{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,11,3]],"date-time":"2026-11-03T03:00:08Z","timestamp":1793674808366,"version":"4.5.1"},"reference-count":58,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2024,8,30]],"date-time":"2024-08-30T00:00:00Z","timestamp":1724976000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"},{"start":{"date-parts":[[2024,8,30]],"date-time":"2024-08-30T00:00:00Z","timestamp":1724976000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Microbiome"],"DOI":"10.1186\/s40168-024-01895-w","type":"journal-article","created":{"date-parts":[[2024,9,2]],"date-time":"2024-09-02T10:02:21Z","timestamp":1725271341000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":11,"title":["CHIKV infection drives shifts in the gastrointestinal microbiome and metabolites in rhesus monkeys"],"prefix":"10.1186","volume":"12","author":[{"given":"Hongyu","family":"Chen","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jiandong","family":"Shi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Cong","family":"Tang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jingwen","family":"Xu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bai","family":"Li","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Junbin","family":"Wang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yanan","family":"Zhou","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yun","family":"Yang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hao","family":"Yang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qing","family":"Huang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wenhai","family":"Yu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Haixuan","family":"Wang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Daoju","family":"Wu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yunzhang","family":"Hu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hongning","family":"Zhou","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qingming","family":"Sun","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shuaiyao","family":"Lu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2024,8,30]]},"reference":[{"key":"1895_CR1","doi-asserted-by":"publisher","first-page":"491","DOI":"10.1038\/nrmicro2368","volume":"8","author":"O Schwartz","year":"2010","unstructured":"Schwartz O, Albert ML. Biology and pathogenesis of chikungunya virus. Nat Rev Microbiol. 2010;8:491\u2013500.","journal-title":"Nat Rev Microbiol"},{"key":"1895_CR2","doi-asserted-by":"publisher","first-page":"674","DOI":"10.1089\/vbz.2015.1795","volume":"15","author":"YJ Huang","year":"2015","unstructured":"Huang YJ, Hsu WW, Higgs S, Vanlandingham DL. Temperature Tolerance and Inactivation of Chikungunya Virus. Vector Borne Zoonotic Dis. 2015;15:674\u20137.","journal-title":"Vector Borne Zoonotic Dis"},{"key":"1895_CR3","doi-asserted-by":"publisher","first-page":"281","DOI":"10.4269\/ajtmh.1999.60.281","volume":"60","author":"M Diallo","year":"1999","unstructured":"Diallo M, Thonnon J, Lamizana-M T, Fontenille D. Vectors of Chikungunya virus in Senegal: current data and transmission cycles. Am J Trop Med Hyg. 1999;60:281\u20136.","journal-title":"Am J Trop Med Hyg"},{"key":"1895_CR4","doi-asserted-by":"publisher","first-page":"6497","DOI":"10.1128\/JVI.01603-09","volume":"84","author":"M Volk Sara","year":"2010","unstructured":"Volk Sara M, Chen R, Tsetsarkin Konstantin A, Adams AP, Garcia Tzintzuni I, SallAmadou A, Nasar F, Schuh Amy J, Holmes Edward C, Higgs S, et al. Genome-scale phylogenetic analyses of chikungunya virus reveal independent emergences of recent epidemics and various evolutionary rates. J Virol. 2010;84:6497\u2013504.","journal-title":"J Virol"},{"key":"1895_CR5","doi-asserted-by":"publisher","first-page":"e00504","DOI":"10.1128\/JVI.00504-19","volume":"93","author":"Y-N Zhang","year":"2019","unstructured":"Zhang Y-N, Deng C-L, Li J-Q, Li N, Zhang Q-Y, Ye H-Q, Yuan Z-M, Zhang B. Infectious Chikungunya Virus (CHIKV) with a complete capsid deletion: a new approach for a CHIKV vaccine. J Virol. 2019;93:e00504-19.","journal-title":"J Virol"},{"key":"1895_CR6","doi-asserted-by":"publisher","first-page":"12321","DOI":"10.1038\/s41598-021-91830-y","volume":"11","author":"H-C Lin","year":"2021","unstructured":"Lin H-C, Chiao D-J, Lin C-C, Kuo S-C. Facile method for delivering chikungunya viral replicons into mosquitoes and mammalian cells. Sci Rep. 2021;11:12321.","journal-title":"Sci Rep"},{"key":"1895_CR7","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1128\/JVI.00504-19","volume":"93","author":"Y-N Zhang","year":"2019","unstructured":"Zhang Y-N, Deng C-L, Li J-Q, Li N, Zhang Q-Y, Ye H-Q, Yuan Z-M, Zhang B. Infectious Chikungunya Virus (CHIKV) with a complete capsid deletion: a new approach for a CHIKV vaccine. J Virol. 2019;93:1\u201316.","journal-title":"J Virol"},{"key":"1895_CR8","doi-asserted-by":"publisher","first-page":"1327","DOI":"10.3201\/eid1408.080201","volume":"14","author":"P Renault","year":"2008","unstructured":"Renault P, Josseran L, Pierre V. Chikungunya-related fatality rates, mauritius, india, and reunion island. Emerg Infect Dis. 2008;14:1327.","journal-title":"Emerg Infect Dis"},{"key":"1895_CR9","doi-asserted-by":"publisher","first-page":"1679","DOI":"10.1007\/s10067-019-04919-1","volume":"39","author":"H Watson","year":"2020","unstructured":"Watson H, Tritsch SR, Encinales L, Cadena A, Cure C, Ramirez AP, Mendoza AR, Chang AY. Stiffness, pain, and joint counts in chronic chikungunya disease: relevance to disability and quality of life. Clin Rheumatol. 2020;39:1679\u201386.","journal-title":"Clin Rheumatol"},{"key":"1895_CR10","doi-asserted-by":"publisher","first-page":"737","DOI":"10.1172\/JCI84417","volume":"127","author":"LA Silva","year":"2017","unstructured":"Silva LA, Dermody TS. Chikungunya virus: epidemiology, replication, disease mechanisms, and prospective intervention strategies. J Clin Invest. 2017;127:737\u201349.","journal-title":"J Clin Invest"},{"key":"1895_CR11","doi-asserted-by":"publisher","first-page":"14","DOI":"10.1016\/j.immuni.2023.12.009","volume":"57","author":"M Arifuzzaman","year":"2024","unstructured":"Arifuzzaman M, Collins N, Guo C-J, Artis D. Nutritional regulation of microbiota-derived metabolites: Implications for immunity and inflammation. Immunity. 2024;57:14\u201327.","journal-title":"Immunity"},{"key":"1895_CR12","doi-asserted-by":"publisher","first-page":"1647","DOI":"10.1053\/j.gastro.2020.12.001","volume":"160","author":"L Jiao","year":"2021","unstructured":"Jiao L, Li H, Xu J, Yang M, Ma C, Li J, Zhao S, Wang H, Yang Y, Yu W, et al. The gastrointestinal tract is an alternative route for SARS-CoV-2 infection in a nonhuman primate model. Gastroenterology. 2021;160:1647\u201361.","journal-title":"Gastroenterology"},{"key":"1895_CR13","doi-asserted-by":"publisher","first-page":"e0168921","DOI":"10.1128\/spectrum.01689-21","volume":"10","author":"T Mizutani","year":"2022","unstructured":"Mizutani T, Ishizaka A, Koga M, Ikeuchi K, Saito M, Adachi E, Yamayoshi S, Iwatsuki-Horimoto K, Yasuhara A, Kiyono H, et al. Correlation analysis between gut microbiota alterations and the cytokine response in patients with coronavirus disease during hospitalization. Microbiol Spectr. 2022;10:e0168921.","journal-title":"Microbiol Spectr"},{"key":"1895_CR14","doi-asserted-by":"publisher","first-page":"321","DOI":"10.1038\/nri3430","volume":"13","author":"N Kamada","year":"2013","unstructured":"Kamada N, Seo S-U, Chen GY, N\u00fa\u00f1ez G. Role of the gut microbiota in immunity and inflammatory disease. Nat Rev Immunol. 2013;13:321\u201335.","journal-title":"Nat Rev Immunol"},{"key":"1895_CR15","doi-asserted-by":"publisher","first-page":"421","DOI":"10.1016\/j.aninu.2020.05.007","volume":"6","author":"J Xue","year":"2020","unstructured":"Xue J, Ajuwon KM, Fang R. Mechanistic insight into the gut microbiome and its interaction with host immunity and inflammation. Anim Nutr. 2020;6:421\u20138.","journal-title":"Anim Nutr"},{"key":"1895_CR16","doi-asserted-by":"publisher","first-page":"415","DOI":"10.1038\/s41584-022-00793-5","volume":"18","author":"N Komatsu","year":"2022","unstructured":"Komatsu N, Takayanagi H. Mechanisms of joint destruction in rheumatoid arthritis \u2014 immune cell\u2013fibroblast\u2013bone interactions. Nat Rev Rheumatol. 2022;18:415\u201329.","journal-title":"Nat Rev Rheumatol"},{"key":"1895_CR17","doi-asserted-by":"publisher","first-page":"3553","DOI":"10.1002\/art.34631","volume":"64","author":"HI Nakaya","year":"2012","unstructured":"Nakaya HI, Gardner J, Poo YS, Major L, Pulendran B, Suhrbier A. Gene profiling of Chikungunya virus arthritis in a mouse model reveals significant overlap with rheumatoid arthritis. Arthritis Rheum. 2012;64:3553\u201363.","journal-title":"Arthritis Rheum"},{"key":"1895_CR18","doi-asserted-by":"publisher","first-page":"2661","DOI":"10.1093\/rheumatology\/keaa232","volume":"59","author":"LE Dedmon","year":"2020","unstructured":"Dedmon LE. The genetics of rheumatoid arthritis. Rheumatology. 2020;59:2661\u201370.","journal-title":"Rheumatology"},{"key":"1895_CR19","doi-asserted-by":"publisher","first-page":"2392","DOI":"10.3390\/nu11102392","volume":"11","author":"J H\u00e4ger","year":"2019","unstructured":"H\u00e4ger J, Bang H, Hagen M, Frech M, Tr\u00e4ger P, Sokolova M, Steffen U, Tascilar K, Sarter K, Schett G, et al. The role of dietary fiber in rheumatoid arthritis patients: a feasibility study. Nutrients. 2019;11:2392.","journal-title":"Nutrients"},{"key":"1895_CR20","doi-asserted-by":"publisher","first-page":"224","DOI":"10.1038\/s41584-021-00585-3","volume":"17","author":"MM Zaiss","year":"2021","unstructured":"Zaiss MM, Joyce Wu H-J, Mauro D, Schett G, Ciccia F. The gut\u2013joint axis in rheumatoid arthritis. Nat Rev Rheumatol. 2021;17:224\u201337.","journal-title":"Nat Rev Rheumatol"},{"key":"1895_CR21","doi-asserted-by":"publisher","first-page":"1041","DOI":"10.1136\/gutjnl-2021-325209","volume":"71","author":"Z Yan","year":"2022","unstructured":"Yan Z, Mingyue C, Liang Z, Luxu Y, Chaofang Z, Yuguo Z, Xue Z, Lei Z, Kang N, Jinxiang H. Hidden link in gut\u2013joint axis: gut microbes promote rheumatoid arthritis at early stage by enhancing ascorbate degradation. Gut. 2022;71:1041.","journal-title":"Gut"},{"key":"1895_CR22","doi-asserted-by":"publisher","first-page":"1015","DOI":"10.1038\/s41419-021-04322-2","volume":"12","author":"X Wang","year":"2021","unstructured":"Wang X, Ning Y, Li C, Gong Y, Huang R, Hu M, Poulet B, Xu K, Zhao G, Zhou R, et al. Alterations in the gut microbiota and metabolite profiles of patients with Kashin-Beck disease, an endemic osteoarthritis in China. Cell Death Dis. 2021;12:1015.","journal-title":"Cell Death Dis"},{"key":"1895_CR23","doi-asserted-by":"publisher","first-page":"e2343","DOI":"10.1371\/journal.pntd.0002343","volume":"7","author":"I Messaoudi","year":"2013","unstructured":"Messaoudi I, Vomaske J, Totonchy T, Kreklywich CN, Haberthur K, Springgay L, Brien JD, Diamond MS, DeFilippis VR, Streblow DN. Chikungunya virus infection results in higher and persistent viral replication in aged rhesus macaques due to defects in anti-viral immunity. PLoS Negl Trop Dis. 2013;7:e2343.","journal-title":"PLoS Negl Trop Dis"},{"key":"1895_CR24","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s12929-021-00778-8","volume":"28","author":"S Khongwichit","year":"2021","unstructured":"Khongwichit S, Chansaenroj J, Chirathaworn C, Poovorawan Y. Chikungunya virus infection: molecular biology, clinical characteristics, and epidemiology in Asian countries. J Biomed Sci. 2021;28:1\u201317.","journal-title":"J Biomed Sci"},{"key":"1895_CR25","doi-asserted-by":"publisher","first-page":"662","DOI":"10.3390\/pathogens4030662","volume":"4","author":"R Broeckel","year":"2015","unstructured":"Broeckel R, Haese N, Messaoudi I, Streblow DN. Nonhuman primate models of Chikungunya Virus Infection and Disease (CHIKV NHP Model). Pathogens. 2015;4:662\u201381.","journal-title":"Pathogens"},{"key":"1895_CR26","doi-asserted-by":"publisher","first-page":"570","DOI":"10.1038\/s41586-018-0121-3","volume":"557","author":"R Zhang","year":"2018","unstructured":"Zhang R, Kim AS, Fox JM, Nair S, Basore K, Klimstra WB, Rimkunas R, Fong RH, Lin H, Poddar S, et al. Mxra8 is a receptor for multiple arthritogenic alphaviruses. Nature. 2018;557:570\u20134.","journal-title":"Nature"},{"key":"1895_CR27","doi-asserted-by":"publisher","first-page":"259","DOI":"10.1038\/s41586-019-1578-4","volume":"574","author":"L Meertens","year":"2019","unstructured":"Meertens L, Hafirassou ML, Couderc T, Bonnet-Madin L, Kril V, K\u00fcmmerer BM, Labeau A, Brugier A, Simon-Loriere E, Burlaud-Gaillard J, et al. FHL1 is a major host factor for chikungunya virus infection. Nature. 2019;574:259\u201363.","journal-title":"Nature"},{"key":"1895_CR28","doi-asserted-by":"publisher","first-page":"581","DOI":"10.1038\/s41586-023-05989-7","volume":"617","author":"D Shalon","year":"2023","unstructured":"Shalon D, Culver RN, Grembi JA, Folz J, Treit PV, Shi H, Rosenberger FA, Dethlefsen L, Meng X, Yaffe E, et al. Profiling the human intestinal environment under physiological conditions. Nature. 2023;617:581\u201391.","journal-title":"Nature"},{"key":"1895_CR29","doi-asserted-by":"publisher","first-page":"2441","DOI":"10.3389\/fimmu.2019.02441","volume":"10","author":"S Negi","year":"2019","unstructured":"Negi S, Das DK, Pahari S, Nadeem S, Agrewala JN. Potential role of gut microbiota in induction and regulation of innate immune memory. Front Immunol. 2019;10:2441.","journal-title":"Front Immunol"},{"key":"1895_CR30","doi-asserted-by":"publisher","first-page":"113","DOI":"10.1038\/s41385-020-0296-4","volume":"14","author":"A Iljazovic","year":"2021","unstructured":"Iljazovic A, Roy U, G\u00e1lvez EJC, Lesker TR, Zhao B, Gronow A, Amend L, Will SE, Hofmann JD, Pils MC, et al. Perturbation of the gut microbiome by Prevotella spp. enhances host susceptibility to mucosal inflammation. Mucosal Immunol. 2021;14:113\u201324.","journal-title":"Mucosal Immunol"},{"key":"1895_CR31","doi-asserted-by":"publisher","first-page":"363","DOI":"10.1111\/imm.12760","volume":"151","author":"JM Larsen","year":"2017","unstructured":"Larsen JM. The immune response to Prevotella bacteria in chronic inflammatory disease. Immunology. 2017;151:363\u201374.","journal-title":"Immunology"},{"key":"1895_CR32","doi-asserted-by":"publisher","first-page":"1140498","DOI":"10.3389\/fmicb.2023.1140498","volume":"14","author":"X Zhong","year":"2023","unstructured":"Zhong X, Zhao Y, Huang L, Liu J, Wang K, Gao X, Zhao X, Wang X. Remodeling of the gut microbiome by Lactobacillus johnsonii alleviates the development of acute myocardial infarction. Front Microbiol. 2023;14:1140498.","journal-title":"Front Microbiol"},{"key":"1895_CR33","doi-asserted-by":"publisher","first-page":"168","DOI":"10.1038\/s41586-022-04985-7","volume":"608","author":"M Bae","year":"2022","unstructured":"Bae M, Cassilly CD, Liu X, Park S-M, Tusi BK, Chen X, Kwon J, Filip\u010d\u00edk P, Bolze AS, Liu Z, et al. Akkermansia muciniphila phospholipid induces homeostatic immune responses. Nature. 2022;608:168\u201373.","journal-title":"Nature"},{"key":"1895_CR34","doi-asserted-by":"publisher","first-page":"3556","DOI":"10.1038\/s41598-020-60564-8","volume":"10","author":"P Xu","year":"2020","unstructured":"Xu P, Shi Y, Liu P, Yang Y, Zhou C, Li G, Luo J, Zhang C, Cao H, Hu G, et al. 16S rRNA gene sequencing reveals an altered composition of the gut microbiota in chickens infected with a nephropathogenic infectious bronchitis virus. Sci Rep. 2020;10:3556.","journal-title":"Sci Rep"},{"key":"1895_CR35","doi-asserted-by":"publisher","first-page":"2946","DOI":"10.1172\/JCI93450","volume":"127","author":"A Pianta","year":"2017","unstructured":"Pianta A, Arvikar SL, Strle K, Drouin EE, Wang Q, Costello CE, Steere AC. Two rheumatoid arthritis\u2013specific autoantigens correlate microbial immunity with autoimmune responses in joints. J Clin Invest. 2017;127:2946\u201356.","journal-title":"J Clin Invest"},{"key":"1895_CR36","doi-asserted-by":"publisher","first-page":"590","DOI":"10.1136\/annrheumdis-2018-214514","volume":"78","author":"D Alpizar-Rodriguez","year":"2019","unstructured":"Alpizar-Rodriguez D, Lesker T, Gronow A, Gilbert B, Raemy E, Lamacchia C, Gabay C, Finckh A, Strowig T. Prevotella copri in individuals at risk for rheumatoid arthritis. Ann Rheum Dis. 2019;78:590\u20133.","journal-title":"Ann Rheum Dis"},{"key":"1895_CR37","doi-asserted-by":"publisher","first-page":"142","DOI":"10.1186\/s13059-017-1271-6","volume":"18","author":"C Wen","year":"2017","unstructured":"Wen C, Zheng Z, Shao T, Liu L, Xie Z, Le Chatelier E, He Z, Zhong W, Fan Y, Zhang L, et al. Quantitative metagenomics reveals unique gut microbiome biomarkers in ankylosing spondylitis. Genome Biol. 2017;18:142.","journal-title":"Genome Biol"},{"key":"1895_CR38","doi-asserted-by":"publisher","first-page":"e01202","DOI":"10.7554\/eLife.01202","volume":"2","author":"JU Scher","year":"2013","unstructured":"Scher JU, Sczesnak A, Longman R, Segata N, Ubeda C, Bielski CM, Rostron T, Cerundolo V, Pamer EG, Abramson SB, et al. Expansion of intestinal Prevotella copri correlates with enhanced susceptibility to arthritis. eLife. 2013;2:e01202.","journal-title":"eLife"},{"key":"1895_CR39","doi-asserted-by":"publisher","first-page":"479","DOI":"10.1038\/nri2800","volume":"10","author":"DJ Cua","year":"2010","unstructured":"Cua DJ, Tato CM. Innate IL-17-producing cells: the sentinels of the immune system. Nat Rev Immunol. 2010;10:479\u201389.","journal-title":"Nat Rev Immunol"},{"key":"1895_CR40","doi-asserted-by":"publisher","first-page":"e13416","DOI":"10.1371\/journal.pone.0013416","volume":"5","author":"M-L Toh","year":"2010","unstructured":"Toh M-L, Gonzales G, Koenders MI, Tournadre A, Boyle D, Lubberts E, Zhou Y, Firestein GS, van den Berg WB, Miossec P. Role of interleukin 17 in arthritis chronicity through survival of synoviocytes via regulation of synoviolin expression. PLoS One. 2010;5:e13416.","journal-title":"PLoS ONE"},{"key":"1895_CR41","doi-asserted-by":"publisher","first-page":"149","DOI":"10.1093\/infdis\/jiq042","volume":"203","author":"A Chow","year":"2011","unstructured":"Chow A, Her Z, Ong EKS, Chen J-M, Dimatatac F, Kwek DJC, Barkham T, Yang H, R\u00e9nia L, Leo Y-S, et al. Persistent arthralgia induced by chikungunya virus infection is associated with interleukin-6 and granulocyte macrophage colony-stimulating factor. J Infect Dis. 2011;203:149\u201357.","journal-title":"J Infect Dis"},{"key":"1895_CR42","doi-asserted-by":"publisher","first-page":"e0028922","DOI":"10.1128\/mbio.00289-22","volume":"13","author":"X Liu","year":"2022","unstructured":"Liu X, Poo Y, Alves J, Almeida R, Mostafavi H, Tang P, Bucala R, Teixeira M, Taylor A, Zaid A, et al. Interleukin-17 contributes to chikungunya virus-induced disease. mBio. 2022;13:e0028922.","journal-title":"mBio"},{"key":"1895_CR43","doi-asserted-by":"publisher","first-page":"588382","DOI":"10.3389\/fimmu.2020.588382","volume":"11","author":"B Neupane","year":"2020","unstructured":"Neupane B, Acharya D, Nazneen F, Gonzalez-Fernandez G, Flynt AS, Bai F. Interleukin-17A facilitates chikungunya virus infection by inhibiting IFN-\u03b12 expression. Front Immunol. 2020;11:588382.","journal-title":"Front Immunol"},{"key":"1895_CR44","doi-asserted-by":"publisher","first-page":"974","DOI":"10.1126\/science.1206095","volume":"332","author":"J Round","year":"2011","unstructured":"Round J, Lee S, Li J, Tran G, Jabri B, Chatila T, Mazmanian S. The toll-like receptor 2 pathway establishes colonization by a commensal of the human microbiota. Science. 2011;332:974\u20137.","journal-title":"Science"},{"key":"1895_CR45","doi-asserted-by":"publisher","first-page":"229","DOI":"10.1093\/ecco-jcc\/jjw142","volume":"11","author":"S Devriese","year":"2017","unstructured":"Devriese S, Eeckhaut V, Geirnaert A, Van den Bossche L, Hindryckx P, van de Wiele T, Van Immerseel F, Ducatelle R, De Vos M, Laukens D. Reduced Mucosa-associated butyricicoccus activity in patients with ulcerative colitis correlates with aberrant claudin-1 expression. J Crohn\u2019s Colitis. 2017;11:229\u201336.","journal-title":"J Crohn\u2019s Colitis"},{"key":"1895_CR46","doi-asserted-by":"publisher","first-page":"523","DOI":"10.1016\/j.tim.2016.02.015","volume":"24","author":"T Konikoff","year":"2016","unstructured":"Konikoff T, Gophna U. Oscillospira: a central, enigmatic component of the human gut microbiota. Trendds Microbiol. 2016;24:523\u20134.","journal-title":"Trendds Microbiol"},{"key":"1895_CR47","doi-asserted-by":"publisher","first-page":"3688","DOI":"10.1128\/aem.60.10.3688-3696.1994","volume":"60","author":"AA Odenyo","year":"1994","unstructured":"Odenyo AA, Mackie RI, Stahl DA, White BA. The use of 16S rRNA-targeted oligonucleotide probes to study competition between ruminal fibrolytic bacteria: development of probes for Ruminococcus species and evidence for bacteriocin production. Appl Environ Microbiol. 1994;60:3688\u201396.","journal-title":"Appl Environ Microbiol"},{"key":"1895_CR48","doi-asserted-by":"publisher","first-page":"1368","DOI":"10.1093\/annonc\/mdx108","volume":"28","author":"N Chaput","year":"2017","unstructured":"Chaput N, Lepage P, Coutzac C, Soularue E, Le Roux K, Monot C, Boselli L, Routier E, Cassard L, Collins M, et al. Baseline gut microbiota predicts clinical response and colitis in metastatic melanoma patients treated with ipilimumab. Ann Oncol. 2017;28:1368\u201379.","journal-title":"Ann Oncol"},{"key":"1895_CR49","doi-asserted-by":"publisher","first-page":"1435","DOI":"10.1093\/cvr\/cvz091","volume":"115","author":"HA Jama","year":"2019","unstructured":"Jama HA, Beale A, Shihata WA, Marques FZ. The effect of diet on hypertensive pathology: is there a link via gut microbiota-driven immunometabolism? Cardiovasc Res. 2019;115:1435\u201347.","journal-title":"Cardiovasc Res"},{"key":"1895_CR50","doi-asserted-by":"publisher","first-page":"685","DOI":"10.1016\/j.cell.2020.06.034","volume":"182","author":"M Bouhaddou","year":"2020","unstructured":"Bouhaddou M, Memon D, Meyer B, White KM, Rezelj VV, Correa Marrero M, Polacco BJ, Melnyk JE, Ulferts S, Kaake RM, et al. The global phosphorylation landscape of SARS-CoV-2 infection. Cell. 2020;182:685-712.e619.","journal-title":"Cell"},{"key":"1895_CR51","doi-asserted-by":"publisher","first-page":"36","DOI":"10.1016\/j.ejphar.2006.07.014","volume":"546","author":"M Ikeda","year":"2006","unstructured":"Ikeda M, Gunji Y, Sonoda H, Oshikawa S, Shimono M, Horie A, Ito K, Yamasaki S. Inhibitory effect of tyrphostin 47 on Shiga toxin-induced cell death. Eur J Pharmacol. 2006;546:36\u20139.","journal-title":"Eur J Pharmacol"},{"key":"1895_CR52","doi-asserted-by":"publisher","first-page":"335","DOI":"10.1038\/s41575-020-00404-2","volume":"18","author":"L Sun","year":"2021","unstructured":"Sun L, Cai J, Gonzalez FJ. The role of farnesoid X receptor in metabolic diseases, and gastrointestinal and liver cancer. Nat Rev Gastroenterol Hepatol. 2021;18:335\u201347.","journal-title":"Nat Rev Gastroenterol Hepatol"},{"key":"1895_CR53","doi-asserted-by":"publisher","first-page":"15","DOI":"10.1002\/ptr.7588","volume":"37","author":"F Liu","year":"2023","unstructured":"Liu F, Yao Y, Wang Q, Zhang F, Wang M, Zhu C, Lin C. Nigakinone alleviates DSS-induced experimental colitis via regulating bile acid profile and FXR\/NLRP3 signaling pathways. Phytother Res. 2023;37:15\u201334.","journal-title":"Phytother Res"},{"key":"1895_CR54","doi-asserted-by":"publisher","first-page":"337","DOI":"10.1126\/science.1198469","volume":"331","author":"K Atarashi","year":"2011","unstructured":"Atarashi K, Tanoue T, Shima T, Imaoka A, Kuwahara T, Momose Y, Cheng G, Yamasaki S, Saito T, Ohba Y, et al. Induction of colonic regulatory T cells by indigenous clostridium species. Science. 2011;331:337\u201341.","journal-title":"Science"},{"key":"1895_CR55","doi-asserted-by":"publisher","first-page":"2205645","DOI":"10.1002\/advs.202205645","volume":"10","author":"A Liu","year":"2023","unstructured":"Liu A, Zhang M, Wu Y, Zhang C, Zhang Q, Su X, Zhu X, Shi W, Liu J, Zhang Y, et al. ASPS exhibits anti-rheumatic effects by reprogramming gut microbiota and increasing serum \u03b3-glutamylcysteine level. Adv Sci. 2023;10:2205645.","journal-title":"Adv Sci"},{"issue":"1","key":"1895_CR56","doi-asserted-by":"publisher","first-page":"2334970","DOI":"10.1080\/19490976.2024.2334970","volume":"16","author":"C Hongyu","year":"2024","unstructured":"Hongyu C, Junbin W, Kaiyun D, Jingwen X, Yun Y, Cong T, Yanan Z, Wenhai Y, Haixuan W, Qing H, et al. Gastrointestinal microbiota and metabolites possibly contribute to distinct pathogenicity of SARS-CoV-2 proto or its variants in rhesus monkeys. Gut Microbes. 2024;16(1):2334970.","journal-title":"Gut Microbes"},{"issue":"14","key":"1895_CR57","doi-asserted-by":"publisher","first-page":"2510","DOI":"10.1016\/j.cell.2022.05.016","volume":"185","author":"Z Hong","year":"2022","unstructured":"Hong Z, Yibin Z, Ziwen L, Yongmei P, Wenyu P, Liangqin T, Jinglin W, Qiyong L, Penghua W, Gong C. A volatile from the skin microbiota of flavivirus-infected hosts promotes mosquito attractiveness. Cell. 2022;185(14):2510-2522.e2516.","journal-title":"Cell"},{"key":"1895_CR58","doi-asserted-by":"publisher","first-page":"484","DOI":"10.1002\/art.40403","volume":"70","author":"A Zaid","year":"2018","unstructured":"Zaid A, G\u00e9rardin P, Taylor A, Mostafavi H, Malvy D, Mahalingam S. Review: chikungunya arthritis: implications of acute and chronic inflammation mechanisms on disease management. Arthritis Rheumatol. 2018;70:484\u201395.","journal-title":"Arthritis Rheumatol"}],"container-title":["Microbiome"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s40168-024-01895-w.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1186\/s40168-024-01895-w\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s40168-024-01895-w.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,2,13]],"date-time":"2025-02-13T09:12:35Z","timestamp":1739437955000},"score":1,"resource":{"primary":{"URL":"https:\/\/microbiomejournal.biomedcentral.com\/articles\/10.1186\/s40168-024-01895-w"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,8,30]]},"references-count":58,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2024,12]]}},"alternative-id":["1895"],"URL":"https:\/\/doi.org\/10.1186\/s40168-024-01895-w","relation":{},"ISSN":["2049-2618"],"issn-type":[{"value":"2049-2618","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,8,30]]},"assertion":[{"value":"22 November 2023","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"30 July 2024","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"30 August 2024","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"All animal procedures in this study were approved by the Institutional Animal Care and Use Committee of the Institute of Medical Biology, Chinese Academy of Medical Science (ethics number: DWSP202110006). All experiments involving live CHIKV were conducted at the ABSL-3 laboratory of the National Kunming High-level Biosafety Primate Research Center.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"All authors have consented to publication.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"The authors declare no competing interests.","order":4,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"161"}}