Perturbations to the gut physical environment, such as changes to pH, temperature, and osmolality, have a drastic - yet underexplored - impact on the establishment and maintenance of microbial communities. While we understand the large impact of physical perturbations, we are still unable to predict microbial dynamics in response to environmental stressors. In this talk, I will discuss approaches to characterize microbial communities in complex environments, including an in-house pipeline developed to detect and quantify absolute microbial counts at high resolution. I will also begin dissecting the impact of the physical environment on microbiome composition, compared to inter-bacterial and host-bacterial interactions. Overall, our goal is to better understand microbial responses to environmental perturbations and ultimately predict microbial composition based on gut physical parameters.