Host Engineering

view profile for Aindrila Mukhopadhyay

Aindrila Mukhopadhyay

Vice President for Biofuels and Bioproducts, and Director of Host Engineering

view profile for Thomas Eng

Thomas Eng

Deputy Director of Host Engineering

view profile for Adam Feist

Adam Feist

Scientific Lead, Host Engineering

view profile for Bernhard Palsson

Bernhard Palsson

Scientific Lead, Host Engineering

view profile for Deepanwita Banerjee

Deepanwita Banerjee

Research Scientist

view profile for Javier Menasalvas

Javier Menasalvas

Research Assistant

view profile for Aparajitha Srinivasan

Aparajitha Srinivasan

Post Doctoral Researcher

view profile for Sunghwa Woo

Sunghwa Woo

Post Doctoral Researcher

Microbes represent an inexhaustible source of beneficial chemicals and can use a range of carbon sources. However, in their native state, most microbes only use a fraction of the carbon types and can produce only small quantities of these molecules. This is an important constraint to be overcome in developing  bioproduction hosts. In the Host Engineering Group, we use genomics and synthetic biology to optimize carbon utilization, the production of desired molecules in engineered microbes. Our goals are to develop microbes that can accumulate high levels of fuel products, tolerate inhibitory pretreatment byproducts and consume all forms of carbon in the biomass. We work closely with other teams at JBEI to achieve this vision, as well as DOE facilities like the JGI and EMSL. We also work closely with researchers at the ABPDU to develop strains that have good performance at commercially relevant scales.


  • Bacterial hosts (Pseudomonas spp, E. coli, C. glutamicum): Discovery and optimization of carbon utilization regimes, tolerance mechanisms to biomass-related inhibitors and final products to generate robust, scalable production platforms
  • Fungal hosts (R. toruloides, S. cerevisiae): Development of new tools and strategies to enable sophisticated strain engineering
  • Adaptive Lab Evolution across a range of strains and final phenotypes (e.g. enhanced tolerance and carbon utilization)
  • Genome Scale metabolic model and functional genomics driven microbial chassis development

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