Background and objectives: As one of the most popular beverages in the world, coffee has long been known to affect bowel functions such as motility, secretion, and absorption. Recent evidence obtained in human and animal studies suggests that coffee has modulating impacts on gut microbiota. We aim to present an overview of the specific effects of coffee on gut microbiota composition, diversity, and growth. We will also critically review the impacts of coffee on bowel functions in health and diseases and discuss whether gut microbiota play a role in the coffee-associated functional changes in the gastrointestinal tract. Methods: We searched the literature up to June 2024 through PubMed, Web of Science, and other sources using search terms such as coffee, caffeine, microbiota, gastrointestinal infection, motility, secretion, gut-brain axis, absorption, and medication interaction. Clinical research in patients and preclinical studies in rodent animals were included. Results: A majority of the studies found that moderate consumption of coffee (<4 cups a day) increased the relative abundance of beneficial bacterial phyla such as Firmicutes and Actinobacteria and decreased Bacteroidetes. Moderate coffee consumption also increased Bifidobacterium spp. and decreased the abundance of Enterobacteria. Coffee consumption is reported to increase gut microbiota diversity. Although the effects of coffee on bowel functions have been known for a long time, it is not until recently that we have recognized that some of the effects of coffee may be partly due to its impacts on microbiota. Conclusions: The current literature suggests that moderate coffee consumption has beneficial effects on oral and gut microbiota and motility function. However, excessive coffee intake (>5 cups a day) is implicated in reflux disorders, periodontal diseases, and progression of Crohn's disease. Further research in the field is needed, as there are many conflicting results regarding the impacts of coffee in the gastrointestinal tract.
Keywords: absorption; caffeine; coffee; dysbiosis; gastrointestinal tract; gut–brain axis; immunity; microbiota; motility; secretion.