Gut Project, which aims to better understand the microbiome that lives inside our body and on our body by collecting numerous samples from all around the world. It’s the largest crowdsourced citizen scientist project in the world. 

“Our experience with the American Gut Project, and its umbrella The Microsetta Initiative, has shown us how much even today’s microbiome data can benefit individual members of the public and research projects that use it as a platform, and we are currently building the next generation of tools to help understand how the microbiome impacts health and disease in both humans and the environment," said Knight.

During the COVID pandemic, Knight and colleagues rapidly built and deployed a detection system that monitored wastewater from 350 San Diego buildings for the SARS-CoV2 virus. The system was optimized to detect even a single asymptomatic person living and working in a building occupied by more than 500 people. Building occupants were notified and advised to test. The research team estimated that their system enabled early detection of 85% of COVID cases on the UC San Diego campus. Before the system was put in place, the only way to detect levels of virus in a community was through clinical testing, which is not feasible at large scales. 

“Congratulations Rob! Election to the National Academy of Engineering marks the highest peer recognition for an engineer or computer scientist. It’s a rare accolade that very few people receive,” said Albert P. Pisano, Dean of the UC San Diego Jacobs School of Engineering, Special Adviser to the Chancellor and an elected member of the National Academy of Engineering. “For Rob Knight, election to the NAE is both well deserved and only part of the story. He has had an outsized impact via the algorithms, software, data platforms and other tools he has created. They have transformed our understanding of microbiomes. What’s more, Rob uses these tools, and the insights and entrepreneurial opportunities that come from them, to improve lives in many different ways.”

Accolades and recognition

Knight’s work has garnered a number of accolades. In 2019, he received the Pioneer Award as part of the High-Risk, High-Reward Research Program of the National Institutes for Health. He also received the 2017 Massry Prize and the 2015 Vilcek Prize in Creative Promise for the Life Sciences. He has co-founded several citizen science efforts to support microbiome studies, including the Earth Microbiome Project and the American Gut Project. He is author of Follow Your Gut: The Enormous Impact of Tiny Microbes and co-author of Dirt is Good: The Advantage of Germs for Your Child’s Developing Immune System, books to help non-scientists understand the importance of a healthy microbiome.

Knight consistently appears in several categories on Clarivate’s Highly Cited Researchers list. He was also named a 2023 Citation Laureate, for computational and experimental research revealing the complex microbial ecosystems of the human body. Citation laureates are notable for producing research papers that were subsequently cited over 2,000 times. 


Prior to joining UC San Diego, Knight was a faculty member at the University of Colorado, Boulder, where he worked on such projects as profiling the microbes found in the saliva of komodo dragons to support conservation efforts and understanding the differences in the microbiomes of babies born via cesarean section or delivered vaginally. 

Knight earned his Bachelor of Science in biochemistry from the University of Otago in New Zealand and his Ph.D. in Ecology, Evolution, and Behavior at Princeton University.

He joins 113 other new NAE members and 21 international members elected in 2024. NAE members, who number more than 2600, are highly accomplished engineering professionals representing a broad spectrum of engineering disciplines working in business, academia, and government.

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