Coffee intervention and gut microbiome-brain axis in Irish adults
269 faecal samples from healthy adult participants in Ireland, studied in an intervention design examining coffee consumption's effects on gut microbiome composition, metabolites, and host cognition. machine-written summary
269 samples · 269 runs · IE · Adult · 2026 · 3.97 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 807 sample values (country, subject id, timepoint) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 1,614 sample values (antibiotic exposure, collection date, health condition, health condition detail, location locality, location site) · PMC13100100 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| – External resources | not covered by the external resources we ingest |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
intervention — arms not resolved
design non_randomized_controlled
longitudinal — not resolved
31 of 60 people sampled more than once (240 samples; median 8, up to 8 per person). Schedule stated by the source: “CD: baseline (V2), withdrawal day2/4 (T2W/T4W), end of 2-wk withdrawal (V3/day14), intervention day2/4/14 (T2I/T4I/T14I), end of 3-wk reintroduction (V4); NCD sampled once (baseline).”; stated follow-up 35 d.
No Sandpiper profile for this project's samples yet.
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 269 | 100% | ||||
| country | 269 | 100% | 269 | |||
| health_condition | 269 | 100% | 269 | |||
| subject_id | 269 | 100% | 269 | |||
| antibiotic_exposure | 269 | 100% | 269 | |||
| collection_date | 269 | 100% | 269 | |||
| detailed_location | 269 | 100% | ||||
| health_condition_detail | 269 | 100% | 269 | |||
| location_locality | 269 | 100% | 269 | |||
| location_site | 269 | 100% | 269 | |||
| timepoint_label | 269 | 100% | 269 |
- Habitual coffee intake shapes the gut microbiome and modifies host physiology and cognition. 2026 PMID 42014402 PMC13100100 own_data
Archive description
Coffee influences multiple physiological processes, including gut function, stress, cognition, and the microbiome. However, the mechanisms underlying these effects remain poorly understood. In this study, we examined coffee’s impact on the microbiota–gut–brain axis—a bidirectional communication pathway between the gut microbiome and the brain—and assessed whether these effects occur independently of caffeine in healthy participants. Significant group differences emerged in faecal microbiome composition, with coffee drinkers showing increased relative abundance of Cryptobacterium and Eggerthella species, alongside reduced levels of the metabolite’s indole-3-propionic acid, indole-3-carboxyaldehyde, and the neurotransmitter γ-aminobutyric acid. Behaviourally, coffee drinkers exhibited greater impulsivity and emotional reactivity, whereas non-coffee drinkers demonstrated better memory performance. Some alterations in the faecal metabolome were reversible following coffee abstinence, and reintroduction triggered acute microbiome changes independent of caffeine. An integrated model identified nine key metabolites—including theophylline, caffeine, and selected phenolic acids—strongly linked to microbial species and cognitive measures. These findings reveal previously unrecognised effects of coffee on the microbiota–gut–brain axis, suggesting that microbiome profiles could potentially predict coffee consumption patterns and highlighting a close association between coffee intake and gut microbial composition.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult by deterministic_prior with confidence 0.90. Assay shotgun_dna.
- host external_curation.infant_catalog · “infant triage reason_code age_adult_only”
- body site study.title · “Coffee Shapes the Gut Microbiome and Host”
- body site study.description · “physiological processes, including gut function, stress, cognition,”
- life stage external_curation.infant_catalog · “infant triage reason_code age_adult_only”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA121646904 | antibiotic_exposure | no | R3 | 0.70 | paper.fulltext.methods | antibiotics/probiotics/prebiotics (minimum 4 weeks of washout to participate) |
| SAMEA121646904 | collection_date | 2021-09/2023-01 | R3 | 0.70 | paper.fulltext.methods | recruited for the study between September 2021 and January 2023 |
| SAMEA121646904 | country | IE | R1 | 0.90 | sample.attr.geographic_location_country_and_or_sea | Ireland |
| SAMEA121646904 | health_condition | healthy_control | R3 | 0.70 | paper.fulltext.methods | healthy adults between 30 and 50 years of age |
| SAMEA121646904 | health_condition_detail | healthy participants; no significant acute or chronic coexisting illness | R3 | 0.70 | paper.fulltext.methods | healthy adults between 30 and 50 years of age |
| SAMEA121646904 | location_locality | Cork | R3 | 0.70 | paper.fulltext.methods | screening visit at University College Cork |
| SAMEA121646904 | location_site | University College Cork | R3 | 0.70 | paper.fulltext.methods | screening visit at University College Cork |
| SAMEA121646904 | subject_id | 003 | R1 | 0.70 | sample.name_rule:sample_alias | 003-CD-T14I_S75_ME |
| SAMEA121646904 | timepoint_label | T14I | R1 | 0.70 | sample.name_rule:sample_alias | 003-CD-T14I_S75_ME |
Sequencing
269 runs over 269 samples · mean 4.31 Gbp per run (median 3.97 Gbp, total 1,159.94 Gbp; 269 runs with a base count) · layout PAIRED 269 · platform ILLUMINA 269 · models Illumina NovaSeq 6000 (269) · 0% of runs with a Sandpiper profile · first public 2026-03-26
Authors (24)
Boscaini S first · Bastiaanssen TFS · Moloney GM · Bergamo F · Zeraik L · O'Leary C · Ferri A · Irfan M · van der Rhee M · Lindemann TIF · Schneider E · Meyyappan AC · Harold KB · Long-Smith CM · Carbia C · O'Riordan KJ · de Alvarenga JFR · Tosi N · Del Rio D · Rosi A · Bresciani L · Mena P · Clarke G · Cryan JF last
Downloads
PRJEB108545.csv.gz (7.6 KB) · parquet (79.9 KB) — all 269 samples, every field with route and confidence · PRJEB108545_determinations.csv.gz (13.3 KB) — 2,421 evidence rows