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.funderNational Recovery and Resilience Plan
dc.contributor.funderDuPont
dc.contributor.funderInstitute for Scientific Information on Coffee
dc.contributor.funderScience Foundation Ireland, SFI
dc.contributor.funderBayer Healthcare
dc.contributor.funderHeel Pharmaceuticals
dc.contributor.funderMinistero dell’Istruzione, dell’Università e della Ricerca, MIUR
dc.contributor.funderIFF
dc.contributor.funderEuropean Research Council, ERC
dc.contributor.funderON Foods - Research and innovation network on food and nutrition Sustainability, Safety and Security – Working ON Foods
dc.contributor.funderEuropean Commission, EU, 1550-PE00000003
dc.contributor.funderMinistero dell'Università e della Ricerca, MUR, CUP D93C22000890001
dc.contributor.funderHorizon 2020 Framework Programme, 950050
dc.contributor.funderIrish Governments’ national development plan, 12/RC/2273_P2
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.sponsorshipWe are grateful to the Institute for Scientific Information on Coffee (ISIC) for funding this research. We would like to thank Aonghus Lavelle, David A. Lachmansingh, Gabriela Ribeiro, Jason Martin, David Kaulmann, Thieza Melo, Antonio Girella, and Eric Kelleher for their support. We also wish to thank all the study participants for their involvement in our study. We acknowledge the use of the APC Microbiome Ireland Flow Cytometry Platform. APC Microbiome Ireland is a research centre funded by Science 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”. Icons were used in the creation of some figures sourced from www.flaticon.com (Icon creator Freepik). J.F.C. has been an invited speaker at conferences organised by Bromotech, Yakult and Nestle and has received research funding from Nutricia, DuPont/IFF, and Nestle. G.C. has received honoraria from Janssen, Probi, Apsen, and Ingelheim Boehringer as an invited speaker
dc.description.sponsorshipis in receipt of research funding from Pharmavite, Fonterra, Reckitt, Nestle and Tate and Lyle
dc.description.sponsorshipand has been paid for consultancy work by Yakult, Zentiva, Bayer Healthcare and Heel Pharmaceuticals. ES has received honorarium from Janssen Sciences Ireland UC. ES also received honorarium from MyNutriWeb for an event that was sponsored by Yakult. This support neither influenced nor constrained the contents of this manuscript. The remaining authors declare no competing interests.
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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