{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,18]],"date-time":"2026-05-18T00:06:56Z","timestamp":1779062816871,"version":"3.51.4"},"reference-count":102,"publisher":"Springer Science and Business Media LLC","issue":"3","license":[{"start":{"date-parts":[[2025,12,5]],"date-time":"2025-12-05T00:00:00Z","timestamp":1764892800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2025,12,5]],"date-time":"2025-12-05T00:00:00Z","timestamp":1764892800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"funder":[{"DOI":"10.13039\/501100001809","name":"MOST | National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["32422017"],"award-info":[{"award-number":["32422017"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"MOST | National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["32370609"],"award-info":[{"award-number":["32370609"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"MOST | National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["92353301"],"award-info":[{"award-number":["92353301"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002855","name":"Ministry of Science and Technology of the People's Republic of China","doi-asserted-by":"publisher","award":["2024YFF1207600"],"award-info":[{"award-number":["2024YFF1207600"]}],"id":[{"id":"10.13039\/501100002855","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100012503","name":"MOST | Dream Project of Ministry of Science and Technology of the People's Republic of China","doi-asserted-by":"publisher","award":["2023YFA1800700"],"award-info":[{"award-number":["2023YFA1800700"]}],"id":[{"id":"10.13039\/501100012503","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004731","name":"MOST | NSFC | NSFC-Zhejiang Joint Fund | \u6d59\u6c5f\u7701\u79d1\u5b66\u6280\u672f\u5385 | Natural Science Foundation of Zhejiang Province","doi-asserted-by":"publisher","award":["LR25C060002"],"award-info":[{"award-number":["LR25C060002"]}],"id":[{"id":"10.13039\/501100004731","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100012226","name":"MOE | Fundamental Research Funds for the Central Universities","doi-asserted-by":"publisher","award":["226-2025-00176"],"award-info":[{"award-number":["226-2025-00176"]}],"id":[{"id":"10.13039\/501100012226","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Zhejiang Provincial Leading Innovation and Entrepreneurship Team Introduction and Cultivation Program","award":["2024R01024"],"award-info":[{"award-number":["2024R01024"]}]},{"name":"Benyuan Foundation","award":["NA"],"award-info":[{"award-number":["NA"]}]},{"DOI":"10.13039\/501100012692","name":"K.C.Wong Education Foundation","doi-asserted-by":"crossref","award":["NA"],"award-info":[{"award-number":["NA"]}],"id":[{"id":"10.13039\/501100012692","id-type":"DOI","asserted-by":"crossref"}]},{"name":"The State Key Laboratory of Transvascular Implantation Devices","award":["012024002"],"award-info":[{"award-number":["012024002"]}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Mol Syst Biol"],"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>\n                    The gut microbiome plays fundamental roles in physiological and pathological processes, yet its interaction with host gene expression and contribution to disease remain underexplored. Here, we integrate the genetic regulatory maps of 116 microbial genera with gene expression quantitative trait loci (eQTLs) and DNA methylation QTLs (mQTLs) in three intestinal tissues to dissect host\u2013microbiome interaction. We identify 6088, 5810, and 2398 gene-to-microbiome regulatory loci in the transverse colon, sigmoid colon, and ileum, respectively. Among these, 13.2% of genes show broad regulatory effects on multiple genera, with functional enrichments in developmental, metabolic, and immune-related pathways. Integrative analysis with genome-wide association studies (GWASs) reveals 283 microbiome-dependent disease loci. We observe pleiotropic effects mediated by the gene-to-microbiome regulation at both microbiome and disease layers. Notably, we predict and experimentally validate the suppressive effect of\n                    <jats:italic>Allisonella<\/jats:italic>\n                    on depression through regulating bile acid abundance, and the regulation of\n                    <jats:italic>Parasutterella<\/jats:italic>\n                    on short-chain fatty acid and its contribution to allergic rhinitis. The gene\u2013microbiome-disease regulatory maps are available at our interactive database (\n                    <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" xlink:href=\"https:\/\/xiongxslab.github.io\/microbiomeMR\/\" ext-link-type=\"uri\">https:\/\/xiongxslab.github.io\/microbiomeMR\/<\/jats:ext-link>\n                    ).\n                  <\/jats:p>","DOI":"10.1038\/s44320-025-00173-7","type":"journal-article","created":{"date-parts":[[2025,12,5]],"date-time":"2025-12-05T14:24:12Z","timestamp":1764944652000},"page":"369-394","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Genetics-mediated regulation of intestinal gene expression on microbiome contributes to human disease heritability"],"prefix":"10.1038","volume":"22","author":[{"ORCID":"https:\/\/orcid.org\/0009-0000-1355-1256","authenticated-orcid":false,"given":"Haochuan","family":"Wang","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chengyu","family":"Li","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zhen","family":"Hu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Haonan","family":"Feng","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Luowei","family":"Chen","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ke","family":"Ding","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jiuhong","family":"Nan","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yuhan","family":"Wu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1207-7449","authenticated-orcid":false,"given":"Jinghao","family":"Sheng","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7090-7503","authenticated-orcid":false,"given":"Xushen","family":"Xiong","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2025,12,5]]},"reference":[{"key":"173_CR1","doi-asserted-by":"crossref","first-page":"68","DOI":"10.1038\/nature15393","volume":"526","author":"A Auton","year":"2015","unstructured":"1000 Genomes Project Consortium, Auton A, Brooks LD, Durbin RM, Garrison EP, Kang HM, Korbel JO, Marchini JL, McCarthy S, McVean GA et al (2015) A global reference for human genetic variation. Nature 526:68\u201374","journal-title":"Nature"},{"key":"173_CR2","doi-asserted-by":"crossref","first-page":"153","DOI":"10.1038\/nature12687","volume":"504","author":"T Alenghat","year":"2013","unstructured":"Alenghat T, Osborne LC, Saenz SA, Kobuley D, Ziegler CGK, Mullican SE, Choi I, Grunberg S, Sinha R, Wynosky-Dolfi M et al (2013) Histone deacetylase 3 coordinates commensal-bacteria-dependent intestinal homeostasis. Nature 504:153\u2013157","journal-title":"Nature"},{"key":"173_CR3","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1038\/75556","volume":"25","author":"M Ashburner","year":"2000","unstructured":"Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT et al (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 25:25\u201329","journal-title":"Nat Genet"},{"key":"173_CR4","doi-asserted-by":"crossref","first-page":"D1305","DOI":"10.1093\/nar\/gkad1051","volume":"52","author":"JA Baron","year":"2024","unstructured":"Baron JA, Johnson CS-B, Schor MA, Olley D, Nickel L, Felix V, Munro JB, Bello SM, Bearer C, Lichenstein R et al (2024) The DO-KB Knowledgebase: a 20-year journey developing the disease open science ecosystem. Nucleic Acids Res 52:D1305\u2013D1314","journal-title":"Nucleic Acids Res"},{"key":"173_CR5","doi-asserted-by":"crossref","unstructured":"Baxter NT, Schmidt AW, Venkataraman A, Kim KS, Waldron C, Schmidt TM (2019) Dynamics of human gut microbiota and short-chain fatty acids in response to dietary interventions with three fermentable fibers. mBio 10:10\u20131128","DOI":"10.1128\/mBio.02566-18"},{"key":"173_CR6","doi-asserted-by":"crossref","first-page":"813","DOI":"10.1038\/s44319-023-00055-9","volume":"25","author":"A Bhattacharya","year":"2024","unstructured":"Bhattacharya A, Torggler R, Reiter W, Romanov N, Licheva M, Ciftci A, Mari M, Kolb L, Kaiser D, Reggiori F et al (2024) Decoding the function of Atg13 phosphorylation reveals a role of Atg11 in bulk autophagy initiation. EMBO Rep 25:813\u2013831","journal-title":"EMBO Rep"},{"key":"173_CR7","doi-asserted-by":"crossref","first-page":"1407","DOI":"10.1038\/ng.3663","volume":"48","author":"MJ Bonder","year":"2016","unstructured":"Bonder MJ, Kurilshikov A, Tigchelaar EF, Mujagic Z, Imhann F, Vila AV, Deelen P, Vatanen T, Schirmer M, Smeekens SP et al (2016) The effect of host genetics on the gut microbiome. Nat Genet 48:1407\u20131412","journal-title":"Nat Genet"},{"key":"173_CR8","doi-asserted-by":"crossref","first-page":"16050","DOI":"10.1073\/pnas.1102999108","volume":"108","author":"JA Bravo","year":"2011","unstructured":"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 108:16050\u201316055","journal-title":"Proc Natl Acad Sci USA"},{"key":"173_CR9","doi-asserted-by":"crossref","first-page":"55","DOI":"10.1038\/nrmicro.2016.142","volume":"15","author":"KF Budden","year":"2017","unstructured":"Budden KF, Gellatly SL, Wood DLA, Cooper MA, Morrison M, Hugenholtz P, Hansbro PM (2017) Emerging pathogenic links between microbiota and the gut-lung axis. Nat Rev Microbiol 15:55\u201363","journal-title":"Nat Rev Microbiol"},{"key":"173_CR10","doi-asserted-by":"crossref","first-page":"291","DOI":"10.1038\/ng.3211","volume":"47","author":"BK Bulik-Sullivan","year":"2015","unstructured":"Bulik-Sullivan BK, Loh P-R, Finucane HK, Ripke S, Yang J, Schizophrenia Working Group of the Psychiatric Genomics Consortium, Patterson N, Daly MJ, Price AL, Neale BM (2015) LD Score regression distinguishes confounding from polygenicity in genome-wide association studies. Nat Genet 47:291\u2013295","journal-title":"Nat Genet"},{"key":"173_CR11","doi-asserted-by":"crossref","first-page":"2304900","DOI":"10.1080\/19490976.2024.2304900","volume":"16","author":"D Chanda","year":"2024","unstructured":"Chanda D, De D (2024) Meta-analysis reveals obesity associated gut microbial alteration patterns and reproducible contributors of functional shift. Gut Microbes 16:2304900","journal-title":"Gut Microbes"},{"key":"173_CR12","doi-asserted-by":"crossref","first-page":"735","DOI":"10.1038\/nrmicro2876","volume":"10","author":"SM Collins","year":"2012","unstructured":"Collins SM, Surette M, Bercik P (2012) The interplay between the intestinal microbiota and the brain. Nat Rev Microbiol 10:735\u2013742","journal-title":"Nat Rev Microbiol"},{"key":"173_CR13","doi-asserted-by":"crossref","first-page":"302","DOI":"10.1080\/19490976.2016.1186334","volume":"7","author":"EH Crost","year":"2016","unstructured":"Crost EH, Tailford LE, Monestier M, Swarbreck D, Henrissat B, Crossman LC, Juge N (2016) The mucin-degradation strategy of Ruminococcus gnavus: the importance of intramolecular trans-sialidases. Gut Microbes 7:302\u2013312","journal-title":"Gut Microbes"},{"key":"173_CR14","doi-asserted-by":"crossref","first-page":"943","DOI":"10.1038\/s42003-024-06628-1","volume":"7","author":"F De Bruyn","year":"2024","unstructured":"De Bruyn F, James K, Cottenet G, Dominick M, Katja J (2024) Combining Bifidobacterium longum subsp. infantis and human milk oligosaccharides synergistically increases short chain fatty acid production ex vivo. Commun Biol 7:943","journal-title":"Commun Biol"},{"key":"173_CR15","doi-asserted-by":"crossref","first-page":"179","DOI":"10.1136\/gutjnl-2013-305112","volume":"63","author":"I Depoortere","year":"2014","unstructured":"Depoortere I (2014) Taste receptors of the gut: emerging roles in health and disease. Gut 63:179\u2013190","journal-title":"Gut"},{"key":"173_CR16","doi-asserted-by":"crossref","first-page":"194","DOI":"10.1053\/j.gastro.2023.09.034","volume":"166","author":"K Desai","year":"2024","unstructured":"Desai K, Gupta S, May FP, Xu G, Shaukat A, Hommes DW, NICE-AA\/CRC-Consortium (2024) Early detection of advanced adenomas and colorectal carcinoma by serum glycoproteome profiling. Gastroenterology 166:194\u2013197.e2","journal-title":"Gastroenterology"},{"key":"173_CR17","doi-asserted-by":"crossref","first-page":"20","DOI":"10.1038\/nrmicro3552","volume":"14","author":"GP Donaldson","year":"2016","unstructured":"Donaldson GP, Lee SM, Mazmanian SK (2016) Gut biogeography of the bacterial microbiota. Nat Rev Microbiol 14:20\u201332","journal-title":"Nat Rev Microbiol"},{"key":"173_CR18","doi-asserted-by":"crossref","DOI":"10.1038\/s41467-023-40874-x","volume":"14","author":"G Ecklu-Mensah","year":"2023","unstructured":"Ecklu-Mensah G, Choo-Kang C, Maseng MG, Donato S, Bovet P, Viswanathan B, Bedu-Addo K, Plange-Rhule J, Oti Boateng P, Forrester TE et al (2023) Gut microbiota and fecal short chain fatty acids differ with adiposity and country of origin: the METS-microbiome study. Nat Commun 14:5160","journal-title":"Nat Commun"},{"key":"173_CR19","doi-asserted-by":"crossref","unstructured":"Elsworth B, Lyon M, Alexander T, Liu Y, Matthews P, Hallett J, Bates P, Palmer T, Haberland V, Smith GD et al (2020) The MRC IEU OpenGWAS data infrastructure. Preprint at bioRxiv https:\/\/www.biorxiv.org\/content\/10.1101\/2020.08.10.244293v1","DOI":"10.1101\/2020.08.10.244293"},{"key":"173_CR20","doi-asserted-by":"publisher","unstructured":"Elsworth B, Lyon M, Alexander T, Liu Y, Matthews P, Hallett J, Bates P, Palmer T, Haberland V, Smith GD et al (2020) OpenGWAS. https:\/\/doi.org\/10.1101\/2020.08.10.244293 (https:\/\/gwas.mrcieu.ac.uk) [DATASET]","DOI":"10.1101\/2020.08.10.244293"},{"key":"173_CR21","doi-asserted-by":"crossref","unstructured":"Engevik MA, Luk B, Chang-Graham AL, Hall A, Herrmann B, Ruan W, Endres BT, Shi Z, Garey KW, Hyser JM et al (2019) Bifidobacterium dentium fortifies the intestinal mucus layer via autophagy and calcium signaling pathways. mBio 10:10\u20131128","DOI":"10.1128\/mBio.01087-19"},{"key":"173_CR22","doi-asserted-by":"crossref","first-page":"1228","DOI":"10.1038\/ng.3404","volume":"47","author":"HK Finucane","year":"2015","unstructured":"Finucane HK, Bulik-Sullivan B, Gusev A, Trynka G, Reshef Y, Loh P-R, Anttila V, Xu H, Zang C, Farh K et al (2015) Partitioning heritability by functional annotation using genome-wide association summary statistics. Nat Genet 47:1228\u20131235","journal-title":"Nat Genet"},{"key":"173_CR23","doi-asserted-by":"crossref","first-page":"124","DOI":"10.1016\/j.ynstr.2017.03.001","volume":"7","author":"JA Foster","year":"2017","unstructured":"Foster JA, Rinaman L, Cryan JF (2017) Stress & the gut-brain axis: regulation by the microbiome. Neurobiol Stress 7:124\u2013136","journal-title":"Neurobiol Stress"},{"key":"173_CR24","doi-asserted-by":"crossref","first-page":"e1004383","DOI":"10.1371\/journal.pgen.1004383","volume":"10","author":"C Giambartolomei","year":"2014","unstructured":"Giambartolomei C, Vukcevic D, Schadt EE, Franke L, Hingorani AD, Wallace C, Plagnol V (2014) Bayesian test for colocalisation between pairs of genetic association studies using summary statistics. PLoS Genet 10:e1004383","journal-title":"PLoS Genet"},{"key":"173_CR25","doi-asserted-by":"crossref","first-page":"2538","DOI":"10.1093\/bioinformatics\/bty147","volume":"34","author":"C Giambartolomei","year":"2018","unstructured":"Giambartolomei C, Zhenli Liu J, Zhang W, Hauberg M, Shi H, Boocock J, Pickrell J, Jaffe AE, CommonMind Consortium, Pasaniuc B et al (2018) A Bayesian framework for multiple trait colocalization from summary association statistics. Bioinformatics 34:2538\u20132545","journal-title":"Bioinformatics"},{"key":"173_CR26","doi-asserted-by":"crossref","first-page":"5650","DOI":"10.1021\/pr3004437","volume":"11","author":"YA Goo","year":"2012","unstructured":"Goo YA, Cain K, Jarrett M, Smith L, Voss J, Tolentino E, Tsuji J, Tsai YS, Panchaud A, Goodlett DR et al (2012) Urinary proteome analysis of irritable bowel syndrome (IBS) symptom subgroups. J Proteome Res 11:5650\u20135662","journal-title":"J Proteome Res"},{"key":"173_CR27","doi-asserted-by":"crossref","first-page":"1318","DOI":"10.1126\/science.aaz1776","volume":"369","author":"GTEx Consortium","year":"2020","unstructured":"GTEx Consortium (2020) The GTEx Consortium atlas of genetic regulatory effects across human tissues. Science 369:1318\u20131330","journal-title":"Science"},{"key":"173_CR28","unstructured":"GTEx Consortium (2020) The Genotype-Tissue Expression (GTEx) Project phs000424.v8. (https:\/\/www.gtexportal.org\/home\/aboutAdultGtex) [DATASET]"},{"key":"173_CR29","doi-asserted-by":"crossref","first-page":"690","DOI":"10.1038\/nrg.2017.63","volume":"18","author":"AB Hall","year":"2017","unstructured":"Hall AB, Tolonen AC, Xavier RJ (2017) Human genetic variation and the gut microbiome in disease. Nat Rev Genet 18:690\u2013699","journal-title":"Nat Rev Genet"},{"key":"173_CR30","volume":"13","author":"W Hao","year":"2022","unstructured":"Hao W, Dian M, Zhou Y, Zhong Q, Pang W, Li Z, Zhao Y, Ma J, Lin X, Luo R et al (2022) Autophagy induction promoted by mA reader YTHDF3 through translation upregulation of FOXO3 mRNA. Nat Commun 13:5845","journal-title":"Nat Commun"},{"key":"173_CR31","doi-asserted-by":"crossref","unstructured":"Hemani G, Zheng J, Elsworth B, Wade KH, Haberland V, Baird D, Laurin C, Burgess S, Bowden J, Langdon R et al (2018) The MR-Base platform supports systematic causal inference across the human phenome.eLife 7:e34408","DOI":"10.7554\/eLife.34408"},{"key":"173_CR32","doi-asserted-by":"crossref","first-page":"26","DOI":"10.1038\/s41531-021-00170-1","volume":"7","author":"MK Herrick","year":"2021","unstructured":"Herrick MK, Tansey MG (2021) Is LRRK2 the missing link between inflammatory bowel disease and Parkinson\u2019s disease?. NPJ Parkinsons Dis 7:26","journal-title":"NPJ Parkinsons Dis"},{"key":"173_CR33","doi-asserted-by":"crossref","first-page":"115","DOI":"10.1038\/s41531-023-00554-5","volume":"9","author":"P Huang","year":"2023","unstructured":"Huang P, Zhang P, Du J, Gao C, Liu J, Tan Y, Chen S (2023) Association of fecal short-chain fatty acids with clinical severity and gut microbiota in essential tremor and its difference from Parkinson\u2019s disease. NPJ Parkinsons Dis 9:115","journal-title":"NPJ Parkinsons Dis"},{"key":"173_CR34","doi-asserted-by":"crossref","first-page":"108","DOI":"10.1136\/gutjnl-2016-312135","volume":"67","author":"F Imhann","year":"2018","unstructured":"Imhann F, Vich Vila A, Bonder MJ, Fu J, Gevers D, Visschedijk MC, Spekhorst LM, Alberts R, Franke L, van Dullemen HM et al (2018) Interplay of host genetics and gut microbiota underlying the onset and clinical presentation of inflammatory bowel disease. Gut 67:108\u2013119","journal-title":"Gut"},{"key":"173_CR35","doi-asserted-by":"crossref","first-page":"496","DOI":"10.1016\/j.chom.2012.09.009","volume":"12","author":"II Ivanov","year":"2012","unstructured":"Ivanov II, Honda K (2012) Intestinal commensal microbes as immune modulators. Cell Host Microbe 12:496\u2013508","journal-title":"Cell Host Microbe"},{"key":"173_CR36","doi-asserted-by":"crossref","first-page":"3635","DOI":"10.1007\/s00018-011-0822-3","volume":"68","author":"MEV Johansson","year":"2011","unstructured":"Johansson MEV, Ambort D, Pelaseyed T, Sch\u00fctte A, Gustafsson JK, Ermund A, Subramani DB, Holm\u00e9n-Larsson JM, Thomsson KA, Bergstr\u00f6m JH et al (2011) Composition and functional role of the mucus layers in the intestine. Cell Mol Life Sci 68:3635\u20133641","journal-title":"Cell Mol Life Sci"},{"key":"173_CR37","doi-asserted-by":"crossref","first-page":"630","DOI":"10.1016\/j.chom.2024.04.003","volume":"32","author":"A Joly","year":"2024","unstructured":"Joly A, De Vadder F (2024) Amino acid bites: Microbial snacking influences host metabolism. Cell Host Microbe 32:630\u2013632","journal-title":"Cell Host Microbe"},{"key":"173_CR38","doi-asserted-by":"crossref","first-page":"119","DOI":"10.1038\/nature11582","volume":"491","author":"L Jostins","year":"2012","unstructured":"Jostins L, Ripke S, Weersma RK, Duerr RH, McGovern DP, Hui KY, Lee JC, Schumm LP, Sharma Y, Anderson CA et al (2012) Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease. Nature 491:119\u2013124","journal-title":"Nature"},{"key":"173_CR39","doi-asserted-by":"crossref","first-page":"109","DOI":"10.1016\/j.jpsychires.2016.07.019","volume":"82","author":"JR Kelly","year":"2016","unstructured":"Kelly JR, Borre Y, O\u2019 Brien C, Patterson E, El Aidy S, Deane J, Kennedy PJ, Beers S, Scott K, Moloney G et al (2016) Transferring the blues: Depression-associated gut microbiota induces neurobehavioural changes in the rat. J Psychiatr Res 82:109\u2013118","journal-title":"J Psychiatr Res"},{"key":"173_CR40","doi-asserted-by":"crossref","first-page":"1725","DOI":"10.1016\/j.neuron.2024.05.007","volume":"112","author":"AS Klein","year":"2024","unstructured":"Klein AS, Kheirbek MA (2024) From bile acids to melancholia. Neuron 112:1725\u20131727","journal-title":"Neuron"},{"key":"173_CR41","doi-asserted-by":"crossref","first-page":"156","DOI":"10.1038\/s41588-020-00763-1","volume":"53","author":"A Kurilshikov","year":"2021","unstructured":"Kurilshikov A, Medina-Gomez C, Bacigalupe R, Radjabzadeh D, Wang J, Demirkan A, Le Roy CI, Raygoza Garay JA, Finnicum CT, Liu X et al (2021) Large-scale association analyses identify host factors influencing human gut microbiome composition. Nat Genet 53:156\u2013165","journal-title":"Nat Genet"},{"key":"173_CR42","doi-asserted-by":"publisher","unstructured":"Kurilshikov A, Medina-Gomez C, Bacigalupe R, Radjabzadeh D, Wang J, Demirkan A, Le Roy CI, Raygoza Garay JA, Finnicum CT, Liu X et al (2021) MiBioGen https:\/\/doi.org\/10.1038\/s41588-020-00763-1 (www.mibiogen.org) [DATASET]","DOI":"10.1038\/s41588-020-00763-1"},{"key":"173_CR43","doi-asserted-by":"crossref","first-page":"806","DOI":"10.1111\/jth.15647","volume":"20","author":"J Lagrange","year":"2022","unstructured":"Lagrange J, Lecompte T, Knopp T, Lacolley P, Regnault V (2022) Alpha-2-macroglobulin in hemostasis and thrombosis: an underestimated old double-edged sword. J Thromb Haemost 20:806\u2013815","journal-title":"J Thromb Haemost"},{"key":"173_CR44","doi-asserted-by":"crossref","first-page":"598","DOI":"10.1038\/nm.4102","volume":"22","author":"B Lamas","year":"2016","unstructured":"Lamas B, Richard ML, Leducq V, Pham H-P, Michel M-L, Da Costa G, Bridonneau C, Jegou S, Hoffmann TW, Natividad JM et al (2016) CARD9 impacts colitis by altering gut microbiota metabolism of tryptophan into aryl hydrocarbon receptor ligands. Nat Med 22:598\u2013605","journal-title":"Nat Med"},{"key":"173_CR45","doi-asserted-by":"crossref","first-page":"38","DOI":"10.1080\/15548627.2019.1635384","volume":"16","author":"A Larabi","year":"2020","unstructured":"Larabi A, Barnich N, Nguyen HTT (2020) New insights into the interplay between autophagy, gut microbiota and inflammatory responses in IBD. Autophagy 16:38\u201351","journal-title":"Autophagy"},{"key":"173_CR46","doi-asserted-by":"crossref","first-page":"787","DOI":"10.1136\/gut.47.6.787","volume":"47","author":"S Lesage","year":"2000","unstructured":"Lesage S, Zouali H, Colombel JF, Belaiche J, C\u00e9zard JP, Tysk C, Almer S, Gassull M, Binder V, Chamaillard M et al (2000) Genetic analyses of chromosome 12 loci in Crohn\u2019s disease. Gut 47:787\u2013791","journal-title":"Gut"},{"key":"173_CR47","doi-asserted-by":"crossref","first-page":"661","DOI":"10.1016\/j.chom.2024.04.004","volume":"32","author":"T-T Li","year":"2024","unstructured":"Li T-T, Chen X, Huo D, Arifuzzaman M, Qiao S, Jin W-B, Shi H, Li XV, JRI Live Cell Bank Consortium, Iliev ID et al (2024a) Microbiota metabolism of intestinal amino acids impacts host nutrient homeostasis and physiology. Cell Host Microbe 32:661\u2013675.e10","journal-title":"Cell Host Microbe"},{"key":"173_CR48","doi-asserted-by":"crossref","first-page":"1795","DOI":"10.1016\/j.neuron.2024.02.019","volume":"112","author":"X-Y Li","year":"2024","unstructured":"Li X-Y, Zhang S-Y, Hong Y-Z, Chen Z-G, Long Y, Yuan D-H, Zhao J-J, Tang S-S, Wang H, Hong H (2024b) TGR5-mediated lateral hypothalamus-dCA3-dorsolateral septum circuit regulates depressive-like behavior in male mice. Neuron 112:1795\u20131814.e10","journal-title":"Neuron"},{"key":"173_CR49","volume":"11","author":"L Lin","year":"2020","unstructured":"Lin L, Zhou G, Chen P, Wang Y, Han J, Chen M, He Y, Zhang S (2020) Which long noncoding RNAs and circular RNAs contribute to inflammatory bowel disease?. Cell Death Dis 11:456","journal-title":"Cell Death Dis"},{"key":"173_CR50","doi-asserted-by":"crossref","first-page":"110739","DOI":"10.1016\/j.cbi.2023.110739","volume":"385","author":"Y Liu","year":"2023","unstructured":"Liu Y, Liu J, Du M, Yang H, Shi R, Shi Y, Zhang S, Zhao Y, Lan J (2023) Short-chain fatty acid\u2014a critical interfering factor for allergic diseases. Chem Biol Interact 385:110739","journal-title":"Chem Biol Interact"},{"key":"173_CR51","doi-asserted-by":"crossref","first-page":"655","DOI":"10.1038\/s41586-019-1237-9","volume":"569","author":"J Lloyd-Price","year":"2019","unstructured":"Lloyd-Price J, Arze C, Ananthakrishnan AN, Schirmer M, Avila-Pacheco J, Poon TW, Andrews E, Ajami NJ, Bonham KS, Brislawn CJ et al (2019) Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases. Nature 569:655\u2013662","journal-title":"Nature"},{"key":"173_CR52","doi-asserted-by":"crossref","first-page":"37","DOI":"10.1038\/s41392-024-01743-1","volume":"9","author":"JS Loh","year":"2024","unstructured":"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 9:37","journal-title":"Signal Transduct Target Ther"},{"key":"173_CR53","doi-asserted-by":"crossref","first-page":"143","DOI":"10.1038\/s41588-021-00992-y","volume":"54","author":"EA Lopera-Maya","year":"2022","unstructured":"Lopera-Maya EA, Kurilshikov A, van der Graaf A, Hu S, Andreu-S\u00e1nchez S, Chen L, Vila AV, Gacesa R, Sinha T, Collij V et al (2022) Effect of host genetics on the gut microbiome in 7,738 participants of the Dutch Microbiome Project. Nat Genet 54:143\u2013151","journal-title":"Nat Genet"},{"key":"173_CR54","doi-asserted-by":"crossref","first-page":"1405","DOI":"10.1126\/science.aay0240","volume":"365","author":"JB Lynch","year":"2019","unstructured":"Lynch JB, Hsiao EY (2019) Microbiomes as sources of emergent host phenotypes. Science 365:1405\u20131409","journal-title":"Science"},{"key":"173_CR55","doi-asserted-by":"crossref","first-page":"298","DOI":"10.1038\/nature10208","volume":"474","author":"KJ Maloy","year":"2011","unstructured":"Maloy KJ, Powrie F (2011) Intestinal homeostasis and its breakdown in inflammatory bowel disease. Nature 474:298\u2013306","journal-title":"Nature"},{"key":"173_CR56","doi-asserted-by":"crossref","first-page":"834","DOI":"10.15252\/msb.20156487","volume":"11","author":"A Mardinoglu","year":"2015","unstructured":"Mardinoglu A, Shoaie S, Bergentall M, Ghaffari P, Zhang C, Larsson E, B\u00e4ckhed F, Nielsen J (2015) The gut microbiota modulates host amino acid and glutathione metabolism in mice. Mol Syst Biol 11:834","journal-title":"Mol Syst Biol"},{"key":"173_CR57","doi-asserted-by":"crossref","first-page":"598093","DOI":"10.3389\/fcimb.2021.598093","volume":"11","author":"Mart\u00ednez-Cuesta","year":"2021","unstructured":"Mart\u00ednez-Cuesta, Del MC, Campo R, Garriga-Garc\u00eda M, Pel\u00e1ez C, Requena T (2021) Taxonomic characterization and short-chain fatty acids production of the obese microbiota. Front Cell Infect Microbiol 11:598093","journal-title":"Front Cell Infect Microbiol"},{"key":"173_CR58","volume":"9","author":"Y Momozawa","year":"2018","unstructured":"Momozawa Y, Dmitrieva J, Th\u00e9\u00e2tre E, Deffontaine V, Rahmouni S, Charloteaux B, Crins F, Docampo E, Elansary M, Gori A-S et al (2018) IBD risk loci are enriched in multigenic regulatory modules encompassing putative causative genes. Nat Commun 9:2427","journal-title":"Nat Commun"},{"key":"173_CR59","unstructured":"Momozawa Y, Dmitrieva J, Th\u00e9\u00e2tre E, Deffontaine V, Rahmouni S, Charloteaux B, Crins F, Docampo E, Elansary M, Gori A-S et al (2018) Correlated Expression & Disease Association Research (CEDAR) E-MTAB-6667 (http:\/\/cedar-web.giga.ulg.ac.be\/) [DATASET]"},{"key":"173_CR60","doi-asserted-by":"crossref","first-page":"241","DOI":"10.1038\/s41579-020-00460-0","volume":"19","author":"LH Morais","year":"2021","unstructured":"Morais LH, Schreiber 4thHL, Mazmanian SK (2021) The gut microbiota-brain axis in behaviour and brain disorders. Nat Rev Microbiol 19:241\u2013255","journal-title":"Nat Rev Microbiol"},{"key":"173_CR61","doi-asserted-by":"crossref","first-page":"3110","DOI":"10.1038\/s41564-024-01865-w","volume":"9","author":"AH Morris","year":"2024","unstructured":"Morris AH, Bohannan BJM (2024) Estimates of microbiome heritability across hosts. Nat Microbiol 9:3110\u20133119","journal-title":"Nat Microbiol"},{"key":"173_CR62","doi-asserted-by":"crossref","DOI":"10.1038\/s41467-024-53670-y","volume":"15","author":"EA Older","year":"2024","unstructured":"Older EA, Zhang J, Ferris ZE, Xue D, Zhong Z, Mitchell MK, Madden M, Wang Y, Chen H, Nagarkatti P et al (2024) Biosynthetic enzyme analysis identifies a protective role for TLR4-acting gut microbial sulfonolipids in inflammatory bowel disease. Nat Commun 15:9371","journal-title":"Nat Commun"},{"key":"173_CR63","doi-asserted-by":"crossref","first-page":"112","DOI":"10.1038\/s41588-022-01248-z","volume":"55","author":"M Oliva","year":"2023","unstructured":"Oliva M, Demanelis K, Lu Y, Chernoff M, Jasmine F, Ahsan H, Kibriya MG, Chen LS, Pierce BL (2023) DNA methylation QTL mapping across diverse human tissues provides molecular links between genetic variation and complex traits. Nat Genet 55:112\u2013122","journal-title":"Nat Genet"},{"key":"173_CR64","unstructured":"Oliva M, Demanelis K, Lu Y, Chernoff M, Jasmine F, Ahsan H, Kibriya MG, Chen LS, Pierce BL (2023) The Genotype-Tissue Expression (GTEx) Project phs000424.v9. (https:\/\/gtexportal.org\/home\/downloads\/egtex\/methylation) [DATASET]"},{"key":"173_CR65","volume":"8","author":"CD Owen","year":"2017","unstructured":"Owen CD, Tailford LE, Monaco S, \u0160uligoj T, Vaux L, Lallement R, Khedri Z, Yu H, Lecointe K, Walshaw J et al (2017) Unravelling the specificity and mechanism of sialic acid recognition by the gut symbiont Ruminococcus gnavus. Nat Commun 8:2196","journal-title":"Nat Commun"},{"key":"173_CR66","doi-asserted-by":"crossref","first-page":"141","DOI":"10.1016\/j.cmet.2012.12.007","volume":"17","author":"BW Parks","year":"2013","unstructured":"Parks BW, Nam E, Org E, Kostem E, Norheim F, Hui ST, Pan C, Civelek M, Rau CD, Bennett BJ et al (2013) Genetic control of obesity and gut microbiota composition in response to high-fat, high-sucrose diet in mice. Cell Metab 17:141\u2013152","journal-title":"Cell Metab"},{"key":"173_CR67","doi-asserted-by":"crossref","first-page":"1229","DOI":"10.1016\/j.tim.2024.05.006","volume":"32","author":"ML Pepke","year":"2024","unstructured":"Pepke ML, Hansen SB, Limborg MT (2024) Unraveling host regulation of gut microbiota through the epigenome-microbiome axis. Trends Microbiol 32:1229\u20131240","journal-title":"Trends Microbiol"},{"key":"173_CR68","doi-asserted-by":"crossref","first-page":"1088","DOI":"10.1136\/gutjnl-2020-321173","volume":"70","author":"J Pujo","year":"2021","unstructured":"Pujo J, Petitfils C, Le Faouder P, Eeckhaut V, Payros G, Maurel S, Perez-Berezo T, Van Hul M, Barreau F, Blanpied C et al (2021) Bacteria-derived long chain fatty acid exhibits anti-inflammatory properties in colitis. Gut 70:1088\u20131097","journal-title":"Gut"},{"key":"173_CR69","doi-asserted-by":"crossref","first-page":"55","DOI":"10.1038\/nature11450","volume":"490","author":"J Qin","year":"2012","unstructured":"Qin J, Li Y, Cai Z, Li S, Zhu J, Zhang F, Liang S, Zhang W, Guan Y, Shen D et al (2012) A metagenome-wide association study of gut microbiota in type 2 diabetes. Nature 490:55\u201360","journal-title":"Nature"},{"key":"173_CR70","doi-asserted-by":"crossref","first-page":"134","DOI":"10.1038\/s41588-021-00991-z","volume":"54","author":"Y Qin","year":"2022","unstructured":"Qin Y, Havulinna AS, Liu Y, Jousilahti P, Ritchie SC, Tokolyi A, Sanders JG, Valsta L, Bro\u017cy\u0144ska M, Zhu Q et al (2022) Combined effects of host genetics and diet on human gut microbiota and incident disease in a single population cohort. Nat Genet 54:134\u2013142","journal-title":"Nat Genet"},{"key":"173_CR71","doi-asserted-by":"crossref","first-page":"1609","DOI":"10.1038\/s41591-020-1021-2","volume":"26","author":"V Ramlall","year":"2020","unstructured":"Ramlall V, Thangaraj PM, Meydan C, Foox J, Butler D, Kim J, May B, De Freitas JK, Glicksberg BS, Mason CE et al (2020) Immune complement and coagulation dysfunction in adverse outcomes of SARS-CoV-2 infection. Nat Med 26:1609\u20131615","journal-title":"Nat Med"},{"key":"173_CR72","doi-asserted-by":"crossref","first-page":"147","DOI":"10.1038\/s41588-020-00747-1","volume":"53","author":"MC R\u00fchlemann","year":"2021","unstructured":"R\u00fchlemann MC, Hermes BM, Bang C, Doms S, Moitinho-Silva L, Thingholm LB, Frost F, Degenhardt F, Wittig M, K\u00e4ssens J et al (2021) Genome-wide association study in 8,956 German individuals identifies influence of ABO histo-blood groups on gut microbiome. Nat Genet 53:147\u2013155","journal-title":"Nat Genet"},{"key":"173_CR73","doi-asserted-by":"crossref","first-page":"100","DOI":"10.1038\/s41588-021-00983-z","volume":"54","author":"S Sanna","year":"2022","unstructured":"Sanna S, Kurilshikov A, van der Graaf A, Fu J, Zhernakova A (2022) Challenges and future directions for studying effects of host genetics on the gut microbiome. Nat Genet 54:100\u2013106","journal-title":"Nat Genet"},{"key":"173_CR74","doi-asserted-by":"crossref","first-page":"600","DOI":"10.1038\/s41588-019-0350-x","volume":"51","author":"S Sanna","year":"2019","unstructured":"Sanna S, van Zuydam NR, Mahajan A, Kurilshikov A, Vich Vila A, V\u00f5sa U, Mujagic Z, Masclee AAM, Jonkers DMAE, Oosting M et al (2019) Causal relationships among the gut microbiome, short-chain fatty acids and metabolic diseases. Nat Genet 51:600\u2013605","journal-title":"Nat Genet"},{"key":"173_CR75","doi-asserted-by":"crossref","first-page":"46","DOI":"10.1038\/s41421-025-00796-y","volume":"11","author":"X Sheng","year":"2025","unstructured":"Sheng X, Jin L, Yao Z, Gu J, Zhu L, Huang A, Peng J, Xu X, Ge X, Zhou W et al (2025) Psychological stress-induced systemic corticosterone directly sabotages intestinal stem cells and exacerbates colitis. Cell Discov 11:46","journal-title":"Cell Discov"},{"key":"173_CR76","doi-asserted-by":"crossref","first-page":"2414805","DOI":"10.1080\/19490976.2024.2414805","volume":"16","author":"X Song","year":"2024","unstructured":"Song X, Dou X, Chang J, Zeng X, Xu Q, Xu C (2024) The role and mechanism of gut-lung axis mediated bidirectional communication in the occurrence and development of chronic obstructive pulmonary disease. Gut Microbes 16:2414805","journal-title":"Gut Microbes"},{"key":"173_CR77","doi-asserted-by":"crossref","DOI":"10.1038\/ncomms3462","volume":"4","author":"G Srinivas","year":"2013","unstructured":"Srinivas G, M\u00f6ller S, Wang J, K\u00fcnzel S, Zillikens D, Baines JF, Ibrahim SM (2013) Genome-wide mapping of gene-microbiota interactions in susceptibility to autoimmune skin blistering. Nat Commun 4:2462","journal-title":"Nat Commun"},{"key":"173_CR78","doi-asserted-by":"crossref","first-page":"2344","DOI":"10.1038\/s41564-024-01739-1","volume":"9","author":"Q Su","year":"2024","unstructured":"Su Q, Wong OWH, Lu W, Wan Y, Zhang L, Xu W, Li MKT, Liu C, Cheung CP, Ching JYL et al (2024) Multikingdom and functional gut microbiota markers for autism spectrum disorder. Nat Microbiol 9:2344\u20132355","journal-title":"Nat Microbiol"},{"key":"173_CR79","doi-asserted-by":"publisher","unstructured":"Sudlow C, Gallacher J, Allen N, Beral V, Burton P, Danesh J, Downey P, Elliott P, Green J, Landray M et al (2015) UK biobank. https:\/\/doi.org\/10.1371\/journal.pmed.1001779 (http:\/\/www.ukbiobank.ac.uk\/) [DATASET]","DOI":"10.1371\/journal.pmed.1001779"},{"key":"173_CR80","doi-asserted-by":"crossref","first-page":"e1001779","DOI":"10.1371\/journal.pmed.1001779","volume":"12","author":"C Sudlow","year":"2015","unstructured":"Sudlow C, Gallacher J, Allen N, Beral V, Burton P, Danesh J, Downey P, Elliott P, Green J, Landray M et al (2015) UK biobank: an open access resource for identifying the causes of a wide range of complex diseases of middle and old age. PLoS Med 12:e1001779","journal-title":"PLoS Med"},{"key":"173_CR81","doi-asserted-by":"crossref","DOI":"10.1038\/ncomms8624","volume":"6","author":"LE Tailford","year":"2015","unstructured":"Tailford LE, Owen CD, Walshaw J, Crost EH, Hardy-Goddard J, Le Gall G, de Vos WM, Taylor GL, Juge N (2015) Discovery of intramolecular trans-sialidases in human gut microbiota suggests novel mechanisms of mucosal adaptation. Nat Commun 6:7624","journal-title":"Nat Commun"},{"key":"173_CR82","doi-asserted-by":"crossref","first-page":"476","DOI":"10.1038\/s41582-022-00681-2","volume":"18","author":"AH Tan","year":"2022","unstructured":"Tan AH, Lim SY, Lang AE (2022) The microbiome-gut-brain axis in Parkinson disease - from basic research to the clinic. Nat Rev Neurol 18:476\u2013495","journal-title":"Nat Rev Neurol"},{"key":"173_CR83","doi-asserted-by":"crossref","first-page":"242","DOI":"10.1038\/nature11552","volume":"489","author":"V Tremaroli","year":"2012","unstructured":"Tremaroli V, B\u00e4ckhed F (2012) Functional interactions between the gut microbiota and host metabolism. Nature 489:242\u2013249","journal-title":"Nature"},{"key":"173_CR84","doi-asserted-by":"crossref","first-page":"2574","DOI":"10.1038\/s41396-021-00937-7","volume":"15","author":"N Tsukuda","year":"2021","unstructured":"Tsukuda N, Yahagi K, Hara T, Watanabe Y, Matsumoto H, Mori H, Higashi K, Tsuji H, Matsumoto S, Kurokawa K et al (2021) Key bacterial taxa and metabolic pathways affecting gut short-chain fatty acid profiles in early life. ISME J 15:2574\u20132590","journal-title":"ISME J"},{"key":"173_CR85","doi-asserted-by":"crossref","first-page":"1413","DOI":"10.1038\/ng.3693","volume":"48","author":"W Turpin","year":"2016","unstructured":"Turpin W, Espin-Garcia O, Xu W, Silverberg MS, Kevans D, Smith MI, Guttman DS, Griffiths A, Panaccione R, Otley A et al (2016) Association of host genome with intestinal microbial composition in a large healthy cohort. Nat Genet 48:1413\u20131417","journal-title":"Nat Genet"},{"key":"173_CR86","volume":"15","author":"F Wang","year":"2024","unstructured":"Wang F, Liao Q, Qin Z, Li J, Wei Q, Li M, Deng H, Xiong W, Tan M, Zhou M (2024) Autophagy: a critical mechanism of N-methyladenosine modification involved in tumor progression and therapy resistance. Cell Death Dis 15:783","journal-title":"Cell Death Dis"},{"key":"173_CR87","doi-asserted-by":"crossref","first-page":"1396","DOI":"10.1038\/ng.3695","volume":"48","author":"J Wang","year":"2016","unstructured":"Wang J, Thingholm LB, Skiecevi\u010dien\u0117 J, Rausch P, Kummen M, Hov JR, Degenhardt F, Heinsen F-A, R\u00fchlemann MC, Szymczak S et al (2016) Genome-wide association analysis identifies variation in vitamin D receptor and other host factors influencing the gut microbiota. Nat Genet 48:1396\u20131406","journal-title":"Nat Genet"},{"key":"173_CR88","volume":"10","author":"S-L Wang","year":"2019","unstructured":"Wang S-L, Shao B-Z, Zhao S-B, Chang X, Wang P, Miao C-Y, Li Z-S, Bai Y (2019a) Intestinal autophagy links psychosocial stress with gut microbiota to promote inflammatory bowel disease. Cell Death Dis 10:391","journal-title":"Cell Death Dis"},{"key":"173_CR89","doi-asserted-by":"crossref","first-page":"787","DOI":"10.1038\/s41422-019-0216-x","volume":"29","author":"X Wang","year":"2019","unstructured":"Wang X, Sun G, Feng T, Zhang J, Huang X, Wang T, Xie Z, Chu X, Yang J, Wang H et al (2019b) Sodium oligomannate therapeutically remodels gut microbiota and suppresses gut bacterial amino acids-shaped neuroinflammation to inhibit Alzheimer\u2019s disease progression. Cell Res 29:787\u2013803","journal-title":"Cell Res"},{"key":"173_CR90","doi-asserted-by":"crossref","first-page":"1339","DOI":"10.1038\/s41588-019-0481-0","volume":"51","author":"K Watanabe","year":"2019","unstructured":"Watanabe K, Stringer S, Frei O, Umi\u0107evi\u0107 Mirkov M, de Leeuw C, Polderman TJC, van der Sluis S, Andreassen OA, Neale BM, Posthuma D (2019) A global overview of pleiotropy and genetic architecture in complex traits. Nat Genet 51:1339\u20131348","journal-title":"Nat Genet"},{"key":"173_CR91","doi-asserted-by":"publisher","unstructured":"Watanabe K, Stringer S, Frei O, Umi\u0107evi\u0107 Mirkov M, de Leeuw C, Polderman TJC, van der Sluis S, Andreassen OA, Neale BM, Posthuma D (2019) GWAS ATLAS. https:\/\/doi.org\/10.1038\/s41588-019-0481-0 (https:\/\/atlas.ctglab.nl) [DATASET]","DOI":"10.1038\/s41588-019-0481-0"},{"key":"173_CR92","doi-asserted-by":"crossref","first-page":"772","DOI":"10.1053\/j.gastro.2017.05.022","volume":"153","author":"AS Wellman","year":"2017","unstructured":"Wellman AS, Metukuri MR, Kazgan N, Xu X, Xu Q, Ren NSX, Czopik A, Shanahan MT, Kang A, Chen W et al (2017) Intestinal epithelial sirtuin 1 regulates intestinal inflammation during aging in mice by altering the intestinal microbiota. Gastroenterology 153:772\u2013786","journal-title":"Gastroenterology"},{"key":"173_CR93","doi-asserted-by":"crossref","first-page":"2022407","DOI":"10.1080\/19490976.2021.2022407","volume":"14","author":"V Woo","year":"2022","unstructured":"Woo V, Alenghat T (2022) Epigenetic regulation by gut microbiota. Gut Microbes 14:2022407","journal-title":"Gut Microbes"},{"key":"173_CR94","doi-asserted-by":"crossref","first-page":"1714","DOI":"10.1016\/j.ccell.2025.07.002","volume":"43","author":"Z-Y Wu","year":"2025","unstructured":"Wu Z-Y, Wu Q-W, Han Y, Xiang S-J, Wang Y-N, Wu W-W, Chen Y-X, Feng Z-Q, Wang Y-Y, Xu Z-G et al (2025) Alistipes finegoldii augments the efficacy of immunotherapy against solid tumors. Cancer Cell 43:1714\u20131730.e12","journal-title":"Cancer Cell"},{"key":"173_CR95","doi-asserted-by":"crossref","first-page":"959","DOI":"10.1016\/j.chom.2021.03.016","volume":"29","author":"C Xing","year":"2021","unstructured":"Xing C, Wang M, Ajibade AA, Tan P, Fu C, Chen L, Zhu M, Hao Z-Z, Chu J, Yu X et al (2021) Microbiota regulate innate immune signaling and protective immunity against cancer. Cell Host Microbe 29:959\u2013974.e7","journal-title":"Cell Host Microbe"},{"key":"173_CR96","doi-asserted-by":"crossref","first-page":"1987783","DOI":"10.1080\/19490976.2021.1987783","volume":"13","author":"J Yang","year":"2021","unstructured":"Yang J, Li Y, Wen Z, Liu W, Meng L, Huang H (2021) Oscillospira\u2014a candidate for the next-generation probiotics. Gut Microbes 13:1987783","journal-title":"Gut Microbes"},{"key":"173_CR97","volume":"14","author":"Z Yang","year":"2022","unstructured":"Yang Z, Chen Z, Lin X, Yao S, Xian M, Ning X, Fu W, Jiang M, Li N, Xiao X et al (2022) Rural environment reduces allergic inflammation by modulating the gut microbiota. Gut Microbes 14:2125733","journal-title":"Gut Microbes"},{"key":"173_CR98","doi-asserted-by":"crossref","first-page":"284","DOI":"10.1089\/omi.2011.0118","volume":"16","author":"G Yu","year":"2012","unstructured":"Yu G, Wang L-G, Han Y, He Q-Y (2012) clusterProfiler: an R package for comparing biological themes among gene clusters. OMICS 16:284\u2013287","journal-title":"OMICS"},{"key":"173_CR99","doi-asserted-by":"crossref","first-page":"608","DOI":"10.1093\/bioinformatics\/btu684","volume":"31","author":"G Yu","year":"2015","unstructured":"Yu G, Wang L-G, Yan G-R, He Q-Y (2015) DOSE: an R\/Bioconductor package for disease ontology semantic and enrichment analysis. Bioinformatics 31:608\u2013609","journal-title":"Bioinformatics"},{"key":"173_CR100","doi-asserted-by":"crossref","first-page":"492","DOI":"10.1038\/s41422-020-0332-7","volume":"30","author":"D Zheng","year":"2020","unstructured":"Zheng D, Liwinski T, Elinav E (2020) Interaction between microbiota and immunity in health and disease. Cell Res 30:492\u2013506","journal-title":"Cell Res"},{"key":"173_CR101","doi-asserted-by":"crossref","first-page":"105272","DOI":"10.1016\/j.micpath.2021.105272","volume":"161","author":"M-S Zhou","year":"2021","unstructured":"Zhou M-S, Zhang B, Gao Z-L, Zheng R-P, Marcellin DFHM, Saro A, Pan J, Chu L, Wang T-S, Huang J-F (2021) Altered diversity and composition of gut microbiota in patients with allergic rhinitis. Micro Pathog 161:105272","journal-title":"Micro Pathog"},{"key":"173_CR102","doi-asserted-by":"crossref","first-page":"481","DOI":"10.1038\/ng.3538","volume":"48","author":"Z Zhu","year":"2016","unstructured":"Zhu Z, Zhang F, Hu H, Bakshi A, Robinson MR, Powell JE, Montgomery GW, Goddard ME, Wray NR, Visscher PM et al (2016) Integration of summary data from GWAS and eQTL studies predicts complex trait gene targets. Nat Genet 48:481\u2013487","journal-title":"Nat Genet"}],"container-title":["Molecular Systems Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1038\/s44320-025-00173-7.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1038\/s44320-025-00173-7","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1038\/s44320-025-00173-7.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,5,17]],"date-time":"2026-05-17T23:42:01Z","timestamp":1779061321000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1038\/s44320-025-00173-7"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,12,5]]},"references-count":102,"journal-issue":{"issue":"3","published-online":{"date-parts":[[2026,3,2]]}},"alternative-id":["173"],"URL":"https:\/\/doi.org\/10.1038\/s44320-025-00173-7","relation":{},"ISSN":["1744-4292"],"issn-type":[{"value":"1744-4292","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,12,5]]},"assertion":[{"value":"20 June 2025","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"17 November 2025","order":2,"name":"revised","label":"Revised","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"20 November 2025","order":3,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"5 December 2025","order":4,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"The authors declare no competing interests.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Disclosure and competing interests statement"}}]}}