Considerations for Best Practices in Studies of Fiber or Other Dietary Components and the Intestinal Microbiome

A two-day workshop organized by NIH and USDA included 16 presentations focused on the role of diet in alterations of the human gastrointestinal microbiome, primarily that of the colon. Although thousands of projects have been funded by United States federal funding agencies to study the intestinal microbiome of humans and a variety of animal models, only a minority address dietary effects and a small subset are described in sufficient detail to allow reproduction of a study. While there are standards being developed for many aspects of microbiome studies such as sample collection, nucleic acid extraction, data handling, etc., none have been proposed for the dietary component. It is important to the research enterprise to foster both rigor in design and reproducibility of published studies. Speakers addressed the influence of the structure of fermentable carbohydrate on the microbiota, the variables to consider in design of studies using animals, in vitro models, and human subjects. For all types of studie...