The composition of microorganisms that reside in the human intestine (gut microbiota) has a profound impact on health. Recent work has shown links between the gut microbiota and conditions such as inflammatory bowel disease, obesity, and drug metabolism. There is great interest in harnessing this knowledge to develop methods of manipulating the gut microbiota as a new way to treat diseases associated with an improper composition of microbes. However, we are limited by our understanding of what manipulations of the community would promote better health because tools to address these questions are lacking. Despite considerable advances in elucidating the relationships between the microbiota and health, the challenge of understanding the contributions of individual bacteria cannot be fully addressed by current technologies. The goal of the proposed research is to address this challenge by developing a novel strategy that would allow the selective elimination of specific bacterial taxa from a community. The approach involves engineering broad host range phages to deliver an endonuclease that selectively cleaves a DNA sequence unique to the genome of the target bacterium, leading to cell death. The effectiveness and specificity of this targeted killing mechanism will be tested and refined in the model bacterium Escherichia coli and in cultured bacteria from the human gut. The germ-free mouse system colonized with bacteria from the human gut will be used as a model to test hypotheses about the functions of specific bacteria in the community. The development of a new technology to eliminate individual members of a microbial community could have profound impacts on the treatment of diseases associated with an imbalance of microbes, as well as those caused by a specific bacterial agent. Furthermore, this strategy could be widely applicable to the study of fundamental aspects of microbial communities.

Public Health Relevance

There is strong evidence that the composition of the human gut microbiota is a significant determinant of health status. Bacteria implicated in promoting health or disease states have been identified, but currently no method exists for tailoring the microbiota to create a healthy profile. This proposal describes a strategy to develop a method of targeting and killing specific members of a microbial community, which could be used to manipulate the human gut microbiota.

National Institute of Health (NIH)
National Institute of Allergy and Infectious Diseases (NIAID)
NIH Director’s New Innovator Awards (DP2)
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Special Emphasis Panel (ZRG1)
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Mills, Melody
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University of California Berkeley
Other Basic Sciences
Earth Sciences/Resources
United States
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Shelton, Amanda N; Seth, Erica C; Mok, Kenny C et al. (2018) Uneven distribution of cobamide biosynthesis and dependence in bacteria predicted by comparative genomics. ISME J :
Abreu, Nicole A; Taga, Michiko E (2016) Decoding molecular interactions in microbial communities. FEMS Microbiol Rev 40:648-63