• Microbial Ecology and Evolution

    Microbial communities form the foundation of our planetary life support system. We study how bacterial populations coalesce to form complex ecological communities in dynamic environments. We are particularly interested in how these evolving communities maintain stability and functional resilience in the face of environmental fluctuations. We focus on microbial communities residing in the mammalian gut. These gut microbes provide crucial services to their hosts. Loss of key bacterial diversity, changes…

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  • Bioinformatic Tools and Methods

    Microbial communities cannot be observed directly. We use molecular techniques to measure DNA, RNA, protein, and lipids, which allow us to infer the form and function of microbial systems. In particular, we employ high-throughput DNA sequencing to quantify the taxonomic and functional content of a microbial community. These data are highly complex, containing many zeros (i.e. sparse), in addition to several forms of technical, sampling, and biological biases/noise that are…

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  • Gut Microbiome and Health

    The gut microbiome is now being recognized as a new organ of the human body. It is not an essential organ, like the liver or the heart, but we have found that proper functioning of the gut microbiome is necessary for long-term wellness and quality of life. Dozens of inflammatory conditions (e.g. inflammatory bowel disease, obesity, and rheumatoid arthritis) have been associated with the microbiome, in addition to several cancers…

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