Coffee consumption is associated with intestinal Lawsonibacter asaccharolyticus abundance and prevalence across multiple cohorts
A large study with open per-microbe results: we load every microbe it tested.
Measured as total coffee intake: 14,647 drink a moderate amount of coffee, 5,730 never or rarely drink coffee (under 20 g a day) and 2,490 drink over 600 g (about 3 cups) of coffee a day.
What the study found
This study included 22,867 people in 5 cohorts in the UK and US. Their gut microbes were read with shotgun metagenomics, which reads the DNA of all the microbes in a stool sample. Coffee intake was self-reported.
For each of 1,932 microbes, the authors calculated a correlation, which shows how closely a microbe's share of gut bacteria goes with coffee intake across everyone in the study. They reported 252 microbes clearly higher and 46 clearly lower in people who drink more coffee.
The strongest clear results were Lawsonibacter asaccharolyticus, Massilioclostridium coli, Clostridia bacterium 12CBH8 and Clostridia bacterium UC5 1 1E11. For Lawsonibacter asaccharolyticus and coffee intake, the authors reported 0.43.
This describes what the study measured. It isn't advice about what to eat.
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How well coffee intake shows in the gut
- Coffee drinking told apart from gut microbes across populations (AUC)
- 0.89
- High coffee drinkers told apart from never drinkers (median AUC across cohorts)
- 0.92
- Moderate coffee drinkers told apart from never drinkers
- 0.86
- Moderate told apart from high coffee drinkers
- 0.63
- Lawsonibacter asaccharolyticus and coffee intake
- 0.43
AUC: how well a model told the groups apart from gut microbes alone, from 0.5 (no better than chance) to 1 (every time).
The microbes, by coffee intake
Higher in people who drink more coffee · 3
Strongest correlation first · 22,867 people
Lawsonibacter asaccharolyticus correlation 0.43 · in 5 of 5 cohorts
Massilioclostridium coli correlation 0.31 · in 5 of 5 cohorts
Massilistercora timonensis correlation 0.10 · in 5 of 5 cohorts
Correlation is the study’s measure of how closely a microbe’s share of gut bacteria goes with total coffee intake, across everyone, carriers or not: a Spearman correlation adjusted for sex, age and BMI, from −1 to 1. An association the authors report, measured once per person.
5 cohorts, 2 countries
| Cohort | Country | People |
|---|---|---|
| ZOE PREDICT 1 | UK | 914 |
| ZOE PREDICT 2 | US | 835 |
| ZOE PREDICT 3 UK22A | UK | 12,222 |
| ZOE PREDICT 3 US22A | US | 8,376 |
| Mind-Body Study and Men's Lifestyle Validation Study | US | 520 |
Why it's a noteworthy study
22,867 people in five cohort groups from the UK and US with diet questionnaires, all shotgun-sequenced; per-microbe correlations with coffee intake per cohort and pooled, in open supplementary tables (CC BY 4.0); relative citation ratio 8.4 (NIH iCite, provisional, 56 citations, checked 2026-10-04).
We load the per-microbe results from 41564_2024_1858_MOESM3_ESM.xlsx (Supplementary Tables 1–22) (Table S6) exactly as reported: partial Spearman's correlation (ρ) between a microbe's relative abundance and total coffee intake, adjusted for sex, age and BMI, per cohort and pooled with a random-effects meta-analysis. A result is clear when its q-value is under 0.001, the authors' threshold. We show it when it's clear and most of its cohorts agree, at least 2. A difference under the usual size for a small one (under 0.2 for a standardized difference, under 0.1 for a correlation) is folded under its pair, labeled "a very small difference", and isn't counted in the lists. It's kept apart from our own GMrepo comparisons and never mixed into them.
606 of the 707 microbes with a species name in its tables are microbes we list.
| Pair | Microbes in the table | Clear in the table | The paper's text says |
|---|---|---|---|
| Total coffee intake | 1,932 | 46 · 252 | 46 · 252 |
Clear counts are lower · higher in people who drink more coffee and so on, by the table's own q-values. We count the table's own q-values; the paper's text gives slightly different counts.
Manghi P et al., Nature Microbiology 2024, CC BY 4.0 · doi:10.1038/s41564-024-01858-9 · Data sources