Recently, longitudinal changes in human gut microbiome composition have been proposed to be more robust markers of host health than cross-sectional variation. However, it is unclear how gut microbiome dynamics are influenced by chronic inflammatory conditions, such as inflammatory bowel disease (IBD), cancer, and obesity. Microbiome features, including species diversity and taxonomic composition, could be evaluated to assess the system’s capacity to resist (degree of change from baseline: resistance) and recover (ability to return to baseline: resilience) following a perturbation. By applying a perturbation to the gut environment, we can observe microbiome features at baseline and post-perturbation to assess both resistance and resilience. Although challenging to measure, resistance and resilience may be related to the health of the host. Given this, we aim to understand the utility of resistance and resilience as potential biomarkers of host health and treatment response in patients with chronic inflammation.