Coffee Consumption and Gut Microbial Diversity: The Role of Polyphenols

A cup of coffee to start the day is, for many people, indispensable and is an integral part of the workday. For some, it acts as an energy stimulant due to its caffeine content, while for others, it is part of a daily ritual, and most coffee lovers, above everything, simply enjoy the aroma. But coffee may offer benefits that go beyond simple enjoyment.

Polyphenols - a modulator of bacterial diversity?

Coffee beans contain dietary compounds known as "polyphenols". Polyphenols are also abundant in fruits and vegetables and, among other compounds, contribute to their colour and flavour and exert numerous health benefits.¹

While these powerful compounds may only be partially absorbed in our digestive tract due to their complex structure, they serve as an excellent source of fuel for the gut bacteria in the large intestine. Gut bacteria metabolise polyphenols, breaking them further down. This can lead to beneficial changes in microbial composition.²

What does the evidence show?

One small study published in 2020 followed 147 healthy individuals and observed an increase in a specific bacteria group called Bacteroides, Prevotella and Porphyromonas group in relation to higher coffee intake.³ Although the sample group was small and there were no significant outcomes for the other bacterial groups tested, this suggests a relation between coffee consumption and our gut microbial composition and further opens the door for future investigations.

A more recent, observational study from 2024 analysed stool samples from over 22,000 participants across different cohorts⁴ and found a strong association between coffee consumption and higher abundance of a particular bacterial species called Lawsonibacter asaccharolyticus.

• Higher consumption of coffee was associated with substantially higher levels of Lawsonibacter asaccharolyticus.

• This was further tested in vitro by adding coffee to the isolated cultures of Lawsonibacter asaccharolyticus, and the result showed increased growth, suggesting that coffee may directly promote bacterial growth.

• The study also interestingly showed that coffee containing caffeine and decaffeinated coffee had similar results, both resulting in growth of Lawsonibacter asaccharolyticus.

What does this mean in practice?

The polyphenols in coffee are fuel for gut bacteria that make up our microbiome. By breaking down the compounds into smaller metabolites, not only do said metabolites exert health benefits on their own, but they also further increase the beneficial growth of bacteria.²

These mechanisms are important for us, as a healthy microbiome has been associated with numerous aspects of health⁵ including:

• our digestion

• our immune health

• our metabolic health

• brain health

  
  

to name just a few. Therefore, consuming coffee, whether it is with caffeine or decaffeinated, may be beneficial for our microbiome due to its polyphenol content.

However, if you are not a coffee lover, there are plenty of other ways to include polyphenols in your diet. Other sources, such as fruits, vegetables, green tea, nuts and cocoa⁶, can all provide us with substantial amounts.

Key takeaway

While we can surely expect more studies in the future that further investigate how coffee influences our microbiome, these findings suggest that we can already assume that our morning coffee might not just wake us up but also give our gut bacteria a little boost of their own.

References:

1. Martirosyan D., Whited S., Kulkarni A. The Effects and Practical Applications of Polyphenols on the Human Gut Microbiome. 2025; 2(11): 221-235. DOI: https://doi.org/10.31989/AFBC.v2i11.1839

2. Wang X, Qi Y, Zheng H. Dietary Polyphenol, Gut Microbiota, and Health Benefits. Antioxidants (Basel). 2022 Jun 20;11(6):1212. doi: 10.3390/antiox11061212. PMID: 35740109; PMCID: PMC9220293.

3. González S, Salazar N, Ruiz-Saavedra S, Gómez-Martín M, de Los Reyes-Gavilán CG, Gueimonde M. Long-Term Coffee Consumption is Associated with Fecal Microbial Composition in Humans. Nutrients. 2020 May 1;12(5):1287. doi: 10.3390/nu12051287. PMID: 32369976; PMCID: PMC7282261.

4. Manghi, P., Bhosle, A., Wang, K. et al. Coffee consumption is associated with intestinal Lawsonibacter asaccharolyticus abundance and prevalence across multiple cohorts. Nat Microbiol 9, 3120–3134 (2024). https://doi.org/10.1038/s41564-024-01858-9

5. Hou, K., Wu, ZX., Chen, XY. et al. Microbiota in health and diseases. Sig Transduct Target Ther 7, 135 (2022). https://doi.org/10.1038/s41392-022-00974-4

6. Pérez-Jiménez J, Neveu V, Vos F, Scalbert A. Identification of the 100 richest dietary sources of polyphenols: an application of the Phenol-Explorer database. Eur J Clin Nutr. 2010 Nov;64 Suppl 3:S112-20. doi: 10.1038/ejcn.2010.221. PMID: 21045839.

Disclaimer: This article is for educational purposes only and does not replace medical advice. Individual needs vary, and personalised guidance from a qualified healthcare professional is recommended for tailored support.