{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,20]],"date-time":"2026-10-20T01:04:13Z","timestamp":1792458253821,"version":"4.5.0"},"reference-count":176,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2026,3,4]],"date-time":"2026-03-04T00:00:00Z","timestamp":1772582400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Aging Neurosci."],"abstract":"<jats:p>The gut microbiome influences brain function through the gut-brain axis via synthesis of neurotransmitters, production of metabolites affecting epithelial barrier integrity and immune modulation and signaling through the vagus nerve. In humans, microbiome diversity reflects healthy aging and predicts survival, while dysbiosis is increasingly implicated in neurodegenerative conditions including Alzheimer\u2019s disease, Parkinson\u2019s disease, multiple sclerosis, and ALS. Fecal transplant studies in germ-free mice demonstrate that microbiome alterations are sufficient to induce cognitive and neuropathological phenotypes, supporting causality in preclinical models. Genetic risk factors and environmental exposures affect both neurodegeneration risk and microbiome composition. In this review, we synthesize evidence from human cohorts and preclinical models on the gut-brain axis in cognitive health and disease. We then present a methodological framework for diet-microbiome-cognition research, addressing causal inference through mediation analysis, supervised approaches for deriving diet scores, validation strategies, and individual heterogeneity. This framework can guide development of microbiome-targeted dietary interventions to improve cognitive outcomes.<\/jats:p>","DOI":"10.3389\/fnagi.2026.1771904","type":"journal-article","created":{"date-parts":[[2026,3,4]],"date-time":"2026-03-04T07:02:00Z","timestamp":1772607720000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":5,"title":["Diet, gut microbiome, and cognition in neurodegeneration: a review and methodological framework"],"prefix":"10.3389","volume":"18","author":[{"given":"Jacob","family":"Raber","sequence":"first","affiliation":[{"name":"Departments of Behavioral Neuroscience, Neurology, and Radiation Medicine, Division of Neuroscience, ONPRC, Oregon Health and Science University","place":["Portland, OR, United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Thomas J.","family":"Sharpton","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Statistics, Linus Pauling Institute, Oregon State University","place":["Corvallis, OR, United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2026,3,4]]},"reference":[{"key":"ref1","doi-asserted-by":"crossref","first-page":"393","DOI":"10.1007\/978-981-99-1737-2_20","volume-title":"Microbial products for future industrialization","author":"Ahmed","year":"2023"},{"key":"ref2","doi-asserted-by":"publisher","first-page":"101049","DOI":"10.1016\/j.bbih.2025.101049","article-title":"Exploring the effects of faecal microbiota transplantation on cognitive function: a review of clinical trials","volume":"48","author":"Alaeddin","year":"2025","journal-title":"Brain Behav. 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Med."},{"key":"ref28","doi-asserted-by":"crossref","first-page":"179","DOI":"10.1016\/S1474-4422(19)30356-4","article-title":"The gut microbiome in neurological disorders","volume":"19","author":"Cryan","year":"2019","journal-title":"Lancet Neurol."},{"key":"ref29","doi-asserted-by":"publisher","first-page":"461","DOI":"10.1038\/s41575-019-0157-3","article-title":"The role of short-chain fatty acids in microbiota\u2013gut\u2013brain communication","volume":"16","author":"Dalile","year":"2019","journal-title":"Nat. Rev. Gastroenterol. 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Med."},{"key":"ref42","doi-asserted-by":"publisher","first-page":"23497","DOI":"10.1038\/s41598-024-75083-z","article-title":"Examining the complex interplay between gut microbiota abundance and short-chain fatty acid production in amyotrophic lateral sclerosis patients shortly after onset of disease","volume":"14","author":"Fontdevila","year":"2024","journal-title":"Sci. Rep."},{"key":"ref43","doi-asserted-by":"publisher","first-page":"3696","DOI":"10.1021\/acssynbio.5c00412","article-title":"Genetic entanglement enables Ultrastable biocontainment in the mammalian gut","volume":"14","author":"Foo","year":"2025","journal-title":"ACS Synth. Biol."},{"key":"ref44","doi-asserted-by":"publisher","first-page":"2287","DOI":"10.1016\/S0140-6736(15)00128-2","article-title":"Global, regional, and national comparative risk assessment of 79 behavioural, environmental and occupational, and metabolic risks or clusters of risks in 188 countries, 1990-2013: a systematic analysis for the global burden of disease study 2013","volume":"386","author":"Forouzanfar","year":"2015","journal-title":"Lancet"},{"key":"ref45","doi-asserted-by":"publisher","first-page":"1314","DOI":"10.1093\/ije\/dyr106","article-title":"Is rigorous retrospective harmonization possible? Application of the DataSHaPER approach across 53 large studies","volume":"40","author":"Fortier","year":"2011","journal-title":"Int. J. Epidemiol."},{"key":"ref46","doi-asserted-by":"publisher","first-page":"305","DOI":"10.1016\/j.tins.2013.01.005","article-title":"Brain axis: how the microbiome influences anxiety and depression","volume":"36","author":"Foster","year":"2013","journal-title":"Trends Neurosci."},{"key":"ref47","doi-asserted-by":"publisher","first-page":"5185","DOI":"10.3390\/nu14235185","article-title":"Comparison of associations between MIND and Mediterranean diet scores with patient-reported outcomes in Parkinson\u2019s disease","volume":"14","author":"Fox","year":"2022","journal-title":"Nutrients"},{"key":"ref48","doi-asserted-by":"publisher","first-page":"541","DOI":"10.1176\/jnp.17.4.541","article-title":"Neuropsychiatric associations of apolipoprotein E alleles in subjects with combat-related posttraumatic stress disorder","volume":"17","author":"Freeman","year":"2005","journal-title":"Clin. Neurosci."},{"key":"ref49","doi-asserted-by":"publisher","first-page":"998","DOI":"10.1016\/j.neuron.2019.02.008","article-title":"Gut microbe to brain Signaling: what happens in Vagus","volume":"101","author":"Fulling","year":"2019","journal-title":"Neuron"},{"key":"ref50","doi-asserted-by":"crossref","first-page":"466","DOI":"10.1093\/jn\/136.2.466","article-title":"Diet quality is associated with the risk of estrogen receptor-negative breast cancer in postmenopausal women","volume":"136","author":"Fung","year":"2006","journal-title":"J. Nutr."},{"key":"ref51","doi-asserted-by":"publisher","first-page":"163","DOI":"10.1093\/ajcn\/82.1.163","article-title":"Diet-quality scores and plasma concentrations of markers of inflammation and endothelial dysfunction","volume":"82","author":"Fung","year":"2005","journal-title":"Am. J. Clin. Nutr."},{"key":"ref52","doi-asserted-by":"publisher","first-page":"10","DOI":"10.1007\/s13668-018-0222-5","article-title":"Mediterranean diet in preventing neurodegenerative diseases","volume":"7","author":"Gardener","year":"2018","journal-title":"Curr Nutr Rep"},{"key":"ref53","doi-asserted-by":"publisher","first-page":"17886","DOI":"10.1038\/s41598-017-18183-3","article-title":"Reinstatement of contextual conditioned anxiety in virtual reality and the effects of transcutaneous vagus nerve stimulation in humans","volume":"7","author":"Genheimer","year":"2017","journal-title":"Sci. Rep."},{"key":"ref54","doi-asserted-by":"publisher","first-page":"2224","DOI":"10.3389\/fmicb.2017.02224","article-title":"Microbiome datasets are compositional: and this is not optional","volume":"8","author":"Gloor","year":"2017","journal-title":"Front. Microbiol."},{"key":"ref55","doi-asserted-by":"publisher","first-page":"311","DOI":"10.1203\/01.PDR.0000135998.08025.FB","article-title":"Developmental origins of disease paradigm: a mechanistic and evolutionary perspective","volume":"56","author":"Gluckman","year":"2004","journal-title":"Pediatr. Res."},{"key":"ref56","doi-asserted-by":"crossref","first-page":"45","DOI":"10.1038\/372045a0","article-title":"Alzheimer\u2019s disease: risky apolipoprotein in brain","volume":"372","author":"Goedert","year":"1994","journal-title":"Nature"},{"key":"ref57","doi-asserted-by":"publisher","first-page":"141","DOI":"10.1146\/annurev-pharmtox-011613-135937","article-title":"Environmental toxins and Parkinson's disease","volume":"54","author":"Goldman","year":"2014","journal-title":"Annu. Rev. Pharmacol. Toxicol."},{"key":"ref58","doi-asserted-by":"crossref","first-page":"27","DOI":"10.1111\/j.1365-2990.1995.tb01025.x","article-title":"Distribution of \u03b2-amyloid protein in the brain following severe head injury","volume":"21","author":"Graham","year":"1995","journal-title":"Neuropathol. Appl. Neurobiol."},{"key":"ref59","doi-asserted-by":"publisher","first-page":"10125298","DOI":"10.3389\/fragi.2022.1012598","article-title":"Mediterranean diet score is associated with greater allocentric processing in the EPAD LCS cohort: a comparative analysis by biogeographical region","volume":"3","author":"Gregory","year":"2022","journal-title":"Frontiers in Aging"},{"key":"ref60","first-page":"93","article-title":"A survey of methods for explaining black box models","volume":"51","author":"Guidotti","year":"2018","journal-title":"ACM Comput. Surv."},{"key":"ref61","doi-asserted-by":"publisher","first-page":"665","DOI":"10.1093\/brain\/awad306","article-title":"Gut microbiome correlates with plasma lipids in amyotrophic lateral sclerosis","volume":"147","author":"Guo","year":"2024","journal-title":"Brain"},{"key":"ref62","doi-asserted-by":"publisher","first-page":"254","DOI":"10.1101\/2024.04.12.589237","article-title":"Fetal programming by the parental microbiome of offspring behavior, and DNA methylation and gene expression within the hippocampus","volume":"13","author":"Gustafson","year":"2025","journal-title":"Microbiome"},{"key":"ref63","doi-asserted-by":"publisher","first-page":"e143777","DOI":"10.1172\/jci143777","article-title":"Brain-gut axis dysfunction in the pathogenesis of traumatic brain injury","volume":"131","author":"Hanscom","year":"2021","journal-title":"J. Clin. Invest."},{"key":"ref64","doi-asserted-by":"crossref","first-page":"921","DOI":"10.1016\/j.jand.2015.12.017","article-title":"No association between dietary patterns and risk for cognitive decline in older women with 9-year follow-up: data from the Women's Health Initiative memory study","volume":"116","author":"Haring","year":"2016","journal-title":"J Acad Nutr Diettetics"},{"key":"ref65","doi-asserted-by":"crossref","first-page":"91","DOI":"10.1080\/21678421.2021.1904994","article-title":"Gut microbiome differences between amyotrophic lateral sclerosis patients and spouse controls","volume":"23","author":"Hertzberg","year":"2023","journal-title":"Amyotroph. Lateral Scler. Frontotemporal Degener."},{"key":"ref66","doi-asserted-by":"crossref","first-page":"935","DOI":"10.1093\/aje\/kwh134","article-title":"Application of a new statistical method to derive dietary patterns in nutritional epidemiology: reduced rank regression","volume":"159","author":"Hoffmann","year":"2004","journal-title":"Am. J. Epidemiol."},{"key":"ref67","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1097\/00041433-200202000-00002","article-title":"Dietary pattern analysis: a new direction in nutritional epidemiology","volume":"13","author":"Hu","year":"2002","journal-title":"Curr. Opin. Lipidol."},{"key":"ref68","first-page":"1541271","article-title":"Higher HEI-2015 score is associated with reduced risk of Parkinson\u2019s disease: a nationwide population-based study","volume":"12","author":"Hu","year":"2025","journal-title":"Clin Nutrition"},{"key":"ref69","doi-asserted-by":"publisher","first-page":"1675","DOI":"10.1128\/mbio.04001-24","article-title":"The same but different: impact of animal facility sanitary status on a transgenic mouse model of Alzheimer\u2019s disease","volume":"16","author":"Ismeurt-Walmsley","year":"2025","journal-title":"MBio"},{"key":"ref70","doi-asserted-by":"publisher","first-page":"2315633","DOI":"10.1080\/19490976.2024.2315633","article-title":"Gut enterotype-dependent modulation of gut microbiota and their metabolism in response to xanthohumol supplementation in healthy adults","volume":"16","author":"Jamieson","year":"2024","journal-title":"Gut Microbes"},{"key":"ref71","doi-asserted-by":"publisher","first-page":"852","DOI":"10.2174\/15672050113109990155","article-title":"Epidemiology and etiology of Alzheimer's disease: from genetic to non- genetic factors","volume":"10","author":"Jiang","year":"2013","journal-title":"Curr. Alzheimer Res."},{"key":"ref72","doi-asserted-by":"publisher","first-page":"2443","DOI":"10.1038\/npp.2015.95","article-title":"ApoE2 exaggerates PTSD-related behavioral, cognitive, and neuroendocrine alterations","volume":"40","author":"Johnson","year":"2015","journal-title":"Neuropsychopharmacology"},{"key":"ref73","first-page":"91","article-title":"Adherence to the Mediterranean diet can beneficially affect the gut microbiota composition: a systematic review","volume":"17","author":"Khavandegar","year":"2024","journal-title":"BMC Med. Genet."},{"key":"ref74","doi-asserted-by":"publisher","first-page":"194","DOI":"10.1002\/da.22138","article-title":"Apolipoprotein E gene polymorphism, alcohol use, and their interactions in combat-related posttraumatic stress disorder","volume":"30","author":"Kim","year":"2013","journal-title":"Depress. 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Microbiol."},{"key":"ref99","doi-asserted-by":"crossref","first-page":"23","DOI":"10.1037\/1082-989X.12.1.23","article-title":"Bias in cross-sectional analyses of longitudinal mediation","volume":"12","author":"Maxwell","year":"2007","journal-title":"Psych Meth"},{"key":"ref100","doi-asserted-by":"publisher","first-page":"3","DOI":"10.1002\/j.2051-5545.2008.tb00139.x","article-title":"Neurobehavioral sequelae of traumatic brain injury: evaluation and management","volume":"7","author":"McAllister","year":"2008","journal-title":"World Psychiatry"},{"key":"ref101","doi-asserted-by":"publisher","first-page":"e2143941","DOI":"10.1001\/jamanetworkopen.2021.43941","article-title":"Association of the gut microbiota with cognitive function in midlife","volume":"5","author":"Meyer","year":"2022","journal-title":"JAMA Netw. 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