Coffee’s Microbial Signature: How a New Bacterium Reveals the Brew’s Hidden Impact on Gut Health

Redacción HC
04/10/2025

Introduction

Coffee is more than a morning ritual—it is the most widely consumed beverage after water and has long been associated with health benefits ranging from lower risk of metabolic disease to increased longevity. Yet, the precise ways in which coffee reshapes the gut microbiome have remained largely unknown.

A large international study published in Nature Microbiology (Manghi et al., 2024) uncovers a striking and reproducible link: regular coffee consumption is strongly associated with the presence and abundance of a previously obscure gut bacterium, Lawsonibacter asaccharolyticus. This discovery provides new insight into how a single dietary component can leave a measurable “microbial fingerprint” and may help explain some of coffee’s health effects.

Investigating the Coffee–Microbiome Connection

While diet is known to be one of the main drivers of gut microbiome composition, identifying species-specific responses to individual foods has been challenging. Coffee’s bioactive compounds and its widespread consumption made it an ideal candidate for a large-scale analysis. The research team—led by scientists from the University of Bologna and Harvard University—asked a simple but ambitious question: does regular coffee drinking consistently favor the growth of specific gut microbes across diverse populations?

Large-Scale, Multi-Layered Methodology

To answer this question, the researchers analyzed an unprecedented dataset: 54,198 fecal metagenomes from 22 cohorts, including major studies such as ZOE PREDICT, the Mind–Body Study, and the Men’s Lifestyle Validation Study. An additional 18,984 publicly available metagenomes were included for cross-population validation.

Dietary data from 22,867 participants, collected through detailed food-frequency questionnaires, enabled classification of coffee intake as never, moderate, or high. Taxonomic profiling used MetaPhlAn 4, and machine learning models—specifically random forest algorithms with cross-validation and a leave-one-dataset-out approach—tested whether gut microbiome composition could predict coffee intake.

The study went further by integrating 438 plasma metabolomic profiles and 364 fecal metatranscriptomes. Finally, in vitro experiments assessed whether Lawsonibacter asaccharolyticus could grow in media enriched with coffee extract.

Key Findings: Meet the “Coffee-Loving” Bacterium

The standout result was a consistent and strong association between coffee consumption and the abundance of Lawsonibacter asaccharolyticus. Across multiple cohorts, random forest models predicted coffee intake with an area under the curve (AUC) exceeding 0.8 and Spearman correlations above 0.5—evidence of a robust microbial signal.

This relationship held true across populations in the United States and United Kingdom, and was further confirmed in independent public metagenomic datasets.

Metabolomic analyses revealed that regular coffee drinkers had higher blood levels of coffee-related bioactive compounds, including quinic acid and trigonelline. These metabolites correlated closely with the abundance of Lawsonibacter asaccharolyticus. Laboratory experiments provided additional support: the bacterium grew more effectively in coffee-supplemented media.

Taken together, these lines of evidence—cross-cohort statistics, metabolomics, and controlled laboratory tests—demonstrate a specific metabolic link between coffee and Lawsonibacter asaccharolyticus.

Implications for Health and Nutrition

Although the study does not establish direct causality in humans, it suggests that coffee can reproducibly shape the gut microbiome in ways that may influence health. The discovery of a “coffee-associated” microbe raises several possibilities for future research:

• Determining whether Lawsonibacter asaccharolyticus contributes to the known metabolic or cardiovascular benefits of coffee.
• Exploring whether the bacterium could serve as an objective dietary biomarker, providing a more reliable measure of coffee intake than self-reported questionnaires.
• Investigating how different coffee preparation methods—such as espresso, filter coffee, or drinks with milk and sugar—affect this microbiome signature, especially in regions like Latin America where coffee culture is diverse and vibrant.

For public health, these findings highlight the potential for precision nutrition strategies that consider both dietary habits and microbiome composition. They also illustrate how single foods can leave a distinct microbial “fingerprint,” paving the way for microbiome-informed dietary recommendations.

Conclusion

This international investigation—led by Paolo Manghi (University of Bologna), Amrisha Bhosle, Kai Wang, and Mingyang Song (Harvard), and Nicola Segata (University of Bologna)—demonstrates that coffee drinking leaves a measurable microbial signature in the human gut. The consistent link between coffee and Lawsonibacter asaccharolyticus provides a new perspective on how everyday dietary choices influence the complex ecosystem within us.

While your morning cup of coffee remains a personal pleasure, it is also, as this research shows, a subtle biological experiment. Future clinical trials will be needed to determine whether modulating Lawsonibacter asaccharolyticus through coffee consumption can help prevent or treat metabolic diseases.

Topics of interest

Biodiversity