Work in the Ottesen lab seeks to understand the structure and function of complex microbial communities, and the ways in which microbes interact with and perceive complex environments. A major focus is the use of molecular ecological tools to observe microbial behavior in the environment. This includes not only observing and tracking changes in which microbes are present in an environment, but also using community transcriptomics to observe changes in microbial gene expression over time. By studying microbial behavior “in the wild”, we hope to gain a better understanding of the roles and significance of diverse members of the uncultured microbial majority. Host and microbial contributions to microbiome stability and dynamics We (and most other higher organisms) are hosts to complex gut microbial communities that aid in digestion and help shape our overall health. We are using the American cockroach (Periplaneta americana) and its gut microbiome as a model system to understand gut microbiome stability and dynamics, particularly responses to dietary perturbation. We use the cockroach as a model host organism because they are robust, low-maintenance insects that reproduce quickly, eat a diverse, omnivorous diet, and their digestive tract hosts a highly diverse gut microbiome dominated by bacterial families found in the guts of many other animals, including mammals and humans. Interestingly, we have found that despite its diversity, the cockroach gut microbiome is highly robust to diet shifts. This makes them an ideal system for understanding host and microbial factors driving gut microbiome stability and resilience. We are now working to understand how the host and microbes work together to maintain this stability. We have established methods for metatranscriptomic and metagenomic investigation of cockroach gut microbiome composition and activity. We have also established a robust system for producing and maintaining gnotobiotic cockroaches in the lab, enabling us to conduct experiments featuring gnoto- and xeno-biotic insects to continue investigating gut community dynamics in the cockroach host. Understanding the assembly and ecological roles of stream and river microbial communities. Streams and rivers play key roles in global biogeochemical cycles and act as the major conduits for the movement of carbon and nutrients between land and sea. We are exploring how streamwater microbial communities form and how this process is influenced by human impacts on the stream and the surrounding landscape.