The role of bacterial interactions in succession of microbial communities in anaerobic environments

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Microorganisms exist in complex communities that are formed through dynamic processes. Succession, the change in the number and abundance of bacterial species over time, regulates many aspects of the resulting community, such as species richness and diversity. With DNA sequencing we can detect the patterns of succession, yet there is a fundamental knowledge gap about the mechanisms that drive these changes. Of the three main forces that drive succession (random, abiotic and biotic), we know the least about biotic forces such as bacteria-bacteria interactions. Competition (negative interactions) occurs through the depletion of shared resources, production of toxic compounds or direct killing. Competition is ubiquitous in the environment but has only begun to be studied in host-associated microbial communities. Cooperation (positive interactions) relevant to succession is through the production of a new resource useful to others (cross-feeding) but under stress can also include the detoxification of molecules like antibiotics. Only a fraction of bacterial interactions are cooperative, however, they have a disproportionately strong impact on microbial communities and succession. My research program aims to determine how bacteria interact with one another, through competition and cooperation, and the impact of these interactions on succession of microbial communities. We will identify and characterize bacteria-bacteria interactions with in vitro culture, molecular taxonomic profiling and synthetic ecology. We will identify influential bacteria within microbial community assembly by collecting empirical data about microbial communities in vitro. The combination of synthetic ecology with empirical data and mathematical modeling will highlight the aspects of community succession that are not fully explained by our synthetic biology approach requiring further study. We expect to quantify, for the first time, the biotic forces during microbial community succession with our simplified model of the gut microbiome from infants. Uncovering these basic mechanisms will contribute directly to the field of microbial ecology since microbial community function, such as productivity, or behavior, such as collapse under stress, are determined through succession. An understanding of how communities get to their final state is essential to the interpretation of all observations of microbial communities and will benefit research within the areas of conservation biology, biodiversity and biotechnology.