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Ultrahigh-throughput single cell profiling

Microbial populations are truly diverse - the human gut microbiome contains hundreds of species, and even individuals of the same species can be very different. For example, two strains of E. coli may share only 50% of their genes! To truly understand this diversity, we must study microbial species as populations of individuals rather than as a monolith. We are researching ways to characterize microbial populations on a cell-by-cell basis using ultrahigh-throughput experimentation. Whether that is by sequencing their single cell genomes, or by assaying for phenotypic differences in each cell.

microbes are highly varied

Ultrahigh-throughput characterization of microbial interactions

microbes cooperate and fight

Most microbes in nature live and interact with other microbes. These interactions determine both the composition, function, and dynamics of microbiomes. Given the enormous diversity of microbes in nature, it is difficult to experimentally characterize all these interactions using traditional approaches. We are researching ways to use ultrahigh-throughput experimentation to characterize the interactions of massive numbers of different microbes within a single experiment, which will give us a better understanding of the forces that shape microbiomes.

Inner angels, inner demons

The microbes living on and within us can significantly affect our lives. The microbes living in our gut form a stable community that can benefit or harm us depending on who is there. Thus far, the microbiome has been implicated in atherosclerosis, cancer, irritable bowel disease, obesity, Parkinson’s disease, mental health, and more. However, knowing which microbes are beneficial or detrimental is only half the battle. For this knowledge to be useful, we also need ways to replace the detrimental microbes with neutral or beneficial ones.

microbes influence our actions
microbes influence our actions

Engineering the human gut microbiome

microbes fight eachother

The human gut microbiome is surprisingly stable given that new microbial invaders are constantly being introduced into the digestive tract. While desirable under most circumstances, this stability can pose a barrier to our attempts to shape it to our liking. We are studying strategies that microbes use to persist within the gut microbial community and leveraging this understanding to research ways to manipulate their presence within the stable microbiome.

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