The human gut microbiome is a complex and individualized ecosystem, formed and shaped by genetics and many environmental factors, such as early experiences, diet, age, stress and antibiotic use. Healthy and taxonomically diverse gut microbiome systems are resilient and can resist disruptions such as viral or bacterial infections, medicines and periods of stress. Dysbiosis, an imbalance or shift in the microbial makeup of the microbiome, causes numerous problems to the host including metabolic disorders, inflammation and has been linked to pathologies such as colon cancer and diabetes. Understanding the bacterial makeup of the gut microbiome as well as its secondary metabolites is crucial to not only develop a comprehensive picture of how bacteria that occupy diverse environmental niches symbiotically thrive in the healthy gut but also respond to challenges such as acute and chronic bio/chemical exposures that contribute to dysbiosis. However, investigating how these factors affect the gut ex vivo is traditionally difficult due to the shortcomings of laboratory culture platforms to sufficiently emulate the complex nature of the lower gastrointestinal tract. Here, we detail a 3D-printed in vitro system that replicates the oxygen gradient across the colon epithelium in a benchtop device and allows for the high-throughput study of the microbiome and its metagenomic profile and metabolic function. Using an organophosphate to model an acute chemical exposure, shifts in microbial function and key metabolites were observed in human fecal microbiome samples. Supplementation with exogenous tryptophan appears to promote resiliency by restoring or preventing perturbations to microbial function. This rapidly prototyped device enables further studies to be performed to understand how environmental factors contribute to dysbiosis, enabling multiplexed screening of measure/countermeasures with diverse gut microbiome samples on the laboratory benchtop.