How do green and black coffee brews and bioactive interaction with gut microbiome affect its health outcomes? Mining evidence from mechanistic studies, metagenomics and clinical trials

The gut microbiome has become a hot topic in recent years with increasing reports on the positive role of a well-balanced gut microbiota composition for one's health and well-being. A number of dietary factors can modulate gut composition, although few publications have focused on common daily beverages impact on the gut microbiome. Coffee is a worldwide beverage consumed mostly as black coffee that is originally derived from green coffee beans post roasting. To enhance the taste and aroma, green coffee is typically roasted and to further affect its chemical composition and rationalize for the different health outcomes. Roasted seeds contain a high caffeine levels versus phenolic acids i.e., chlorogenic acid enrichment in green coffee suggestive that they interact differently with gut microbiota and to affect its metabolism. The present review provides a mechanistic insight on the effects of black and green coffee chemicals on the gut microbiome. We present herein the first comprehensive review of how coffee natural bioactive such as caffeine and chlorogenic acid and its process derived chemicals i.e., melanoidins can specifically influence gut homeostasis, and likewise via gut microbiota-mediated coffee chemicals metabolism. The role of gut microbiota in affecting coffee chemicals and the potential of mining metagenomics data to uncover gut microbiome community and carbohydrate active enzyme (CAZyme) profile associated with coffee consumption are presented for the first time. Moreover, our metagenomics analysis in silico showed a decrease in abundance in either Desulfofarcimen or Mycoplasma genera, confirmed the basic coffee-gut microbial enzymes repertoire found in the literature and highlights for the first time the coffee CAZyme biomarkers encoded by the human gut microbiome.