Habitual coffee intake shapes the gut microbiome and modifies host physiology and cognition

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dc.contributor.authorBoscaini, Serena
dc.contributor.authorBastiaanssen, Thomaz F. S.
dc.contributor.authorMoloney, Gerard M.
dc.contributor.authorBergamo, Federica
dc.contributor.authorZeraik, Laila
dc.contributor.authorO’Leary, Caroline
dc.contributor.authorFerri, Aimone
dc.contributor.authorIrfan, Maha
dc.contributor.authorvan der Rhee, Maaike
dc.contributor.authorLindemann, Thaïs I. F.
dc.contributor.authorSchneider, Elizabeth
dc.contributor.authorMeyyappan, Arthi Chinna
dc.contributor.authorHarold, Kirsten Berding
dc.contributor.authorLong-Smith, Caitríona M.
dc.contributor.authorCarbia, Carina
dc.contributor.authorO’Riordan, Kenneth J.
dc.contributor.authorde Alvarenga, José Fernando Rinaldi
dc.contributor.authorTosi, Nicole
dc.contributor.authorRio, Daniele Del
dc.contributor.authorRosi, Alice
dc.contributor.authorBresciani, Letizia
dc.contributor.authorMena, Pedro
dc.contributor.authorClarke, Gerard
dc.contributor.authorCryan, John F.
dc.contributor.funderScience Foundation Ireland(SFI)
dc.contributor.funderEuropean Research Council
dc.contributor.funderHorizon 2020
dc.date.accessioned2026-05-22T11:50:06Z
dc.date.available2026-05-22T11:50:06Z
dc.date.issued2026-04-21
dc.description.abstractCoffee 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. Our primary outcome was microbiota composition and function, whereas the secondary outcome was gut microbial metabolites and coffee-related metabolites (NCT05927038 and NCT05927103). 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.en
dc.description.sponsorshipScience Foundation Ireland (SFI), through the Irish Governments’ national development plan (grant no. 12/RC/2273_P2). This work was also partially supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (PREDICT-CARE project, grant agreement No 950050) and the National Recovery and Resilience Plan (NRRP), Mission 4 Component 2 Investment 1.3 - Call for tender No. 341 of March 15, 2022 of Italian Ministry of University and Research funded by the European Union – NextGenerationEU
dc.description.sponsorshipAward Number: Project code PE00000003, Concession Decree No. 1550 of October 11, 2022 adopted by the Italian Ministry of University and Research, CUP D93C22000890001, Project title “ON Foods - Research and innovation network on food and nutrition Sustainability, Safety and Security – Working ON Foods”.
dc.description.versionPublished Version
dc.format.extent20
dc.format.mimetypeapplication/pdfen
dc.identifier.articleid3439
dc.identifier.authororcidBoscaini, Serena
dc.identifier.authororcidBastiaanssen, Thomaz F. S.
dc.identifier.authororcidMoloney, Gerard M.§0000-0002-3672-1390
dc.identifier.authororcidBergamo, Federica
dc.identifier.authororcidZeraik, Laila
dc.identifier.authororcidO’Leary, Caroline
dc.identifier.authororcidFerri, Aimone
dc.identifier.authororcidIrfan, Maha
dc.identifier.authororcidvan der Rhee, Maaike
dc.identifier.authororcidLindemann, Thaïs I. F.
dc.identifier.authororcidSchneider, Elizabeth§0000-0002-1711-0877
dc.identifier.authororcidMeyyappan, Arthi Chinna
dc.identifier.authororcidHarold, Kirsten Berding
dc.identifier.authororcidLong-Smith, Caitríona M.
dc.identifier.authororcidCarbia, Carina
dc.identifier.authororcidO’Riordan, Kenneth J.
dc.identifier.authororcidde Alvarenga, José Fernando Rinaldi
dc.identifier.authororcidTosi, Nicole
dc.identifier.authororcidRio, Daniele Del
dc.identifier.authororcidRosi, Alice
dc.identifier.authororcidBresciani, Letizia
dc.identifier.authororcidMena, Pedro
dc.identifier.authororcidClarke, Gerard§0000-0001-9771-3979
dc.identifier.authororcidCryan, John F.§0000-0001-5887-2723
dc.identifier.citationBoscaini, S, Bastiaanssen, T F S, Moloney, G M, Bergamo, F, Zeraik, L, O’Leary, C, Ferri, A, Irfan, M, van der Rhee, M, Lindemann, T I F, Schneider, E, Meyyappan, A C, Harold, K B, Long-Smith, C M, Carbia, C, O’Riordan, K J, de Alvarenga, J F R, Tosi, N, Rio, D D, Rosi, A, Bresciani, L, Mena, P, Clarke, G & Cryan, J F 2026, 'Habitual coffee intake shapes the gut microbiome and modifies host physiology and cognition', Nature Communications, vol. 17, no. 1, 3439, pp. 1-20. https://doi.org/10.1038/s41467-026-71264-8
dc.identifier.doi10.1038/s41467-026-71264-8
dc.identifier.endpage20
dc.identifier.issn2041-1723
dc.identifier.issued1
dc.identifier.journaltitleNature Communications
dc.identifier.otherORCID: /0000-0002-3672-1390/work/212423756
dc.identifier.otherORCID: /0000-0001-5887-2723/work/215518084
dc.identifier.otherORCID: /0000-0002-1711-0877/work/215518142
dc.identifier.startpage1
dc.identifier.urihttps://hdl.handle.net/10468/18834
dc.identifier.volume17
dc.language.isoen
dc.publisherNature Research
dc.relation.urihttps://www.scopus.com/pages/publications/105036456765
dc.rights© 2026, the Authors. Open Access. This article is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License, which permits any non-commercial use, sharing, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if you modified the licensed material.
dc.rights.accessrightsopen access
dc.rights.licensenameAttribution-NonCommercial-NoDerivatives 4.0 International
dc.rights.urihttps://creativecommons.org/licenses/by-nc-nd/4.0/
dc.statusPeer reviewed
dc.subjectCoffee
dc.subjectGut microbiome
dc.subjectHost physiology and cognition
dc.subject[APCMicrobiome]
dc.subject[AppliedPsychology]
dc.subject[Medicine]
dc.subject[OVPRI]
dc.titleHabitual coffee intake shapes the gut microbiome and modifies host physiology and cognitionen
dc.typeArticle (peer-reviewed)
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