(7bh) Genome- and Biome-Scale Microbial Engineering Using Synthetic Biology, Robotic Automation, and Mass Spectrometry Imaging

Microorganisms play essential and fascinating roles in various ecosystems and show important applications in biotechnology and medicine. Lying at the interface of chemistry, biology and engineering, my research centers on high-throughput technologies for basic and applied research in microbial systems, seeking to push the scale limit of natural and artificial diversities we can analyze and program. Studies of microbial diversities in high throughput not only help to create and isolate valuable microbial hosts and products, but also enable large-scale genotype-phenotype mapping to advance fundamental understanding of biology.

During my graduate study, I focused on genome and metabolic engineering of yeast as a microbial cell factory, and one notable project is the development of automated multiplex genome-scale engineering in yeast. Current genomic libraries are mainly limited to single-gene, single-mode mutations in very few strains. Multiplex genome-scale engineering is essential in rewiring complex cellular networks for optimizing a target trait, but extremely challenging, especially in yeast, due to the lack of efficient tools. I developed standardized genetic parts for iterative, modular introduction of diverse mutations on a genome scale using CRISPR/Cas and RNAi. Such standardization and modularization permit the use of defined workflows and hence robotic automation, which is critical when creating and screening such enormous diversity. For custom yeast strains, the impact of both overexpression and knockdown mutations of >90% genes on a select phenotype can be tracked simultaneously. Also, up to 40 genes can be targeted in a single cell to explore genetic interaction. These capacities enable optimization of a wide range of fermentation traits including substrate utilization, protein/metabolite overproduction, and inhibitor resistance.

My postdoctoral work has broadened my horizons in two aspects: (1) mass spectrometry (MS) imaging as a general structure-based screening modality, and (2) biomedical research. For microbial metabolites, most screening schemes rely on photometric or biological properties specific to a target molecule, requiring case-by-case, time-consuming assay development. MS detects hundreds of compounds simultaneously with high selectivity but has not been widely applied in microbial screening. I developed optically-guided MS profiling that utilizes machine vision to aid automated MS measurement at randomly distributed colonies. The resulting MS datasets were visualized in a straightforward manner similar to colorimetric readouts. When applied to screen the variant library of a lanthipeptide antibiotic, a structure-activity relationship was rapidly established, and new analogs with improved activity were identified. Optically-guided MS profiling was also applied to characterize microbial communities. Unique microbial strains were isolated in high throughput from rat gut microbiota based on proteomic signatures. For isolated microbes, metabolomic profiles were correlated with host responses, such as pancreatic peptide secretion from ex vivo islet models, which provides valuable insights into the molecular mechanism of host-microbe interaction. MS imaging was also used to characterize surface-associated biofilms, a major contributor to medical device-associated infections, revealing spatial heterogeneity and interplays of community signaling, gene regulation, and metabolite production.

Looking forward, I seek to establish an independent research program focusing on the understanding and engineering of human-associated microbial communities. Complementary to current microbiota studies that mainly monitor compositional changes using DNA sequencing, high-throughput molecular and imaging methods will be developed for in vitro and ex vivo models for hypothesis-driven research, aiming to pinpoint key chemicals and corresponding pathways mediating microbe-microbe and host-microbe interactions, to analyze and control horizontal gene transfer for in situ microbiome engineering, and to engineer probiotic strains for therapeutic reprogramming of microbiota.

Teaching Interests:

I consider myself a beneficiary of innovative education programs mainly including (1) an undergraduate degree at the chemistry-biology interface with an emphasis on lab research; (2) the graduate Mavis Future Faculty Fellowship focusing on non-research skills in proposal writing, teaching, and service; and (3) the postdoctoral fellowship at the Carl R. Woese Institute for Genomic Biology encouraging research across disciplines. Therefore, I will dedicate to continuing innovation in teaching to train the next generation of researchers and professionals in chemical engineering.

For introductory courses, such as biochemical engineering and chemical reaction engineering, while ensuring solid coverage of the fundamentals, I plan to introduce new pedagogy techniques to flip the classroom, including problem-based learning, peer teaching, field visits, and so on. These measures are not merely to appeal to students’ interests, but also to equip them with learning skills and collaborative mindsets that are critical in the current workplace with evolving challenges and technological landscapes. For advanced courses such as synthetic biology, I will emphasize the qualities needed as an interdisciplinary researcher, for example, the ability to effectively communicate with people from diverse scientific backgrounds, and to formulate research strategies to tackle complicated, real-world problems in feasible steps. As for student mentoring, in addition to graduate students and postdoctoral fellows from different research groups, I have been working closely with 12 undergraduate research assistants. There is nothing more rewarding to me than the achievements of the undergraduate mentees, such as dream school offers, summer research fellowships, and presentation awards. Furthermore, I have been frequently involved in outreach activities, including hands-on activities targeting K-12 students and public lectures, with the firm belief that it is important to improve public acceptance and attract young minds for the continuing prosperity of a relatively new research area such as synthetic biology.