Malnourishment results in a cycle that degrades the ability to effectively absorb nutrients even after adequate food has been consumed due to a disruption of gut homeostasis. We aim to better understand impaired nutrient absorption in malnourished individuals through a microfluidic based lab-on-a-chip approach. We are developing a malnourished model of an intestine into existing gut-on-a-chip device design fabricated through soft lithography techniques. In order to develop a more physiologically relevant model, we have studied the effects of different components of bacteria on the mechanical properties of the gut cells. Whole bacteria, spheroplasts, and the endotoxin lipopolysaccharide (LPS) were all introduced to the gut cell layer to determine their adverse effects on the stability of the cells. We characterized this malnourished model by studying the tight junction integrity along with cytoskeletal organization of the microvilli in both healthy and malnourished models. Additionally, we have looked at the permeability of the monolayer as an indicator of epithelial integrity. Our work would be useful in many areas including evaluating malnourished nutritional absorption in vitro as well as demonstrating the response of malnourished cells in a more physiologically relevant assay.