Dan Knights


What can we learn from immigrants’ gut microbiomes and how they are influenced by health inequities?


Dan Knights develops computational methods for doing precision medicine with gut bacterial communities, or microbiomes, and he applies those methods to study human disease. Trillions of bacteria live in our guts, protecting us from infection and aiding our digestion, yet these communities are so complex that we need advanced computational methods to study them. In his multidisciplinary research lab Dan combines expertise in data mining and biology to learn about how modern lifestyles and medical practices are affecting our microbiomes and leading to increases in modern diseases. Dan received his PhD in Computer Science from the University of Colorado, followed by a post-doctoral fellowship at Harvard Medical School. Dan has co-authored over 70 highly cited articles in top multidisciplinary journals. In 2015 he was named a McKnight Land-Grant Professor by the University of Minnesota. His lab is building a next-generation informatics pipeline for microbiome-targeted drug discovery, linking nutrition and microbial activity to clinical outcomes. 


The Missing Microbes, by Marty Blaser.

This is a great read and extremely thorough exploration of the unintended consequences of antibiotics and other modern exposures on our inner microbial ecosystem.


Microbiome Discovery YouTube course: An online YouTube course that I teach to introduce learners to challenges and progress in microbiome analysis.


Most germs are not bad. In fact, we should treat them as honored guests inside our bodies. They help digest our food, protect us from infection, and keep our immune system balanced. As they serve us, we can also serve them by eating more fiber and avoiding unnecessary antibiotics.
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Computational Microbiologist