Principal Investigators
The GutWorks team is led by PIs who are pioneering novel cultivation methods, synthetic biology approaches, electroporation for genetic transformation, host models, and tools for assessing gene function in vitro and in vivo.
Our combined expertise spans bacteriology, microfluidics, high-throughput screening, host-microbe interactions, and imaging.
Dr. Cullen Buie (MIT)
Cullen is an expert in the areas of electrokinetic phenomena, genetic transformation of microbes, electrochemistry, and heat and mass transfer. Over the past seven years, his lab has focused on the impacts of microscale transport phenomena on prokaryotic and micro-eukaryotic organisms. His lab has developed microfluidic electroporation platforms that facilitate high-throughput, automated genetic transformation of bacteria. He has also pioneered microfluidic assays for rapid discovery of genetic transformation conditions for previously intractable microbes. Together, these systems will serve as an enabling platform for GutWork’s efforts to illuminate the physiology of the diverse organisms that compose the human gut microbiome.
Dr. Adam Deutschbauer (LBL)
Adam is an expert in bacterial functional genomics and systems biology. For the past 10 years, his lab has focused on the development and application of genetic tools to rapidly characterize uncharacterized genes from diverse bacteria. His lab makes extensive use of laboratory automation, chemical libraries, and multiplexed assays to generate extensive genetic datasets in bacteria. More recently, he has been interested in understanding the roles of microorganisms in their natural environment, with a focus on rhizosphere bacteria. The Deutschbauer group is part of a large DOE-funded project and as such, is highly collaborative. In the past 5 years, his laboratory has provided guidance and resources to dozens of labs interested in high-throughput genetics. Since 2018, he has also been an adjunct assistant professor in the Plant and Microbial Biology Department at UC Berkeley.
Dr. KC Huang (Stanford)
KC is a bacterial cell biologist and biophysicist, with a strong focus on the organizational principles of microbial communities and the physiology of gut commensal bacteria. Huang has broad expertise in computational physics and biology, with specific training in the physical modeling of bacterial physiology. His group has developed experimental synthetic biology tools that enable novel interdisciplinary studies of the role of physical forces in cellular organization. In recent years, his lab has applied these tools to complex microbial communities such as the intestinal microbiome. His group has developed a powerful experimental and computational framework for quantifying the spatial organization of the gut, which has revealed strong effects of diet on the structure of the community surrounding the mucus. His group has also developed high-throughput approaches for imaging single bacterial cells that GutWorks will use for forward genetic screens of genomic-scale libraries.
Dr. Justin Sonnenburg (Stanford)
Justin is an expert in the microbiota and its relationship with disease. His overarching goal is to define the mechanisms that connect changes in the gut environment, such as dietary change or presence of a pathogen, to the microbiota’s response and its impact on host biology. His lab applies molecular-genetic and systems-level tools to intestinal microbiology and uses gnotobiotic mouse models to unravel the complexities of interactions in the gastrointestinal tract. He colonizes ex-germ-free mice with defined model microbiotas to gain insights into the dynamics of a microbial ecosystem in an in vivo model. New approaches include (i) quantitative image analysis of the microbiota within the gut to address a major gap in understanding the spatial organization of the intestinal ecosystem, and (ii) synthetic biology applications to engineer gut symbionts that can record their own life experiences, detect inflammation, or execute site-specific therapeutic delivery.
Dr. Carlotta Ronda (Innovative Genomics Institute, UC Berkeley)
Carlotta is an expert in CRISPR editing of microbiome communities. She is a Principal Investigator and WIES Fellow at the Innovative Genomics Institute at UC Berkeley. Her research has focused on genetic modification of non-model organisms and microbial communities. As a Simons Junior Fellow at Columbia University, she pioneered a landmark platform to edit microbial communities in vivo using CRISPR technology, paving the way for future microbiome-based therapies. Her recent work opens new avenues for targeted functional metagenomics in situ, enhancing our understanding of microbial communities in their native milieu. Her lab applies systems biology principles to modulate the gut microbiome and develops innovative platforms to decipher bi-directional host-microbiome signaling. Leveraging cutting-edge gut organoid co-culturing systems, CRISPR technologies, and microbiome engineering platforms, her team combines in vitro and in vivo studies with mouse models to map the host-microbiome interactome. These efforts include creating genetic and molecular systems in diverse bacterial chassis and mammalian cells, using -omic technologies to characterize fundamental genetic mechanisms.