The intestinal microbiota is comprises a diverse community of micro-organisms that interact with many host processes. Innate immune responses to the gut microbiota are of particular importance as they influence many other downstream responses. This fascinating host-microbe crosstalk is a rapidly expanding field of study; thus, it is critical to ensure reproducibility between studies and applicability to human clinical trials through standardization of experiments. We discuss here recent advances in the field including the spectrum of colonization statuses available, the critical importance of colonization timing, the dynamics of the microbial community, and the required housing of animals, as they pertain to appropriate experimental control and design.
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