Microbial communities within the human gut play an important role in our overall health and wellbeing. Understanding how microgravity affects these microbial communities provides greater insight into the health of astronauts on board the ISS and what may occur during Deep Space explorations. Previous experiments have measured differential gene expression of single culture bacteria exposed to simulated microgravity, allowing us to map which genes are selected for or against in that environment. Using fecal pellets from mice exposed to simulated microgravity and space radiation, we are constructing and sequencing RNA and DNA libraries to study the metatranscriptome and changes in gut microbiota. These comparisons will allow us to gain a better understanding of how microbial communities are affected by space environments and what that may entail for the gut health of astronauts.