Decoding the Gut Microbiota: Mechanisms of Host-Microbe Interactions and Inflammatory Pathologies

Microbes residing in the gastrointestinal tract are intertwined with the immune development and overall health of the host throughout stages of life. It is well established that these microbes can have both positive and negative impacts on host health, making understanding the interactions with the host critical in understanding gastrointestinal health. This complex and highly individualized relationship of microbes interacting within the host results in an ever-changing landscape in the gastrointestinal tract, whether due to host conditions or microbial conditions including microbe-microbe and microbe-host interactions. The vastness and complexity of the gut microbiota contribute to the challenge of quantifying not only a community of microbes in the gut environment, but also maintaining resolution to investigate individual microbes, capturing the network of interactions coinciding in the gastrointestinal tract. Functional capacity of microbes in the gut environment can vary widely due to microbial diversity, as well as host conditions, therefore understanding these interactions that have direct host impacts is important in gastrointestinal health and understanding inflammatory triggers. Here, we discuss the importance of high-resolution study of the gut microbiota, which include discussion of the potential modern approaches for analyzing the gut microbiota and consider the challenges and aspects necessary for robust investigation of the gut microbiota.