Abstract: 

Microbes are everywhere in nature and they live in diverse communities that show remarkable metabolic capabilities and robustness. On the other hand, disruption of microbiome homeostasis and associated changes in the community’s structure/function underlies numerous health or environmental issues. My lab has been developing and expanding a technological framework, based on nanoliter-scale water-in-oil microfluidic droplets, to co-cultivate microbial communities in a high-throughput manner and to elucidate the mechanisms governing these complex ecosystems. We start by utilizing droplets as highly parallel miniaturized bioreactors to encapsulate and co-cultivate individual cells distributed across droplets according to the Poisson distribution. Protocols have been developed for a wide variety of microbes, such as aerobes, anaerobes, and phototrophs. Droplets containing co-cultivated mini-communities are then characterized through a number of methods, including microscopy, sequencing, or outgrowth followed by assays accessible to larger-volume cell cultures. Additionally, these droplets can be sorted based on fluorescence signals to screen for target properties such as enhanced co-growth.  

These modules can be integrated to create pipelines tailored for specific applications spanning the range of naturally occurring microbiomes and synthetic co-cultures.

A second distinct yet complementary research thrust in my lab, inspired by naturally occurring synergistic microbial communities, has been the design and construction of synthetic consortia for biomanufacturing and bioremediation. For instance, to make use of lignocellulosic biomass, we designed and optimized a consortium consisting of a cellulolytic fungus capable of hydrolyzing hemicellulose and cellulose (main components of lignocellulosic biomass) into mono and oligosaccharides and a genetically engineered bacterium for converting mono and oligosaccharides into isobutanol, an advanced biofuel. The general framework of engineering defined co-cultures of coordinated specialists offers tremendous potential for developing novel biotechnologies for numerous applications.

Bio: 

Prof. Xiaoxia “Nina” Lin obtained her bachelor's degree in chemical engineering and a minor in computer science from Tsinghua University in 1997. She then moved to the United States and pursued a PhD degree in process systems engineering with Chris Floudas at Princeton University. Afterwards, Nina furthered her training as a postdoc in the emerging field of systems and synthetic biology with George Church at Harvard Medical School. Since 2006, Nina has been directing her own research group at the University of Michigan - Ann Arbor. Her group’s research has been funded by U.S. government agencies (e.g. NSF, NIH, DOE) and the industry. Nina is the recipient of a 2011 CAREER Award and a 2022 MCA award from the U.S. National Science Foundation, a University of Michigan Elizabeth C. Crosby Research Award in 2007 and 2011, and invited participant/speaker at two frontier symposia sponsored by the U.S. National Academies of Engineering and Science.