From correlation to causation: The missing point in the study of functional foods and gut microbiota

[Display omitted] •The missing point in the current study of functional foods and gut microbiota is discussed.•Methods for establishing causation in the study of functional foods and gut microbiota are summarized.•Future study in the field of functional foods and gut microbiota should move from correlation to causation. Recently, there has been an unprecedented interest in the study of gut microbiota during treatment of diseases by functional foods. However, although great progresses have been made, a significant knowledge gap still exists. The knowledge gap, as argued here, is that in most of the studies we failed to establish a cause–effect relationship between attenuation of the diseases and changes of the gut microbiota. The lack of causation studies deteriorates the foundation for the use of functional foods in disease management that aim to target the gut microbiota. In this sense, we propose here that future studies on the interactions of functional foods and gut microbiota during the treatment of diseases must move beyond correlation to causation, and only after a cause–effect relationship has been established can we fully realize the therapeutic potential of functional foods in the upcoming era of microbiota targeted precision nutrition.