---
title: Coffee & The Microbiome
description: Compelling evidence has been uncovered outlining the relationship between coffee consumption and the composition of the gut microbiome. Multi-omic analysis of comprehensive dietary data and metagenomic sequencing of stool samples from 22,867 participants across the US and UK revealed 115 distinct microbial strains associated with long-term coffee intake. These findings were then integrated with public data from 54,198 diverse samples, including healthy individuals, non-Westernized populations, newborns, ancient microbiomes, non-human primates, and those with specific diseases.
---

[Biotics Research Blog ](https://blog.bioticsresearch.com)

# [Coffee & The Microbiome](https://blog.bioticsresearch.com/coffeemicrobiome)

 Written by [The Biotics Education Team](https://blog.bioticsresearch.com/author/the-biotics-education-team) | Jan 14, 2025 8:47:32 PM

[Compelling evidence](https://www.nature.com/articles/s41564-024-01858-9) has been uncovered outlining the relationship between coffee consumption and the composition of the gut microbiome. Multi-omic analysis of comprehensive dietary data and metagenomic sequencing of stool samples from 22,867 participants across the US and UK revealed 115 distinct microbial strains associated with long-term coffee intake. These findings were then integrated with public data from 54,198 diverse samples, including healthy individuals, non-Westernized populations, newborns, ancient microbiomes, non-human primates, and those with specific diseases.

Of all the microbial species tied to coffee consumption, the presence and abundance of the microorganism, *Lawsonibacter asaccharolyticus,* was demonstrated to be the most robust. Remarkably, this finding was consistent across populations of individuals in 25 diverse countries. In fact, *Lawsonibacter asaccharolyticus *was shown to be six to eight times more plentiful in the gut microbiome of individuals considered to be ‘high’ coffee drinkers (defined by more than three cups a day), compared to those who rarely drank coffee (defined by less than three cups per month). These results suggest coffee may stimulate the growth of *Lawsonibacter asaccharolyticus. * 

Indeed, scientists confirmed this hypothesis by demonstrating* in vitro* that coffee—including decaffeinated—promotes the growth of this bacteria. Compellingly, it was also demonstrated that infants do not inhabit this microorganism, further in support of these findings. 

Researchers additionally discovered the top ten microbial strains most strongly correlated with coffee consumption were also associated with decaf. These findings, therefore, suggest that coffee’s unique chemistry, aside from caffeine, may contribute to the distinct observed effects in the microbiome of habitual coffee drinkers.  

These results were consistent with previous [research](https://pmc.ncbi.nlm.nih.gov/articles/PMC8353542/) published in* Nature Medicine *demonstrating that among more than 150 dietary items, coffee yielded the most substantial impact in terms of its effects on the composition of the microbiome in 1,098 individuals.  

Coffee consists of polyphenols and fiber, in addition to subsequent bioactive [compounds](https://pubmed.ncbi.nlm.nih.gov/38370073/), which have been demonstrated to influence and enrich microbiome composition, while exerting various health benefits. The presence of *L. asaccharolyticus* in the gut microbiome of coffee consumers is particularly noteworthy, as metabolites produced by this microbiota have been associated with improved markers of systemic health.  

Beneficial microbiota play essential roles in transforming and secreting an array of metabolites, enzymes and vitamins, while also extracting nutrients from food and modulating metabolic responses. In fact, each diverse strain of microbiota has been shown to have the ability to interact with other strains—to promote or inhibit their growth—while some work in conjunction to enhance metabolic functions. 

One of the primary mechanisms in which microbiota influence health is through the production of metabolites that diffuse into systemic circulation, or into the bloodstream. Researchers discovered that chlorogenic acid, a potent polyphenol in coffee, is metabolized by *Lawsonibacter asaccharolyticus. *As other strains of microbiota feed on *L. asaccharolyticus* they also produce various subsequent important compounds, including [quinic acid](https://www.sciencedirect.com/science/article/pii/S2772753X24000893), a derivative of chlorogenic acid. This strong antioxidant has also been suggested to exhibit anti-inflammatory, metabolic and possibly antimicrobial properties. 

[Hippurate](https://pmc.ncbi.nlm.nih.gov/articles/PMC5651863/) is a further beneficial compound metabolized by this strain of microbiota, and has been implicated as a metabolomic marker of gut microbiome diversity. [Butyrate](https://www.microbiologyresearch.org/content/journal/ijsem/10.1099/ijsem.0.002800), a short chain fatty acid, is also produced by *Lawsonibacter asaccharolyticus,* [conferring](https://pubmed.ncbi.nlm.nih.gov/36763294/) various health benefits, such as improving intestinal barrier function and mucosal immunity, while exerting anti-inflammatory properties.  

Increased levels of these compounds have been [linked](https://pubmed.ncbi.nlm.nih.gov/18844285/) to improved markers of antioxidants, metabolic and gut health by enriching microbial [diversity](https://pmc.ncbi.nlm.nih.gov/articles/PMC5651863/). These related coffee compounds were also found in elevated levels in the blood of coffee consumers inhabiting this microbiota (*L. asaccharolyticus*). Plasma metabolomics analysis of 438 samples revealed increased concentrations of these metabolites among regular coffee consumers.This is important as greater microbiome diversity has been shown to be a [protective](https://pubmed.ncbi.nlm.nih.gov/36377581/) factor against various health [conditions](https://pmc.ncbi.nlm.nih.gov/articles/PMC6366966/).  

This research also aligns with previous studies demonstrating that coffee is linked to increased microbiome diversity, having vast health implications. For such, a smaller 2020 [study](https://pubmed.ncbi.nlm.nih.gov/32369976/) of 147 individuals published in* Nutrients *demonstrated an increase in *Bacteroides, Porphyromonas* and *Prevotella *among coffee drinkers utilizing quantitative PCR.  

The results of these studies provide novel insights into how coffee influences and modulates various aspects of health through its effects on beneficial microbiota and the metabolites they produce. This expanding body of research highlights the profound impact the gut microbiome has on overall health, as it has been demonstrated to govern nearly all of the body’s systems — including [metabolism](https://pmc.ncbi.nlm.nih.gov/articles/PMC9874984/), [immunity](https://pubmed.ncbi.nlm.nih.gov/34985325/), [hormones](https://pmc.ncbi.nlm.nih.gov/articles/PMC6469458/), and the nervous system.

Studies also indicate that a diverse gut microbiome helps mitigate [systemic](https://pmc.ncbi.nlm.nih.gov/articles/PMC7589951/) and [neuro-inflammation](https://pmc.ncbi.nlm.nih.gov/articles/PMC9167715/), which have been implicated in a number of chronic diseases and mental health conditions. These findings also establish a distinct metabolic link between specific gut microbiota and coffee, shedding light on the various metabolic pathways involved.  

This research provides compelling insights into how the unique compounds found in this widely consumed beverage can influence the gut microbiome in favorable ways that support our health.  

Coffee, therefore (including decaf), may offer protective health benefits, in conjunction with a nutrient dense diet and healthy lifestyle. 

Related Biotics Research Products: 

[View full post](https://blog.bioticsresearch.com/coffeemicrobiome)

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