Coffee intake induces enterotype-specific restructuring of the human gut microbiome
Coffee is one of the most widely consumed beverages worldwide and has been associated with multiple health benefits, potentially mediated through interactions with the gut microbiome. However, the extent to which coffee intake alters gut microbial composition and whether these responses differ according to host enterotype remain poorly understood. In this study, we investigated dose-dependent and enterotype-specific responses of the human gut microbiome to coffee intake in healthy adults. Participants were classified into Bacteroides-dominant (B-type) and Prevotella-dominant (P-type) enterotypes based on baseline microbiome composition. Fecal samples were collected longitudinally across six time points representing baseline (T0), low-dose coffee intake (2 shots; T1–T2), washout (T3), and high-dose coffee intake (4 shots; T4–T5). Gut microbial composition was analyzed using 16S rRNA gene sequencing, and microbial functional potential was predicted using PICRUSt2. In addition, subject-aware Random Forest models were applied to identify microbial signatures associated with coffee intake stages. Overall microbial diversity and global community structure remained largely stable across sampling time points. However, high-dose coffee intake was associated with a significant reduction in microbial community distances, indicating increased convergence of gut microbiota composition across individuals. Taxonomic analysis revealed enterotype-dependent microbial responses, with the B-type enterotype showing more pronounced shifts in several dominant genera, including increases in Roseburia, Fusicatenibacter, and Lachnospiraceae-related taxa, and decreases in Bifidobacterium. Functional prediction suggested corresponding alterations in microbial metabolic pathways, particularly those involved in amino acid metabolism and energy-related pathways. Machine-learning analysis further demonstrated that microbiome states associated with coffee intake could be distinguished across sampling stages, with improved classification performance during the high-dose coffee phase. Collectively, these findings indicate that coffee intake induces enterotype-specific restructuring of the human gut microbiome, with microbial responses becoming more distinguishable under higher intake conditions. Our results highlight the importance of host enterotype in shaping microbiome responses to dietary exposures and provide new insights into the interaction between coffee consumption and gut microbial ecology.
Coffee is one of the most widely consumed beverages worldwide and has been associated with multiple health benefits, potentially mediated through interactions with the gut microbiome. However, the extent to which coffee intake alters gut microbial composition and whether these responses differ according to host enterotype remain poorly understood. In this study, we investigated dose-dependent and enterotype-specific responses of the human gut microbiome to coffee intake in healthy adults. Participants were classified into Bacteroides-dominant (B-type) and Prevotella-dominant (P-type) enterotypes based on baseline microbiome composition. Fecal samples were collected longitudinally across six time points representing baseline (T0), low-dose coffee intake (2 shots; T1–T2), washout (T3), and high-dose coffee intake (4 shots; T4–T5). Gut microbial composition was analyzed using 16S rRNA gene sequencing, and microbial functional potential was predicted using PICRUSt2. In addition, subject-aware Random Forest models were applied to identify microbial signatures associated with coffee intake stages. Overall microbial diversity and global community structure remained largely stable across sampling time points. However, high-dose coffee intake was associated with a significant reduction in microbial community distances, indicating increased convergence of gut microbiota composition across individuals. Taxonomic analysis revealed enterotype-dependent microbial responses, with the B-type enterotype showing more pronounced shifts in several dominant genera, including increases in Roseburia, Fusicatenibacter, and Lachnospiraceae-related taxa, and decreases in Bifidobacterium. Functional prediction suggested corresponding alterations in microbial metabolic pathways, particularly those involved in amino acid metabolism and energy-related pathways. Machine-learning analysis further demonstrated that microbiome states associated with coffee intake could be distinguished across sampling stages, with improved classification performance during the high-dose coffee phase. Collectively, these findings indicate that coffee intake induces enterotype-specific restructuring of the human gut microbiome, with microbial responses becoming more distinguishable under higher intake conditions. Our results highlight the importance of host enterotype in shaping microbiome responses to dietary exposures and provide new insights into the interaction between coffee consumption and gut microbial ecology.
University of California San Diego Microbiome Initiative