RUI: Engineered Microbe Colonization and Community Response in a Model Microbial Community

Communities of microbes live in human bodies and all around, impacting the environment, the food system, and human health. Much like stable human communities, stable microbial communities are composed of many different members. Each member pursues their own strategies for survival, while at the same time interacting with each other and the physical environment in positive and negative ways to create a stable “neighborhood.” Like human communities encountering natural disasters or gentrification, microbial communities often encounter natural or human-caused disruption.

This project aims to determine and characterize the features that determine if a microbial community can be resilient or malleable to change when disrupted. This question will be addressed by creating simplified models of microbial communities, introducing disruptions like newcomer microbes or genetically altering existing community members, and then seeing how the community composition and behavior changes as a result of these disruptions.

This research aims to uncover general rules that will allow more accurate predictions of microbial community responses to disruptions, which will allow for the design of interactions with natural microbial communities in ways that benefit humans and their environments. This project will train undergraduate students from diverse socio-economic and cultural backgrounds.

The human microbiota and the microbial communities of the environments that humans interact with shape human biology and lives. Previous observational studies have identified compositional features of some of these communities, and a mechanistic understanding how these microbial communities interact with humans is beginning to take shape. The question of how the members in these microbial communities influence each other, however, remains.

Bioengineering has the potential to introduce genetically designed microorganisms to human and environmental communities to improve and modify their functions, but fundamental questions about microbe community behavior and device engineering remain unanswered. For example, can a genetically-modified organism enter an existing community and establish itself as a member?

The rules that govern how organisms naturally enter or leave the community are unknown. Once there, how will the community affect the behavior of the genetic device and vice versa? These questions will be addressed mechanistically by first developing in vitro microbial community models ranging from pairs of representative organisms grown in batch culture to complex environmental inocula grown in continuous culture.

These in vitro models will allow for inexpensive and rapid experimentation compared to currently existing in vivo models. Then, newcomer microbes will be introduced and changes in model community composition and gene expression will be identified through RNA-seq. Tn-seq screening will identify the mechanism by which successful newcomer microbes establish themselves in the model communities.

Concurrently, commonly used promoters and reporter genes will be constructed, and their performance quantified at the RNA and protein levels and compared between pure culture and community culture. This data will be used to uncover rules for designing devices that are tuned for optimal function in microbial communities.

This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.