Physical Structure and Inter-Species Interactions in Gut Microbial Communities

Resident within each of our intestines are trillions of microbes representing hundreds of species. These microorganisms compete, cooperate, and interact with each other and with our human cells and organs, and in doing so influence both normal physiological processes and a wide range of challenging diseases. Our understanding of how intestinal ecosystems are structured, how structure influences function, and how structure and composition can be altered remain minimal, in part because these ecosystems are not easily recapitulated in in “petri dish” studies. The gut microbiome operates under strong physical constraints. Species coexist at high densities, forcing them close to boundaries as well as competitors, and are subject to vigorous flows as the gut transports and processes food. Understanding the structure of the gut microbiome therefore requires observation and quantitative characterization of real intestinal environments, motivating this award. The investigators’ labs have pioneered the use of three-dimensional microscopy of larval zebrafish to gain insights into physical aspects of the gut microbiome. Zebrafish share many physiological similarities with humans and other vertebrates, making them an excellent animal model. At young ages they are quite transparent, and the recently developed technique of “light sheet fluorescence microscopy” enables fast, three-dimensional imaging over fields of view spanning the entire intestine, with resolution capable of discerning individual gut bacteria. Past work has shown that many gut bacterial species form aggregates: three-dimensional colonies with populations ranging from a few cells to tens of thousands of members. These observations raise fundamental questions about the nature and consequences of intestinal aggregation that this project aims to answer. First: Are there structural signatures of interactions among bacterial species? In zebrafish prepared such that only a single bacterial species is resident in the gut, the investigators have shown that the statistical distribution of aggregate sizes reflects physical processes of coalescence, fragmentation, and intestinal transport. In addition, multi-species communities coexist to a much greater degree than would be expected, for reasons that remain mysterious. The investigators suspect that the characteristics of aggregates, for example how aggregates of competing species are situated in the intestinal landscape and how species alter other species’ aggregation behaviors, can explain gut bacterial community structure. Second: Can aggregation state predict susceptibility to invasion? Intestinal microbes are constantly visited by new bacteria, but the reasons for resistance or susceptibility to invaders are poorly understood. This project focuses on a bacterial invader capable of altering the physical environment of the gut, namely a strain that enhances the strength of gut mechanical contractions. The investigators hypothesize that aggregation state is a major factor in invasion susceptibility, as large aggregates are readily transported and expelled by the contractions of the gut. This award involves the construction of intestinal communities in zebrafish composed of different numbers and types of species, linking observations of microbiome organization with invasion outcomes. In addition, experiments that select for invasion-resistant communities may be of particular importance for generating intestinal resilience in other animal species, including humans. In addition to the experiments and analyses described above, the investigators will design educational activities that use microbiome data to illustrate the intersection between biological imaging and computational analysis. These will be implemented in a day camp that targets low socio-economic status high school students. 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.