Emily Balskus

Professor of Chemistry and Chemical Biology, Co-director Chemical Biology PhD Program

Department of Chemistry and Chemical Biology
Mallinckrodt 303N
12 Oxford Street
Cambridge, MA 02138
Tel: 617-496-9921

Lab Size: Between 10-15


The focus of our research is the discovery of new enzymatic and non-enzymatic chemistry in living systems. We are particularly inspired by the breadth of reactions used by microorganisms in both primary and secondary metabolism. Microbes are Nature’s synthetic chemists, continually evolving elegant chemical solutions for problems inherent to their growth and survival in diverse environments. Understanding microbial chemistry is important; in addition to playing significant roles in the ecology of producing organisms, small molecules made and manipulated by bacteria and fungi have medicinal and industrial applications. The emerging field of synthetic biology has also fueled interest in engineering microbial metabolism to produce small molecules of natural and non-natural origins; such efforts will greatly benefit from the ability to introduce new chemistry, both enzymatic and non-enzymatic, into designed pathways.
One area of interest is the discovery of new biosynthetic pathways and enzymes using a genome mining approach heavily influenced by our deep understanding of chemical reactivity. We are targeting pathways from both primary and secondary microbial metabolism. Within secondary metabolism, we focus on uncovering biosynthetic pathways for natural products of unusual molecular architecture and characterizing metabolic pathways from the gut microbiota that may influence various aspects of human health.
We are also investigating whether it is possible to chemically modify small molecules in the presence of microorganisms using methods and design principles from synthetic chemistry. Our long-term goals in this area are to unite the fields of synthetic and biological chemistry by developing biocompatible chemistry: non-enzymatic reactions that can alter the structures of cellular metabolites. Ultimately, we will apply our methods to address problems in the areas of synthetic biology and medicine.


Haiser, Henry J.; Gootenberg, David B.; Chatman, Kelly; Sirasani, Gopal; Balskus, Emily P.; Turnbaugh, Peter J. “Predicting and Manipulating Cardiac Drug Inactivation by the Human Gut Microbe Eggerthella lenta” Science 2013, 341, 295–298.

Nakamura, Hitomi; Balskus, Emily P. “Using Chemical Knowledge to Uncover New Biological Function: Discovery of the Cylindrocyclophane Biosynthetic Pathway” Synlett,2013, 24, 1464–1470.

Brotherton, Carolyn A.; Balskus, Emily P. “A Prodrug Mechanism is Involved in Colibactin Biosynthesis and Cytotoxicity” Journal of the American Chemical Society, 2013, 135, 3359–3362.

Craciun, Smaranda; Balskus, Emily P. “Microbial Conversion of Choline to Trimethylamine Requires a Glycyl Radical Enzyme” Proceedings of the National Academy of Sciences USA 2012, 109, 21307–21312.

Nakamura, Hitomi; Hamer, Hilary A.; Sirasani, Gopal; Balskus, Emily P. “Cylindrocyclophane Biosynthesis Involves Functionalization of an Unactivated Carbon Center” Journal of the American Chemical Society 2012, 134, 18518–18521.