*Result*: Microbiome: A Key Regulator of Body-Brain Interactions.

Microbiome: A Key Regulator of Body-Brain Interactions.

O'Riordan KJ; APC Microbiome Ireland, University College Cork, Cork, Ireland., Aburto MR; APC Microbiome Ireland, University College Cork, Cork, Ireland.; Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland., Nagpal J; APC Microbiome Ireland, University College Cork, Cork, Ireland.; Department of Pharmacology and Therapeutics, School of Medicine, and School of Pharmacy, University College Cork, Cork, Ireland., Clarke G; APC Microbiome Ireland, University College Cork, Cork, Ireland.; Department of Psychiatry and Neurobehavioural Science, University College Cork, Cork, Ireland., Cryan JF; APC Microbiome Ireland, University College Cork, Cork, Ireland. j.cryan@ucc.ie.; Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland. j.cryan@ucc.ie.

Advances in experimental medicine and biology [Adv Exp Med Biol] 2025; Vol. 1477, pp. 139-203.

Journal Article; Review

English

Publisher: Kluwer Academic/Plenum Publishers Country of Publication: United States NLM ID: 0121103 Publication Model: Print Cited Medium: Print ISSN: 0065-2598 (Print) Linking ISSN: 00652598 NLM ISO Abbreviation: Adv Exp Med Biol Subsets: MEDLINE

Publication: 1998- : New York : Kluwer Academic/Plenum Publishers
Original Publication: New York, Plenum Press.

Gastrointestinal Microbiome*/physiology , Brain*/physiology , Brain*/microbiology , Brain-Gut Axis*/physiology, Humans ; Animals

Abbott RD, Petrovitch H, White LR, Masaki KH, Tanner CM, Curb JD, Grandinetti A, Blanchette PL, Popper JS, Ross GW (2001) Frequency of bowel movements and the future risk of Parkinson’s disease. Neurology 57(3):456–462. https://doi.org/10.1212/wnl.57.3.456. (PMID: 10.1212/wnl.57.3.45611502913)
Aburto MR, Cryan JF (2024) Gastrointestinal and brain barriers: unlocking gates of communication across the microbiota-gut-brain axis. Nat Rev Gastroenterol Hepatol 21(4):222–247. https://doi.org/10.1038/s41575-023-00890-0. (PMID: 10.1038/s41575-023-00890-038355758)
Adiguzel E, Cicek B, Unal G, Aydin MF, Barlak-Keti D (2022) Probiotics and prebiotics alleviate behavioral deficits, inflammatory response, and gut dysbiosis in prenatal VPA-induced rodent model of autism. Physiol Behav 256:113961. https://doi.org/10.1016/j.physbeh.2022.113961. (PMID: 10.1016/j.physbeh.2022.11396136100109)
Agahi A, Hamidi GA, Daneshvar R, Hamdieh M, Soheili M, Alinaghipour A, Esmaeili Taba SM, Salami M (2018) Does severity of Alzheimer’s disease contribute to its responsiveness to modifying gut microbiota? a double blind clinical trial. Front Neurol 9:662. https://doi.org/10.3389/fneur.2018.00662. (PMID: 10.3389/fneur.2018.00662301588976104449)
Agans R, Rigsbee L, Kenche H, Michail S, Khamis HJ, Paliy O (2011) Distal gut microbiota of adolescent children is different from that of adults. FEMS Microbiol Ecol 77(2):404–412. https://doi.org/10.1111/j.1574-6941.2011.01120.x. (PMID: 10.1111/j.1574-6941.2011.01120.x21539582)
de Aguiar Vallim TQ, Tarling EJ, Edwards PA (2013) Pleiotropic roles of bile acids in metabolism. Cell Metab 17(5):657–669. https://doi.org/10.1016/j.cmet.2013.03.013. (PMID: 10.1016/j.cmet.2013.03.013236024483654004)
Ahmadvand A, Sepehrmanesh Z, Shahzeidi A, Mansournia M, Ghaderi A (2021) Clinical and metabolic reaction to probiotic supplement in children suffering attention-deficit hyperactivity disorder: a randomized, double-blind, placebo-controlled experiment. Int Arch Health Sci 8(2):90–96. https://doi.org/10.4103/iahs.iahs_112_20. (PMID: 10.4103/iahs.iahs_112_20)
Ahrens AP, Hyotylainen T, Petrone JR, Igelstrom K, George CD, Garrett TJ, Oresic M, Triplett EW, Ludvigsson J (2024) Infant microbes and metabolites point to childhood neurodevelopmental disorders. Cell 187(8):1853–1873 e1815. https://doi.org/10.1016/j.cell.2024.02.035. (PMID: 10.1016/j.cell.2024.02.03538574728)
Ait-Belgnaoui A, Payard I, Rolland C, Harkat C, Braniste V, Theodorou V, Tompkins TA (2018) Bifidobacterium longum and Lactobacillus helveticus synergistically suppress stress-related visceral hypersensitivity through hypothalamic-pituitary-adrenal axis modulation. J Neurogastroenterol Motil 24(1):138–146. https://doi.org/10.5056/jnm16167. (PMID: 10.5056/jnm16167292916145753912)
Akbari E, Asemi Z, Daneshvar Kakhaki R, Bahmani F, Kouchaki E, Tamtaji OR, Hamidi GA, Salami M (2016) Effect of probiotic supplementation on cognitive function and metabolic status in Alzheimer’s disease: a randomized, double-blind and controlled trial. Front Aging Neurosci 8:256. https://doi.org/10.3389/fnagi.2016.00256. (PMID: 10.3389/fnagi.2016.00256278910895105117)
Akkasheh G, Kashani-Poor Z, Tajabadi-Ebrahimi M, Jafari P, Akbari H, Taghizadeh M, Memarzadeh MR, Asemi Z, Esmaillzadeh A (2016) Clinical and metabolic response to probiotic administration in patients with major depressive disorder: a randomized, double-blind, placebo-controlled trial. Nutrition 32(3):315–320. https://doi.org/10.1016/j.nut.2015.09.003. (PMID: 10.1016/j.nut.2015.09.00326706022)
Allahyari P, Abbas Torki S, Aminnezhad Kavkani B, Mahmoudi Z, Mousavi Hoseini MS, Moradi M, Alami F, Keshavarz Mohammadian M, Bahoo Sele Bani S, Abbasi Mobarakeh K, Shafaei H, Khoshdooz S, Hajipour A, Doaei S, Gholamalizadeh M (2024) A systematic review of the beneficial effects of prebiotics, probiotics, and synbiotics on ADHD. Neuropsychopharmacol Rep 44(2):300–307. https://doi.org/10.1002/npr2.12437. (PMID: 10.1002/npr2.124373862392911144606)
Allan NP, Yamamoto BY, Kunihiro BP, Nunokawa CKL, Rubas NC, Wells RK, Umeda L, Phankitnirundorn K, Torres A, Peres R, Takahashi E, Maunakea AK (2024) Ketogenic diet induced shifts in the gut microbiome associate with changes to inflammatory cytokines and brain-related miRNAs in children with autism spectrum disorder. Nutrients 16(10). https://doi.org/10.3390/nu16101401.
Altaha B, Heddes M, Pilorz V, Niu Y, Gorbunova E, Gigl M, Kleigrewe K, Oster H, Haller D, Kiessling S (2022) Genetic and environmental circadian disruption induce weight gain through changes in the gut microbiome. Mol Metab 66:101628. https://doi.org/10.1016/j.molmet.2022.101628. (PMID: 10.1016/j.molmet.2022.101628363348979672454)
American Psychiatric Association (2013) Diagnostic and statistical manual of mental disorders, 5th edn. American Psychiatric Association. (PMID: 10.1176/appi.books.9780890425596)
Andreani NA, Sharma A, Dahmen B, Specht HE, Mannig N, Ruan V, Keller L, Baines JF, Herpertz-Dahlmann B, Dempfle A, Seitz J (2024) Longitudinal analysis of the gut microbiome in adolescent patients with anorexia nervosa: microbiome-related factors associated with clinical outcome. Gut Microbes 16(1):2304158. https://doi.org/10.1080/19490976.2024.2304158. (PMID: 10.1080/19490976.2024.23041583829486710832965)
Archie EA, Tung J (2015) Social behavior and the microbiome. Curr Opin Behav Sci 6:28–34. https://doi.org/10.1016/j.cobeha.2015.07.008. (PMID: 10.1016/j.cobeha.2015.07.008)
Arentsen T, Qian Y, Gkotzis S, Femenia T, Wang T, Udekwu K, Forssberg H, Diaz Heijtz R (2017) The bacterial peptidoglycan-sensing molecule Pglyrp2 modulates brain development and behavior. Mol Psychiatry 22(2):257–266. https://doi.org/10.1038/mp.2016.182. (PMID: 10.1038/mp.2016.18227843150)
Arifuzzaman M, Won TH, Li TT, Yano H, Digumarthi S, Heras AF, Zhang W, Parkhurst CN, Kashyap S, Jin WB, Putzel GG, Tsou AM, Chu C, Wei Q, Grier A, Consortium JILCB, Worgall S, Guo CJ, Schroeder FC, Artis D (2022) Inulin fibre promotes microbiota-derived bile acids and type 2 inflammation. Nature 611(7936):578–584. https://doi.org/10.1038/s41586-022-05380-y. (PMID: 10.1038/s41586-022-05380-y3632377810576985)
Armet AM, Deehan EC, O’Sullivan AF, Mota JF, Field CJ, Prado CM, Lucey AJ, Walter J (2022) Rethinking healthy eating in light of the gut microbiome. Cell Host Microbe 30(6):764–785. https://doi.org/10.1016/j.chom.2022.04.016. (PMID: 10.1016/j.chom.2022.04.01635679823)
Arnold SE, Arvanitakis Z, Macauley-Rambach SL, Koenig AM, Wang HY, Ahima RS, Craft S, Gandy S, Buettner C, Stoeckel LE, Holtzman DM, Nathan DM (2018) Brain insulin resistance in type 2 diabetes and Alzheimer disease: concepts and conundrums. Nat Rev Neurol 14(3):168–181. https://doi.org/10.1038/nrneurol.2017.185. (PMID: 10.1038/nrneurol.2017.185293770106098968)
Aron-Wisnewsky J, Clement K (2014) The effects of gastrointestinal surgery on gut microbiota: potential contribution to improved insulin sensitivity. Curr Atheroscler Rep 16(11):454. https://doi.org/10.1007/s11883-014-0454-9. (PMID: 10.1007/s11883-014-0454-925214424)
Audet MC (2019) Stress-induced disturbances along the gut microbiota-immune-brain axis and implications for mental health: does sex matter? Front Neuroendocrinol 54:100772. https://doi.org/10.1016/j.yfrne.2019.100772. (PMID: 10.1016/j.yfrne.2019.10077231302116)
Audet MC (2021) Beyond the neuro-immune interplay in depression: could gut microbes be the missing link? Brain Behave Immune Health 16:100308. https://doi.org/10.1016/j.bbih.2021.100308. (PMID: 10.1016/j.bbih.2021.100308)
Avolio E, Olivito I, Rosina E, Romano L, Angelone T, De Bartolo A, Scimeca M, Bellizzi D, D’Aquila P, Passarino G, Alo R, Facciolo RM, Bagni C, De Lorenzo A, Canonaco M (2022) Modifications of behavior and inflammation in mice following transplant with fecal microbiota from children with autism. Neuroscience 498:174–189. https://doi.org/10.1016/j.neuroscience.2022.06.038. (PMID: 10.1016/j.neuroscience.2022.06.03835792193)
Awan A, Bartlett A, Blakeley-Ruiz JA, Richie T, Theriot CM, Kleiner M (2024) Dietary protein from different sources escapes host digestion and is differentially modified by the microbiota. bioRxiv. https://doi.org/10.1101/2024.06.26.600830.
Ayala FJ (2009) Darwin and the scientific method. Proc Natl Acad Sci USA 106 Suppl 1(Suppl 1):10033–10039. https://doi.org/10.1073/pnas.0901404106. (PMID: 10.1073/pnas.090140410619528662)
Balasubramanian R, Schneider E, Gunnigle E, Cotter PD, Cryan JF (2024) Fermented foods: harnessing their potential to modulate the microbiota-gut-brain axis for mental health. Neurosci Biobehav Rev 158:105562. https://doi.org/10.1016/j.neubiorev.2024.105562. (PMID: 10.1016/j.neubiorev.2024.10556238278378)
Baldi S, Pagliai G, Dinu M, Di Gloria L, Nannini G, Curini L, Pallecchi M, Russo E, Niccolai E, Danza G, Benedettelli S, Ballerini G, Colombini B, Bartolucci G, Ramazzotti M, Sofi F, Amedei A (2022) Effect of ancient Khorasan wheat on gut microbiota, inflammation, and short-chain fatty acid production in patients with fibromyalgia. World J Gastroenterol 28(18):1965–1980. https://doi.org/10.3748/wjg.v28.i18.1965. (PMID: 10.3748/wjg.v28.i18.1965356649589150053)
Bang S, Shin YH, Park SM, Deng L, Williamson RT, Graham DB, Xavier RJ, Clardy J (2025) Unusual phospholipids from Morganella morganii linked to depression. J Am Chem Soc. https://doi.org/10.1021/jacs.4c15158.
Bansal T, Alaniz RC, Wood TK, Jayaraman A (2010) The bacterial signal indole increases epithelial-cell tight-junction resistance and attenuates indicators of inflammation. Proc Natl Acad Sci USA 107(1):228–233. https://doi.org/10.1073/pnas.0906112107. (PMID: 10.1073/pnas.090611210719966295)
Barone M, Ramayo-Caldas Y, Estelle J, Tambosco K, Chadi S, Maillard F, Gallopin M, Planchais J, Chain F, Kropp C, Rios-Covian D, Sokol H, Brigidi P, Langella P, Martin R (2023) Gut barrier-microbiota imbalances in early life lead to higher sensitivity to inflammation in a murine model of C-section delivery. Microbiome 11(1):140. https://doi.org/10.1186/s40168-023-01584-0. (PMID: 10.1186/s40168-023-01584-03739442810316582)
Barroso A, Mahler JV, Fonseca-Castro PH, Quintana FJ (2021) The aryl hydrocarbon receptor and the gut-brain axis. Cell Mol Immunol 18(2):259–268. https://doi.org/10.1038/s41423-020-00585-5. (PMID: 10.1038/s41423-020-00585-5334083408027889)
Bartlett A, Kleiner M (2022) Dietary protein and the intestinal microbiota: an understudied relationship. iScience 25(11):105313. https://doi.org/10.1016/j.isci.2022.105313. (PMID: 10.1016/j.isci.2022.105313363392709626677)
Basafa-Roodi P, Jazayeri S, Hadi F, Paghaleh SJ, Khosravi-Darani K, Malakouti SK (2024) Effects of synbiotic supplementation on the components of metabolic syndrome in patients with schizophrenia: a randomized, double-blind, placebo-controlled trial. BMC Psychiatry 24(1):669. https://doi.org/10.1186/s12888-024-06061-y. (PMID: 10.1186/s12888-024-06061-y3938518911462647)
Basso PJ, Camara NOS, Sales-Campos H (2018) Microbial-based therapies in the treatment of inflammatory bowel disease - an overview of human studies. Front Pharmacol 9:1571. https://doi.org/10.3389/fphar.2018.01571. (PMID: 10.3389/fphar.2018.0157130687107)
Bastiaanssen TFS, Cowan CSM, Claesson MJ, Dinan TG, Cryan JF (2019) Making sense of ... the microbiome in psychiatry. Int J Neuropsychopharmacol 22(1):37–52. https://doi.org/10.1093/ijnp/pyy067. (PMID: 10.1093/ijnp/pyy06730099552)
Bastiaanssen TFS, Cussotto S, Claesson MJ, Clarke G, Dinan TG, Cryan JF (2020) Gutted! unraveling the role of the microbiome in major depressive disorder. Harv Rev Psychiatry 28(1):26–39. https://doi.org/10.1097/HRP.0000000000000243. (PMID: 10.1097/HRP.0000000000000243319139807012351)
Bastiaanssen TFS, Gururajan A, van de Wouw M, Moloney GM, Ritz NL, Long-Smith CM, Wiley NC, Murphy AB, Lyte JM, Fouhy F, Stanton C, Claesson MJ, Dinan TG, Cryan JF (2021) Volatility as a concept to understand the impact of stress on the microbiome. Psychoneuroendocrinology 124:105047. https://doi.org/10.1016/j.psyneuen.2020.105047. (PMID: 10.1016/j.psyneuen.2020.10504733307493)
Bastiaanssen TFS, Quinn TP, Loughman A (2022) Treating bugs as features: a compositional guide to the statistical analysis of the microbiome-gut-brain axis. Arxiv.
Bayrer JR, Castro J, Venkataraman A, Touhara KK, Rossen ND, Morrie RD, Maddern J, Hendry A, Braverman KN, Garcia-Caraballo S, Schober G, Brizuela M, Castro Navarro FM, Bueno-Silva C, Ingraham HA, Brierley SM, Julius D (2023) Gut enterochromaffin cells drive visceral pain and anxiety. Nature 616(7955):137–142. https://doi.org/10.1038/s41586-023-05829-8. (PMID: 10.1038/s41586-023-05829-83694919210827380)
Beaumont W (1833) Experiments and observations on the gastric juice and the physiology of digestion. Maclachlan and Stewart, Edinburgh.
Benakis C, Brea D, Caballero S, Faraco G, Moore J, Murphy M, Sita G, Racchumi G, Ling L, Pamer EG, Iadecola C, Anrather J (2016) Commensal microbiota affects ischemic stroke outcome by regulating intestinal gammadelta T cells. Nat Med 22(5):516–523. https://doi.org/10.1038/nm.4068. (PMID: 10.1038/nm.4068270193274860105)
Benarroch EE (2007) Enteric nervous system: functional organization and neurologic implications. Neurology 69(20):1953–1957. https://doi.org/10.1212/01.wnl.0000281999.56102.b5. (PMID: 10.1212/01.wnl.0000281999.56102.b517998487)
Berding K, Cryan JF (2022) Microbiota-targeted interventions for mental health. Curr Opin Psychiatry 35(1):3–9. https://doi.org/10.1097/YCO.0000000000000758. (PMID: 10.1097/YCO.000000000000075834750307)
Berding K, Long-Smith CM, Carbia C, Bastiaanssen TFS, van de Wouw M, Wiley N, Strain CR, Fouhy F, Stanton C, Cryan JF, Dinan TG (2021) A specific dietary fibre supplementation improves cognitive performance-an exploratory randomised, placebo-controlled, crossover study. Psychopharmacology 238(1):149–163. https://doi.org/10.1007/s00213-020-05665-y. (PMID: 10.1007/s00213-020-05665-y32951067)
Berding K, Bastiaanssen TFS, Moloney GM, Boscaini S, Strain CR, Anesi A, Long-Smith C, Mattivi F, Stanton C, Clarke G, Dinan TG, Cryan JF (2023) Feed your microbes to deal with stress: a psychobiotic diet impacts microbial stability and perceived stress in a healthy adult population. Mol Psychiatry 28(2):601–610. https://doi.org/10.1038/s41380-022-01817-y. (PMID: 10.1038/s41380-022-01817-y36289300)
Berer K, Gerdes LA, Cekanaviciute E, Jia X, Xiao L, Xia Z, Liu C, Klotz L, Stauffer U, Baranzini SE, Kumpfel T, Hohlfeld R, Krishnamoorthy G, Wekerle H (2017) Gut microbiota from multiple sclerosis patients enables spontaneous autoimmune encephalomyelitis in mice. Proc Natl Acad Sci USA 114(40):10719–10724. https://doi.org/10.1073/pnas.1711233114. (PMID: 10.1073/pnas.1711233114288939945635914)
Bernard C (1878) Lectures on phenomena of life common to animals and plants. JB Balliere and Son, Paris.
Bernard, C. (1949 (Originally 1865)) An introduction to the study of experimental medicine. Henry Schuman, Inc, Paris.
Beyond bacteria: early-life gut virome link with childhood asthma development (2024) Nat Med 30(1):43–44. https://doi.org/10.1038/s41591-023-02747-0. (PMID: 10.1038/s41591-023-02747-0)
Bhattarai Y, Williams BB, Battaglioli EJ, Whitaker WR, Till L, Grover M, Linden DR, Akiba Y, Kandimalla KK, Zachos NC, Kaunitz JD, Sonnenburg JL, Fischbach MA, Farrugia G, Kashyap PC (2018) Gut microbiota-produced tryptamine activates an Epithelial G-Protein-Coupled receptor to increase colonic secretion. Cell Host Microbe 23(6):775–785 e775. https://doi.org/10.1016/j.chom.2018.05.004. (PMID: 10.1016/j.chom.2018.05.004299024416055526)
Bizzozero-Peroni B, Martinez-Vizcaino V, Fernandez-Rodriguez R, Jimenez-Lopez E, Nunez de Arenas-Arroyo S, Saz-Lara A, Diaz-Goni V, Mesas AE (2024) The impact of the Mediterranean diet on alleviating depressive symptoms in adults: a systematic review and meta-analysis of randomized controlled trials. Nutr Rev. https://doi.org/10.1093/nutrit/nuad176.
Block CL, Eroglu O, Mague SD, Smith CJ, Ceasrine AM, Sriworarat C, Blount C, Beben KA, Malacon KE, Ndubuizu N, Talbot A, Gallagher NM, Chan Jo Y, Nyangacha T, Carlson DE, Dzirasa K, Eroglu C, Bilbo SD (2022) Prenatal environmental stressors impair postnatal microglia function and adult behavior in males. Cell Rep 40(5):111161. https://doi.org/10.1016/j.celrep.2022.111161. (PMID: 10.1016/j.celrep.2022.111161359264559438555)
Boehme M, van de Wouw M, Bastiaanssen TFS, Olavarria-Ramirez L, Lyons K, Fouhy F, Golubeva AV, Moloney GM, Minuto C, Sandhu KV, Scott KA, Clarke G, Stanton C, Dinan TG, Schellekens H, Cryan JF (2020) Mid-life microbiota crises: middle age is associated with pervasive neuroimmune alterations that are reversed by targeting the gut microbiome. Mol Psychiatry 25(10):2567–2583. https://doi.org/10.1038/s41380-019-0425-1. (PMID: 10.1038/s41380-019-0425-131092898)
Boehme M, Guzzetta KE, Bastiaanssen TFS, van de Wouw M, Moloney GM, Gual-Grau A, Spichak S, Olavarria-Ramirez L, Fitzgerald P, Morillas E, Ritz NL, Jaggar M, Cowan CSM, Crispie F, Donoso F, Halitzki E, Neto MC, Sichetti M, Golubeva AV et al (2021) Microbiota from young mice counteracts selective age-associated behavioral deficits. Nat Aging 1(8):666–676. https://doi.org/10.1038/s43587-021-00093-9. (PMID: 10.1038/s43587-021-00093-937117767)
Boles JS, Krueger ME, Jernigan JE, Cole CL, Neighbarger NK, Uriarte Huarte O, Tansey MG (2024) A leaky gut dysregulates gene networks in the brain associated with immune activation, oxidative stress, and myelination in a mouse model of colitis. Brain Behav Immun 117:473–492. https://doi.org/10.1016/j.bbi.2024.02.007. (PMID: 10.1016/j.bbi.2024.02.00738341052)
Bonaz BL, Bernstein CN (2013) Brain-gut interactions in inflammatory bowel disease. Gastroenterology 144(1):36–49. https://doi.org/10.1053/j.gastro.2012.10.003. (PMID: 10.1053/j.gastro.2012.10.00323063970)
Bordenstein SR, Theis KR (2015) Host biology in light of the microbiome: ten principles of holobionts and hologenomes. PLoS Biol 13(8):e1002226. https://doi.org/10.1371/journal.pbio.1002226. (PMID: 10.1371/journal.pbio.1002226262847774540581)
Boscaini S, Leigh SJ, Lavelle A, Garcia-Cabrerizo R, Lipuma T, Clarke G, Schellekens H, Cryan JF (2022) Microbiota and body weight control: weight watchers within? Mol Metab 57:101427. https://doi.org/10.1016/j.molmet.2021.101427. (PMID: 10.1016/j.molmet.2021.10142734973469)
Bostock EC, Kirkby KC, Taylor BV (2017) The current status of the ketogenic diet in psychiatry. Front Psych 8:43. https://doi.org/10.3389/fpsyt.2017.00043. (PMID: 10.3389/fpsyt.2017.00043)
Braga JD, Thongngam M, Kumrungsee T (2024) Gamma-aminobutyric acid as a potential postbiotic mediator in the gut-brain axis. NPJ Sci Food 8(1):16. https://doi.org/10.1038/s41538-024-00253-2. (PMID: 10.1038/s41538-024-00253-23856556710987602)
Bravo JA, Forsythe P, Chew MV, Escaravage E, Savignac HM, Dinan TG, Bienenstock J, Cryan JF (2011) Ingestion of Lactobacillus strain regulates emotional behavior and central GABA receptor expression in a mouse via the vagus nerve. Proc Natl Acad Sci USA 108(38):16050–16055. https://doi.org/10.1073/pnas.1102999108. (PMID: 10.1073/pnas.1102999108218761503179073)
Brea D, Poon C, Benakis C, Lubitz G, Murphy M, Iadecola C, Anrather J (2021) Stroke affects intestinal immune cell trafficking to the central nervous system. Brain Behav Immun 96:295–302. https://doi.org/10.1016/j.bbi.2021.05.008. (PMID: 10.1016/j.bbi.2021.05.008339897428672365)
Bretler T, Weisberg H, Koren O, Neuman H (2019) The effects of antipsychotic medications on microbiome and weight gain in children and adolescents. BMC Med 17(1):112. https://doi.org/10.1186/s12916-019-1346-1. (PMID: 10.1186/s12916-019-1346-1312154946582584)
Breton J, Massart S, Vandamme P, De Brandt E, Pot B, Foligne B (2013) Ecotoxicology inside the gut: impact of heavy metals on the mouse microbiome. BMC Pharmacol Toxicol 14:62. https://doi.org/10.1186/2050-6511-14-62. (PMID: 10.1186/2050-6511-14-62243259433874687)
Bruce-Keller AJ, Salbaum JM, Luo M, Blanchard ET, Taylor CM, Welsh DA, Berthoud HR (2015) Obese-type gut microbiota induce neurobehavioral changes in the absence of obesity. Biol Psychiatry 77(7):607–615. https://doi.org/10.1016/j.biopsych.2014.07.012. (PMID: 10.1016/j.biopsych.2014.07.01225173628)
Brushett S, Gacesa R, Vich Vila A, Brandao Gois MF, Andreu-Sanchez S, Swarte JC, Klaassen MAY, Collij V, Sinha T, Bolte LA, Wu J, Swertz M, de Kroon MLA, Reijneveld SA, Wijmenga C, Weersma RK, Fu J, van Loo HM, Kurilshikov A, Zhernakova A (2023) Gut feelings: the relations between depression, anxiety, psychotropic drugs and the gut microbiome. Gut Microbes 15(2):2281360. https://doi.org/10.1080/19490976.2023.2281360. (PMID: 10.1080/19490976.2023.22813603801766210730195)
Buzun E, Hsu CY, Sejane K, Oles RE, Vasquez Ayala A, Loomis LR, Zhao J, Rossitto LA, McGrosso DM, Gonzalez DJ, Bode L, Chu H (2024) A bacterial sialidase mediates early-life colonization by a pioneering gut commensal. Cell Host Microbe 32(2):181–190 e189. https://doi.org/10.1016/j.chom.2023.12.014. (PMID: 10.1016/j.chom.2023.12.0143822814310922750)
Cabre S, Ratsika A, Rea K, Stanton C, Cryan JF (2022) Animal models for assessing impact of C-section delivery on biological systems. Neurosci Biobehav Rev 135:104555. https://doi.org/10.1016/j.neubiorev.2022.104555. (PMID: 10.1016/j.neubiorev.2022.10455535122781)
Caffrey EB, Sonnenburg JL, Devkota S (2024) Our extended microbiome: the human-relevant metabolites and biology of fermented foods. Cell Metab 36(4):684–701. https://doi.org/10.1016/j.cmet.2024.03.007. (PMID: 10.1016/j.cmet.2024.03.00738569469)
Campbell JP, Turner JE (2018) Debunking the myth of exercise-induced immune suppression: redefining the impact of exercise on immunological health across the lifespan [Review]. Front Immunol 9:648. https://doi.org/10.3389/fimmu.2018.00648. (PMID: 10.3389/fimmu.2018.00648297133195911985)
Campbell BCV, De Silva DA, Macleod MR, Coutts SB, Schwamm LH, Davis SM, Donnan GA (2019) Ischaemic stroke. Nat Rev Dis Primers 5(1):70. https://doi.org/10.1038/s41572-019-0118-8. (PMID: 10.1038/s41572-019-0118-831601801)
Cannavale CN, Mysonhimer AR, Bailey MA, Cohen NJ, Holscher HD, Khan NA (2023) Consumption of a fermented dairy beverage improves hippocampal-dependent relational memory in a randomized, controlled cross-over trial. Nutr Neurosci 26(3):265–274. https://doi.org/10.1080/1028415X.2022.2046963. (PMID: 10.1080/1028415X.2022.204696335282787)
Cantoni C, Lin Q, Dorsett Y, Ghezzi L, Liu Z, Pan Y, Chen K, Han Y, Li Z, Xiao H, Gormley M, Liu Y, Bokoliya S, Panier H, Suther C, Evans E, Deng L, Locca A, Mikesell R et al (2022) Alterations of host-gut microbiome interactions in multiple sclerosis. EBioMedicine 76:103798. https://doi.org/10.1016/j.ebiom.2021.103798. (PMID: 10.1016/j.ebiom.2021.103798350949618814376)
Carabotti M, Scirocco A, Maselli MA, Severi C (2015) The gut-brain axis: interactions between enteric microbiota, central and enteric nervous systems. Ann Gastroenterol 28(2):203–209. (PMID: 258305584367209)
Carbia C, Bastiaanssen TFS, Iannone LF, Garcia-Cabrerizo R, Boscaini S, Berding K, Strain CR, Clarke G, Stanton C, Dinan TG, Cryan JF (2023) The microbiome-gut-brain axis regulates social cognition & craving in young binge drinkers. EBioMedicine 89:104442. https://doi.org/10.1016/j.ebiom.2023.104442. (PMID: 10.1016/j.ebiom.2023.1044423673923810025767)
Castillo-Ruiz A, Gars A, Sturgeon H, Ronczkowski NM, Pyaram DN, Dauriat CJG, Chassaing B, Forger NG (2023) Brain effects of gestating germ-free persist in mouse neonates despite acquisition of a microbiota at birth. Front Neurosci 17:1130347. https://doi.org/10.3389/fnins.2023.1130347. (PMID: 10.3389/fnins.2023.11303473720717910188942)
Castro-Nallar E, Bendall ML, Perez-Losada M, Sabuncyan S, Severance EG, Dickerson FB, Schroeder JR, Yolken RH, Crandall KA (2015) Composition, taxonomy and functional diversity of the oropharynx microbiome in individuals with schizophrenia and controls. PeerJ 3:e1140. https://doi.org/10.7717/peerj.1140. (PMID: 10.7717/peerj.1140263366374556144)
Cattaneo A, Cattane N, Galluzzi S, Provasi S, Lopizzo N, Festari C, Ferrari C, Guerra UP, Paghera B, Muscio C, Bianchetti A, Volta GD, Turla M, Cotelli MS, Gennuso M, Prelle A, Zanetti O, Lussignoli G, Mirabile D et al (2017) Association of brain amyloidosis with pro-inflammatory gut bacterial taxa and peripheral inflammation markers in cognitively impaired elderly. Neurobiol Aging 49:60–68. https://doi.org/10.1016/j.neurobiolaging.2016.08.019. (PMID: 10.1016/j.neurobiolaging.2016.08.01927776263)
Cekanaviciute E, Yoo BB, Runia TF, Debelius JW, Singh S, Nelson CA, Kanner R, Bencosme Y, Lee YK, Hauser SL, Crabtree-Hartman E, Sand IK, Gacias M, Zhu Y, Casaccia P, Cree BAC, Knight R, Mazmanian SK, Baranzini SE (2017) Gut bacteria from multiple sclerosis patients modulate human T cells and exacerbate symptoms in mouse models. Proc Natl Acad Sci USA 114(40):10713–10718. https://doi.org/10.1073/pnas.1711235114. (PMID: 10.1073/pnas.1711235114288939785635915)
Cervantes-Barragan L, Chai JN, Tianero MD, Di Luccia B, Ahern PP, Merriman J, Cortez VS, Caparon MG, Donia MS, Gilfillan S, Cella M, Gordon JI, Hsieh CS, Colonna M (2017) Lactobacillus reuteri induces gut intraepithelial CD4(+)CD8alphaalpha(+) T cells. Science 357(6353):806–810. https://doi.org/10.1126/science.aah5825. (PMID: 10.1126/science.aah5825287752135687812)
Chen JJ, Zeng BH, Li WW, Zhou CJ, Fan SH, Cheng K, Zeng L, Zheng P, Fang L, Wei H, Xie P (2017) Effects of gut microbiota on the microRNA and mRNA expression in the hippocampus of mice. Behav Brain Res 322(Pt A):34–41. https://doi.org/10.1016/j.bbr.2017.01.021. (PMID: 10.1016/j.bbr.2017.01.02128093256)
Chen X, Hu C, Yan C, Tao E, Zhu Z, Shu X, Guo R, Jiang M (2023) Maternal separation leads to dynamic changes of visceral hypersensitivity and fecal metabolomics from childhood to adulthood. Sci Rep 13(1):7670. https://doi.org/10.1038/s41598-023-34792-7. (PMID: 10.1038/s41598-023-34792-73716984710175246)
Chen D, Lou Q, Song XJ, Kang F, Liu A, Zheng C, Li Y, Wang D, Qun S, Zhang Z, Cao P, Jin Y (2024) Microglia govern the extinction of acute stress-induced anxiety-like behaviors in male mice. Nat Commun 15(1):449. https://doi.org/10.1038/s41467-024-44704-6. (PMID: 10.1038/s41467-024-44704-63820002310781988)
Cheng L, Wu H, Cai X, Zhang Y, Yu S, Hou Y, Yin Z, Yan Q, Wang Q, Sun T, Wang G, Yuan Y, Zhang X, Hao H, Zheng X (2024) A Gpr35-tuned gut microbe-brain metabolic axis regulates depressive-like behavior. Cell Host Microbe 32(2):227–243 e226. https://doi.org/10.1016/j.chom.2023.12.009. (PMID: 10.1016/j.chom.2023.12.00938198925)
Chilton PM, Ghare SS, Charpentier BT, Myers SA, Rao AV, Petrosino JF, Hoffman KL, Greenwell JC, Tyagi N, Behera J, Wang Y, Sloan LJ, Zhang J, Shields CB, Cooper GE, Gobejishvili L, Whittemore SR, McClain CJ, Barve SS (2024) Age-associated temporal decline in butyrate-producing bacteria plays a key pathogenic role in the onset and progression of neuropathology and memory deficits in 3xTg-AD mice. Gut Microbes 16(1):2389319. https://doi.org/10.1080/19490976.2024.2389319. (PMID: 10.1080/19490976.2024.23893193918222711346541)
Chimerel C, Emery E, Summers DK, Keyser U, Gribble FM, Reimann F (2014) Bacterial metabolite indole modulates incretin secretion from intestinal enteroendocrine L cells. Cell Rep 9(4):1202–1208. https://doi.org/10.1016/j.celrep.2014.10.032. (PMID: 10.1016/j.celrep.2014.10.032254561224308618)
Chiu IM, Heesters BA, Ghasemlou N, Von Hehn CA, Zhao F, Tran J, Wainger B, Strominger A, Muralidharan S, Horswill AR, Bubeck Wardenburg J, Hwang SW, Carroll MC, Woolf CJ (2013) Bacteria activate sensory neurons that modulate pain and inflammation. Nature 501(7465):52–57. https://doi.org/10.1038/nature12479. (PMID: 10.1038/nature12479239656273773968)
Chiu K, Warner G, Nowak RA, Flaws JA, Mei W (2020) The impact of environmental chemicals on the gut microbiome. Toxicol Sci 176(2):253–284. https://doi.org/10.1093/toxsci/kfaa065. (PMID: 10.1093/toxsci/kfaa065323923067416318)
Cho NA, Sales KM, Sampsell K, Wang W, Noye Tuplin EW, Lowry DE, Reimer RA (2021) C-section birth increases offspring obesity risk dependent on maternal diet and obesity status in rats. Obesity (Silver Spring) 29(10):1664–1675. https://doi.org/10.1002/oby.23258. (PMID: 10.1002/oby.2325834464518)
Chong HX, Yusoff NAA, Hor YY, Lew LC, Jaafar MH, Choi SB, Yusoff MSB, Wahid N, Abdullah M, Zakaria N, Ong KL, Park YH, Liong MT (2019) Lactobacillus plantarum DR7 alleviates stress and anxiety in adults: a randomised, double-blind, placebo-controlled study. Benef Microbes 10(4):355–373. https://doi.org/10.3920/BM2018.0135. (PMID: 10.3920/BM2018.013530882244)
Church JS, Bannish JAM, Adrian LA, Rojas Martinez K, Henshaw A, Schwartzer JJ (2023) Serum short chain fatty acids mediate hippocampal BDNF and correlate with decreasing neuroinflammation following high pectin fiber diet in mice. Front Neurosci 17:1134080. https://doi.org/10.3389/fnins.2023.1134080. (PMID: 10.3389/fnins.2023.11340803712336510130583)
Clarke G, Quigley EM, Cryan JF, Dinan TG (2009) Irritable bowel syndrome: towards biomarker identification. Trends Mol Med 15(10):478–489. https://doi.org/10.1016/j.molmed.2009.08.001. (PMID: 10.1016/j.molmed.2009.08.00119811951)
Clarke TB, Davis KM, Lysenko ES, Zhou AY, Yu Y, Weiser JN (2010) Recognition of peptidoglycan from the microbiota by Nod1 enhances systemic innate immunity. Nat Med 16(2):228–231. https://doi.org/10.1038/nm.2087. (PMID: 10.1038/nm.2087200818634497535)
Clarke G, Cryan JF, Dinan TG, Quigley EM (2012a) Review article: probiotics for the treatment of irritable bowel syndrome--focus on lactic acid bacteria. Aliment Pharmacol Ther 35(4):403–413. https://doi.org/10.1111/j.1365-2036.2011.04965.x. (PMID: 10.1111/j.1365-2036.2011.04965.x22225517)
Clarke G, McKernan DP, Gaszner G, Quigley EM, Cryan JF, Dinan TG (2012b) A distinct profile of tryptophan metabolism along the Kynurenine Pathway Downstream of toll-like receptor activation in irritable Bowel Syndrome. Front Pharmacol 3:90. https://doi.org/10.3389/fphar.2012.00090. (PMID: 10.3389/fphar.2012.00090226619473357104)
Clarke SF, Murphy EF, Nilaweera K, Ross PR, Shanahan F, O’Toole PW, Cotter PD (2012c) The gut microbiota and its relationship to diet and obesity: new insights. Gut Microbes 3(3):186–202. https://doi.org/10.4161/gmic.20168. (PMID: 10.4161/gmic.20168225728303427212)
Clarke G, Grenham S, Scully P, Fitzgerald P, Moloney RD, Shanahan F, Dinan TG, Cryan JF (2013) The microbiome-gut-brain axis during early life regulates the hippocampal serotonergic system in a sex-dependent manner [Article]. Mol Psychiatry 18(6):666–673. https://doi.org/10.1038/mp.2012.77. (PMID: 10.1038/mp.2012.7722688187)
Claus SP, Guillou H, Ellero-Simatos S (2016) The gut microbiota: a major player in the toxicity of environmental pollutants? NPJ Biofilms Microbiomes 2:16003. https://doi.org/10.1038/npjbiofilms.2016.3. (PMID: 10.1038/npjbiofilms.2016.3287212425515271)
Coelho LP, Alves R, Del Rio AR, Myers PN, Cantalapiedra CP, Giner-Lamia J, Schmidt TS, Mende DR, Orakov A, Letunic I, Hildebrand F, Van Rossum T, Forslund SK, Khedkar S, Maistrenko OM, Pan S, Jia L, Ferretti P, Sunagawa S et al (2022) Towards the biogeography of prokaryotic genes. Nature 601(7892):252–256. https://doi.org/10.1038/s41586-021-04233-4. (PMID: 10.1038/s41586-021-04233-434912116)
Collins SM (2014) A role for the gut microbiota in IBS. Nat Rev Gastroenterol Hepatol 11(8):497–505. https://doi.org/10.1038/nrgastro.2014.40. (PMID: 10.1038/nrgastro.2014.4024751910)
Colloca L, Ludman T, Bouhassira D, Baron R, Dickenson AH, Yarnitsky D, Freeman R, Truini A, Attal N, Finnerup NB, Eccleston C, Kalso E, Bennett DL, Dworkin RH, Raja SN (2017) Neuropathic pain. Nat Rev Dis Primers 3(1):17002. https://doi.org/10.1038/nrdp.2017.2. (PMID: 10.1038/nrdp.2017.2282055745371025)
Conti S, Perdixi E, Bernini S, Jesuthasan N, Severgnini M, Prinelli F, NutBrain Study, G (2024) Adherence to Mediterranean diet is inversely associated with depressive symptoms in older women: findings from the NutBrain Study. Br J Nutr 131(11):1892–1901. https://doi.org/10.1017/S0007114524000461. (PMID: 10.1017/S000711452400046138361447)
Cotillard A, Cartier-Meheust A, Litwin NS, Chaumont S, Saccareau M, Lejzerowicz F, Tap J, Koutnikova H, Lopez DG, McDonald D, Song SJ, Knight R, Derrien M, Veiga P (2022) A posteriori dietary patterns better explain variations of the gut microbiome than individual markers in the American Gut Project. Am J Clin Nutr 115(2):432–443. https://doi.org/10.1093/ajcn/nqab332. (PMID: 10.1093/ajcn/nqab33234617562)
Craig AD (2009) How do you feel--now? The anterior insula and human awareness. Nat Rev Neurosci 10(1):59–70. https://doi.org/10.1038/nrn2555. (PMID: 10.1038/nrn255519096369)
Crouzet L, Gaultier E, Del’Homme C, Cartier C, Delmas E, Dapoigny M, Fioramonti J, Bernalier-Donadille A (2013) The hypersensitivity to colonic distension of IBS patients can be transferred to rats through their fecal microbiota. Neurogastroenterol Motil 25(4):e272–e282. https://doi.org/10.1111/nmo.12103. (PMID: 10.1111/nmo.1210323433203)
Cruz-Pereira JS, Moloney GM, Bastiaanssen TFS, Boscaini S, Fitzgerald P, Clarke G, Cryan JF (2023) Age-associated deficits in social behaviour are microbiota-dependent. Brain Behav Immun 110:119–124. https://doi.org/10.1016/j.bbi.2023.02.008. (PMID: 10.1016/j.bbi.2023.02.00836791892)
Cryan JF, O’Riordan KJ, Cowan CSM, Sandhu KV, Bastiaanssen TFS, Boehme M, Codagnone MG, Cussotto S, Fulling C, Golubeva AV, Guzzetta KE, Jaggar M, Long-Smith CM, Lyte JM, Martin JA, Molinero-Perez A, Moloney G, Morelli E, Morillas E et al (2019) The microbiota-gut-brain axis. Physiol Rev 99(4):1877–2013. https://doi.org/10.1152/physrev.00018.2018. (PMID: 10.1152/physrev.00018.201831460832)
Cryan JF, O’Riordan KJ, Sandhu K, Peterson V, Dinan TG (2020) The gut microbiome in neurological disorders. Lancet Neurol 19(2):179–194. https://doi.org/10.1016/S1474-4422(19)30356-4. (PMID: 10.1016/S1474-4422(19)30356-431753762)
Cull C, Singu VK, Cull BJ, Lechtenberg KF, Amachawadi RG, Schutz JS, Bryan KA (2022) Efficacy of two probiotic products fed daily to reduce clostridium perfringens-based adverse health and performance effects in dairy calves. Antibiotics (Basel) 11(11). https://doi.org/10.3390/antibiotics11111513.
Curtis MA, Dhamsania RK, Branco RC, Guo JD, Creeden J, Neifer KL, Black CA, Winokur EJ, Andari E, Dias BG, Liu RC, Gourley SL, Miller GW, Burkett JP (2023) Developmental pyrethroid exposure causes a neurodevelopmental disorder phenotype in mice. PNAS Nexus 2(4):pgad085. https://doi.org/10.1093/pnasnexus/pgad085. (PMID: 10.1093/pnasnexus/pgad0853711397810129348)
Cussotto S, Sandhu KV, Dinan TG, Cryan JF (2018) The neuroendocrinology of the microbiota-gut-brain axis: a behavioural perspective. Front Neuroendocrinol 51:80–101. https://doi.org/10.1016/j.yfrne.2018.04.002. (PMID: 10.1016/j.yfrne.2018.04.00229753796)
Cussotto S, Clarke G, Dinan TG, Cryan JF (2019a) Psychotropics and the microbiome: a chamber of secrets. Psychopharmacology 236(5):1411–1432. https://doi.org/10.1007/s00213-019-5185-8. (PMID: 10.1007/s00213-019-5185-8308067446598948)
Cussotto S, Strain CR, Fouhy F, Strain RG, Peterson VL, Clarke G, Stanton C, Dinan TG, Cryan JF (2019b) Differential effects of psychotropic drugs on microbiome composition and gastrointestinal function. Psychopharmacology 236(5):1671–1685. https://doi.org/10.1007/s00213-018-5006-5. (PMID: 10.1007/s00213-018-5006-530155748)
Cussotto S, Clarke G, Dinan TG, Cryan JF (2021a) Psychotropic drugs and the microbiome. Mod Trends Psychiatry 32:113–133. https://doi.org/10.1159/000510423. (PMID: 10.1159/00051042334032649)
Cussotto S, Walsh J, Golubeva AV, Zhdanov AV, Strain CR, Fouhy F, Stanton C, Dinan TG, Hyland NP, Clarke G, Cryan JF, Griffin BT (2021b) The gut microbiome influences the bioavailability of olanzapine in rats. EBioMedicine 66:103307. https://doi.org/10.1016/j.ebiom.2021.103307. (PMID: 10.1016/j.ebiom.2021.103307338197418047500)
Dalile B, Van Oudenhove L, Vervliet B, Verbeke K (2019) The role of short-chain fatty acids in microbiota-gut-brain communication. Nat Rev Gastroenterol Hepatol 16(8):461–478. https://doi.org/10.1038/s41575-019-0157-3. (PMID: 10.1038/s41575-019-0157-331123355)
Dalile B, Vervliet B, Bergonzelli G, Verbeke K, Van Oudenhove L (2020) Colon-delivered short-chain fatty acids attenuate the cortisol response to psychosocial stress in healthy men: a randomized, placebo-controlled trial. Neuropsychopharmacology 45(13):2257–2266. https://doi.org/10.1038/s41386-020-0732-x. (PMID: 10.1038/s41386-020-0732-x325215387784980)
Dalile B, Fuchs A, La Torre D, Vervliet B, Van Oudenhove L, Verbeke K (2024) Colonic butyrate administration modulates fear memory but not the acute stress response in men: a randomized, triple-blind, placebo-controlled trial. Prog Neuro-Psychopharmacol Biol Psychiatry 131:110939. https://doi.org/10.1016/j.pnpbp.2024.110939. (PMID: 10.1016/j.pnpbp.2024.110939)
Daly DM, Park SJ, Valinsky WC, Beyak MJ (2011) Impaired intestinal afferent nerve satiety signalling and vagal afferent excitability in diet induced obesity in the mouse. J Physiol 589(Pt 11):2857–2870. https://doi.org/10.1113/jphysiol.2010.204594. (PMID: 10.1113/jphysiol.2010.204594214867623112560)
Dapoigny M, Piche T, Ducrotte P, Lunaud B, Cardot JM, Bernalier-Donadille A (2012) Efficacy and safety profile of LCR35 complete freeze-dried culture in irritable bowel syndrome: a randomized, double-blind study. World J Gastroenterol 18(17):2067–2075. https://doi.org/10.3748/wjg.v18.i17.2067. (PMID: 10.3748/wjg.v18.i17.2067225631943342605)
Darwin C (1859) On the origin of species by means of natural selection. J Murray Page view. http://hdllocgov/locrbc/General174731.
Davidson GL, Cienfuegos IA, Dalesman S (2024) Antibiotic-altered gut microbiota explain host memory plasticity and disrupt pace-of-life covariation for an aquatic snail. ISME J 18(1). https://doi.org/10.1093/ismejo/wrae078.
De Palma G, Lynch MD, Lu J, Dang VT, Deng Y, Jury J, Umeh G, Miranda PM, Pigrau Pastor M, Sidani S, Pinto-Sanchez MI, Philip V, McLean PG, Hagelsieb MG, Surette MG, Bergonzelli GE, Verdu EF, Britz-McKibbin P, Neufeld JD et al (2017) Transplantation of fecal microbiota from patients with irritable bowel syndrome alters gut function and behavior in recipient mice. Sci Transl Med 9(379). https://doi.org/10.1126/scitranslmed.aaf6397.
De Vadder F, Grasset E, Manneras Holm L, Karsenty G, Macpherson AJ, Olofsson LE, Backhed F (2018) Gut microbiota regulates maturation of the adult enteric nervous system via enteric serotonin networks. Proc Natl Acad Sci USA 115(25):6458–6463. https://doi.org/10.1073/pnas.1720017115. (PMID: 10.1073/pnas.1720017115298668436016808)
Deaver JA, Eum SY, Toborek M (2018) Circadian disruption changes gut microbiome taxa and functional gene composition. Front Microbiol 9:737. https://doi.org/10.3389/fmicb.2018.00737. (PMID: 10.3389/fmicb.2018.00737297069475909328)
Degirolamo C, Rainaldi S, Bovenga F, Murzilli S, Moschetta A (2014) Microbiota modification with probiotics induces hepatic bile acid synthesis via downregulation of the Fxr-Fgf15 axis in mice. Cell Rep 7(1):12–18. https://doi.org/10.1016/j.celrep.2014.02.032. (PMID: 10.1016/j.celrep.2014.02.03224656817)
Dendrou CA, Fugger L, Friese MA (2015) Immunopathology of multiple sclerosis. Nat Rev Immunol 15(9):545–558. https://doi.org/10.1038/nri3871. (PMID: 10.1038/nri387126250739)
Desbonnet L, Clarke G, Traplin A, O’Sullivan O, Crispie F, Moloney RD, Cotter PD, Dinan TG, Cryan JF (2015) Gut microbiota depletion from early adolescence in mice: implications for brain and behaviour. Brain Behav Immun 48:165–173. https://doi.org/10.1016/j.bbi.2015.04.004. (PMID: 10.1016/j.bbi.2015.04.00425866195)
Dharshika C, Gulbransen BD (2023) Enteric neuromics: how high-throughput “Omics” deepens our understanding of enteric nervous system genetic architecture. Cell Mol Gastroenterol Hepatol 15(2):487–504. https://doi.org/10.1016/j.jcmgh.2022.10.019. (PMID: 10.1016/j.jcmgh.2022.10.01936368612)
Diaz Heijtz R (2024) Gut microbiota: a key susceptibility factor in social anxiety disorder. Proc Natl Acad Sci USA 121(5):e2320425121. https://doi.org/10.1073/pnas.2320425121. (PMID: 10.1073/pnas.23204251213825281610835049)
Dickerson F, Adamos M, Katsafanas E, Khushalani S, Origoni A, Savage C, Schweinfurth L, Stallings C, Sweeney K, Goga J, Yolken RH (2018) Adjunctive probiotic microorganisms to prevent rehospitalization in patients with acute mania: a randomized controlled trial. Bipolar Disord 20(7):614–621. https://doi.org/10.1111/bdi.12652. (PMID: 10.1111/bdi.1265229693757)
Dinan TG, Butler MI, Cryan JF (2021) Psychobiotics: evolution of novel antidepressants. Mod Trends Psychiatry 32:134–143. https://doi.org/10.1159/000510424. (PMID: 10.1159/00051042434032650)
Dinan TG, Kennedy PJ, Morais LH, Murphy A, Long-Smith CM, Moloney GM, Bastiaanssen TFS, Allen AP, Collery A, Mullins D, Cusack AM, Berding K, O’Toole PW, Clarke G, Stanton C, Cryan JF (2022) Altered stress responses in adults born by Caesarean section. Neurobiol Stress 16:100425. https://doi.org/10.1016/j.ynstr.2021.100425. (PMID: 10.1016/j.ynstr.2021.10042535024387)
Diop L, Guillou S, Durand H (2008) Probiotic food supplement reduces stress-induced gastrointestinal symptoms in volunteers: a double-blind, placebo-controlled, randomized trial. Nutr Res 28(1):1–5. https://doi.org/10.1016/j.nutres.2007.10.001. (PMID: 10.1016/j.nutres.2007.10.00119083380)
Dollish HK, Tsyglakova M, McClung CA (2024) Circadian rhythms and mood disorders: time to see the light. Neuron 112(1):25–40. https://doi.org/10.1016/j.neuron.2023.09.023. (PMID: 10.1016/j.neuron.2023.09.02337858331)
Domènech L, Willis J, Alemany-Navarro M, Morell M, Real E, Escaramís G, Bertolín S, Sánchez Chinchilla D, Balcells S, Segalàs C, Estivill X, Menchón JM, Gabaldón T, Alonso P, Rabionet R (2022) Changes in the stool and oropharyngeal microbiome in obsessive-compulsive disorder. Sci Rep 12(1):1448. https://doi.org/10.1038/s41598-022-05480-9. (PMID: 10.1038/s41598-022-05480-9350871238795436)
Donoso F, Egerton S, Bastiaanssen TFS, Fitzgerald P, Gite S, Fouhy F, Ross RP, Stanton C, Dinan TG, Cryan JF (2020) Polyphenols selectively reverse early-life stress-induced behavioural, neurochemical and microbiota changes in the rat. Psychoneuroendocrinology 116:104673. https://doi.org/10.1016/j.psyneuen.2020.104673. (PMID: 10.1016/j.psyneuen.2020.10467332334345)
Doyle WI, Dinser JA, Cansler HL, Zhang X, Dinh DD, Browder NS, Riddington IM, Meeks JP (2016) Faecal bile acids are natural ligands of the mouse accessory olfactory system [Article]. Nat Commun 7:11936. https://doi.org/10.1038/ncomms11936. (PMID: 10.1038/ncomms11936273244394919516)
Drewes AM, Olesen AE, Farmer AD, Szigethy E, Rebours V, Olesen SS (2020) Gastrointestinal pain. Nat Rev Dis Primers 6(1):1. https://doi.org/10.1038/s41572-019-0135-7. (PMID: 10.1038/s41572-019-0135-731907359)
Dzamko N (2023) Cytokine activity in Parkinson’s disease. Neuronal Signals 7(4):NS20220063. https://doi.org/10.1042/NS20220063. (PMID: 10.1042/NS20220063)
Eijsbouts C, Zheng T, Kennedy NA, Bonfiglio F, Anderson CA, Moutsianas L, Holliday J, Shi J, Shringarpure S, andMe Research, T, Voda AI, Bellygenes I, Farrugia G, Franke A, Hubenthal M, Abecasis G, Zawistowski M, Skogholt AH, Ness-Jensen E et al (2021) Genome-wide analysis of 53,400 people with irritable bowel syndrome highlights shared genetic pathways with mood and anxiety disorders. Nat Genet 53(11):1543–1552. https://doi.org/10.1038/s41588-021-00950-8. (PMID: 10.1038/s41588-021-00950-8347411638571093)
El-Salhy M, Valeur J, Hausken T, Gunnar Hatlebakk J (2021) Changes in fecal short-chain fatty acids following fecal microbiota transplantation in patients with irritable bowel syndrome. Neurogastroenterol Motil 33(2):e13983. https://doi.org/10.1111/nmo.13983. (PMID: 10.1111/nmo.1398332945066)
Enck P, Aziz Q, Barbara G, Farmer AD, Fukudo S, Mayer EA, Niesler B, Quigley EM, Rajilic-Stojanovic M, Schemann M, Schwille-Kiuntke J, Simren M, Zipfel S, Spiller RC (2016) Irritable bowel syndrome. Nat Rev Dis Primers 2:16014. https://doi.org/10.1038/nrdp.2016.14. (PMID: 10.1038/nrdp.2016.14271596385001845)
Fackelmann G, Manghi P, Carlino N, Heidrich V, Piccinno G, Ricci L, Piperni E, Arre A, Bakker E, Creedon AC, Francis L, Capdevila Pujol J, Davies R, Wolf J, Bermingham KM, Berry SE, Spector TD, Asnicar F, Segata N (2025) Gut microbiome signatures of vegan, vegetarian and omnivore diets and associated health outcomes across 21,561 individuals. Nat Microbiol 10(1):41–52. https://doi.org/10.1038/s41564-024-01870-z. (PMID: 10.1038/s41564-024-01870-z3976243511726441)
Fahur Bottino G, Bonham KS, Patel F, McCann S, Zieff M, Naspolini N, Ho D, Portlock T, Joos R, Midani FS, Schuroff P, Das A, Shennon I, Wilson BC, O’Sullivan JM, Britton RA, Murray DM, Kiely ME, Taddei CR et al (2025) Early life microbial succession in the gut follows common patterns in humans across the globe. Nat Commun 16(1):660. https://doi.org/10.1038/s41467-025-56072-w. (PMID: 10.1038/s41467-025-56072-w3980976811733223)
Fan Y, Stoving RK, Berreira Ibraim S, Hyotylainen T, Thirion F, Arora T, Lyu L, Stankevic E, Hansen TH, Dechelotte P, Sinioja T, Ragnarsdottir O, Pons N, Galleron N, Quinquis B, Levenez F, Roume H, Falony G, Vieira-Silva S et al (2023) The gut microbiota contributes to the pathogenesis of anorexia nervosa in humans and mice. Nat Microbiol 8(5):787–802. https://doi.org/10.1038/s41564-023-01355-5. (PMID: 10.1038/s41564-023-01355-53706939910159860)
Felice VD, Moloney RD, Cryan JF, Dinan TG, O’Mahony SM (2015) Visceral pain and psychiatric disorders. Mod Trends Pharmacopsychiatry 30:103–119. https://doi.org/10.1159/000435936. (PMID: 10.1159/00043593626436661)
Ferrier L, Eutamene H, Siegwald L, Marquard AM, Tondereau V, Chevalier J, Jacot GE, Favre L, Theodorou V, Vicario M, Rytz A, Bergonzelli G, Garcia-Rodenas CL (2022) Human milk oligosaccharides alleviate stress-induced visceral hypersensitivity and associated microbiota dysbiosis. J Nutr Biochem 99:108865. https://doi.org/10.1016/j.jnutbio.2021.108865. (PMID: 10.1016/j.jnutbio.2021.10886534582967)
Filippi M, Bar-Or A, Piehl F, Preziosa P, Solari A, Vukusic S, Rocca MA (2018) Multiple sclerosis. Nat Rev Dis Prime 4(1):43. https://doi.org/10.1038/s41572-018-0041-4. (PMID: 10.1038/s41572-018-0041-4)
Fouladi F, Bulik-Sullivan EC, Glenny EM, Thornton LM, Reed KK, Thomas S, Kleiman S, Watters A, Oakes J, Huh EY, Tang Q, Liu J, Djukic Z, Harper L, Trillo-Ordonez Y, Sun S, Blakely I, Mehler PS, Fodor AA et al (2022) Reproducible changes in the anorexia nervosa gut microbiota following inpatient therapy remain distinct from non-eating disorder controls. Gut Microbes 14(1):2143217. https://doi.org/10.1080/19490976.2022.2143217. (PMID: 10.1080/19490976.2022.2143217363988629678007)
Fransen F, van Beek AA, Borghuis T, Aidy SE, Hugenholtz F, van der Gaast-de Jongh C, Savelkoul HFJ, De Jonge MI, Boekschoten MV, Smidt H, Faas MM, de Vos P (2017) Aged gut microbiota contributes to systemical inflammaging after transfer to germ-free mice [Original Research]. Front Immunol 8(1385):1385. https://doi.org/10.3389/fimmu.2017.01385. (PMID: 10.3389/fimmu.2017.01385291634745674680)
Fulling C, Dinan TG, Cryan JF (2019) Gut microbe to brain signaling: what happens in Vagus. Neuron 101(6):998–1002. https://doi.org/10.1016/j.neuron.2019.02.008. (PMID: 10.1016/j.neuron.2019.02.00830897366)
Fulling C, Lach G, Bastiaanssen TFS, Fouhy F, O’Donovan AN, Ventura-Silva AP, Stanton C, Dinan TG, Cryan JF (2020) Adolescent dietary manipulations differentially affect gut microbiota composition and amygdala neuroimmune gene expression in male mice in adulthood. Brain Behav Immun 87:666–678. https://doi.org/10.1016/j.bbi.2020.02.013. (PMID: 10.1016/j.bbi.2020.02.01332119901)
Fung TC (2020) The microbiota-immune axis as a central mediator of gut-brain communication. Neurobiol Dis 136:104714. https://doi.org/10.1016/j.nbd.2019.104714. (PMID: 10.1016/j.nbd.2019.10471431846737)
Gabanyi I, Lepousez G, Wheeler R, Vieites-Prado A, Nissant A, Chevalier G, Wagner S, Moigneu C, Dulauroy S, Hicham S, Polomack B, Verny F, Rosenstiel P, Renier N, Boneca IG, Eberl G, Lledo PM (2022) Bacterial sensing via neuronal Nod2 regulates appetite and body temperature. Science 376(6590):eabj3986. https://doi.org/10.1126/science.abj3986. (PMID: 10.1126/science.abj398635420957)
Gacesa R, Kurilshikov A, Vich Vila A, Sinha T, Klaassen MAY, Bolte LA, Andreu-Sanchez S, Chen L, Collij V, Hu S, Dekens JAM, Lenters VC, Bjork JR, Swarte JC, Swertz MA, Jansen BH, Gelderloos-Arends J, Jankipersadsing S, Hofker M et al (2022) Environmental factors shaping the gut microbiome in a Dutch population. Nature 604(7907):732–739. https://doi.org/10.1038/s41586-022-04567-7. (PMID: 10.1038/s41586-022-04567-735418674)
Gama J, Neves B, Pereira A (2022) Chronic effects of dietary pesticides on the gut microbiome and neurodevelopment. Front Microbiol 13:931440. https://doi.org/10.3389/fmicb.2022.931440. (PMID: 10.3389/fmicb.2022.931440358470889279132)
Garcia-Cabrerizo R, Cryan JF (2024) A gut (microbiome) feeling about addiction: interactions with stress and social systems. Neurobiol Stress 30:100629. https://doi.org/10.1016/j.ynstr.2024.100629. (PMID: 10.1016/j.ynstr.2024.1006293858488010995916)
Garcia-Cabrerizo R, Carbia C, KJ OR, Schellekens H, Cryan JF (2021) Microbiota-gut-brain axis as a regulator of reward processes. J Neurochem 157(5):1495–1524. https://doi.org/10.1111/jnc.15284. (PMID: 10.1111/jnc.1528433368280)
Garcia-Cabrerizo R, Barros-Santos T, Campos D, Cryan JF (2023) The gut microbiota alone and in combination with a social stimulus regulates cocaine reward in the mouse. Brain Behav Immun 107:286–291. https://doi.org/10.1016/j.bbi.2022.10.020. (PMID: 10.1016/j.bbi.2022.10.02036341966)
Gatarek P, Kaluzna-Czaplinska J (2021) Trimethylamine N-oxide (TMAO) in human health. EXCLI J 20:301–319. https://doi.org/10.17179/excli2020-3239. (PMID: 10.17179/excli2020-3239337466647975634)
Ge X, Pan J, Liu Y, Wang H, Zhou W, Wang X (2018) Intestinal crosstalk between microbiota and serotonin and its impact on gut motility. Curr Pharm Biotechnol 19(3):190–195. https://doi.org/10.2174/1389201019666180528094202. (PMID: 10.2174/138920101966618052809420229804531)
Gee LMV, Barron-Millar B, Leslie J, Richardson C, Zaki MYW, Luli S, Burgoyne RA, Cameron RIT, Smith GR, Brain JG, Innes B, Jopson L, Dyson JK, McKay KRC, Pechlivanis A, Holmes E, Berlinguer-Palmini R, Victorelli S, Mells GF et al (2023) Anti-Cholestatic therapy with obeticholic acid improves short-term memory in bile duct-ligated mice. Am J Pathol 193(1):11–26. https://doi.org/10.1016/j.ajpath.2022.09.005. (PMID: 10.1016/j.ajpath.2022.09.00536243043)
Geier TJ, Atkinson SN, Pan AY, Mantz-Wichman M, Jazinski-Chambers K, Hillard CJ, de Roon-Cassini TA (2024) Differences in intestinal bacteria in traumatic injury survivors with and without probable posttraumatic stress disorder. J Affect Disord 361:528–535. https://doi.org/10.1016/j.jad.2024.06.075. (PMID: 10.1016/j.jad.2024.06.07538914163)
Gheorghe CE, Cryan JF, Clarke G (2022) Debugging the gut-brain axis in depression. Cell Host Microbe 30(3):281–283. https://doi.org/10.1016/j.chom.2022.02.007. (PMID: 10.1016/j.chom.2022.02.00735271799)
Gheorghe CE, Leigh SJ, Tofani GSS, Bastiaanssen TFS, Lyte JM, Gardellin E, Govindan A, Strain C, Martinez-Herrero S, Goodson MS, Kelley-Loughnane N, Cryan JF, Clarke G (2024) The microbiota drives diurnal rhythms in tryptophan metabolism in the stressed gut. Cell Rep 43(4):114079. https://doi.org/10.1016/j.celrep.2024.114079. (PMID: 10.1016/j.celrep.2024.11407938613781)
Ghosh TS, Shanahan F, O’Toole PW (2022) The gut microbiome as a modulator of healthy ageing. Nat Rev Gastroenterol Hepatol 19(9):565–584. https://doi.org/10.1038/s41575-022-00605-x. (PMID: 10.1038/s41575-022-00605-x354689529035980)
Ghuge S, Rahman Z, Bhale NA, Dikundwar AG, Dandekar MP (2023) Multistrain probiotic rescinds quinpirole-induced obsessive-compulsive disorder phenotypes by reshaping of microbiota gut-brain axis in rats. Pharmacol Biochem Behav 232:173652. https://doi.org/10.1016/j.pbb.2023.173652. (PMID: 10.1016/j.pbb.2023.17365237804865)
Gkougka D, Mitropoulos K, Tzanakaki G, Panagouli E, Psaltopoulou T, Thomaidis L, Tsolia M, Sergentanis TN, Tsitsika A (2022) Gut microbiome and attention deficit/hyperactivity disorder: a systematic review. Pediatr Res 92(6):1507–1519. https://doi.org/10.1038/s41390-022-02027-6. (PMID: 10.1038/s41390-022-02027-635354932)
Goehler LE, Gaykema RP, Opitz N, Reddaway R, Badr N, Lyte M (2005) Activation in vagal afferents and central autonomic pathways: early responses to intestinal infection with Campylobacter jejuni. Brain Behav Immun 19(4):334–344. https://doi.org/10.1016/j.bbi.2004.09.002. (PMID: 10.1016/j.bbi.2004.09.00215944073)
Gois MFB, Fernandez-Pato A, Huss A, Gacesa R, Wijmenga C, Weersma RK, Fu J, Vermeulen RCH, Zhernakova A, Lenters VC, Kurilshikov A (2023) Impact of occupational pesticide exposure on the human gut microbiome. Front Microbiol 14:1223120. https://doi.org/10.3389/fmicb.2023.1223120. (PMID: 10.3389/fmicb.2023.12231203763710410448898)
Golubeva AV, Joyce SA, Moloney G, Burokas A, Sherwin E, Arboleya S, Flynn I, Khochanskiy D, Moya-Perez A, Peterson V, Rea K, Murphy K, Makarova O, Buravkov S, Hyland NP, Stanton C, Clarke G, Gahan CGM, Dinan TG, Cryan JF (2017) Microbiota-related changes in bile acid & tryptophan metabolism are associated with gastrointestinal dysfunction in a mouse model of autism. EBioMedicine 24:166–178. https://doi.org/10.1016/j.ebiom.2017.09.020. (PMID: 10.1016/j.ebiom.2017.09.020289658765652137)
González-Muniesa P, Mártinez-González M-A, Hu FB, Després J-P, Matsuzawa Y, Loos RJF, Moreno LA, Bray GA, Martinez JA (2017) Obesity. Nat Rev Dis Prime 3(1):17034. https://doi.org/10.1038/nrdp.2017.34. (PMID: 10.1038/nrdp.2017.34)
Gonzalez-Santana A, Diaz Heijtz R (2020) Bacterial peptidoglycans from microbiota in neurodevelopment and behavior. Trends Mol Med 26(8):729–743. https://doi.org/10.1016/j.molmed.2020.05.003. (PMID: 10.1016/j.molmed.2020.05.00332507655)
Goodrich JK, Waters JL, Poole AC, Sutter JL, Koren O, Blekhman R, Beaumont M, Van Treuren W, Knight R, Bell JT, Spector TD, Clark AG, Ley RE (2014) Human genetics shape the gut microbiome. Cell 159(4):789–799. https://doi.org/10.1016/j.cell.2014.09.053. (PMID: 10.1016/j.cell.2014.09.053254171564255478)
Gora B, Gofron Z, Grosiak M, Aptekorz M, Kazek B, Kocelak P, Radosz-Komoniewska H, Chudek J, Martirosian G (2018) Toxin profile of fecal Clostridium perfringens strains isolated from children with autism spectrum disorders. Anaerobe 51:73–77. https://doi.org/10.1016/j.anaerobe.2018.03.005. (PMID: 10.1016/j.anaerobe.2018.03.00529526827)
Grabrucker S, Marizzoni M, Silajdzic E, Lopizzo N, Mombelli E, Nicolas S, Dohm-Hansen S, Scassellati C, Moretti DV, Rosa M, Hoffmann K, Cryan JF, O’Leary OF, English JA, Lavelle A, O’Neill C, Thuret S, Cattaneo A, Nolan YM (2023) Microbiota from Alzheimer’s patients induce deficits in cognition and hippocampal neurogenesis. Brain 146(12):4916–4934. https://doi.org/10.1093/brain/awad303. (PMID: 10.1093/brain/awad3033784923410689930)
Grant ET, De Franco H, Desai MS (2025) Non-SCFA microbial metabolites associated with fiber fermentation and host health. Trends Endocrinol Metab 36(1):70–82. https://doi.org/10.1016/j.tem.2024.06.009. (PMID: 10.1016/j.tem.2024.06.00938991905)
Green JE, Davis JA, Berk M, Hair C, Loughman A, Castle D, Athan E, Nierenberg AA, Cryan JF, Jacka F, Marx W (2020) Efficacy and safety of fecal microbiota transplantation for the treatment of diseases other than Clostridium difficile infection: a systematic review and meta-analysis. Gut Microbes 12(1):1–25. https://doi.org/10.1080/19490976.2020.1854640. (PMID: 10.1080/19490976.2020.185464033345703)
Green JE, Berk M, Mohebbi M, Loughman A, McGuinness AJ, Castle D, Chatterton ML, Perez J, Strandwitz P, Athan E, Hair C, Nierenberg AA, Cryan JF, Jacka F (2023) Feasibility, acceptability, and safety of faecal microbiota transplantation in the treatment of major depressive disorder: a pilot randomized controlled trial. Can J Psychiatr 68(5):315–326. https://doi.org/10.1177/07067437221150508. (PMID: 10.1177/07067437221150508)
Group, N. H. W, Peterson J, Garges S, Giovanni M, McInnes P, Wang L, Schloss JA, Bonazzi V, McEwen JE, Wetterstrand KA, Deal C, Baker CC, Di Francesco V, Howcroft TK, Karp RW, Lunsford RD, Wellington CR, Belachew T, Wright M et al (2009) The NIH human microbiome project. Genome Res 19(12):2317–2323. https://doi.org/10.1101/gr.096651.109. (PMID: 10.1101/gr.096651.109)
Grundy D, Al-Chaer ED, Aziz Q, Collins SM, Ke M, Tache Y, Wood JD (2006) Fundamentals of neurogastroenterology: basic science. Gastroenterology 130(5):1391–1411. https://doi.org/10.1053/j.gastro.2005.11.060. (PMID: 10.1053/j.gastro.2005.11.06016678554)
Guo G, Jia KR, Shi Y, Liu XF, Liu KY, Qi W, Guo Y, Zhang WJ, Wang T, Xiao B, Zou QM (2009) Psychological stress enhances the colonization of the stomach by Helicobacter pylori in the BALB/c mouse. Stress 12(6):478–485. https://doi.org/10.3109/10253890802642188. (PMID: 10.3109/1025389080264218820102319)
Gupta VK, Rajendraprasad S, Ozkan M, Ramachandran D, Ahmad S, Bakken JS, Laudanski K, Gajic O, Bauer B, Zec S, Freeman DW, Khanna S, Shah A, Skalski JH, Sung J, Karnatovskaia LV (2024) Safety, feasibility, and impact on the gut microbiome of kefir administration in critically ill adults. BMC Med 22(1):80. https://doi.org/10.1186/s12916-024-03299-x. (PMID: 10.1186/s12916-024-03299-x3837856810880344)
Guzior DV, Quinn RA (2021) Review: microbial transformations of human bile acids. Microbiome 9(1):140. https://doi.org/10.1186/s40168-021-01101-1. (PMID: 10.1186/s40168-021-01101-1341270708204491)
Guzzetta KE, Cryan JF, O’Leary OF (2022) Microbiota-Gut-Brain axis regulation of adult Hippocampal Neurogenesis. Brain Plast 8(1):97–119. https://doi.org/10.3233/BPL-220141. (PMID: 10.3233/BPL-220141364480399661352)
Gyles TM, Nestler EJ, Parise EM (2024) Advancing preclinical chronic stress models to promote therapeutic discovery for human stress disorders. Neuropsychopharmacology 49(1):215–226. https://doi.org/10.1038/s41386-023-01625-0. (PMID: 10.1038/s41386-023-01625-037349475)
Hao Z, Wang W, Guo R, Liu H (2019) Faecalibacterium prausnitzii (ATCC 27766) has preventive and therapeutic effects on chronic unpredictable mild stress-induced depression-like and anxiety-like behavior in rats. Psychoneuroendocrinology 104:132–142. https://doi.org/10.1016/j.psyneuen.2019.02.025. (PMID: 10.1016/j.psyneuen.2019.02.02530844607)
Hata T, Asano Y, Yoshihara K, Kimura-Todani T, Miyata N, Zhang XT, Takakura S, Aiba Y, Koga Y, Sudo N (2017) Regulation of gut luminal serotonin by commensal microbiota in mice. PLoS One 12(7):e0180745. https://doi.org/10.1371/journal.pone.0180745. (PMID: 10.1371/journal.pone.0180745286830935500371)
Heddes M, Altaha B, Niu Y, Reitmeier S, Kleigrewe K, Haller D, Kiessling S (2022) The intestinal clock drives the microbiome to maintain gastrointestinal homeostasis. Nat Commun 13(1):6068. https://doi.org/10.1038/s41467-022-33609-x. (PMID: 10.1038/s41467-022-33609-x362416509568547)
Heinzel S, Jureczek J, Kainulainen V, Nieminen AI, Suenkel U, von Thaler AK, Kaleta C, Eschweiler GW, Brockmann K, Aho VTE, Auvinen P, Maetzler W, Berg D, Scheperjans F (2024) Elevated fecal calprotectin is associated with gut microbial dysbiosis, altered serum markers and clinical outcomes in older individuals. Sci Rep 14(1):13513. https://doi.org/10.1038/s41598-024-63893-0. (PMID: 10.1038/s41598-024-63893-03886691411169261)
Heppner N, Reitmeier S, Heddes M, Merino MV, Schwartz L, Dietrich A, List M, Gigl M, Meng C, van der Veen DR, Schirmer M, Kleigrewe K, Omer H, Kiessling S, Haller D (2024) Diurnal rhythmicity of infant fecal microbiota and metabolites: a randomized controlled interventional trial with infant formula. Cell Host Microbe 32(4):573–587 e575. https://doi.org/10.1016/j.chom.2024.02.015. (PMID: 10.1016/j.chom.2024.02.01538569545)
Hill C, Guarner F, Reid G, Gibson GR, Merenstein DJ, Pot B, Morelli L, Canani RB, Flint HJ, Salminen S, Calder PC, Sanders ME (2014) Expert consensus document. The International Scientific Association for probiotics and prebiotics consensus statement on the scope and appropriate use of the term probiotic. Nat Rev Gastroenterol Hepatol 11(8):506–514. https://doi.org/10.1038/nrgastro.2014.66. (PMID: 10.1038/nrgastro.2014.6624912386)
Hillman CH, Erickson KI, Kramer AF (2008) Be smart, exercise your heart: exercise effects on brain and cognition. Nat Rev Neurosci 9(1):58–65. https://doi.org/10.1038/nrn2298. (PMID: 10.1038/nrn229818094706)
Hilton D, Stephens M, Kirk L, Edwards P, Potter R, Zajicek J, Broughton E, Hagan H, Carroll C (2014) Accumulation of alpha-synuclein in the bowel of patients in the pre-clinical phase of Parkinson’s disease. Acta Neuropathol 127(2):235–241. https://doi.org/10.1007/s00401-013-1214-6. (PMID: 10.1007/s00401-013-1214-624240814)
Holmqvist S, Chutna O, Bousset L, Aldrin-Kirk P, Li W, Bjorklund T, Wang ZY, Roybon L, Melki R, Li JY (2014) Direct evidence of Parkinson pathology spread from the gastrointestinal tract to the brain in rats. Acta Neuropathol 128(6):805–820. https://doi.org/10.1007/s00401-014-1343-6. (PMID: 10.1007/s00401-014-1343-625296989)
Holzer P, Farzi A, Hassan AM, Zenz G, Jacan A, Reichmann F (2017) Visceral inflammation and immune activation stress the brain. Front Immunol 8:1613. https://doi.org/10.3389/fimmu.2017.01613. (PMID: 10.3389/fimmu.2017.01613292132715702648)
Hontelez S, Stobernack T, Pelsser LM, van Baarlen P, Frankena K, Groefsema MM, Kleerebezem M, Rodrigues Pereira R, Postma EM, Smeets PAM, Stopyra MA, Zwiers MP, Aarts E (2021) Correlation between brain function and ADHD symptom changes in children with ADHD following a few-foods diet: an open-label intervention trial. Sci Rep 11(1):22205. https://doi.org/10.1038/s41598-021-01684-7. (PMID: 10.1038/s41598-021-01684-7347729968589974)
Hopkins MJ, Sharp R, Macfarlane GT (2001) Age and disease related changes in intestinal bacterial populations assessed by cell culture, 16S rRNA abundance, and community cellular fatty acid profiles. Gut 48(2):198–205. https://doi.org/10.1136/gut.48.2.198. (PMID: 10.1136/gut.48.2.198111566401728209)
Horne R, Foster JA (2018) Metabolic and microbiota measures as peripheral biomarkers in major depressive disorder. Front Psych 9:513. https://doi.org/10.3389/fpsyt.2018.00513. (PMID: 10.3389/fpsyt.2018.00513)
Howard AL, Robinson M, Smith GJ, Ambrosini GL, Piek JP, Oddy WH (2011) ADHD is associated with a “Western” dietary pattern in adolescents. J Atten Disord 15(5):403–411. https://doi.org/10.1177/1087054710365990. (PMID: 10.1177/108705471036599020631199)
Hsiao EY, McBride SW, Hsien S, Sharon G, Hyde ER, McCue T, Codelli JA, Chow J, Reisman SE, Petrosino JF, Patterson PH, Mazmanian SK (2013) Microbiota modulate behavioral and physiological abnormalities associated with neurodevelopmental disorders. Cell 155(7):1451–1463. https://doi.org/10.1016/j.cell.2013.11.024. (PMID: 10.1016/j.cell.2013.11.024243154843897394)
Human Microbiome Project, C (2012) Structure, function and diversity of the healthy human microbiome. Nature 486(7402):207–214. https://doi.org/10.1038/nature11234. (PMID: 10.1038/nature11234)
Hung LY, Margolis KG (2024) Autism spectrum disorders and the gastrointestinal tract: insights into mechanisms and clinical relevance. Nat Rev Gastroenterol Hepatol 21(3):142–163. https://doi.org/10.1038/s41575-023-00857-1. (PMID: 10.1038/s41575-023-00857-138114585)
Hutkins R, Walter J, Gibson GR, Bedu-Ferrari C, Scott K, Tancredi DJ, Wijeyesekera A, Sanders ME (2025) Classifying compounds as prebiotics — scientific perspectives and recommendations. Nat Rev Gastroenterol Hepatol 22(1):54–70. https://doi.org/10.1038/s41575-024-00981-6. (PMID: 10.1038/s41575-024-00981-639358591)
Hyland NP, Cryan JF (2016) Microbe-host interactions: influence of the gut microbiota on the enteric nervous system. Dev Biol 417(2):182–187. https://doi.org/10.1016/j.ydbio.2016.06.027. (PMID: 10.1016/j.ydbio.2016.06.02727343895)
Imhann F, Bonder MJ, Vich Vila A, Fu J, Mujagic Z, Vork L, Tigchelaar EF, Jankipersadsing SA, Cenit MC, Harmsen HJ, Dijkstra G, Franke L, Xavier RJ, Jonkers D, Wijmenga C, Weersma RK, Zhernakova A (2016) Proton pump inhibitors affect the gut microbiome. Gut 65(5):740–748. https://doi.org/10.1136/gutjnl-2015-310376. (PMID: 10.1136/gutjnl-2015-31037626657899)
Itzhaki RF, Lathe R, Balin BJ, Ball MJ, Bearer EL, Braak H, Bullido MJ, Carter C, Clerici M, Cosby SL, Del Tredici K, Field H, Fulop T, Grassi C, Griffin WS, Haas J, Hudson AP, Kamer AR, Kell DB et al (2016) Microbes and Alzheimer’s disease. J Alzheimers Dis 51(4):979–984. https://doi.org/10.3233/JAD-160152. (PMID: 10.3233/JAD-160152269672295457904)
Jacka FN, O’Neil A, Opie R, Itsiopoulos C, Cotton S, Mohebbi M, Castle D, Dash S, Mihalopoulos C, Chatterton ML, Brazionis L, Dean OM, Hodge AM, Berk M (2017) A randomised controlled trial of dietary improvement for adults with major depression (the ‘SMILES’ trial). BMC Med 15(1):23. https://doi.org/10.1186/s12916-017-0791-y. (PMID: 10.1186/s12916-017-0791-y281372475282719)
Jaggar M, Rea K, Spichak S, Dinan TG, Cryan JF (2020) You’ve got male: sex and the microbiota-gut-brain axis across the lifespan. Front Neuroendocrinol 56:100815. https://doi.org/10.1016/j.yfrne.2019.100815. (PMID: 10.1016/j.yfrne.2019.10081531805290)
Jänig W (2006) The integrative action of the autonomic nervous system neurobiology of homeostasis introduction. In: Integrative action of the autonomic nervous system: neurobiology of homeostasis. Cambridge University Press, pp 1–9. (PMID: 10.1017/CBO9780511541667)
Jasarevic E, Hill EM, Kane PJ, Rutt L, Gyles T, Folts L, Rock KD, Howard CD, Morrison KE, Ravel J, Bale TL (2021) The composition of human vaginal microbiota transferred at birth affects offspring health in a mouse model. Nat Commun 12(1):6289. https://doi.org/10.1038/s41467-021-26634-9. (PMID: 10.1038/s41467-021-26634-9347253598560944)
Jia J, Ning Y, Chen M, Wang S, Yang H, Li F, Ding J, Li Y, Zhao B, Lyu J, Yang S, Yan X, Wang Y, Qin W, Wang Q, Li Y, Zhang J, Liang F, Liao Z, Wang S (2024) Biomarker changes during 20 Years preceding Alzheimer’s disease. N Engl J Med 390(8):712–722. https://doi.org/10.1056/NEJMoa2310168. (PMID: 10.1056/NEJMoa231016838381674)
Jiang H, Ling Z, Zhang Y, Mao H, Ma Z, Yin Y, Wang W, Tang W, Tan Z, Shi J, Li L, Ruan B (2015) Altered fecal microbiota composition in patients with major depressive disorder. Brain Behav Immun 48:186–194. https://doi.org/10.1016/j.bbi.2015.03.016. (PMID: 10.1016/j.bbi.2015.03.01625882912)
Jiang J, Tang B, Wang L, Huo Q, Tan S, Misrani A, Han Y, Li H, Hu H, Wang J, Cheng T, Tabassum S, Chen M, Xie W, Long C, Yang L (2022) Systemic LPS-induced microglial activation results in increased GABAergic tone: a mechanism of protection against neuroinflammation in the medial prefrontal cortex in mice. Brain Behav Immun 99:53–69. https://doi.org/10.1016/j.bbi.2021.09.017. (PMID: 10.1016/j.bbi.2021.09.01734582995)
Jie Z, Yu X, Liu Y, Sun L, Chen P, Ding Q, Gao Y, Zhang X, Yu M, Liu Y, Zhang Y, Kristiansen K, Jia H, Brix S, Cai K (2021) The baseline gut microbiota directs dieting-induced weight loss trajectories. Gastroenterology 160(6):2029–2042 e2016. https://doi.org/10.1053/j.gastro.2021.01.029. (PMID: 10.1053/j.gastro.2021.01.02933482223)
Jin H, Li M, Jeong E, Castro-Martinez F, Zuker CS (2024) A body-brain circuit that regulates body inflammatory responses. Nature 630(8017):695–703. https://doi.org/10.1038/s41586-024-07469-y. (PMID: 10.1038/s41586-024-07469-y3869228511186780)
Johnsen PH, Hilpusch F, Cavanagh JP, Leikanger IS, Kolstad C, Valle PC, Goll R (2018) Faecal microbiota transplantation versus placebo for moderate-to-severe irritable bowel syndrome: a double-blind, randomised, placebo-controlled, parallel-group, single-centre trial. Lancet Gastroenterol Hepatol 3(1):17–24. https://doi.org/10.1016/S2468-1253(17)30338-2. (PMID: 10.1016/S2468-1253(17)30338-229100842)
Jomova K, Alomar SY, Nepovimova E, Kuca K, Valko M (2025) Heavy metals: toxicity and human health effects. Arch Toxicol 99(1):153–209. https://doi.org/10.1007/s00204-024-03903-2. (PMID: 10.1007/s00204-024-03903-239567405)
Joos R, Boucher K, Lavelle A, Arumugam M, Blaser MJ, Claesson MJ, Clarke G, Cotter PD, De Sordi L, Dominguez-Bello MG, Dutilh BE, Ehrlich SD, Ghosh TS, Hill C, Junot C, Lahti L, Lawley TD, Licht TR, Maguin E et al (2024) Examining the healthy human microbiome concept. Nat Rev Microbiol. https://doi.org/10.1038/s41579-024-01107-0.
Kaelberer MM, Rupprecht LE, Liu WW, Weng P, Bohorquez DV (2020) Neuropod cells: the emerging biology of gut-brain sensory transduction. Annu Rev Neurosci 43:337–353. https://doi.org/10.1146/annurev-neuro-091619-022657. (PMID: 10.1146/annurev-neuro-091619-022657321014837573801)
Kang JI, Seo JH, Park CI, Kim ST, Kim YK, Jang JK, Kwon CO, Jeon S, Kim HW, Kim SJ (2023) Microbiome analysis of circulating bacterial extracellular vesicles in obsessive-compulsive disorder. Psychiatry Clin Neurosci 77(12):646–652. https://doi.org/10.1111/pcn.13593. (PMID: 10.1111/pcn.1359337646189)
Kawai T, Akira S (2009) The roles of TLRs, RLRs and NLRs in pathogen recognition. Int Immunol 21(4):317–337. https://doi.org/10.1093/intimm/dxp017. (PMID: 10.1093/intimm/dxp017192465542721684)
Kemp KM, Orihuela CA, Morrow CD, Judd SE, Evans RR, Mrug S (2024) Associations between dietary habits, socio-demographics and gut microbial composition in adolescents. Br J Nutr 131(5):809–820. https://doi.org/10.1017/S0007114523002271. (PMID: 10.1017/S000711452300227137850446)
Kennedy AR, Pissios P, Otu H, Roberson R, Xue B, Asakura K, Furukawa N, Marino FE, Liu FF, Kahn BB, Libermann TA, Maratos-Flier E (2007) A high-fat, ketogenic diet induces a unique metabolic state in mice. Am J Physiol Endocrinol Metab 292(6):E1724–E1739. https://doi.org/10.1152/ajpendo.00717.2006. (PMID: 10.1152/ajpendo.00717.200617299079)
Kennedy KM, de Goffau MC, Perez-Munoz ME, Arrieta MC, Backhed F, Bork P, Braun T, Bushman FD, Dore J, de Vos WM, Earl AM, Eisen JA, Elovitz MA, Ganal-Vonarburg SC, Ganzle MG, Garrett WS, Hall LJ, Hornef MW, Huttenhower C et al (2023) Questioning the fetal microbiome illustrates pitfalls of low-biomass microbial studies. Nature 613(7945):639–649. https://doi.org/10.1038/s41586-022-05546-8. (PMID: 10.1038/s41586-022-05546-83669786211333990)
Khan MF, Khodve G, Yadav S, Mallick K, Banerjee S (2025) Probiotic treatment improves post-traumatic stress disorder outcomes in mice. Behav Brain Res 476:115246. https://doi.org/10.1016/j.bbr.2024.115246. (PMID: 10.1016/j.bbr.2024.11524639255901)
Kim S, Kwon SH, Kam TI, Panicker N, Karuppagounder SS, Lee S, Lee JH, Kim WR, Kook M, Foss CA, Shen C, Lee H, Kulkarni S, Pasricha PJ, Lee G, Pomper MG, Dawson VL, Dawson TM, Ko HS (2019) Transneuronal propagation of pathologic alpha-Synuclein from the gut to the brain models Parkinson’s disease. Neuron 103(4):627–641 e627. https://doi.org/10.1016/j.neuron.2019.05.035. (PMID: 10.1016/j.neuron.2019.05.035312554876706297)
Kim MS, Kim Y, Choi H, Kim W, Park S, Lee D, Kim DK, Kim HJ, Choi H, Hyun DW, Lee JY, Choi EY, Lee DS, Bae JW, Mook-Jung I (2020) Transfer of a healthy microbiota reduces amyloid and tau pathology in an Alzheimer’s disease animal model. Gut 69(2):283–294. https://doi.org/10.1136/gutjnl-2018-317431. (PMID: 10.1136/gutjnl-2018-31743131471351)
Kimmel M, Jin W, Xia K, Lun K, Azcarate-Peril A, Plantinga A, Wu M, Ataei S, Rackers H, Carroll I, Meltzer-Brody S, Fransson E, Knickmeyer R (2022) Metabolite trajectories across the perinatal period and mental health: a preliminary study of tryptophan-related metabolites, bile acids and microbial composition. Behav Brain Res 418:113635. https://doi.org/10.1016/j.bbr.2021.113635. (PMID: 10.1016/j.bbr.2021.11363534755640)
Knopman DS, Amieva H, Petersen RC, Chetelat G, Holtzman DM, Hyman BT, Nixon RA, Jones DT (2021) Alzheimer disease. Nat Rev Dis Primers 7(1):33. https://doi.org/10.1038/s41572-021-00269-y. (PMID: 10.1038/s41572-021-00269-y339863018574196)
Knox EG, Aburto MR, Clarke G, Cryan JF, O’Driscoll CM (2022a) The blood-brain barrier in aging and neurodegeneration. Mol Psychiatry 27(6):2659–2673. https://doi.org/10.1038/s41380-022-01511-z. (PMID: 10.1038/s41380-022-01511-z353619059156404)
Knox EG, Aburto MR, Tessier C, Nagpal J, Clarke G, O’Driscoll CM, Cryan JF (2022b) Microbial-derived metabolites induce actin cytoskeletal rearrangement and protect blood-brain barrier function. iScience 25(12):105648. https://doi.org/10.1016/j.isci.2022.105648. (PMID: 10.1016/j.isci.2022.105648365059349732410)
Knox EG, Lynch CMK, Lee YS, O’Driscoll CM, Clarke G, Cryan JF, Aburto MR (2023) The gut microbiota is important for the maintenance of blood-cerebrospinal fluid barrier integrity. Eur J Neurosci 57(2):233–241. https://doi.org/10.1111/ejn.15878. (PMID: 10.1111/ejn.1587836453579)
Kolobaric A, Andreescu C, Jasarevic E, Hong CH, Roh HW, Cheong JY, Kim YK, Shin TS, Kang CS, Kwon CO, Yoon SY, Hong SW, Aizenstein HJ, Karim HT, Son SJ (2024) Gut microbiome predicts cognitive function and depressive symptoms in late life. Mol Psychiatry 29(10):3064–3075. https://doi.org/10.1038/s41380-024-02551-3. (PMID: 10.1038/s41380-024-02551-33866449011449789)
Komulainen P, Tuomilehto J, Savonen K, Mannikko R, Hassinen M, Lakka TA, Hanninen T, Kiviniemi V, Jacobs DR, Kivipelto M, Rauramaa R (2021) Exercise, diet, and cognition in a 4-year randomized controlled trial: Dose-Responses to Exercise Training (DR’s EXTRA). Am J Clin Nutr 113(6):1428–1439. https://doi.org/10.1093/ajcn/nqab018. (PMID: 10.1093/ajcn/nqab018337421948244125)
Kong G, Cao KL, Judd LM, Li S, Renoir T, Hannan AJ (2020) Microbiome profiling reveals gut dysbiosis in a transgenic mouse model of Huntington’s disease. Neurobiol Dis 135:104268. https://doi.org/10.1016/j.nbd.2018.09.001. (PMID: 10.1016/j.nbd.2018.09.00130194046)
Konturek SJ, Konturek JW, Pawlik T, Brzozowski T (2004) Brain-gut axis and its role in the control of food intake. J Physiol Pharmacol 55(1 Pt 2):137–154. https://www.ncbi.nlm.nih.gov/pubmed/15082874. (PMID: 15082874)
Korpela K, de Vos WM (2022) Infant gut microbiota restoration: state of the art. Gut Microbes 14(1):2118811. https://doi.org/10.1080/19490976.2022.2118811. (PMID: 10.1080/19490976.2022.2118811360936119467569)
Korpela K, Kallio S, Salonen A, Hero M, Kukkonen AK, Miettinen PJ, Savilahti E, Kohva E, Kariola L, Suutela M, Tarkkanen A, de Vos WM, Raivio T, Kuitunen M (2021) Gut microbiota develop towards an adult profile in a sex-specific manner during puberty. Sci Rep 11(1):23297. https://doi.org/10.1038/s41598-021-02375-z. (PMID: 10.1038/s41598-021-02375-z348578148640005)
Koutzoumis DN, Vergara M, Pino J, Buddendorff J, Khoshbouei H, Mandel RJ, Torres GE (2020) Alterations of the gut microbiota with antibiotics protects dopamine neuron loss and improve motor deficits in a pharmacological rodent model of Parkinson’s disease. Exp Neurol 325:113159. https://doi.org/10.1016/j.expneurol.2019.113159. (PMID: 10.1016/j.expneurol.2019.11315931843492)
Kraeuter AK, van den Buuse M, Sarnyai Z (2019) Ketogenic diet prevents impaired prepulse inhibition of startle in an acute NMDA receptor hypofunction model of schizophrenia. Schizophr Res 206:244–250. https://doi.org/10.1016/j.schres.2018.11.011. (PMID: 10.1016/j.schres.2018.11.01130466960)
Kragsnaes MS, Kjeldsen J, Horn HC, Munk HL, Pedersen FM, Holt HM, Pedersen JK, Holm DK, Glerup H, Andersen V, Fredberg U, Kristiansen K, Christensen R, Ellingsen T (2018) Efficacy and safety of faecal microbiota transplantation in patients with psoriatic arthritis: protocol for a 6-month, double-blind, randomised, placebo-controlled trial. BMJ Open 8(4):e019231. https://doi.org/10.1136/bmjopen-2017-019231. (PMID: 10.1136/bmjopen-2017-019231297038515922473)
Kullberg RFJ, Wikki I, Haak BW, Kauko A, Galenkamp H, Peters-Sengers H, Butler JM, Havulinna AS, Palmu J, McDonald D, Benchraka C, Abdel-Aziz MI, Prins M, Maitland van der Zee AH, van den Born BJ, Jousilahti P, de Vos WM, Salomaa V, Knight R et al (2024) Association between butyrate-producing gut bacteria and the risk of infectious disease hospitalisation: results from two observational, population-based microbiome studies. Lancet Microbe 5(9):100864. https://doi.org/10.1016/S2666-5247(24)00079-X. (PMID: 10.1016/S2666-5247(24)00079-X38909617)
Lachmansingh DA, Lavelle A, Cryan JF, Clarke G (2023) Microbiota-Gut-Brain axis and antidepressant treatment. Curr Top Behav Neurosci. https://doi.org/10.1007/7854_2023_449.
Lagomarsino VN, Kostic AD, Chiu IM (2021) Mechanisms of microbial-neuronal interactions in pain and nociception. Neurobiol Pain 9:100056. https://doi.org/10.1016/j.ynpai.2020.100056. (PMID: 10.1016/j.ynpai.2020.10005633392418)
Lai KP, Chung YT, Li R, Wan HT, Wong CK (2016) Bisphenol A alters gut microbiome: comparative metagenomics analysis. Environ Pollut 218:923–930. https://doi.org/10.1016/j.envpol.2016.08.039. (PMID: 10.1016/j.envpol.2016.08.03927554980)
Lane MM, Gamage E, Du S, Ashtree DN, McGuinness AJ, Gauci S, Baker P, Lawrence M, Rebholz CM, Srour B, Touvier M, Jacka FN, O’Neil A, Segasby T, Marx W (2024) Ultra-processed food exposure and adverse health outcomes: umbrella review of epidemiological meta-analyses. BMJ 384:e077310. https://doi.org/10.1136/bmj-2023-077310. (PMID: 10.1136/bmj-2023-0773103841808210899807)
Larraufie P, Martin-Gallausiaux C, Lapaque N, Dore J, Gribble FM, Reimann F, Blottiere HM (2018) SCFAs strongly stimulate PYY production in human enteroendocrine cells. Sci Rep 8(1):74. https://doi.org/10.1038/s41598-017-18259-0. (PMID: 10.1038/s41598-017-18259-0293116175758799)
Lathe R, Schultek NM, Balin BJ, Ehrlich GD, Auber LA, Perry G, Breitschwerdt EB, Corry DB, Doty RL, Rissman RA, Nara PL, Itzhaki R, Eimer WA, Tanzi RE, Intracell Research Group Consortium, C (2023) Establishment of a consensus protocol to explore the brain pathobiome in patients with mild cognitive impairment and Alzheimer’s disease: research outline and call for collaboration. Alzheimers Dement 19(11):5209–5231. https://doi.org/10.1002/alz.13076. (PMID: 10.1002/alz.1307637283269)
Lavelle A, Sokol H (2020) Gut microbiota-derived metabolites as key actors in inflammatory bowel disease. Nat Rev Gastroenterol Hepatol 17(4):223–237. https://doi.org/10.1038/s41575-019-0258-z. (PMID: 10.1038/s41575-019-0258-z32076145)
Lay C, Chu CW, Purbojati RW, Acerbi E, Drautz-Moses DI, de Sessions PF, Jie S, Ho E, Kok YJ, Bi X, Chen S, Mak SY, Chua MC, Goh AEN, Chiang WC, Rao R, Chaithongwongwatthana S, Khemapech N, Chongsrisawat V et al (2021) A synbiotic intervention modulates meta-omics signatures of gut redox potential and acidity in elective caesarean born infants. BMC Microbiol 21(1):191. https://doi.org/10.1186/s12866-021-02230-1. (PMID: 10.1186/s12866-021-02230-1341720128229302)
Leal Rodriguez C, Shah SA, Rasmussen MA, Thorsen J, Boulund U, Pedersen CT, Castro-Mejia JL, Poulsen CE, Poulsen CS, Deng L, Larsen FAN, Widdowson M, Zhang Y, Sorensen SJ, Moineau S, Petit MA, Chawes B, Bonnelykke K, Nielsen DS, Stokholm J (2024) The infant gut virome is associated with preschool asthma risk independently of bacteria. Nat Med 30(1):138–148. https://doi.org/10.1038/s41591-023-02685-x. (PMID: 10.1038/s41591-023-02685-x38102298)
LeDoux J (2003) The emotional brain, fear, and the amygdala [journal article]. Cell Mol Neurobiol 23(4–5):727–738. https://doi.org/10.1023/a:1025048802629. (PMID: 10.1023/a:10250488026291451402711530156)
Lee JH, Wood TK, Lee J (2015) Roles of indole as an interspecies and interkingdom signaling molecule. Trends Microbiol 23(11):707–718. https://doi.org/10.1016/j.tim.2015.08.001. (PMID: 10.1016/j.tim.2015.08.00126439294)
Lee JJ, Piras E, Tamburini S, Bu K, Wallach DS, Remsen B, Cantor A, Kong J, Goetz D, Hoffman KW, Bonner M, Joe P, Mueller BR, Robinson-Papp J, Lotan E, Gonen O, Malaspina D, Clemente JC (2023) Gut and oral microbiome modulate molecular and clinical markers of schizophrenia-related symptoms: a transdiagnostic, multilevel pilot study. Psychiatry Res 326:115279. https://doi.org/10.1016/j.psychres.2023.115279. (PMID: 10.1016/j.psychres.2023.1152793733106810595250)
Leigh SJ, Uhlig F, Wilmes L, Sanchez-Diaz P, Gheorghe CE, Goodson MS, Kelley-Loughnane N, Hyland NP, Cryan JF, Clarke G (2023) The impact of acute and chronic stress on gastrointestinal physiology and function: a microbiota-gut-brain axis perspective. J Physiol 601(20):4491–4538. https://doi.org/10.1113/JP281951. (PMID: 10.1113/JP28195137756251)
Lessard-Lord J, Roussel C, Lupien-Meilleur J, Genereux P, Richard V, Guay V, Roy D, Desjardins Y (2024) Short term supplementation with cranberry extract modulates gut microbiota in human and displays a bifidogenic effect. NPJ Biofilms Microbiomes 10(1):18. https://doi.org/10.1038/s41522-024-00493-w. (PMID: 10.1038/s41522-024-00493-w3844845210918075)
Ley RE, Backhed F, Turnbaugh P, Lozupone CA, Knight RD, Gordon JI (2005) Obesity alters gut microbial ecology. Proc Natl Acad Sci USA 102(31):11070–11075. https://doi.org/10.1073/pnas.0504978102. (PMID: 10.1073/pnas.0504978102160338671176910)
Leyrolle Q, Decoeur F, Dejean C, Briere G, Leon S, Bakoyiannis I, Baroux E, Sterley TL, Bosch-Bouju C, Morel L, Amadieu C, Lecours C, St-Pierre MK, Bordeleau M, De Smedt-Peyrusse V, Sere A, Schwendimann L, Gregoire S, Bretillon L et al (2022) N-3 PUFA deficiency disrupts oligodendrocyte maturation and myelin integrity during brain development. Glia 70(1):50–70. https://doi.org/10.1002/glia.24088. (PMID: 10.1002/glia.2408834519378)
Li D, Wu M (2021) Pattern recognition receptors in health and diseases. Signal Transduct Target Ther 6(1):291. https://doi.org/10.1038/s41392-021-00687-0. (PMID: 10.1038/s41392-021-00687-0343448708333067)
Li J, Jia H, Cai X, Zhong H, Feng Q, Sunagawa S, Arumugam M, Kultima JR, Prifti E, Nielsen T, Juncker AS, Manichanh C, Chen B, Zhang W, Levenez F, Wang J, Xu X, Xiao L, Liang S et al (2014) An integrated catalog of reference genes in the human gut microbiome. Nat Biotechnol 32(8):834–841. https://doi.org/10.1038/nbt.2942. (PMID: 10.1038/nbt.294224997786)
Li H, Sun J, Du J, Wang F, Fang R, Yu C, Xiong J, Chen W, Lu Z, Liu J (2018) Clostridium butyricum exerts a neuroprotective effect in a mouse model of traumatic brain injury via the gut-brain axis. Neurogastroenterol Motil 30(5):e13260. https://doi.org/10.1111/nmo.13260. (PMID: 10.1111/nmo.1326029193450)
Lim MY, Nam YD (2023) Gut microbiome in healthy aging versus those associated with frailty. Gut Microbes 15(2):2278225. https://doi.org/10.1080/19490976.2023.2278225. (PMID: 10.1080/19490976.2023.22782253796883710730223)
Lin CH, Chen CC, Chiang HL, Liou JM, Chang CM, Lu TP, Chuang EY, Tai YC, Cheng C, Lin HY, Wu MS (2019) Altered gut microbiota and inflammatory cytokine responses in patients with Parkinson’s disease. J Neuroinflammation 16(1):129. https://doi.org/10.1186/s12974-019-1528-y. (PMID: 10.1186/s12974-019-1528-y312484246598278)
Lin L, Zhang K, Xiong Q, Zhang J, Cai B, Huang Z, Yang B, Wei B, Chen J, Niu Q (2023) Gut microbiota in pre-clinical rheumatoid arthritis: from pathogenesis to preventing progression. J Autoimmun 141:103001. https://doi.org/10.1016/j.jaut.2023.103001. (PMID: 10.1016/j.jaut.2023.10300136931952)
Link VM, Subramanian P, Cheung F, Han KL, Stacy A, Chi L, Sellers BA, Koroleva G, Courville AB, Mistry S, Burns A, Apps R, Hall KD, Belkaid Y (2024) Differential peripheral immune signatures elicited by vegan versus ketogenic diets in humans. Nat Med 30(2):560–572. https://doi.org/10.1038/s41591-023-02761-2. (PMID: 10.1038/s41591-023-02761-23829130110878979)
Liou AP, Paziuk M, Luevano JM Jr, Machineni S, Turnbaugh PJ, Kaplan LM (2013) Conserved shifts in the gut microbiota due to gastric bypass reduce host weight and adiposity. Sci Transl Med 5(178):178ra141. https://doi.org/10.1126/scitranslmed.3005687. (PMID: 10.1126/scitranslmed.3005687)
Lippert RN, Bruning JC (2022) Maternal metabolic programming of the developing central nervous system: unified pathways to metabolic and psychiatric disorders. Biol Psychiatry 91(10):898–906. https://doi.org/10.1016/j.biopsych.2021.06.002. (PMID: 10.1016/j.biopsych.2021.06.00234330407)
Liu B, Fang F, Pedersen NL, Tillander A, Ludvigsson JF, Ekbom A, Svenningsson P, Chen H, Wirdefeldt K (2017a) Vagotomy and Parkinson disease: a Swedish register-based matched-cohort study. Neurology 88(21):1996–2002. https://doi.org/10.1212/WNL.0000000000003961. (PMID: 10.1212/WNL.0000000000003961284466535440238)
Liu F, Li P, Chen M, Luo Y, Prabhakar M, Zheng H, He Y, Qi Q, Long H, Zhang Y, Sheng H, Zhou H (2017b) Fructooligosaccharide (FOS) and Galactooligosaccharide (GOS) increase bifidobacterium but reduce butyrate producing bacteria with adverse glycemic metabolism in healthy young population. Sci Rep 7(1):11789. https://doi.org/10.1038/s41598-017-10722-2. (PMID: 10.1038/s41598-017-10722-2289241435603605)
Liu H, Wang J, He T, Becker S, Zhang G, Li D, Ma X (2018a) Butyrate: a double-edged sword for health? Adv Nutr 9(1):21–29. https://doi.org/10.1093/advances/nmx009. (PMID: 10.1093/advances/nmx009294384626333934)
Liu S, Marcelin G, Blouet C, Jeong JH, Jo YH, Schwartz GJ, Chua S Jr (2018b) A gut-brain axis regulating glucose metabolism mediated by bile acids and competitive fibroblast growth factor actions at the hypothalamus. Mol Metab 8:37–50. https://doi.org/10.1016/j.molmet.2017.12.003. (PMID: 10.1016/j.molmet.2017.12.00329290621)
Liu L, Ji G, Li G, Hu Y, Jin Q, Hu C, Zhao J, Meng Q, von Deneen KM, Chen A, Cui G, Wang H, Zhao Q, Wu K, Tian J, Shokri-Kojori E, Tomasi D, Volkow ND, Nie Y et al (2019) Structural changes in brain regions involved in executive-control and self-referential processing after sleeve gastrectomy in obese patients. Brain Imaging Behav 13(3):830–840. https://doi.org/10.1007/s11682-018-9904-2. (PMID: 10.1007/s11682-018-9904-229948904)
Liu XF, Shao JH, Liao YT, Wang LN, Jia Y, Dong PJ, Liu ZZ, He DD, Li C, Zhang X (2023) Regulation of short-chain fatty acids in the immune system. Front Immunol 14:1186892. https://doi.org/10.3389/fimmu.2023.1186892. (PMID: 10.3389/fimmu.2023.11868923721514510196242)
Llor C, Bjerrum L (2014) Antimicrobial resistance: risk associated with antibiotic overuse and initiatives to reduce the problem. Ther Adv Drug Saf 5(6):229–241. https://doi.org/10.1177/2042098614554919. (PMID: 10.1177/2042098614554919254361054232501)
Loh JS, Mak WQ, Tan LKS, Ng CX, Chan HH, Yeow SH, Foo JB, Ong YS, How CW, Khaw KY (2024) Microbiota-gut-brain axis and its therapeutic applications in neurodegenerative diseases. Signal Transduct Target Ther 9(1):37. https://doi.org/10.1038/s41392-024-01743-1. (PMID: 10.1038/s41392-024-01743-13836086210869798)
Long SL, Gahan CGM, Joyce SA (2017) Interactions between gut bacteria and bile in health and disease. Mol Asp Med 56:54–65. https://doi.org/10.1016/j.mam.2017.06.002. (PMID: 10.1016/j.mam.2017.06.002)
Lonstein JS, Meinhardt TA, Pavlidi P, Kokras N, Dalla C, Charlier TD, Pawluski JL (2024) Maternal probiotic Lactocaseibacillus rhamnosus HN001 treatment alters postpartum anxiety, cortical monoamines, and the gut microbiome. Psychoneuroendocrinology 165:107033. https://doi.org/10.1016/j.psyneuen.2024.107033. (PMID: 10.1016/j.psyneuen.2024.10703338569396)
Lopera-Maya EA, Kurilshikov A, van der Graaf A, Hu S, Andreu-Sanchez S, Chen L, Vila AV, Gacesa R, Sinha T, Collij V, Klaassen MAY, Bolte LA, Gois MFB, Neerincx PBT, Swertz MA, LifeLines Cohort S, Harmsen HJM, Wijmenga C, Fu J et al (2022) Effect of host genetics on the gut microbiome in 7,738 participants of the Dutch Microbiome Project. Nat Genet 54(2):143–151. https://doi.org/10.1038/s41588-021-00992-y. (PMID: 10.1038/s41588-021-00992-y35115690)
Lowe J, Briggs A, Whittle S, Hoon E, Stephenson M (2018) Effectiveness of probiotics in the management of inflammatory arthritis: a systematic review protocol. JBI Database System Rev Implement Rep 16(12):2295–2303. https://doi.org/10.11124/JBISRIR-2017-003692. (PMID: 10.11124/JBISRIR-2017-00369230096059)
Lu K, Abo RP, Schlieper KA, Graffam ME, Levine S, Wishnok JS, Swenberg JA, Tannenbaum SR, Fox JG (2014) Arsenic exposure perturbs the gut microbiome and its metabolic profile in mice: an integrated metagenomics and metabolomics analysis. Environ Health Perspect 122(3):284–291. https://doi.org/10.1289/ehp.1307429. (PMID: 10.1289/ehp.1307429244132863948040)
Lynch CMK, Cowan CSM, Bastiaanssen TFS, Moloney GM, Theune N, van de Wouw M, Florensa Zanuy E, Ventura-Silva AP, Codagnone MG, Villalobos-Manriquez F, Segalla M, Koc F, Stanton C, Ross P, Dinan TG, Clarke G, Cryan JF (2023) Critical windows of early-life microbiota disruption on behaviour, neuroimmune function, and neurodevelopment. Brain Behav Immun 108:309–327. https://doi.org/10.1016/j.bbi.2022.12.008. (PMID: 10.1016/j.bbi.2022.12.00836535610)
Lynch CMK, Nagpal J, Luczynski P, McVey Neufeld K-A, Dinan TG, Clarke G, Cryan JF (2024) Germ-free animals. In: Hyland N, Stanton C (eds) The gut-brain axis. Academic Press, pp 401–454. https://doi.org/10.1016/b978-0-323-99971-7.00012-6. (PMID: 10.1016/b978-0-323-99971-7.00012-6)
Lyte M, Daniels KM, Schmitz-Esser S (2019) Fluoxetine-induced alteration of murine gut microbial community structure: evidence for a microbial endocrinology-based mechanism of action responsible for fluoxetine-induced side effects. PeerJ 7:e6199. https://doi.org/10.7717/peerj.6199. (PMID: 10.7717/peerj.6199306437016330042)
Lyte JM, Gheorghe CE, Goodson MS, Kelley-Loughnane N, Dinan TG, Cryan JF, Clarke G (2020) Gut-brain axis serotonergic responses to acute stress exposure are microbiome-dependent. Neurogastroenterol Motil 32(11):e13881. https://doi.org/10.1111/nmo.13881. (PMID: 10.1111/nmo.1388132391630)
Ma J, Piao X, Mahfuz S, Long S, Wang J (2022) The interaction among gut microbes, the intestinal barrier and short chain fatty acids. Anim Nutr 9:159–174. https://doi.org/10.1016/j.aninu.2021.09.012. (PMID: 10.1016/j.aninu.2021.09.01235573092)
Macpherson AJ, Pachnis V, Prinz M (2023) Boundaries and integration between microbiota, the nervous system, and immunity. Immunity 56(8):1712–1726. https://doi.org/10.1016/j.immuni.2023.07.011. (PMID: 10.1016/j.immuni.2023.07.01137557080)
Madra M, Ringel R, Margolis KG (2020) Gastrointestinal issues and autism spectrum disorder. Child Adolesc Psychiatr Clin N Am 29(3):501–513. https://doi.org/10.1016/j.chc.2020.02.005. (PMID: 10.1016/j.chc.2020.02.005324715988608248)
Mandelbaum N, Zhang L, Carasso S, Ziv T, Lifshiz-Simon S, Davidovich I, Luz I, Berinstein E, Gefen T, Cooks T, Talmon Y, Balskus EP, Geva-Zatorsky N (2023) Extracellular vesicles of the Gram-positive gut symbiont Bifidobacterium longum induce immune-modulatory, anti-inflammatory effects. npj Biofilms Microbiomes 9(1):30. https://doi.org/10.1038/s41522-023-00400-9. (PMID: 10.1038/s41522-023-00400-93727055410239484)
Manor O, Dai CL, Kornilov SA, Smith B, Price ND, Lovejoy JC, Gibbons SM, Magis AT (2020) Health and disease markers correlate with gut microbiome composition across thousands of people. Nat Commun 11(1):5206. https://doi.org/10.1038/s41467-020-18871-1. (PMID: 10.1038/s41467-020-18871-1330605867562722)
Manyi-Loh C, Mamphweli S, Meyer E, Okoh A (2018) Antibiotic use in agriculture and its consequential resistance in environmental sources: potential public health implications. Molecules 23(4). https://doi.org/10.3390/molecules23040795.
Marco ML, Sanders ME, Ganzle M, Arrieta MC, Cotter PD, De Vuyst L, Hill C, Holzapfel W, Lebeer S, Merenstein D, Reid G, Wolfe BE, Hutkins R (2021) The International Scientific Association for Probiotics and Prebiotics (ISAPP) consensus statement on fermented foods. Nat Rev Gastroenterol Hepatol 18(3):196–208. https://doi.org/10.1038/s41575-020-00390-5. (PMID: 10.1038/s41575-020-00390-5333981127925329)
Martinez KB, Leone V, Chang EB (2017) Western diets, gut dysbiosis, and metabolic diseases: are they linked? Gut Microbes 8(2):130–142. https://doi.org/10.1080/19490976.2016.1270811. (PMID: 10.1080/19490976.2016.1270811280596145390820)
Marungruang N, Kovalenko T, Osadchenko I, Voss U, Huang F, Burleigh S, Ushakova G, Skibo G, Nyman M, Prykhodko O, Hallenius FF (2020) Lingonberries and their two separated fractions differently alter the gut microbiota, improve metabolic functions, reduce gut inflammatory properties, and improve brain function in ApoE−/− mice fed high-fat diet. Nutr Neurosci 23(8):600–612. https://doi.org/10.1080/1028415X.2018.1536423. (PMID: 10.1080/1028415X.2018.153642330353787)
Marx W, Lane MM, Hockey M, Aslam H, Walder K, Borsini A, Firth J, Pariante CM, Berding K, Cryan JF, Clarke G, Craig JM, Su KP, Mischoulon D, Gomez-Pinilla F, Foster JA, Cani PD, Thuret S, Staudacher HM et al (2022) Diet and depression: future needs to unlock the potential. Mol Psychiatry 27(2):778–780. https://doi.org/10.1038/s41380-021-01360-2. (PMID: 10.1038/s41380-021-01360-234754110)
Marx W, Penninx B, Solmi M, Furukawa TA, Firth J, Carvalho AF, Berk M (2023) Major depressive disorder. Nat Rev Dis Primers 9(1):44. https://doi.org/10.1038/s41572-023-00454-1. (PMID: 10.1038/s41572-023-00454-137620370)
Matsuzaki R, Gunnigle E, Geissen V, Clarke G, Nagpal J, Cryan JF (2023) Pesticide exposure and the microbiota-gut-brain axis. ISME J 17(8):1153–1166. https://doi.org/10.1038/s41396-023-01450-9. (PMID: 10.1038/s41396-023-01450-93732857010356795)
Mayer EA (2000) The neurobiology of stress and gastrointestinal disease. Gut 47(6):861–869. https://doi.org/10.1136/gut.47.6.861. (PMID: 10.1136/gut.47.6.861110768881728136)
Mayer EA, Ryu HJ, Bhatt RR (2023) The neurobiology of irritable bowel syndrome. Mol Psychiatry 28(4):1451–1465. https://doi.org/10.1038/s41380-023-01972-w. (PMID: 10.1038/s41380-023-01972-w3673258610208985)
Mazzoli R, Pessione E (2016) The neuro-endocrinological role of microbial glutamate and GABA signaling. Front Microbiol 7:1934. https://doi.org/10.3389/fmicb.2016.01934. (PMID: 10.3389/fmicb.2016.01934279656545127831)
Mazzone L, Dooling SW, Volpe E, Uljarevic M, Waters JL, Sabatini A, Arturi L, Abate R, Riccioni A, Siracusano M, Pereira M, Engstrand L, Cristofori F, Adduce D, Francavilla R, Costa-Mattioli M, Hardan AY (2024) Precision microbial intervention improves social behavior but not autism severity: a pilot double-blind randomized placebo-controlled trial. Cell Host Microbe 32(1):106–116 e106. https://doi.org/10.1016/j.chom.2023.11.021. (PMID: 10.1016/j.chom.2023.11.02138113884)
McColgan P, Tabrizi SJ (2018) Huntington’s disease: a clinical review. Eur J Neurol 25(1):24–34. https://doi.org/10.1111/ene.13413. (PMID: 10.1111/ene.1341328817209)
McDonald D, Hyde E, Debelius JW, Morton JT, Gonzalez A, Ackermann G, Aksenov AA, Behsaz B, Brennan C, Chen Y, DeRight Goldasich L, Dorrestein PC, Dunn RR, Fahimipour AK, Gaffney J, Gilbert JA, Gogul G, Green JL, Hugenholtz P et al (2018) American gut: an open platform for citizen science microbiome research. mSystems 3(3). https://doi.org/10.1128/mSystems.00031-18.
McEvoy CT, Jennings A, Steves CJ, Macgregor A, Spector T, Cassidy A (2024) Diet patterns and cognitive performance in a UK Female Twin Registry (TwinsUK). Alzheimers Res Ther 16(1):17. https://doi.org/10.1186/s13195-024-01387-x. (PMID: 10.1186/s13195-024-01387-x3826327110804649)
McGuinness AJ, Loughman A, Foster JA, Jacka F (2024) Mood disorders: the gut bacteriome and beyond. Biol Psychiatry 95(4):319–328. https://doi.org/10.1016/j.biopsych.2023.08.020. (PMID: 10.1016/j.biopsych.2023.08.02037661007)
McKernan DP, Fitzgerald P, Dinan TG, Cryan JF (2010) The probiotic Bifidobacterium infantis 35624 displays visceral antinociceptive effects in the rat. Neurogastroenterol Motil 22(9):1029–1035, e1268. https://doi.org/10.1111/j.1365-2982.2010.01520.x. (PMID: 10.1111/j.1365-2982.2010.01520.x20518856)
McNamara MP, Singleton JM, Cadney MD, Ruegger PM, Borneman J, Garland T (2021) Early-life effects of juvenile Western diet and exercise on adult gut microbiome composition in mice. J Exp Biol 224(Pt 4). https://doi.org/10.1242/jeb.239699.
Medawar E, Beyer F, Thieleking R, Haange SB, Rolle-Kampczyk U, Reinicke M, Chakaroun R, von Bergen M, Stumvoll M, Villringer A, Witte AV (2024) Prebiotic diet changes neural correlates of food decision-making in overweight adults: a randomised controlled within-subject cross-over trial. Gut 73(2):298–310. https://doi.org/10.1136/gutjnl-2023-330365. (PMID: 10.1136/gutjnl-2023-33036537793780)
Medzhitov R (2007) Recognition of microorganisms and activation of the immune response. Nature 449(7164):819–826. https://doi.org/10.1038/nature06246. (PMID: 10.1038/nature0624617943118)
Michaudel C, Danne C, Agus A, Magniez A, Aucouturier A, Spatz M, Lefevre A, Kirchgesner J, Rolhion N, Wang Y, Lavelle A, Galbert C, Da Costa G, Poirier M, Lapiere A, Planchais J, Nadvornik P, Illes P, Oeuvray C et al (2023) Rewiring the altered tryptophan metabolism as a novel therapeutic strategy in inflammatory bowel diseases. Gut 72(7):1296–1307. https://doi.org/10.1136/gutjnl-2022-327337. (PMID: 10.1136/gutjnl-2022-32733736270778)
Millan MJ (2002) Descending control of pain. Prog Neurobiol 66(6):355–474. https://doi.org/10.1016/s0301-0082(02)00009-6. (PMID: 10.1016/s0301-0082(02)00009-612034378)
Miller JE, Goldacre R, Moore HC, Zeltzer J, Knight M, Morris C, Nowell S, Wood R, Carter KW, Fathima P, de Klerk N, Strunk T, Li J, Nassar N, Pedersen LH, Burgner DP (2020) Mode of birth and risk of infection-related hospitalisation in childhood: a population cohort study of 7.17 million births from 4 high-income countries. PLoS Med 17(11):e1003429. https://doi.org/10.1371/journal.pmed.1003429. (PMID: 10.1371/journal.pmed.1003429332116967676705)
Minnebo Y, De Paepe K, Raes J, Van de Wiele T (2023) Eating patterns contribute to shaping the gut microbiota in the mucosal simulator of the human intestinal microbial ecosystem. FEMS Microbiol Ecol 99(12). https://doi.org/10.1093/femsec/fiad149.
Minter MR, Hinterleitner R, Meisel M, Zhang C, Leone V, Zhang X, Oyler-Castrillo P, Zhang X, Musch MW, Shen X, Jabri B, Chang EB, Tanzi RE, Sisodia SS (2017) Antibiotic-induced perturbations in microbial diversity during post-natal development alters amyloid pathology in an aged APP(SWE)/PS1(DeltaE9) murine model of Alzheimer’s disease. Sci Rep 7(1):10411. https://doi.org/10.1038/s41598-017-11047-w. (PMID: 10.1038/s41598-017-11047-w288748325585265)
Mir H-D, Milman A, Monnoye M, Douard V, Philippe C, Aubert A, Castanon N, Vancassel S, Guérineau NC, Naudon L, Rabot S (2020) The gut microbiota metabolite indole increases emotional responses and adrenal medulla activity in chronically stressed male mice. Psychoneuroendocrinology 119:104750. https://doi.org/10.1016/j.psyneuen.2020.104750. (PMID: 10.1016/j.psyneuen.2020.10475032569990)
Mir H-D, Yang Q, Maximin E, Montardy Q, Ji S, Cheng Q, Shan X, Wang L, Naudon L, Rabot S, Li L (2024) Indole induces anxiety-like behaviour in mice mediated by brainstem locus coeruleus activation. Neurobiol Dis 200:106606. https://doi.org/10.1016/j.nbd.2024.106606. (PMID: 10.1016/j.nbd.2024.10660639019292)
Mischoulon D, Dunlop BW, Kinkead B, Schettler PJ, Lamon-Fava S, Rakofsky JJ, Nierenberg AA, Clain AJ, Mletzko Crowe T, Wong A, Felger JC, Sangermano L, Ziegler TR, Cusin C, Fisher LB, Fava M, Rapaport MH (2022) Omega-3 fatty acids for major depressive disorder with high inflammation: a randomized dose-finding clinical trial. J Clin Psychiatry 83(5). https://doi.org/10.4088/JCP.21m14074.
Misiak B, Pawlak E, Rembacz K, Kotas M, Zebrowska-Rozanska P, Kujawa D, Laczmanski L, Piotrowski P, Bielawski T, Samochowiec J, Samochowiec A, Karpinski P (2024) Associations of gut microbiota alterations with clinical, metabolic, and immune-inflammatory characteristics of chronic schizophrenia. J Psychiatr Res 171:152–160. https://doi.org/10.1016/j.jpsychires.2024.01.036. (PMID: 10.1016/j.jpsychires.2024.01.03638281465)
Moeller AH, Foerster S, Wilson ML, Pusey AE, Hahn BH, Ochman H (2016) Social behavior shapes the chimpanzee pan-microbiome. Sci Adv 2(1):e1500997. https://doi.org/10.1126/sciadv.1500997. (PMID: 10.1126/sciadv.1500997268240724730854)
Mohle L, Mattei D, Heimesaat MM, Bereswill S, Fischer A, Alutis M, French T, Hambardzumyan D, Matzinger P, Dunay IR, Wolf SA (2016) Ly6C(hi) monocytes provide a link between antibiotic-induced changes in gut microbiota and adult hippocampal neurogenesis. Cell Rep 15(9):1945–1956. https://doi.org/10.1016/j.celrep.2016.04.074. (PMID: 10.1016/j.celrep.2016.04.07427210745)
Moloney GM, Viola MF, Hoban AE, Dinan TG, Cryan JF (2018) Faecal microRNAs: indicators of imbalance at the host-microbe interface? Benef Microbes 9(2):175–183. https://doi.org/10.3920/BM2017.0013. (PMID: 10.3920/BM2017.001329264965)
Moloney GM, Dinan TG, Clarke G, Cryan JF (2019) Microbial regulation of microRNA expression in the brain-gut axis. Curr Opin Pharmacol 48:120–126. https://doi.org/10.1016/j.coph.2019.08.005. (PMID: 10.1016/j.coph.2019.08.00531590111)
Morais LH, Golubeva AV, Moloney GM, Moya-Perez A, Ventura-Silva AP, Arboleya S, Bastiaanssen TFS, O’Sullivan O, Rea K, Borre Y, Scott KA, Patterson E, Cherry P, Stilling R, Hoban AE, El Aidy S, Sequeira AM, Beers S, Moloney RD et al (2020) Enduring behavioral effects induced by birth by caesarean section in the mouse. Curr Biol 30(19):3761–3774 e3766. https://doi.org/10.1016/j.cub.2020.07.044. (PMID: 10.1016/j.cub.2020.07.04432822606)
Morais S, Winkler S, Zorea A, Levin L, Nagies FSP, Kapust N, Lamed E, Artan-Furman A, Bolam DN, Yadav MP, Bayer EA, Martin WF, Mizrahi I (2024) Cryptic diversity of cellulose-degrading gut bacteria in industrialized humans. Science 383(6688):eadj9223. https://doi.org/10.1126/science.adj9223. (PMID: 10.1126/science.adj9223384840697615765)
Morales-Soto W, Gonzales J, Jackson WF, Gulbransen BD (2023) Enteric glia promote visceral hypersensitivity during inflammation through intercellular signaling with gut nociceptors. Sci Signal 16(812):eadg1668. https://doi.org/10.1126/scisignal.adg1668. (PMID: 10.1126/scisignal.adg16683798845410733972)
Morin C, Faure F, Mollet J, Guenoun D, Heydari-Olya A, Sautet I, Diao S, Faivre V, Pansiot J, Tabet L, Hua J, Schwendimann L, Mokhtari A, Martin-Rosique R, Chadi S, Laforge M, Demene C, Delahaye-Duriez A, Diaz-Heijtz R et al (2025) C-section and systemic inflammation synergize to disrupt the neonatal gut microbiota and brain development in a model of prematurity. Brain Behav Immun 123:824–837. https://doi.org/10.1016/j.bbi.2024.10.023. (PMID: 10.1016/j.bbi.2024.10.02339442636)
Morton JT, Jin DM, Mills RH, Shao Y, Rahman G, McDonald D, Zhu Q, Balaban M, Jiang Y, Cantrell K, Gonzalez A, Carmel J, Frankiensztajn LM, Martin-Brevet S, Berding K, Needham BD, Zurita MF, David M, Averina OV et al (2023) Multi-level analysis of the gut-brain axis shows autism spectrum disorder-associated molecular and microbial profiles. Nat Neurosci 26(7):1208–1217. https://doi.org/10.1038/s41593-023-01361-0. (PMID: 10.1038/s41593-023-01361-03736531310322709)
Mueller NT, Differding MK, Ostbye T, Hoyo C, Benjamin-Neelon SE (2021a) Association of birth mode of delivery with infant faecal microbiota, potential pathobionts, and short chain fatty acids: a longitudinal study over the first year of life. BJOG 128(8):1293–1303. https://doi.org/10.1111/1471-0528.16633. (PMID: 10.1111/1471-0528.16633333382928211907)
Mueller NT, Differding MK, Zhang M, Maruthur NM, Juraschek SP, Miller ER 3rd, Appel LJ, Yeh HC (2021b) Metformin affects gut microbiome composition and function and circulating short-chain fatty acids: a randomized trial. Diabetes Care 44(7):1462–1471. https://doi.org/10.2337/dc20-2257. (PMID: 10.2337/dc20-2257340065658323185)
Mullish BH, Michael DR, Dabcheva M, Webberley TS, Coates N, John DA, Wang D, Luo Y, Plummer SF, Marchesi JR (2024) A double-blind, randomized, placebo-controlled study assessing the impact of probiotic supplementation on the symptoms of irritable bowel syndrome in females. Neurogastroenterol Motil 36(4):e14751. https://doi.org/10.1111/nmo.14751. (PMID: 10.1111/nmo.1475138287443)
Murray N, Al Khalaf S, Bastiaanssen TFS, Kaulmann D, Lonergan E, Cryan JF, Clarke G, Khashan AS, O’Connor K (2023) Compositional and functional alterations in intestinal microbiota in patients with psychosis or schizophrenia: a systematic review and meta-analysis. Schizophr Bull 49(5):1239–1255. https://doi.org/10.1093/schbul/sbad049. (PMID: 10.1093/schbul/sbad0493721059410483467)
Muth AK, Park SQ (2021) The impact of dietary macronutrient intake on cognitive function and the brain. Clin Nutr 40(6):3999–4010. https://doi.org/10.1016/j.clnu.2021.04.043. (PMID: 10.1016/j.clnu.2021.04.04334139473)
Mysonhimer AR, Brown MD, Alvarado DA, Cornman E, Esmail M, Abdiel T, Gutierrez K, Vasquez J, Cannavale CN, Miller MJ, Khan NA, Holscher HD (2024) Honey added to yogurt with Bifidobacterium animalis subsp. lactis DN-173 010/CNCM I-2494 supports probiotic enrichment but does not reduce intestinal transit time in healthy adults: a randomized, controlled, crossover trial. J Nutr 154(8):2396–2410. https://doi.org/10.1016/j.tjnut.2024.05.028. (PMID: 10.1016/j.tjnut.2024.05.0283883047211375456)
Nagpal J, Cryan JF (2021a) Host genetics, the microbiome & behaviour-a ‘Holobiont’ perspective. Cell Res 31(8):832–833. https://doi.org/10.1038/s41422-021-00512-x. (PMID: 10.1038/s41422-021-00512-x339907868324890)
Nagpal J, Cryan JF (2021b) Microbiota-brain interactions: moving toward mechanisms in model organisms. Neuron 109(24):3930–3953. https://doi.org/10.1016/j.neuron.2021.09.036. (PMID: 10.1016/j.neuron.2021.09.03634653349)
Nguyen TT, Kosciolek T, Maldonado Y, Daly RE, Martin AS, McDonald D, Knight R, Jeste DV (2019) Differences in gut microbiome composition between persons with chronic schizophrenia and healthy comparison subjects. Schizophr Res 204:23–29. https://doi.org/10.1016/j.schres.2018.09.014. (PMID: 10.1016/j.schres.2018.09.01430268819)
Nguyen TT, Kosciolek T, Daly RE, Vazquez-Baeza Y, Swafford A, Knight R, Jeste DV (2021) Gut microbiome in schizophrenia: altered functional pathways related to immune modulation and atherosclerotic risk. Brain Behav Immun 91:245–256. https://doi.org/10.1016/j.bbi.2020.10.003. (PMID: 10.1016/j.bbi.2020.10.00333098964)
Ni Lochlainn M, Bowyer RCE, Moll JM, Garcia MP, Wadge S, Baleanu AF, Nessa A, Sheedy A, Akdag G, Hart D, Raffaele G, Seed PT, Murphy C, Harridge SDR, Welch AA, Greig C, Whelan K, Steves CJ (2024) Effect of gut microbiome modulation on muscle function and cognition: the PROMOTe randomised controlled trial. Nat Commun 15(1):1859. https://doi.org/10.1038/s41467-024-46116-y. (PMID: 10.1038/s41467-024-46116-y3842409910904794)
Nicolas S, Leime CSO, Hoban AE, Hueston CM, Cryan JF, Nolan YM (2022a) Enduring effects of an unhealthy diet during adolescence on systemic but not neurobehavioural measures in adult rats. Nutr Neurosci 25(4):657–669. https://doi.org/10.1080/1028415X.2020.1796041. (PMID: 10.1080/1028415X.2020.179604132723167)
Nicolas S, McGovern AJ, Hueston CM, O’Mahony SM, Cryan JF, O’Leary OF, Nolan YM (2022b) Prior maternal separation stress alters the dendritic complexity of new hippocampal neurons and neuroinflammation in response to an inflammatory stressor in juvenile female rats. Brain Behav Immun 99:327–338. https://doi.org/10.1016/j.bbi.2021.10.016. (PMID: 10.1016/j.bbi.2021.10.01634732365)
Nicolas S, Dohm-Hansen S, Lavelle A, Bastiaanssen TFS, English JA, Cryan JF, Nolan YM (2024) Exercise mitigates a gut microbiota-mediated reduction in adult hippocampal neurogenesis and associated behaviours in rats. Transl Psychiatry 14(1):195. https://doi.org/10.1038/s41398-024-02904-0. (PMID: 10.1038/s41398-024-02904-03865854711043361)
Nikolova VL, Smith MRB, Hall LJ, Cleare AJ, Stone JM, Young AH (2021) Perturbations in gut microbiota composition in psychiatric disorders: a review and meta-analysis. JAMA Psychiatry 78(12):1343–1354. https://doi.org/10.1001/jamapsychiatry.2021.2573. (PMID: 10.1001/jamapsychiatry.2021.257334524405)
Noetel M, Sanders T, Gallardo-Gomez D, Taylor P, Del Pozo Cruz B, van den Hoek D, Smith JJ, Mahoney J, Spathis J, Moresi M, Pagano R, Pagano L, Vasconcellos R, Arnott H, Varley B, Parker P, Biddle S, Lonsdale C (2024) Effect of exercise for depression: systematic review and network meta-analysis of randomised controlled trials. BMJ 384:e075847. https://doi.org/10.1136/bmj-2023-075847. (PMID: 10.1136/bmj-2023-0758473835515410870815)
Nota MHC, Nicolas S, O’Leary OF, Nolan YM (2023) Outrunning a bad diet: interactions between exercise and a Western-style diet for adolescent mental health, metabolism and microbes. Neurosci Biobehav Rev 149:105147. https://doi.org/10.1016/j.neubiorev.2023.105147. (PMID: 10.1016/j.neubiorev.2023.10514736990371)
O’Connor R, van De Wouw M, Moloney GM, Ventura-Silva AP, O’Riordan K, Golubeva AV, Dinan TG, Schellekens H, Cryan JF (2021) Strain differences in behaviour and immunity in aged mice: relevance to autism. Behav Brain Res 399:113020. https://doi.org/10.1016/j.bbr.2020.113020. (PMID: 10.1016/j.bbr.2020.11302033227245)
Obata Y, Pachnis V (2016) The effect of microbiota and the immune system on the development and organization of the enteric nervous system. Gastroenterology 151(5):836–844. https://doi.org/10.1053/j.gastro.2016.07.044. (PMID: 10.1053/j.gastro.2016.07.04427521479)
O’Riordan KJ, Collins MK, Moloney GM, Knox EG, Aburto MR, Fulling C, Morley SJ, Clarke G, Schellekens H, Cryan JF (2022) Short chain fatty acids: microbial metabolites for gut-brain axis signalling. Mol Cell Endocrinol 546:111572. https://doi.org/10.1016/j.mce.2022.111572. (PMID: 10.1016/j.mce.2022.11157235066114)
Osman A, Mervosh NL, Strat AN, Euston TJ, Zipursky G, Pollak RM, Meckel KR, Tyler SR, Chan KL, Buxbaum Grice A, Drapeau E, Litichevskiy L, Gill J, Zeldin SM, Thaiss CA, Buxbaum JD, Breen MS, Kiraly DD (2023) Acetate supplementation rescues social deficits and alters transcriptional regulation in prefrontal cortex of Shank3 deficient mice. Brain Behav Immun 114:311–324. https://doi.org/10.1016/j.bbi.2023.08.020. (PMID: 10.1016/j.bbi.2023.08.0203765764310955506)
Otaru N, Kourouma L, Pugin B, Constancias F, Braegger C, Mansuy IM, Lacroix C (2024) Transgenerational effects of early life stress on the fecal microbiota in mice. Commun Biol 7(1):670. https://doi.org/10.1038/s42003-024-06279-2. (PMID: 10.1038/s42003-024-06279-23882206111143345)
Palmer C, Bik EM, DiGiulio DB, Relman DA, Brown PO (2007) Development of the human infant intestinal microbiota. PLoS Biol 5(7):e177. https://doi.org/10.1371/journal.pbio.0050177. (PMID: 10.1371/journal.pbio.0050177175941761896187)
Palomar MM, Maldonado Galdeano C, Perdigon G (2014) Influence of a probiotic lactobacillus strain on the intestinal ecosystem in a stress model mouse. Brain Behav Immun 35:77–85. https://doi.org/10.1016/j.bbi.2013.08.015. (PMID: 10.1016/j.bbi.2013.08.01524016865)
Paoli A, Rubini A, Volek JS, Grimaldi KA (2013) Beyond weight loss: a review of the therapeutic uses of very-low-carbohydrate (ketogenic) diets. Eur J Clin Nutr 67(8):789–796. https://doi.org/10.1038/ejcn.2013.116. (PMID: 10.1038/ejcn.2013.116238010973826507)
Park G, Kadyan S, Hochuli N, Pollak J, Wang B, Salazar G, Chakrabarty P, Efron P, Sheffler J, Nagpal R (2024) A modified Mediterranean-style diet enhances brain function via specific gut-microbiome-brain mechanisms. Gut Microbes 16(1):2323752. https://doi.org/10.1080/19490976.2024.2323752. (PMID: 10.1080/19490976.2024.23237523844439210936641)
Partty A, Kalliomaki M, Wacklin P, Salminen S, Isolauri E (2015) A possible link between early probiotic intervention and the risk of neuropsychiatric disorders later in childhood: a randomized trial [Article]. Pediatr Res 77(6):823–828. https://doi.org/10.1038/pr.2015.51. (PMID: 10.1038/pr.2015.5125760553)
de Paula GC, Brunetta HS, Engel DF, Gaspar JM, Velloso LA, Engblom D, de Oliveira J, de Bem AF (2021) Hippocampal function is impaired by a short-term high-fat diet in mice: increased blood-brain barrier permeability and neuroinflammation as triggering events. Front Neurosci 15:734158. https://doi.org/10.3389/fnins.2021.734158. (PMID: 10.3389/fnins.2021.734158348035838600238)
Pavlov I (1897) Lectures on activities of major gastrointestinal glands (Lekcji o rabotie glawnych piszcziewaritielnych zielez). St Petersburg.
Pavlov VA, Tracey KJ (2005) The cholinergic anti-inflammatory pathway. Brain Behav Immun 19(6):493–499. https://doi.org/10.1016/j.bbi.2005.03.015. (PMID: 10.1016/j.bbi.2005.03.01515922555)
Perez-Burgos A, Wang L, McVey Neufeld KA, Mao YK, Ahmadzai M, Janssen LJ, Stanisz AM, Bienenstock J, Kunze WA (2015) The TRPV1 channel in rodents is a major target for antinociceptive effect of the probiotic Lactobacillus reuteri DSM 17938. J Physiol 593(17):3943–3957. https://doi.org/10.1113/JP270229. (PMID: 10.1113/JP270229260844094575579)
Petrican R, Fornito A, Boyland E (2024) Lifestyle factors counteract the neurodevelopmental impact of genetic risk for accelerated brain aging in adolescence. Biol Psychiatry 95(5):453–464. https://doi.org/10.1016/j.biopsych.2023.06.023. (PMID: 10.1016/j.biopsych.2023.06.02337393046)
Pinto-Sanchez MI, Hall GB, Ghajar K, Nardelli A, Bolino C, Lau JT, Martin FP, Cominetti O, Welsh C, Rieder A, Traynor J, Gregory C, De Palma G, Pigrau M, Ford AC, Macri J, Berger B, Bergonzelli G, Surette MG et al (2017) Probiotic Bifidobacterium longum NCC3001 reduces depression scores and alters brain activity: a pilot study in patients with irritable bowel syndrome. Gastroenterology 153(2):448–459 e448. https://doi.org/10.1053/j.gastro.2017.05.003. (PMID: 10.1053/j.gastro.2017.05.00328483500)
Plovier H, Cani PD (2017) Enteroendocrine cells: metabolic relays between microbes and their host. In: Developmental biology of gastrointestinal hormones, vol 32. Karger Publishers, pp 139–164. (PMID: 10.1159/000475736)
Poewe W, Seppi K, Tanner CM, Halliday GM, Brundin P, Volkmann J, Schrag AE, Lang AE (2017) Parkinson disease. Nat Rev Dis Primers 3(1):17013. https://doi.org/10.1038/nrdp.2017.13. (PMID: 10.1038/nrdp.2017.1328332488)
Potter HG, Kowash HM, Woods RM, Revill G, Grime A, Deeney B, Burgess MA, Aarons T, Glazier JD, Neill JC, Hager R (2023) Maternal behaviours and adult offspring behavioural deficits are predicted by maternal TNFalpha concentration in a rat model of neurodevelopmental disorders. Brain Behav Immun 108:162–175. https://doi.org/10.1016/j.bbi.2022.12.003. (PMID: 10.1016/j.bbi.2022.12.00336503051)
Prestinaci F, Pezzotti P, Pantosti A (2015) Antimicrobial resistance: a global multifaceted phenomenon. Pathog Glob Health 109(7):309–318. https://doi.org/10.1179/2047773215Y.0000000030. (PMID: 10.1179/2047773215Y.0000000030263432524768623)
Prince N, Peralta Marzal LN, Markidi A, Ahmed S, Adolfs Y, Pasterkamp RJ, Kumar H, Roeselers G, Garssen J, Kraneveld AD, Perez-Pardo P (2024) Prebiotic diet normalizes aberrant immune and behavioral phenotypes in a mouse model of autism spectrum disorder. Acta Pharmacol Sin 45(8):1591–1603. https://doi.org/10.1038/s41401-024-01268-x. (PMID: 10.1038/s41401-024-01268-x3858969011272935)
Pusceddu MM, Gareau MG (2018) Visceral pain: gut microbiota, a new hope? J Biomed Sci 25(1):73. https://doi.org/10.1186/s12929-018-0476-7. (PMID: 10.1186/s12929-018-0476-7303093676182804)
Quigley EMM (2018) The gut-brain axis and the microbiome: clues to pathophysiology and opportunities for novel management strategies in Irritable Bowel Syndrome (IBS). J Clin Med 7(1):6. https://doi.org/10.3390/jcm7010006. (PMID: 10.3390/jcm7010006293013805791014)
Radjabzadeh D, Bosch JA, Uitterlinden AG, Zwinderman AH, Ikram MA, van Meurs JBJ, Luik AI, Nieuwdorp M, Lok A, van Duijn CM, Kraaij R, Amin N (2022) Gut microbiome-wide association study of depressive symptoms. Nat Commun 13(1):7128. https://doi.org/10.1038/s41467-022-34502-3. (PMID: 10.1038/s41467-022-34502-3364738529726982)
Radulescu CI, Garcia-Miralles M, Sidik H, Bardile CF, Yusof N, Lee HU, Ho EXP, Chu CW, Layton E, Low D, De Sessions PF, Pettersson S, Ginhoux F, Pouladi MA (2019) Manipulation of microbiota reveals altered callosal myelination and white matter plasticity in a model of Huntington disease. Neurobiol Dis 127:65–75. https://doi.org/10.1016/j.nbd.2019.02.011. (PMID: 10.1016/j.nbd.2019.02.01130802499)
Ratsika A, Cruz Pereira JS, Lynch CMK, Clarke G, Cryan JF (2023) Microbiota-immune-brain interactions: a lifespan perspective. Curr Opin Neurobiol 78:102652. https://doi.org/10.1016/j.conb.2022.102652. (PMID: 10.1016/j.conb.2022.10265236463579)
Rea K, O’Mahony SM, Dinan TG, Cryan JF (2017) The role of the gastrointestinal microbiota in visceral pain. Handb Exp Pharmacol 239:269–287. https://doi.org/10.1007/164_2016_115. (PMID: 10.1007/164_2016_11528035535)
Rea K, SM OM, Cryan JF (2021) High and Mighty? Cannabinoids and the microbiome in pain. Neurobiol Pain 9:100061. https://doi.org/10.1016/j.ynpai.2021.100061. (PMID: 10.1016/j.ynpai.2021.100061336654797905370)
Rein B, Raymond K, Boustani C, Tuy S, Zhang J, St Laurent R, Pomrenze MB, Boroon P, Heifets B, Smith M, Malenka RC (2024) MDMA enhances empathy-like behaviors in mice via 5-HT release in the nucleus accumbens. Sci Adv 10(17):eadl6554. https://doi.org/10.1126/sciadv.adl6554. (PMID: 10.1126/sciadv.adl65543865705711042730)
Ren L, Liang H, Zhu L, Yang X, Zhang H, Sun N, Huang D, Feng J, Wu Y, Xiong L, Ke X, Li M, Zhang A (2024) Dietary restriction improves perioperative neurocognitive disorders by inhibiting neuroinflammation and gut microbial dysbiosis. Neuroscience 540:48–67. https://doi.org/10.1016/j.neuroscience.2024.01.012. (PMID: 10.1016/j.neuroscience.2024.01.01238272300)
Ribeiro G, Camacho M, Fernandes AB, Cotovio G, Torres S, Oliveira-Maia AJ (2021) Reward-related gustatory and psychometric predictors of weight loss following bariatric surgery: a multicenter cohort study. Am J Clin Nutr 113(3):751–761. https://doi.org/10.1093/ajcn/nqaa349. (PMID: 10.1093/ajcn/nqaa349335588947948842)
Rinaman L (2010) Ascending projections from the caudal visceral nucleus of the solitary tract to brain regions involved in food intake and energy expenditure. Brain Res 1350:18–34. https://doi.org/10.1016/j.brainres.2010.03.059. (PMID: 10.1016/j.brainres.2010.03.059203537642909454)
Ritz NL, Bastiaanssen TFS, Cowan CSM, Smith L, Theune N, Brocka M, Myers EM, Moloney RD, Moloney GM, Shkoporov AN, Draper LA, Hill C, Dinan TG, Slattery DA, Cryan JF (2024a) Social fear extinction susceptibility is associated with Microbiota-Gut-Brain axis alterations. Brain Behav Immun 120:315–326. https://doi.org/10.1016/j.bbi.2024.06.009. (PMID: 10.1016/j.bbi.2024.06.00938852762)
Ritz NL, Draper LA, Bastiaanssen TFS, Turkington CJR, Peterson VL, van de Wouw M, Vlckova K, Fulling C, Guzzetta KE, Burokas A, Harris H, Dalmasso M, Crispie F, Cotter PD, Shkoporov AN, Moloney GM, Dinan TG, Hill C, Cryan JF (2024b) The gut virome is associated with stress-induced changes in behaviour and immune responses in mice. Nat Microbiol 9(2):359–376. https://doi.org/10.1038/s41564-023-01564-y. (PMID: 10.1038/s41564-023-01564-y3831692910847049)
Roager HM, Licht TR (2018) Microbial tryptophan catabolites in health and disease. Nat Commun 9(1):3294. https://doi.org/10.1038/s41467-018-05470-4. (PMID: 10.1038/s41467-018-05470-4301202226098093)
Roager HM, Stanton C, Hall LJ (2023) Microbial metabolites as modulators of the infant gut microbiome and host-microbial interactions in early life. Gut Microbes 15(1):2192151. https://doi.org/10.1080/19490976.2023.2192151. (PMID: 10.1080/19490976.2023.21921513694288310038037)
Rodino-Janeiro BK, Vicario M, Alonso-Cotoner C, Pascua-Garcia R, Santos J (2018) A review of microbiota and irritable bowel syndrome: future in therapies. Adv Ther 35(3):289–310. https://doi.org/10.1007/s12325-018-0673-5. (PMID: 10.1007/s12325-018-0673-5294980195859043)
Rodrigues KB, Weng Z, Graham ZA, Lavin K, McAdam J, Tuggle SC, Peoples B, Seay R, Yang S, Bamman MM, Broderick TJ, Montgomery SB (2025) Exercise intensity and training alter the innate immune cell type and chromosomal origins of circulating cell-free DNA in humans. Proc Natl Acad Sci USA 122(3):e2406954122. https://doi.org/10.1073/pnas.2406954122. (PMID: 10.1073/pnas.240695412239805013)
Rogers MAM, Aronoff DM (2016) The influence of non-steroidal anti-inflammatory drugs on the gut microbiome. Clin Microbiol Infect 22(2):178 e171–178 e179. https://doi.org/10.1016/j.cmi.2015.10.003. (PMID: 10.1016/j.cmi.2015.10.003)
Romani-Perez M, Liebana-Garcia R, Flor-Duro A, Bonillo-Jimenez D, Bullich-Vilarrubias C, Olivares M, Sanz Y (2024a) Obesity and the gut microbiota: implications of neuroendocrine and immune signaling. FEBS J. https://doi.org/10.1111/febs.17249.
Romani-Perez M, Lopez-Almela I, Bullich-Vilarrubias C, Evtoski Z, Benitez-Paez A, Sanz Y (2024b) Bacteroides uniformis CECT 7771 requires adaptive immunity to improve glucose tolerance but not to prevent body weight gain in diet-induced obese mice. Microbiome 12(1):103. https://doi.org/10.1186/s40168-024-01810-3. (PMID: 10.1186/s40168-024-01810-33884504911155119)
Romano S, Savva GM, Bedarf JR, Charles IG, Hildebrand F, Narbad A (2021) Meta-analysis of the Parkinson’s disease gut microbiome suggests alterations linked to intestinal inflammation. NPJ Parkinsons Dis 7(1):27. https://doi.org/10.1038/s41531-021-00156-z. (PMID: 10.1038/s41531-021-00156-z336923567946946)
Rosin S, Xia K, Azcarate-Peril MA, Carlson AL, Propper CB, Thompson AL, Grewen K, Knickmeyer RC (2021) A preliminary study of gut microbiome variation and HPA axis reactivity in healthy infants. Psychoneuroendocrinology 124:105046. https://doi.org/10.1016/j.psyneuen.2020.105046. (PMID: 10.1016/j.psyneuen.2020.10504633254059)
Ross FC, Mayer DE, Gupta A, Gill CIR, Del Rio D, Cryan JF, Lavelle A, Ross RP, Stanton C, Mayer EA (2024a) Existing and future strategies to manipulate the gut microbiota with diet as a potential adjuvant treatment for psychiatric disorders. Biol Psychiatry 95(4):348–360. https://doi.org/10.1016/j.biopsych.2023.10.018. (PMID: 10.1016/j.biopsych.2023.10.01837918459)
Ross FC, Patangia D, Grimaud G, Lavelle A, Dempsey EM, Ross RP, Stanton C (2024b) The interplay between diet and the gut microbiome: implications for health and disease. Nat Rev Microbiol 22(11):671–686. https://doi.org/10.1038/s41579-024-01068-4. (PMID: 10.1038/s41579-024-01068-439009882)
Rudzki L, Ostrowska L, Pawlak D, Malus A, Pawlak K, Waszkiewicz N, Szulc A (2019) Probiotic Lactobacillus Plantarum 299v decreases kynurenine concentration and improves cognitive functions in patients with major depression: a double-blind, randomized, placebo controlled study. Psychoneuroendocrinology 100:213–222. https://doi.org/10.1016/j.psyneuen.2018.10.010. (PMID: 10.1016/j.psyneuen.2018.10.01030388595)
Rueda GH, Causada-Calo N, Borojevic R, Nardelli A, Pinto-Sanchez MI, Constante M, Libertucci J, Mohan V, Langella P, Loonen LMP, Wells JM, Collins SM, Sokol H, Verdu EF, Bercik P (2024) Oral tryptophan activates duodenal aryl hydrocarbon receptor in healthy subjects: a crossover randomized controlled trial. Am J Physiol Gastrointest Liver Physiol 326(6):G687–G696. https://doi.org/10.1152/ajpgi.00306.2023. (PMID: 10.1152/ajpgi.00306.202338591144)
Rusch JA, Layden BT, Dugas LR (2023) Signalling cognition: the gut microbiota and hypothalamic-pituitary-adrenal axis. Front Endocrinol (Lausanne) 14:1130689. https://doi.org/10.3389/fendo.2023.1130689. (PMID: 10.3389/fendo.2023.113068937404311)
Salehipour Z, Haghmorad D, Sankian M, Rastin M, Nosratabadi R, Soltan Dallal MM, Tabasi N, Khazaee M, Nasiraii LR, Mahmoudi M (2017) Bifidobacterium animalis in combination with human origin of Lactobacillus plantarum ameliorate neuroinflammation in experimental model of multiple sclerosis by altering CD4+ T cell subset balance. Biomed Pharmacother 95:1535–1548. https://doi.org/10.1016/j.biopha.2017.08.117. (PMID: 10.1016/j.biopha.2017.08.11728946394)
Salia S, Burke FF, Hinks ME, Randell AM, Matheson MA, Walling SG, Swift-Gallant A (2025) Gut microbiota transfer from the preclinical maternal immune activation model of autism is sufficient to induce sex-specific alterations in immune response and behavioural outcomes. Brain Behav Immun 123:813–823. https://doi.org/10.1016/j.bbi.2024.10.030. (PMID: 10.1016/j.bbi.2024.10.03039471905)
Salminen S, Collado MC, Endo A, Hill C, Lebeer S, Quigley EMM, Sanders ME, Shamir R, Swann JR, Szajewska H, Vinderola G (2021) The International Scientific Association of Probiotics and Prebiotics (ISAPP) consensus statement on the definition and scope of postbiotics. Nat Rev Gastroenterol Hepatol 18(9):649–667. https://doi.org/10.1038/s41575-021-00440-6. (PMID: 10.1038/s41575-021-00440-6339480258387231)
Samara J, Moossavi S, Alshaikh B, Ortega VA, Pettersen VK, Ferdous T, Hoops SL, Soraisham A, Vayalumkal J, Dersch-Mills D, Gerber JS, Mukhopadhyay S, Puopolo K, Tompkins TA, Knights D, Walter J, Amin H, Arrieta MC (2022) Supplementation with a probiotic mixture accelerates gut microbiome maturation and reduces intestinal inflammation in extremely preterm infants. Cell Host Microbe 30(5):696–711 e695. https://doi.org/10.1016/j.chom.2022.04.005. (PMID: 10.1016/j.chom.2022.04.00535550672)
Sampson TR, Debelius JW, Thron T, Janssen S, Shastri GG, Ilhan ZE, Challis C, Schretter CE, Rocha S, Gradinaru V, Chesselet MF, Keshavarzian A, Shannon KM, Krajmalnik-Brown R, Wittung-Stafshede P, Knight R, Mazmanian SK (2016) Gut microbiota regulate motor deficits and neuroinflammation in a model of Parkinson’s disease. Cell 167(6):1469–1480 e1412. https://doi.org/10.1016/j.cell.2016.11.018. (PMID: 10.1016/j.cell.2016.11.018279120575718049)
Sanchez M, Darimont C, Panahi S, Drapeau V, Marette A, Taylor VH, Dore J, Tremblay A (2017) Effects of a diet-based weight-reducing program with probiotic supplementation on satiety efficiency, eating behaviour traits, and psychosocial behaviours in obese individuals. Nutrients 9(3). https://doi.org/10.3390/nu9030284.
Sanidad KZ, Rager SL, Carrow HC, Ananthanarayanan A, Callaghan R, Hart LR, Li T, Ravisankar P, Brown JA, Amir M, Jin JC, Savage AR, Luo R, Rowdo FM, Martin ML, Silver RB, Guo CJ, Krumsiek J, Inohara N, Zeng MY (2024) Gut bacteria-derived serotonin promotes immune tolerance in early life. Sci Immunol 9(93):eadj4775. https://doi.org/10.1126/sciimmunol.adj4775. (PMID: 10.1126/sciimmunol.adj47753848935211328322)
Sanmarco LM, Chao CC, Wang YC, Kenison JE, Li Z, Rone JM, Rejano-Gordillo CM, Polonio CM, Gutierrez-Vazquez C, Piester G, Plasencia A, Li L, Giovannoni F, Lee HG, Faust Akl C, Wheeler MA, Mascanfroni I, Jaronen M, Alsuwailm M et al (2022) Identification of environmental factors that promote intestinal inflammation. Nature 611(7937):801–809. https://doi.org/10.1038/s41586-022-05308-6. (PMID: 10.1038/s41586-022-05308-6362665819898826)
Santangelo A, Corsello A, Spolidoro GCI, Trovato CM, Agostoni C, Orsini A, Milani GP, Peroni DG (2023) The influence of ketogenic diet on gut microbiota: potential benefits, risks and indications. Nutrients 15(17). https://doi.org/10.3390/nu15173680.
Sarathy J, Detloff SJ, Ao M, Khan N, French S, Sirajuddin H, Nair T, Rao MC (2017) The Yin and Yang of bile acid action on tight junctions in a model colonic epithelium. Physiol Rep 5(10):e13294. https://doi.org/10.14814/phy2.13294. (PMID: 10.14814/phy2.13294285549665449568)
Sarnyai Z, Kraeuter AK, Palmer CM (2019) Ketogenic diet for schizophrenia: clinical implication. Curr Opin Psychiatry 32(5):394–401. https://doi.org/10.1097/YCO.0000000000000535. (PMID: 10.1097/YCO.000000000000053531192814)
Savignac HM, Kiely B, Dinan TG, Cryan JF (2014) Bifidobacteria exert strain-specific effects on stress-related behavior and physiology in BALB/c mice. Neurogastroenterol Motil 26(11):1615–1627. https://doi.org/10.1111/nmo.12427. (PMID: 10.1111/nmo.1242725251188)
Schellekens H, Torres-Fuentes C, van de Wouw M, Long-Smith CM, Mitchell A, Strain C, Berding K, Bastiaanssen TFS, Rea K, Golubeva AV, Arboleya S, Verpaalen M, Pusceddu MM, Murphy A, Fouhy F, Murphy K, Ross P, Roy BL, Stanton C et al (2021) Bifidobacterium longum counters the effects of obesity: partial successful translation from rodent to human. EBioMedicine 63:103176. https://doi.org/10.1016/j.ebiom.2020.103176. (PMID: 10.1016/j.ebiom.2020.10317633349590)
Schellekens H, Ribeiro G, Cuesta-Marti C, Cryan JF (2023) The microbiome-gut-brain axis in nutritional neuroscience. Nutr Neurosci 26(11):1159–1171. https://doi.org/10.1080/1028415X.2022.2128007. (PMID: 10.1080/1028415X.2022.212800736222323)
Schneider KM, Thaiss CA (2022) When the brain feels the bugs. Immunity 55(6):976–978. https://doi.org/10.1016/j.immuni.2022.05.008. (PMID: 10.1016/j.immuni.2022.05.00835705000)
Schneider KM, Blank N, Alvarez Y, Thum K, Lundgren P, Litichevskiy L, Sleeman M, Bahnsen K, Kim J, Kardo S, Patel S, Dohnalova L, Uhr GT, Descamps HC, Kircher S, McSween AM, Ardabili AR, Nemec KM, Jimenez MT et al (2023) The enteric nervous system relays psychological stress to intestinal inflammation. Cell 186(13):2823–2838 e2820. https://doi.org/10.1016/j.cell.2023.05.001. (PMID: 10.1016/j.cell.2023.05.0013723619310330875)
Schneider E, Balasubramanian R, Ferri A, Cotter PD, Clarke G, Cryan JF (2024a) Conference on ‘Diet and lifestyle strategies for prevention and management of multimorbidity’ Symposium three: diet and the gut-brain-heart connection fibre & fermented foods: differential effects on the microbiota-gut-brain axis. Proc Nutr Soc 25:1–16. https://doi.org/10.1017/S0029665124004907. (PMID: 10.1017/S0029665124004907)
Schneider E, Balasubramanian R, Ferri A, Cotter PD, Clarke G, Cryan JF (2024b) Fibre & fermented foods: differential effects on the microbiota-gut-brain axis. Proc Nutr Soc:1–16. https://doi.org/10.1017/S0029665124004907.
Schumacher SM, Doyle WJ, Hill K, Ochoa-Reparaz J (2024) Gut microbiota in multiple sclerosis and animal models. FEBS J. https://doi.org/10.1111/febs.17161.
Selma-Royo M, Dubois L, Manara S, Armanini F, Cabrera-Rubio R, Valles-Colomer M, Gonzalez S, Parra-Llorca A, Escuriet R, Bode L, Martinez-Costa C, Segata N, Collado MC (2024) Birthmode and environment-dependent microbiota transmission dynamics are complemented by breastfeeding during the first year. Cell Host Microbe 32(6):996–1010 e1014. https://doi.org/10.1016/j.chom.2024.05.005. (PMID: 10.1016/j.chom.2024.05.0053887090611183301)
Sen P, Sherwin E, Sandhu K, Bastiaanssen TFS, Moloney GM, Golubeva A, Fitzgerald P, Paula Ventura Da Silva A, Chruscicka-Smaga B, Olavarria-Ramirez L, Druelle C, Campos D, Jayaprakash P, Rea K, Jeffery IB, Savignac H, Chetal S, Mulder I, Schellekens H et al (2022) The live biotherapeutic Blautia stercoris MRx0006 attenuates social deficits, repetitive behaviour, and anxiety-like behaviour in a mouse model relevant to autism. Brain Behav Immun 106:115–126. https://doi.org/10.1016/j.bbi.2022.08.007. (PMID: 10.1016/j.bbi.2022.08.00735995237)
Sens JP, Hofford RS, Kiraly DD (2023) Effect of germ-free status on transcriptional profiles in the nucleus accumbens and transcriptomic response to chronic morphine. Mol Cell Neurosci 126:103874. https://doi.org/10.1016/j.mcn.2023.103874. (PMID: 10.1016/j.mcn.2023.1038743731587710921993)
Serebrinsky-Duek K, Barra M, Danino T, Garrido D (2023) Engineered bacteria for short-chain-fatty-acid-repressed expression of biotherapeutic molecules. Microbiol Spectr 11(2):e0004923. https://doi.org/10.1128/spectrum.00049-23. (PMID: 10.1128/spectrum.00049-2336939337)
Shao Y, Forster SC, Tsaliki E, Vervier K, Strang A, Simpson N, Kumar N, Stares MD, Rodger A, Brocklehurst P, Field N, Lawley TD (2019) Stunted microbiota and opportunistic pathogen colonization in caesarean-section birth. Nature 574(7776):117–121. https://doi.org/10.1038/s41586-019-1560-1. (PMID: 10.1038/s41586-019-1560-1315342276894937)
Sharkey KA, Mawe GM (2023) The enteric nervous system. Physiol Rev 103(2):1487–1564. https://doi.org/10.1152/physrev.00018.2022. (PMID: 10.1152/physrev.00018.202236521049)
Sheng JA, Bales NJ, Myers SA, Bautista AI, Roueinfar M, Hale TM, Handa RJ (2020) The hypothalamic-pituitary-adrenal axis: development, programming actions of hormones, and maternal-fetal interactions. Front Behav Neurosci 14:601939. https://doi.org/10.3389/fnbeh.2020.601939. (PMID: 10.3389/fnbeh.2020.60193933519393)
Siciliano RA, Reale A, Mazzeo MF, Morandi S, Silvetti T, Brasca M (2021) Paraprobiotics: a new perspective for functional foods and nutraceuticals. Nutrients 13(4). https://doi.org/10.3390/nu13041225.
Siegler Lathrop T, Perego S, Bastiaanssen TFS, van Hemert S, Chronakis IS, Diaz Heijtz R (2024) Multispecies probiotic intake during pregnancy modulates neurodevelopmental trajectories of offspring: aiming towards precision microbial intervention. Brain Behav Immun 122:547–554. https://doi.org/10.1016/j.bbi.2024.08.050. (PMID: 10.1016/j.bbi.2024.08.05039197545)
Silva YP, Bernardi A, Frozza RL (2020) The role of short-chain fatty acids from gut microbiota in gut-brain communication. Front Endocrinol (Lausanne) 11:25. https://doi.org/10.3389/fendo.2020.00025. (PMID: 10.3389/fendo.2020.0002532082260)
Simren M, Tack J (2018) New treatments and therapeutic targets for IBS and other functional bowel disorders. Nat Rev Gastroenterol Hepatol 15(10):589–605. https://doi.org/10.1038/s41575-018-0034-5. (PMID: 10.1038/s41575-018-0034-529930260)
Simren M, Ohman L, Olsson J, Svensson U, Ohlson K, Posserud I, Strid H (2010) Clinical trial: the effects of a fermented milk containing three probiotic bacteria in patients with irritable bowel syndrome - a randomized, double-blind, controlled study. Aliment Pharmacol Ther 31(2):218–227. https://doi.org/10.1111/j.1365-2036.2009.04183.x. (PMID: 10.1111/j.1365-2036.2009.04183.x19863495)
Singh V, Sadler R, Heindl S, Llovera G, Roth S, Benakis C, Liesz A (2018) The gut microbiome primes a cerebroprotective immune response after stroke. J Cereb Blood Flow Metab 38(8):1293–1298. https://doi.org/10.1177/0271678X18780130. (PMID: 10.1177/0271678X18780130298461306092773)
Slykerman RF, Davies N, Vlckova K, O’Riordan KJ, Bassett SA, Dekker J, Schellekens H, Hyland NP, Clarke G, Patterson E (2025) Precision psychobiotics for gut–brain axis health: advancing the discovery pipelines to deliver mechanistic pathways and proven health efficacy. Microb Biotechnol 18(1):e70079. https://doi.org/10.1111/1751-7915.70079. (PMID: 10.1111/1751-7915.700793981567111735468)
Smolensky I, Zajac-Bakri K, Odermatt TS, Bregere C, Cryan JF, Guzman R, Timper K, Inta D (2023) Sex-specific differences in metabolic hormone and adipose tissue dynamics induced by moderate low-carbohydrate and ketogenic diet. Sci Rep 13(1):16465. https://doi.org/10.1038/s41598-023-43587-9. (PMID: 10.1038/s41598-023-43587-93777752810542803)
Song X, Zhao Z, Zhao Y, Wang Z, Wang C, Yang G, Li S (2022) Lactobacillus plantarum DP189 prevents cognitive dysfunction in D-galactose/AlCl(3) induced mouse model of Alzheimer’s disease via modulating gut microbiota and PI3K/Akt/GSK-3beta signaling pathway. Nutr Neurosci 25(12):2588–2600. https://doi.org/10.1080/1028415X.2021.1991556. (PMID: 10.1080/1028415X.2021.199155634755592)
Sonnenburg JL, Backhed F (2016) Diet-microbiota interactions as moderators of human metabolism. Nature 535(7610):56–64. https://doi.org/10.1038/nature18846. (PMID: 10.1038/nature18846273839805991619)
Sonnenburg JL, Sonnenburg ED (2019) Vulnerability of the industrialized microbiota. Science 366(6464). https://doi.org/10.1126/science.aaw9255.
Stachulski AV, Knausenberger TB, Shah SN, Hoyles L, McArthur S (2023) A host-gut microbial amino acid co-metabolite, p-cresol glucuronide, promotes blood-brain barrier integrity in vivo. Tissue Barriers 11(1):2073175. https://doi.org/10.1080/21688370.2022.2073175. (PMID: 10.1080/21688370.2022.207317535596559)
Stagaman K, Kmiecik MJ, Wetzel M, Aslibekyan S, Sonmez TF, Fontanillas P, Auton A, Babalola E, Bell RK, Bielenberg J, Bowes J, Bryc K, Chaudhary NS, Coker D, Das S, DelloRusso E, Elson SL, Eriksson N, Filshtein T et al (2024) Oral and gut microbiome profiles in people with early idiopathic Parkinson’s disease. Commun Med 4(1):209. https://doi.org/10.1038/s43856-024-00630-8. (PMID: 10.1038/s43856-024-00630-83944363411499922)
Stilling RM, Bordenstein SR, Dinan TG, Cryan JF (2014) Friends with social benefits: host-microbe interactions as a driver of brain evolution and development? Front Cell Infect Microbiol 4:147. https://doi.org/10.3389/fcimb.2014.00147. (PMID: 10.3389/fcimb.2014.00147254010924212686)
Strandwitz P (2018) Neurotransmitter modulation by the gut microbiota. Brain Res 1693(Pt B):128–133. https://doi.org/10.1016/j.brainres.2018.03.015. (PMID: 10.1016/j.brainres.2018.03.015299036156005194)
Sudo N, Chida Y, Aiba Y, Sonoda J, Oyama N, Yu XN, Kubo C, Koga Y (2004) Postnatal microbial colonization programs the hypothalamic-pituitary-adrenal system for stress response in mice. J Physiol 558(Pt 1):263–275. https://doi.org/10.1113/jphysiol.2004.063388. (PMID: 10.1113/jphysiol.2004.063388151330621664925)
Sun J, Wang F, Ling Z, Yu X, Chen W, Li H, Jin J, Pang M, Zhang H, Yu J, Liu J (2016) Clostridium butyricum attenuates cerebral ischemia/reperfusion injury in diabetic mice via modulation of gut microbiota. Brain Res 1642:180–188. https://doi.org/10.1016/j.brainres.2016.03.042. (PMID: 10.1016/j.brainres.2016.03.04227037183)
Sun J, Zhang Y, Kong Y, Ye T, Yu Q, Kumaran Satyanarayanan S, Su KP, Liu J (2022) Microbiota-derived metabolite indoles induced aryl hydrocarbon receptor activation and inhibited neuroinflammation in APP/PS1 mice. Brain Behav Immun 106:76–88. https://doi.org/10.1016/j.bbi.2022.08.003. (PMID: 10.1016/j.bbi.2022.08.00335961580)
Swanson KS, Gibson GR, Hutkins R, Reimer RA, Reid G, Verbeke K, Scott KP, Holscher HD, Azad MB, Delzenne NM, Sanders ME (2020) The International Scientific Association for Probiotics and Prebiotics (ISAPP) consensus statement on the definition and scope of synbiotics. Nat Rev Gastroenterol Hepatol 17(11):687–701. https://doi.org/10.1038/s41575-020-0344-2. (PMID: 10.1038/s41575-020-0344-2328269667581511)
Tabouy L, Getselter D, Ziv O, Karpuj M, Tabouy T, Lukic I, Maayouf R, Werbner N, Ben-Amram H, Nuriel-Ohayon M, Koren O, Elliott E (2018) Dysbiosis of microbiome and probiotic treatment in a genetic model of autism spectrum disorders. Brain Behav Immun 73:310–319. https://doi.org/10.1016/j.bbi.2018.05.015. (PMID: 10.1016/j.bbi.2018.05.01529787855)
Takeda K, Akira S (2004) Microbial recognition by Toll-like receptors. J Dermatol Sci 34(2):73–82. https://doi.org/10.1016/j.jdermsci.2003.10.002. (PMID: 10.1016/j.jdermsci.2003.10.00215033189)
Takeuchi T, Kubota T, Nakanishi Y, Tsugawa H, Suda W, Kwon AT, Yazaki J, Ikeda K, Nemoto S, Mochizuki Y, Kitami T, Yugi K, Mizuno Y, Yamamichi N, Yamazaki T, Takamoto I, Kubota N, Kadowaki T, Arner E et al (2023) Gut microbial carbohydrate metabolism contributes to insulin resistance. Nature 621(7978):389–395. https://doi.org/10.1038/s41586-023-06466-x. (PMID: 10.1038/s41586-023-06466-x3764885210499599)
Tames H, Sabater C, Royo F, Margolles A, Falcon JM, Ruas-Madiedo P, Ruiz L (2024) Mouse intestinal microbiome modulation by oral administration of a GABA-producing Bifidobacterium adolescentis strain. Microbiol Spectr 12(1):e0258023. https://doi.org/10.1128/spectrum.02580-23. (PMID: 10.1128/spectrum.02580-2337991375)
Tamtaji OR, Kouchaki E, Salami M, Aghadavod E, Akbari E, Tajabadi-Ebrahimi M, Asemi Z (2017) The effects of probiotic supplementation on gene expression related to inflammation, insulin, and lipids in patients with multiple sclerosis: a randomized, double-blind, placebo-controlled trial. J Am Coll Nutr 36(8):660–665. https://doi.org/10.1080/07315724.2017.1347074. (PMID: 10.1080/07315724.2017.134707428922099)
Tanelian A, Nankova B, Miari M, Nahvi RJ, Sabban EL (2022) Resilience or susceptibility to traumatic stress: potential influence of the microbiome. Neurobiol Stress 19:100461. https://doi.org/10.1016/j.ynstr.2022.100461. (PMID: 10.1016/j.ynstr.2022.100461357897699250071)
Teichman EM, O’Riordan KJ, Gahan CGM, Dinan TG, Cryan JF (2020) When rhythms meet the blues: circadian interactions with the microbiota-gut-brain axis. Cell Metab 31(3):448–471. https://doi.org/10.1016/j.cmet.2020.02.008. (PMID: 10.1016/j.cmet.2020.02.00832130879)
Tette FM, Kwofie SK, Wilson MD (2022) Therapeutic anti-depressant potential of microbial GABA produced by Lactobacillus rhamnosus strains for GABAergic signaling restoration and inhibition of addiction-induced HPA Axis hyperactivity. Curr Issues Mol Biol 44(4):1434–1451. https://doi.org/10.3390/cimb44040096. (PMID: 10.3390/cimb44040096357233549164062)
Theis KR, Dheilly NM, Klassen JL, Brucker RM, Baines JF, Bosch TC, Cryan JF, Gilbert SF, Goodnight CJ, Lloyd EA, Sapp J, Vandenkoornhuyse P, Zilber-Rosenberg I, Rosenberg E, Bordenstein SR (2016) Getting the hologenome concept right: an eco-evolutionary framework for hosts and their microbiomes. mSystems 1(2). https://doi.org/10.1128/mSystems.00028-16.
Thompson KN, Oulhote Y, Weihe P, Wilkinson JE, Ma S, Zhong H, Li J, Kristiansen K, Huttenhower C, Grandjean P (2022) Effects of lifetime exposures to environmental contaminants on the adult gut microbiome. Environ Sci Technol 56(23):16985–16995. https://doi.org/10.1021/acs.est.2c03185. (PMID: 10.1021/acs.est.2c0318536394280)
Tian Z, Zhuang X, Luo M, Yin W, Xiong L (2020) The propionic acid and butyric acid in serum but not in feces are increased in patients with diarrhea-predominant irritable bowel syndrome. BMC Gastroenterol 20(1):73. https://doi.org/10.1186/s12876-020-01212-3. (PMID: 10.1186/s12876-020-01212-3321786257077160)
Tian YE, Di Biase MA, Mosley PE, Lupton MK, Xia Y, Fripp J, Breakspear M, Cropley V, Zalesky A (2023) Evaluation of brain-body health in individuals with common neuropsychiatric disorders. JAMA Psychiatry 80(6):567–576. https://doi.org/10.1001/jamapsychiatry.2023.0791. (PMID: 10.1001/jamapsychiatry.2023.07913709931310134046)
Ticinesi A, Milani C, Lauretani F, Nouvenne A, Mancabelli L, Lugli GA, Turroni F, Duranti S, Mangifesta M, Viappiani A, Ferrario C, Maggio M, Ventura M, Meschi T (2017) Gut microbiota composition is associated with polypharmacy in elderly hospitalized patients. Sci Rep 7(1):11102. https://doi.org/10.1038/s41598-017-10734-y. (PMID: 10.1038/s41598-017-10734-y288941835593887)
Tofani GSS, Leigh SJ, Gheorghe CE, Bastiaanssen TFS, Wilmes L, Sen P, Clarke G, Cryan JF (2025) Gut microbiota regulates stress responsivity via the circadian system. Cell Metab 37(1):138–153 e135. https://doi.org/10.1016/j.cmet.2024.10.003. (PMID: 10.1016/j.cmet.2024.10.00339504963)
Torres-Fuentes C, Schellekens H, Dinan TG, Cryan JF (2017) The microbiota-gut-brain axis in obesity. Lancet Gastroenterol Hepatol 2(10):747–756. https://doi.org/10.1016/S2468-1253(17)30147-4. (PMID: 10.1016/S2468-1253(17)30147-428844808)
Tremmel M, Gerdtham UG, Nilsson PM, Saha S (2017) Economic burden of obesity: a systematic literature review. Int J Environ Res Public Health 14(4). https://doi.org/10.3390/ijerph14040435.
Tschop M, Weyer C, Tataranni PA, Devanarayan V, Ravussin E, Heiman ML (2001) Circulating ghrelin levels are decreased in human obesity. Diabetes 50(4):707–709. https://doi.org/10.2337/diabetes.50.4.707. (PMID: 10.2337/diabetes.50.4.70711289032)
Tuck CJ, Abu Omar A, De Palma G, Osman S, Jimenez-Vargas NN, Yu Y, Bennet SM, Lopez-Lopez C, Jaramillo-Polanco JO, Baker CC, Bennett AS, Guzman-Rodriguez M, Tsang Q, Alward T, Rolland S, Morissette C, Verdu EF, Bercik P, Vanner SJ et al (2022) Changes in signalling from faecal neuroactive metabolites following dietary modulation of IBS pain. Gut. https://doi.org/10.1136/gutjnl-2022-327260.
Turna J, Grosman Kaplan K, Anglin R, Patterson B, Soreni N, Bercik P, Surette MG, Van Ameringen M (2020) The gut microbiome and inflammation in obsessive-compulsive disorder patients compared to age- and sex-matched controls: a pilot study. Acta Psychiatr Scand 142(4):337–347. https://doi.org/10.1111/acps.13175. (PMID: 10.1111/acps.1317532307692)
Turnbaugh PJ, Backhed F, Fulton L, Gordon JI (2008) Diet-induced obesity is linked to marked but reversible alterations in the mouse distal gut microbiome. Cell Host Microbe 3(4):213–223. https://doi.org/10.1016/j.chom.2008.02.015. (PMID: 10.1016/j.chom.2008.02.015184070653687783)
Turnbaugh PJ, Ridaura VK, Faith JJ, Rey FE, Knight R, Gordon JI (2009) The effect of diet on the human gut microbiome: a metagenomic analysis in humanized gnotobiotic mice. Sci Transl Med 1(6):6ra14. https://doi.org/10.1126/scitranslmed.3000322. (PMID: 10.1126/scitranslmed.3000322203681782894525)
Turner EH, Loftis JM, Blackwell AD (2006) Serotonin a la carte: supplementation with the serotonin precursor 5-hydroxytryptophan. Pharmacol Ther 109(3):325–338. https://doi.org/10.1016/j.pharmthera.2005.06.004. (PMID: 10.1016/j.pharmthera.2005.06.00416023217)
Ulker İ, Yildiran H (2019) The effects of bariatric surgery on gut microbiota in patients with obesity: a review of the literature. Biosci Microbiota Food Health 38(1):3–9. https://doi.org/10.12938/bmfh.18-018. (PMID: 10.12938/bmfh.18-01830705797)
Val-Laillet D, Guerin S, Coquery N, Nogret I, Formal M, Rome V, Le Normand L, Meurice P, Randuineau G, Guilloteau P, Malbert CH, Parnet P, Lalles JP, Segain JP (2018) Oral sodium butyrate impacts brain metabolism and hippocampal neurogenesis, with limited effects on gut anatomy and function in pigs. FASEB J 32(4):2160–2171. https://doi.org/10.1096/fj.201700547RR. (PMID: 10.1096/fj.201700547RR29242276)
Valles-Colomer M, Falony G, Darzi Y, Tigchelaar EF, Wang J, Tito RY, Schiweck C, Kurilshikov A, Joossens M, Wijmenga C, Claes S, Van Oudenhove L, Zhernakova A, Vieira-Silva S, Raes J (2019) The neuroactive potential of the human gut microbiota in quality of life and depression. Nat Microbiol 4(4):623–632. https://doi.org/10.1038/s41564-018-0337-x. (PMID: 10.1038/s41564-018-0337-x30718848)
Vasileva SS, Yang Y, Baker A, Siskind D, Gratten J, Eyles D (2024) Associations of the gut microbiome with treatment resistance in schizophrenia. JAMA Psychiatry 81(3):292–302. https://doi.org/10.1001/jamapsychiatry.2023.5371. (PMID: 10.1001/jamapsychiatry.2023.53713829480510831632)
Vermeulen W, De Man JG, Pelckmans PA, De Winter BY (2014) Neuroanatomy of lower gastrointestinal pain disorders. World J Gastroenterol 20(4):1005–1020. https://doi.org/10.3748/wjg.v20.i4.1005. (PMID: 10.3748/wjg.v20.i4.1005245747733921524)
Verstockt B, Ferrante M, Vermeire S, Van Assche G (2018) New treatment options for inflammatory bowel diseases. J Gastroenterol 53(5):585–590. https://doi.org/10.1007/s00535-018-1449-z. (PMID: 10.1007/s00535-018-1449-z295567265910475)
Viel JF, Rouget F, Warembourg C, Monfort C, Limon G, Cordier S, Chevrier C (2017) Behavioural disorders in 6-year-old children and pyrethroid insecticide exposure: the PELAGIE mother-child cohort. Occup Environ Med 74(4):275–281. https://doi.org/10.1136/oemed-2016-104035. (PMID: 10.1136/oemed-2016-10403528250046)
Vogt NM, Kerby RL, Dill-McFarland KA, Harding SJ, Merluzzi AP, Johnson SC, Carlsson CM, Asthana S, Zetterberg H, Blennow K, Bendlin BB, Rey FE (2017) Gut microbiome alterations in Alzheimer’s disease. Sci Rep 7(1):13537. https://doi.org/10.1038/s41598-017-13601-y. (PMID: 10.1038/s41598-017-13601-y290515315648830)
Voigt RM, Summa KC, Forsyth CB, Green SJ, Engen P, Naqib A, Vitaterna MH, Turek FW, Keshavarzian A (2016) The circadian clock mutation promotes intestinal dysbiosis. Alcohol Clin Exp Res 40(2):335–347. https://doi.org/10.1111/acer.12943. (PMID: 10.1111/acer.12943268422524977829)
Wallace Fitzsimons SE, Chruscicka B, Druelle C, Stamou P, Nally K, Dinan TG, Cryan JF, Schellekens H (2019) A ghrelin receptor and oxytocin receptor heterocomplex impairs oxytocin mediated signalling. Neuropharmacology 152:90–101. https://doi.org/10.1016/j.neuropharm.2018.12.022. (PMID: 10.1016/j.neuropharm.2018.12.02230582955)
Walsh J, Olavarria-Ramirez L, Lach G, Boehme M, Dinan TG, Cryan JF, Griffin BT, Hyland NP, Clarke G (2020) Impact of host and environmental factors on beta-glucuronidase enzymatic activity: implications for gastrointestinal serotonin. Am J Physiol Gastrointest Liver Physiol 318(4):G816–G826. https://doi.org/10.1152/ajpgi.00026.2020. (PMID: 10.1152/ajpgi.00026.202032146834)
Walter J, Hornef MW (2021) A philosophical perspective on the prenatal in utero microbiome debate. Microbiome 9(1):5. https://doi.org/10.1186/s40168-020-00979-7. (PMID: 10.1186/s40168-020-00979-7334360937805158)
Wang LJ, Yang CY, Chou WJ, Lee MJ, Chou MC, Kuo HC, Yeh YM, Lee SY, Huang LH, Li SC (2020) Gut microbiota and dietary patterns in children with attention-deficit/hyperactivity disorder. Eur Child Adolesc Psychiatry 29(3):287–297. https://doi.org/10.1007/s00787-019-01352-2. (PMID: 10.1007/s00787-019-01352-231119393)
Wang B, Zhou Y, Mao Y, Gong L, Li X, Xu S, Wang F, Guo Q, Zhang H, Li W (2021) Dietary supplementation with lactobacillus plantarum ameliorates compromise of growth performance by modulating short-chain fatty acids and intestinal dysbiosis in broilers under clostridium perfringens challenge. Front Nutr 8:706148. https://doi.org/10.3389/fnut.2021.706148. (PMID: 10.3389/fnut.2021.706148347226028551491)
Wang M, Zhang H, Liang J, Huang J, Chen N (2023) Exercise suppresses neuroinflammation for alleviating Alzheimer’s disease. J Neuroinflammation 20(1):76. https://doi.org/10.1186/s12974-023-02753-6. (PMID: 10.1186/s12974-023-02753-63693551110026496)
Wang G, Fan Y, Zhang G, Cai S, Ma Y, Yang L, Wang Y, Yu H, Qiao S, Zeng X (2024) Microbiota-derived indoles alleviate intestinal inflammation and modulate microbiome by microbial cross-feeding. Microbiome 12(1):59. https://doi.org/10.1186/s40168-024-01750-y. (PMID: 10.1186/s40168-024-01750-y3850438310949743)
Warda AK, Clooney AG, Ryan F, de Almeida Bettio PH, Di Benedetto G, Ross RP, Hill C (2021) A postbiotic consisting of heat-treated lactobacilli has a bifidogenic effect in pure culture and in human fermented faecal communities. Appl Environ Microbiol 87(8). https://doi.org/10.1128/AEM.02459-20.
Warren JL, Hunter GR, Gower BA, Bamman MM, Windham ST, Moellering DR, Fisher G (2020) Exercise effects on mitochondrial function and lipid metabolism during energy balance. Med Sci Sports Exerc 52(4):827–834. https://doi.org/10.1249/MSS.0000000000002190. (PMID: 10.1249/MSS.0000000000002190316522457117801)
Waters JL, Ley RE (2019) The human gut bacteria Christensenellaceae are widespread, heritable, and associated with health. BMC Biol 17(1):83. https://doi.org/10.1186/s12915-019-0699-4. (PMID: 10.1186/s12915-019-0699-4316609486819567)
Wehrwein EA, Orer HS, Barman SM (2016) Overview of the anatomy, physiology, and pharmacology of the autonomic nervous system. Compr Physiol 6(3):1239–1278. https://doi.org/10.1002/cphy.c150037. (PMID: 10.1002/cphy.c15003727347892)
Wei S, Jespersen ML, Baunwall SMD, Myers PN, Smith EM, Dahlerup JF, Rasmussen S, Nielsen HB, Licht TR, Bahl MI, Hvas CL (2022) Cross-generational bacterial strain transfer to an infant after fecal microbiota transplantation to a pregnant patient: a case report. Microbiome 10(1):193. https://doi.org/10.1186/s40168-022-01394-w. (PMID: 10.1186/s40168-022-01394-w363524609647999)
Wei N, Ju M, Su X, Zhang Y, Huang Y, Rao X, Cui L, Lin Z, Dong Y (2024) Transplantation of gut microbiota derived from patients with schizophrenia induces schizophrenia-like behaviors and dysregulated brain transcript response in mice. Schizophrenia (Heidelb) 10(1):44. https://doi.org/10.1038/s41537-024-00460-6. (PMID: 10.1038/s41537-024-00460-638589422)
Whelan K, Martin LD, Staudacher HM, Lomer MCE (2018) The low FODMAP diet in the management of irritable bowel syndrome: an evidence-based review of FODMAP restriction, reintroduction and personalisation in clinical practice. J Hum Nutr Diet 31(2):239–255. https://doi.org/10.1111/jhn.12530. (PMID: 10.1111/jhn.1253029336079)
Wiley NC, Cryan JF, Dinan TG, Ross RP, Stanton C (2021) Production of psychoactive metabolites by gut bacteria. Mod Trends Psychiatr 32:74–99. https://doi.org/10.1159/000510419. (PMID: 10.1159/000510419)
Wilmes L, Collins JM, O’Riordan KJ, O’Mahony SM, Cryan JF, Clarke G (2021) Of bowels, brain and behavior: a role for the gut microbiota in psychiatric comorbidities in irritable bowel syndrome. Neurogastroenterol Motil 33(3):e14095. https://doi.org/10.1111/nmo.14095. (PMID: 10.1111/nmo.1409533580895)
Woolf CJ, Bennett GJ, Doherty M, Dubner R, Kidd B, Koltzenburg M, Lipton R, Loeser JD, Payne R, Torebjork E (1998) Towards a mechanism-based classification of pain? Pain 77(3):227–229. https://doi.org/10.1016/S0304-3959(98)00099-2. (PMID: 10.1016/S0304-3959(98)00099-29808347)
van de Wouw M, Walsh CJ, Vigano GMD, Lyte JM, Boehme M, Gual-Grau A, Crispie F, Walsh AM, Clarke G, Dinan TG, Cotter PD, Cryan JF (2021) Kefir ameliorates specific microbiota-gut-brain axis impairments in a mouse model relevant to autism spectrum disorder. Brain Behav Immun 97:119–134. https://doi.org/10.1016/j.bbi.2021.07.004. (PMID: 10.1016/j.bbi.2021.07.00434252569)
Wu HJ, Wu E (2012) The role of gut microbiota in immune homeostasis and autoimmunity. Gut Microbes 3(1):4–14. https://doi.org/10.4161/gmic.19320. (PMID: 10.4161/gmic.19320223568533337124)
Wu WL, Adame MD, Liou CW, Barlow JT, Lai TT, Sharon G, Schretter CE, Needham BD, Wang MI, Tang W, Ousey J, Lin YY, Yao TH, Abdel-Haq R, Beadle K, Gradinaru V, Ismagilov RF, Mazmanian SK (2021) Microbiota regulate social behaviour via stress response neurons in the brain. Nature 595(7867):409–414. https://doi.org/10.1038/s41586-021-03669-y. (PMID: 10.1038/s41586-021-03669-y341940388346519)
Xu F, Xie Q, Kuang W, Dong Z (2023a) Interactions between antidepressants and intestinal microbiota. Neurotherapeutics 20(2):359–371. https://doi.org/10.1007/s13311-023-01362-8. (PMID: 10.1007/s13311-023-01362-83688135110121977)
Xu W, Rustenhoven J, Nelson CA, Dykstra T, Ferreiro A, Papadopoulos Z, Burnham CD, Dantas G, Fremont DH, Kipnis J (2023b) A novel immune modulator IM33 mediates a glia-gut-neuronal axis that controls lifespan. Neuron 111(20):3244–3254 e3248. https://doi.org/10.1016/j.neuron.2023.07.010. (PMID: 10.1016/j.neuron.2023.07.0103758236610592285)
Yang D, Almanzar N, Chiu IM (2023) The role of cellular and molecular neuroimmune crosstalk in gut immunity. Cell Mol Immunol 20(11):1259–1269. https://doi.org/10.1038/s41423-023-01054-5. (PMID: 10.1038/s41423-023-01054-53733698910616093)
Yatsunenko T, Rey FE, Manary MJ, Trehan I, Dominguez-Bello MG, Contreras M, Magris M, Hidalgo G, Baldassano RN, Anokhin AP, Heath AC, Warner B, Reeder J, Kuczynski J, Caporaso JG, Lozupone CA, Lauber C, Clemente JC, Knights D et al (2012) Human gut microbiome viewed across age and geography. Nature 486(7402):222–227. https://doi.org/10.1038/nature11053. (PMID: 10.1038/nature11053226996113376388)
Yin J, Liao SX, He Y, Wang S, Xia GH, Liu FT, Zhu JJ, You C, Chen Q, Zhou L, Pan SY, Zhou HW (2015) Dysbiosis of gut microbiota with reduced Trimethylamine-N-Oxide level in patients with large-artery atherosclerotic stroke or transient ischemic attack. J Am Heart Assoc 4(11). https://doi.org/10.1161/JAHA.115.002699.
Yolken R, Adamos M, Katsafanas E, Khushalani S, Origoni A, Savage C, Schweinfurth L, Stallings C, Sweeney K, Dickerson F (2016) Individuals hospitalized with acute mania have increased exposure to antimicrobial medications. Bipolar Disord 18(5):404–409. https://doi.org/10.1111/bdi.12416. (PMID: 10.1111/bdi.12416274255975508736)
Yoon HS, Cho CH, Yun MS, Jang SJ, You HJ, Kim JH, Han D, Cha KH, Moon SH, Lee K, Kim YJ, Lee SJ, Nam TW, Ko G (2021) Akkermansia muciniphila secretes a glucagon-like peptide-1-inducing protein that improves glucose homeostasis and ameliorates metabolic disease in mice. Nat Microbiol 6(5):563–573. https://doi.org/10.1038/s41564-021-00880-5. (PMID: 10.1038/s41564-021-00880-533820962)
Yu Y, Daly DM, Adam IJ, Kitsanta P, Hill CJ, Wild J, Shorthouse A, Grundy D, Jiang W (2016) Interplay between mast cells, enterochromaffin cells, and sensory signaling in the aging human bowel. Neurogastroenterol Motil 28(10):1465–1479. https://doi.org/10.1111/nmo.12842. (PMID: 10.1111/nmo.12842272066895053273)
Yu L, Han X, Cen S, Duan H, Feng S, Xue Y, Tian F, Zhao J, Zhang H, Zhai Q, Chen W (2020) Beneficial effect of GABA-rich fermented milk on insomnia involving regulation of gut microbiota. Microbiol Res 233:126409. https://doi.org/10.1016/j.micres.2020.126409. (PMID: 10.1016/j.micres.2020.12640931927503)
Yue Y, Sun X, Tian S, Yan S, Sun W, Miao J, Huang S, Diao J, Zhou Z, Zhu W (2024) Multi-omics and gut microbiome: unveiling the pathogenic mechanisms of early-life pesticide exposure. Pestic Biochem Physiol 199:105770. https://doi.org/10.1016/j.pestbp.2024.105770. (PMID: 10.1016/j.pestbp.2024.10577038458664)
Zachariassen LF, Sorensen DB, Krych L, Hansen AK, Hansen CHF (2021) Effects of delivery mode on behavior in mouse offspring. Physiol Behav 230:113285. https://doi.org/10.1016/j.physbeh.2020.113285. (PMID: 10.1016/j.physbeh.2020.11328533309952)
Zelante T, Iannitti RG, Cunha C, De Luca A, Giovannini G, Pieraccini G, Zecchi R, D’Angelo C, Massi-Benedetti C, Fallarino F, Carvalho A, Puccetti P, Romani L (2013) Tryptophan catabolites from microbiota engage aryl hydrocarbon receptor and balance mucosal reactivity via interleukin-22. Immunity 39(2):372–385. https://doi.org/10.1016/j.immuni.2013.08.003. (PMID: 10.1016/j.immuni.2013.08.00323973224)
Zengeler KE, Shapiro DA, Bruch KR, Lammert CR, Ennerfelt H, Lukens JR (2023) SSRI treatment modifies the effects of maternal inflammation on in utero physiology and offspring neurobiology. Brain Behav Immun 108:80–97. https://doi.org/10.1016/j.bbi.2022.10.024. (PMID: 10.1016/j.bbi.2022.10.02436343752)
Zha X, Liu X, Wei M, Huang H, Cao J, Liu S, Bian X, Zhang Y, Xiao F, Xie Y, Wang W, Zhang C (2025) Microbiota-derived lysophosphatidylcholine alleviates Alzheimer’s disease pathology via suppressing ferroptosis. Cell Metab 37(1):169–186 e169. https://doi.org/10.1016/j.cmet.2024.10.006. (PMID: 10.1016/j.cmet.2024.10.00639510074)
Zhai L, Huang C, Ning Z, Zhang Y, Zhuang M, Yang W, Wang X, Wang J, Zhang L, Xiao H, Zhao L, Asthana P, Lam YY, Chow CFW, Huang JD, Yuan S, Chan KM, Yuan CS, Lau JY et al (2023) Ruminococcus gnavus plays a pathogenic role in diarrhea-predominant irritable bowel syndrome by increasing serotonin biosynthesis. Cell Host Microbe 31(1):33–44 e35. https://doi.org/10.1016/j.chom.2022.11.006. (PMID: 10.1016/j.chom.2022.11.00636495868)
Zhang X, Gerard P (2022) Diet-gut microbiota interactions on cardiovascular disease. Comput Struct Biotechnol J 20:1528–1540. https://doi.org/10.1016/j.csbj.2022.03.028. (PMID: 10.1016/j.csbj.2022.03.028354229668983311)
Zhang S, Jin Y, Zeng Z, Liu Z, Fu Z (2015) Subchronic exposure of mice to cadmium perturbs their hepatic energy metabolism and gut microbiome. Chem Res Toxicol 28(10):2000–2009. https://doi.org/10.1021/acs.chemrestox.5b00237. (PMID: 10.1021/acs.chemrestox.5b0023726352046)
Zhang Z, Lin T, Meng Y, Hu M, Shu L, Jiang H, Gao R, Ma J, Wang C, Zhou X (2021b) FOS/GOS attenuates high-fat diet induced bone loss via reversing microbiota dysbiosis, high intestinal permeability and systemic inflammation in mice. Metabolism 119:154767. https://doi.org/10.1016/j.metabol.2021.154767. (PMID: 10.1016/j.metabol.2021.15476733753088)
Zhang Y, Li Y, Barber AF, Noya SB, Williams JA, Li F, Daniel SG, Bittinger K, Fang J, Sehgal A (2023) The microbiome stabilizes circadian rhythms in the gut. Proc Natl Acad Sci USA 120(5):e2217532120. https://doi.org/10.1073/pnas.2217532120. (PMID: 10.1073/pnas.2217532120366896619945975)
Zhang S, Meng R, Jiang M, Qing H, Ni J (2024a) Emerging roles of microglia in blood-brain barrier integrity in aging and neurodegeneration. Curr Neuropharmacol 22(7):1189–1204. https://doi.org/10.2174/1570159X21666230203103910. (PMID: 10.2174/1570159X216662302031039103674079910964094)
Zhang YD, Shi DD, Liao BB, Li Y, Zhang S, Gao J, Lin LJ, Wang Z (2024b) Human microbiota from drug-naive patients with obsessive-compulsive disorder drives behavioral symptoms and neuroinflammation via succinic acid in mice. Mol Psychiatry 29(6):1782–1797. https://doi.org/10.1038/s41380-024-02424-9. (PMID: 10.1038/s41380-024-02424-938273106)
Zheng Z, Zong Y, Ma Y, Tian Y, Pang Y, Zhang C, Gao J (2024) Glucagon-like peptide-1 receptor: mechanisms and advances in therapy. Signal Transduct Target Ther 9(1):234. https://doi.org/10.1038/s41392-024-01931-z. (PMID: 10.1038/s41392-024-01931-z3928933911408715)
Zhernakova DV, Wang D, Liu L, Andreu-Sanchez S, Zhang Y, Ruiz-Moreno AJ, Peng H, Plomp N, Del Castillo-Izquierdo A, Gacesa R, Lopera-Maya EA, Temba GS, Kullaya VI, van Leeuwen SS, Lifelines Cohort S, Xavier RJ, de Mast Q, Joosten LAB, Riksen NP et al (2024) Host genetic regulation of human gut microbial structural variation. Nature 625(7996):813–821. https://doi.org/10.1038/s41586-023-06893-w. (PMID: 10.1038/s41586-023-06893-w3817263710808065)
Zhou R, Qian S, Cho WCS, Zhou J, Jin C, Zhong Y, Wang J, Zhang X, Xu Z, Tian M, Chan LWC, Zhang H (2022) Microbiota-microglia connections in age-related cognition decline. Aging Cell 21(5):e13599. https://doi.org/10.1111/acel.13599. (PMID: 10.1111/acel.13599353497469124309)
Zhou L, Qiu W, Wang J, Zhao A, Zhou C, Sun T, Xiong Z, Cao P, Shen W, Chen J, Lai X, Zhao LH, Wu Y, Li M, Qiu F, Yu Y, Xu ZZ, Zhou H, Jia W et al (2023) Effects of vaginal microbiota transfer on the neurodevelopment and microbiome of cesarean-born infants: a blinded randomized controlled trial. Cell Host Microbe 31(7):1232–1247 e1235. https://doi.org/10.1016/j.chom.2023.05.022. (PMID: 10.1016/j.chom.2023.05.02237327780)
Zhu Y, Lin X, Zhao F, Shi X, Li H, Li Y, Zhu W, Xu X, Li C, Zhou G (2015) Meat, dairy and plant proteins alter bacterial composition of rat gut bacteria. Sci Rep 5:15220. https://doi.org/10.1038/srep15220. (PMID: 10.1038/srep15220264632714604471)
Zhu W, Romano KA, Li L, Buffa JA, Sangwan N, Prakash P, Tittle AN, Li XS, Fu X, Androjna C, DiDonato AJ, Brinson K, Trapp BD, Fischbach MA, Rey FE, Hajjar AM, DiDonato JA, Hazen SL (2021) Gut microbes impact stroke severity via the trimethylamine N-oxide pathway. Cell Host Microbe 29(7):1199–1208 e1195. https://doi.org/10.1016/j.chom.2021.05.002. (PMID: 10.1016/j.chom.2021.05.002341391738288076)
Zhu L, Ming Y, Wu M, Zhang X, Wang X, Li H, Lin Z, Gao F, Zhu Y (2024a) Effect of fiber-rich diet and rope skipping on memory, executive function, and gut microbiota in young adults: a randomized controlled trial. Mol Nutr Food Res 68(3):e2300673. https://doi.org/10.1002/mnfr.202300673. (PMID: 10.1002/mnfr.20230067338072647)
Zhu Q, Chen B, Zhang F, Zhang B, Guo Y, Pang M, Huang L, Wang T (2024b) Toxic and essential metals: metabolic interactions with the gut microbiota and health implications. Front Nutr 11:1448388. https://doi.org/10.3389/fnut.2024.1448388. (PMID: 10.3389/fnut.2024.14483883913555711317476)
Zhuang ZQ, Shen LL, Li WW, Fu X, Zeng F, Gui L, Lu Y, Cai M, Zhu C, Tan YL, Zheng P, Li HY, Zhu J, Zhou HD, Bu XL, Wang YJ (2018) Gut microbiota is altered in patients with Alzheimer’s disease. J Alzheimers Dis 63(4):1337–1346. https://doi.org/10.3233/JAD-180176. (PMID: 10.3233/JAD-18017629758946)
Zilber-Rosenberg I, Rosenberg E (2008) Role of microorganisms in the evolution of animals and plants: the hologenome theory of evolution. FEMS Microbiol Rev 32(5):723–735. https://doi.org/10.1111/j.1574-6976.2008.00123.x. (PMID: 10.1111/j.1574-6976.2008.00123.x18549407)
Zuffa S, Schimmel P, Gonzalez-Santana A, Belzer C, Knol J, Bolte S, Falck-Ytter T, Forssberg H, Swann J, Diaz Heijtz R (2023) Early-life differences in the gut microbiota composition and functionality of infants at elevated likelihood of developing autism spectrum disorder. Transl Psychiatry 13(1):257. https://doi.org/10.1038/s41398-023-02556-6. (PMID: 10.1038/s41398-023-02556-63744335910344877)

Keywords: Blood-Brain Barrier (BBB); Gut Microbiota; Microbiota-Gut-Brain Axis; Neurodevelopment; Neuroinflammation; Psychobiotics; Short-Chain Fatty Acids (SCFAs); Vagus Nerve

Date Created: 20250529 Date Completed: 20250530 Latest Revision: 20250529

20260130

10.1007/978-3-031-89525-8_6

40442386

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