{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,12]],"date-time":"2026-09-12T05:09:25Z","timestamp":1789189765814,"version":"build-2803163510"},"reference-count":60,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2026,9,12]],"date-time":"2026-09-12T00:00:00Z","timestamp":1789171200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2026,9,12]],"date-time":"2026-09-12T00:00:00Z","timestamp":1789171200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"funder":[{"name":"Guangdong Basic and Applied Basic Research","award":["2024A1515030013"],"award-info":[{"award-number":["2024A1515030013"]}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Bioresour. Bioprocess."],"DOI":"10.1186\/s40643-026-01129-x","type":"journal-article","created":{"date-parts":[[2026,9,12]],"date-time":"2026-09-12T03:09:55Z","timestamp":1789182595000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Elucidating the beneficial effects of gut microbiota-derived metabolites in treating hepatocellular carcinoma: an integrated network pharmacology, molecular docking, and single-cell sequencing analysis"],"prefix":"10.1186","volume":"13","author":[{"given":"Jinlin","family":"Huo","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wenqian","family":"Song","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yuan","family":"Sun","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jun","family":"Lu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0009-6301-3232","authenticated-orcid":false,"given":"Maolin","family":"Wang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2026,9,12]]},"reference":[{"issue":"6","key":"1129_CR1","doi-asserted-by":"publisher","first-page":"716","DOI":"10.1016\/j.chom.2018.05.003","volume":"23","author":"A Agus","year":"2018","unstructured":"Agus A, Planchais J, Sokol H (2018) Gut microbiota regulation of tryptophan metabolism in health and disease. Cell Host Microbe 23(6):716\u2013724","journal-title":"Cell Host Microbe"},{"issue":"3","key":"1129_CR2","doi-asserted-by":"publisher","first-page":"558","DOI":"10.1016\/j.jhep.2019.10.003","volume":"72","author":"A Albillos","year":"2020","unstructured":"Albillos A, de Gottardi A, Rescigno M (2020) The gut-liver axis in liver disease: pathophysiological basis for therapy. J Hepatol 72(3):558\u2013577","journal-title":"J Hepatol"},{"issue":"6","key":"1129_CR3","doi-asserted-by":"publisher","first-page":"1384","DOI":"10.1016\/j.jhep.2011.10.027","volume":"56","author":"G Baffy","year":"2012","unstructured":"Baffy G, Brunt EM, Caldwell SH (2012) Hepatocellular carcinoma in non-alcoholic fatty liver disease: an emerging menace. J Hepatol 56(6):1384\u20131391","journal-title":"J Hepatol"},{"key":"1129_CR4","doi-asserted-by":"publisher","first-page":"W513","DOI":"10.1093\/nar\/gkae303","volume":"52","author":"P Banerjee","year":"2024","unstructured":"Banerjee P, Kemmler E, Dunkel M, Preissner R (2024) ProTox 3.0: a webserver for the prediction of toxicity of chemicals. Nucleic Acids Res 52:W513\u2013W520","journal-title":"Nucleic Acids Res"},{"key":"1129_CR5","unstructured":"Basolo, A., Hohenadel, M., Ang, Q. Y., Piaggi, P., Heinitz, S., Walter, M., Walter, P., Parrington, S., Trinidad, D. D., von Schwartzenberg, R. J., Turnbaugh, P. J. & Krakoff, J. (2020)"},{"issue":"8","key":"1129_CR6","doi-asserted-by":"publisher","first-page":"1337","DOI":"10.1038\/bjc.2012.409","volume":"107","author":"LB Bindels","year":"2012","unstructured":"Bindels LB, Porporato P, Dewulf EM, Verrax J, Neyrinck AM, Martin JC, Scott KP, Buc Calderon P, Feron O, Muccioli GG, Sonveaux P, Cani PD, Delzenne NM (2012) Gut microbiota-derived propionate reduces cancer cell proliferation in the liver. Br J Cancer 107(8):1337\u20131344","journal-title":"Br J Cancer"},{"issue":"4","key":"1129_CR7","doi-asserted-by":"publisher","first-page":"220","DOI":"10.3390\/metabo15040220","volume":"15","author":"E Caradonna","year":"2025","unstructured":"Caradonna E, Abate F, Schiano E, Paparella F, Ferrara F, Vanoli E, Difruscolo R, Goffredo VM, Amato B, Setacci C, Setacci F, Novellino E (2025) Trimethylamine-N-Oxide (TMAO) as a rising-star metabolite: implications for human health. Metabolites 15(4):220","journal-title":"Metabolites"},{"key":"1129_CR8","doi-asserted-by":"publisher","first-page":"18","DOI":"10.1016\/j.neo.2022.01.001","volume":"25","author":"DS Chandrashekar","year":"2022","unstructured":"Chandrashekar DS, Karthikeyan SK, Korla PK, Patel H, Shovon AR, Athar M, Netto GJ, Qin ZS, Kumar S, Manne U, Creighton CJ, Varambally S (2022) UALCAN: an update to the integrated cancer data analysis platform. Neoplasia 25:18\u201327","journal-title":"Neoplasia"},{"issue":"1","key":"1129_CR9","doi-asserted-by":"publisher","first-page":"88","DOI":"10.1097\/HEP.0000000000000047","volume":"78","author":"Y Che","year":"2023","unstructured":"Che Y, Chen G, Guo Q, Duan Y, Feng H, Xia Q (2023) Gut microbial metabolite butyrate improves anticancer therapy by regulating intracellular calcium homeostasis. Hepatology 78(1):88\u2013102","journal-title":"Hepatology"},{"issue":"52","key":"1129_CR10","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.2203894119","volume":"119","author":"W Chen","year":"2022","unstructured":"Chen W, Wen L, Bao Y, Tang Z, Zhao J, Zhang X, Wei T, Zhang J, Ma T, Zhang Q, Zhi X, Li J, Zhang C, Ni L, Li M, Liang T (2022) Gut flora disequilibrium promotes the initiation of liver cancer by modulating tryptophan metabolism and up-regulating SREBP2. Proc Natl Acad Sci U S A 119(52):e2203894119","journal-title":"Proc Natl Acad Sci U S A"},{"key":"1129_CR11","first-page":"1","volume":"149","author":"S Chidambaranathan-Reghupaty","year":"2021","unstructured":"Chidambaranathan-Reghupaty S, Fisher PB, Sarkar D (2021) Hepatocellular carcinoma (HCC): epidemiology, etiology and molecular classification. Adv Cancer Res 149:1\u201361","journal-title":"Adv Cancer Res"},{"key":"1129_CR12","doi-asserted-by":"publisher","first-page":"42717","DOI":"10.1038\/srep42717","volume":"7","author":"A Daina","year":"2017","unstructured":"Daina A, Michielin O, Zoete V (2017) SwissADME: a free web tool to evaluate pharmacokinetics, drug-likeness and medicinal chemistry friendliness of small molecules. Sci Rep 7:42717","journal-title":"Sci Rep"},{"issue":"2","key":"1129_CR13","doi-asserted-by":"publisher","first-page":"181","DOI":"10.1016\/S0092-8674(03)00042-4","volume":"112","author":"R Eferl","year":"2003","unstructured":"Eferl R, Ricci R, Kenner L, Zenz R, David JP, Rath M, Wagner EF (2003) Liver tumor development. c-Jun antagonizes the proapoptotic activity of p53. Cell 112(2):181\u2013192","journal-title":"Cell"},{"issue":"1","key":"1129_CR14","doi-asserted-by":"publisher","first-page":"2467235","DOI":"10.1080\/19490976.2025.2467235","volume":"17","author":"H Gao","year":"2025","unstructured":"Gao H, Sun M, Li A, Gu Q, Kang D, Feng Z, Li X, Wang X, Chen L, Yang H, Cong Y, Liu Z (2025) Microbiota-derived IPA alleviates intestinal mucosal inflammation through upregulating Th1\/Th17 cell apoptosis in inflammatory bowel disease. Gut Microbes 17(1):2467235","journal-title":"Gut Microbes"},{"issue":"1","key":"1129_CR15","doi-asserted-by":"publisher","first-page":"156","DOI":"10.1016\/j.jhep.2020.07.041","volume":"74","author":"S Gaul","year":"2021","unstructured":"Gaul S, Leszczynska A, Alegre F, Kaufmann B, Johnson CD, Adams LA, Wree A, Damm G, Seehofer D, Calvente CJ, Povero D, Kisseleva T, Eguchi A, McGeough MD, Hoffman HM, Pelegrin P, Laufs U, Feldstein AE (2021) Hepatocyte pyroptosis and release of inflammasome particles induce stellate cell activation and liver fibrosis. J Hepatol 74(1):156\u2013167","journal-title":"J Hepatol"},{"issue":"15","key":"1129_CR16","doi-asserted-by":"publisher","first-page":"2488","DOI":"10.3390\/nu16152488","volume":"16","author":"W Gong","year":"2024","unstructured":"Gong W, Sun P, Li X, Wang X, Zhang X, Cui H, Yang J (2024) Investigating the molecular mechanisms of resveratrol in treating cardiometabolic multimorbidity: a network pharmacology and bioinformatics approach with molecular docking validation. Nutrients 16(15):2488","journal-title":"Nutrients"},{"issue":"1","key":"1129_CR17","doi-asserted-by":"publisher","first-page":"146","DOI":"10.1186\/s13046-020-01654-3","volume":"39","author":"M Hong","year":"2020","unstructured":"Hong M, Lee S, Clayton J, Yake W, Li J (2020) Genipin suppression of growth and metastasis in hepatocellular carcinoma through blocking activation of STAT-3. J Exp Clin Cancer Res 39(1):146","journal-title":"J Exp Clin Cancer Res"},{"issue":"10","key":"1129_CR18","doi-asserted-by":"publisher","first-page":"1110","DOI":"10.1038\/nbt1007-1110","volume":"25","author":"AL Hopkins","year":"2007","unstructured":"Hopkins AL (2007) Network pharmacology. Nat Biotechnol 25(10):1110\u20131111","journal-title":"Nat Biotechnol"},{"issue":"11","key":"1129_CR19","doi-asserted-by":"publisher","first-page":"719","DOI":"10.1038\/s41579-023-00904-3","volume":"21","author":"CL Hsu","year":"2023","unstructured":"Hsu CL, Schnabl B (2023) The gut-liver axis and gut microbiota in health and liver disease. Nat Rev Microbiol 21(11):719\u2013733","journal-title":"Nat Rev Microbiol"},{"issue":"7","key":"1129_CR20","doi-asserted-by":"publisher","first-page":"2257","DOI":"10.1039\/C5FO00248F","volume":"6","author":"P Hu","year":"2015","unstructured":"Hu P, Song W, Shan Y, Du M, Huang M, Song C, Zhang L (2015) Lactobacillus paracasei subsp. paracasei M5L induces cell cycle arrest and calreticulin translocation via the generation of reactive oxygen species in HT-29 cell apoptosis. Food Funct 6(7):2257\u20132265","journal-title":"Food Funct"},{"issue":"1","key":"1129_CR21","doi-asserted-by":"publisher","first-page":"48","DOI":"10.1002\/hep.32449","volume":"77","author":"C Hu","year":"2023","unstructured":"Hu C, Xu B, Wang X, Wan WH, Lu J, Kong D, Jin Y, You W, Sun H, Mu X, Feng D, Chen Y (2023) Gut microbiota-derived short-chain fatty acids regulate group 3 innate lymphoid cells in HCC. Hepatology (Baltimore, MD) 77(1):48\u201364","journal-title":"Hepatology (Baltimore, MD)"},{"issue":"7","key":"1129_CR22","doi-asserted-by":"publisher","first-page":"1651","DOI":"10.1016\/j.cell.2024.02.022","volume":"187","author":"D Jia","year":"2024","unstructured":"Jia D, Wang Q, Qi Y, Jiang Y, He J, Lin Y, Sun Y, Xu J, Chen W, Fan L, Yan R, Zhang W, Ren G, Xu C, Ge Q, Wang L, Liu W, Xu F, Wu P, Wang Y, Chen S, Wang L (2024) Microbial metabolite enhances immunotherapy efficacy by modulating T cell stemness in pan-cancer. Cell 187(7):1651-1665 e1621","journal-title":"Cell"},{"issue":"2","key":"1129_CR23","doi-asserted-by":"publisher","first-page":"113","DOI":"10.1159\/000521358","volume":"11","author":"Y Kang","year":"2022","unstructured":"Kang Y, Cai Y, Yang Y (2022) The gut microbiome and hepatocellular carcinoma: implications for early diagnostic biomarkers and novel therapies. Liver Cancer (Basel) 11(2):113\u2013125","journal-title":"Liver Cancer (Basel)"},{"issue":"20","key":"1129_CR24","doi-asserted-by":"publisher","first-page":"4578","DOI":"10.1038\/s44318-024-00188-0","volume":"43","author":"Y Kurlishchuk","year":"2024","unstructured":"Kurlishchuk Y, Cindric Vranesic A, Jessen M, Kipping A, Ritter C, Kim K, Cramer P, von Eyss B (2024) A non-canonical repressor function of JUN restrains YAP activity and liver cancer growth. EMBO J 43(20):4578\u20134603","journal-title":"EMBO J"},{"issue":"W1","key":"1129_CR25","doi-asserted-by":"publisher","first-page":"W242","DOI":"10.1093\/nar\/gkab418","volume":"49","author":"C Li","year":"2021","unstructured":"Li C, Tang Z, Zhang W, Ye Z, Liu F (2021a) GEPIA2021: integrating multiple deconvolution-based analysis into GEPIA. Nucleic Acids Res 49(W1):W242\u2013W246","journal-title":"Nucleic Acids Res"},{"issue":"4","key":"1129_CR26","doi-asserted-by":"publisher","first-page":"507","DOI":"10.1055\/s-0041-1730926","volume":"41","author":"N Li","year":"2021","unstructured":"Li N, Yamamoto G, Fuji H, Kisseleva T (2021b) Interleukin-17 in liver disease pathogenesis. Semin Liver Dis 41(4):507\u2013515","journal-title":"Semin Liver Dis"},{"issue":"2","key":"1129_CR27","doi-asserted-by":"publisher","first-page":"154","DOI":"10.1016\/j.trecan.2024.11.003","volume":"11","author":"S Li","year":"2025","unstructured":"Li S, Duan Y, Luo S, Zhou F, Wu Q, Lu Z (2025) Short-chain fatty acids and cancer. Trends Cancer 11(2):154\u2013168","journal-title":"Trends Cancer"},{"key":"1129_CR28","doi-asserted-by":"publisher","DOI":"10.1136\/jitc-2021-003069","author":"B Liu","year":"2022","unstructured":"Liu B, Zhou Z, Jin Y, Lu J, Feng D, Peng R, Sun H, Mu X, Li C, Chen Y (2022a) Hepatic stellate cell activation and senescence induced by intrahepatic microbiota disturbances drive progression of liver cirrhosis toward hepatocellular carcinoma. J Immunother Cancer. https:\/\/doi.org\/10.1136\/jitc-2021-003069","journal-title":"J Immunother Cancer"},{"issue":"W1","key":"1129_CR29","doi-asserted-by":"publisher","first-page":"W159","DOI":"10.1093\/nar\/gkac394","volume":"50","author":"Y Liu","year":"2022","unstructured":"Liu Y, Yang X, Gan J, Chen S, Xiao ZX, Cao Y (2022b) CB-Dock2: improved protein-ligand blind docking by integrating cavity detection, docking and homologous template fitting. Nucleic Acids Res 50(W1):W159\u2013W164","journal-title":"Nucleic Acids Res"},{"issue":"9","key":"1129_CR30","doi-asserted-by":"publisher","DOI":"10.1002\/adhm.202402773","volume":"14","author":"Y Lv","year":"2025","unstructured":"Lv Y, Jiang M, Ouyang Y, Zheng X, Zhang L, Yao J, Hu L, Zhao J, Li Z, Wang S (2025) Sodium butyrate-loaded microspheres with enhanced bioavailability for targeted treatment of intestinal barrier injury. Adv Healthc Mater 14(9):e2402773","journal-title":"Adv Healthc Mater"},{"issue":"5","key":"1129_CR31","doi-asserted-by":"publisher","first-page":"946","DOI":"10.1016\/j.jhep.2019.12.016","volume":"72","author":"HY Ma","year":"2020","unstructured":"Ma HY, Yamamoto G, Xu J, Liu X, Karin D, Kim JY, Alexandrov LB, Koyama Y, Nishio T, Benner C, Heinz S, Rosenthal SB, Liang S, Sun M, Karin G, Zhao P, Brodt P, McKillop IH, Quehenberger O, Dennis E, Saltiel A, Tsukamoto H, Gao B, Karin M, Brenner DA, Kisseleva T (2020) IL-17 signaling in steatotic hepatocytes and macrophages promotes hepatocellular carcinoma in alcohol-related liver disease. J Hepatol 72(5):946\u2013959","journal-title":"J Hepatol"},{"issue":"1","key":"1129_CR32","doi-asserted-by":"publisher","first-page":"2297846","DOI":"10.1080\/19490976.2023.2297846","volume":"16","author":"H Ma","year":"2024","unstructured":"Ma H, Yang L, Liang Y, Liu F, Hu J, Zhang R, Li Y, Yuan L, Feng F (2024) B. thetaiotaomicron-derived acetic acid modulate immune microenvironment and tumor growth in hepatocellular carcinoma. Gut Microbes 16(1):2297846","journal-title":"Gut Microbes"},{"issue":"8","key":"1129_CR33","doi-asserted-by":"publisher","first-page":"577","DOI":"10.1038\/s41577-024-01014-8","volume":"24","author":"ER Mann","year":"2024","unstructured":"Mann ER, Lam YK, Uhlig HH (2024) Short-chain fatty acids: linking diet, the microbiome and immunity. Nat Rev Immunol 24(8):577\u2013595","journal-title":"Nat Rev Immunol"},{"issue":"1","key":"1129_CR34","doi-asserted-by":"publisher","first-page":"10","DOI":"10.1038\/sj.leu.2401981","volume":"15","author":"TA McDonald","year":"2001","unstructured":"McDonald TA, Holland NT, Skibola C, Duramad P, Smith MT (2001) Hypothesis: phenol and hydroquinone derived mainly from diet and gastrointestinal flora activity are causal factors in leukemia. Leukemia 15(1):10\u201320","journal-title":"Leukemia"},{"issue":"11","key":"1129_CR35","doi-asserted-by":"publisher","first-page":"2717","DOI":"10.1016\/j.cell.2024.03.034","volume":"187","author":"Q Nie","year":"2024","unstructured":"Nie Q, Luo X, Wang K, Ding Y, Jia S, Zhao Q, Li M, Zhang J, Zhuo Y, Lin J, Guo C, Zhang Z, Liu H, Zeng G, You J, Sun L, Lu H, Ma M, Jia Y, Zheng MH, Pang Y, Qiao J, Jiang C (2024) Gut symbionts alleviate MASH through a secondary bile acid biosynthetic pathway. Cell 187(11):2717-2734 e2733","journal-title":"Cell"},{"issue":"2","key":"1129_CR36","doi-asserted-by":"publisher","first-page":"136","DOI":"10.1016\/j.tips.2021.11.004","volume":"43","author":"C Nogales","year":"2022","unstructured":"Nogales C, Mamdouh ZM, List M, Kiel C, Casas AI, Schmidt H (2022) Network pharmacology: curing causal mechanisms instead of treating symptoms. Trends Pharmacol Sci 43(2):136\u2013150","journal-title":"Trends Pharmacol Sci"},{"issue":"W1","key":"1129_CR37","doi-asserted-by":"publisher","first-page":"W398","DOI":"10.1093\/nar\/gkae253","volume":"52","author":"Z Pang","year":"2024","unstructured":"Pang Z, Lu Y, Zhou G, Hui F, Xu L, Viau C, Spigelman AF, MacDonald PE, Wishart DS, Li S, Xia J (2024) MetaboAnalyst 6.0: towards a unified platform for metabolomics data processing, analysis and interpretation. Nucleic Acids Res 52(W1):W398\u2013W406","journal-title":"Nucleic Acids Res"},{"issue":"5","key":"1129_CR38","doi-asserted-by":"publisher","first-page":"1873","DOI":"10.1172\/JCI90327","volume":"127","author":"C Patitucci","year":"2017","unstructured":"Patitucci C, Couchy G, Bagattin A, Caneque T, de Reynies A, Scoazec JY, Rodriguez R, Pontoglio M, Zucman-Rossi J, Pende M, Panasyuk G (2017) Hepatocyte nuclear factor 1alpha suppresses steatosis-associated liver cancer by inhibiting PPARgamma transcription. J Clin Invest 127(5):1873\u20131888","journal-title":"J Clin Invest"},{"key":"1129_CR39","doi-asserted-by":"publisher","DOI":"10.3390\/ijms20184331","author":"L Pinzi","year":"2019","unstructured":"Pinzi L, Rastelli G (2019) Molecular docking: shifting paradigms in drug discovery. Int J Mol Sci. https:\/\/doi.org\/10.3390\/ijms20184331","journal-title":"Int J Mol Sci"},{"issue":"1","key":"1129_CR40","doi-asserted-by":"publisher","first-page":"107","DOI":"10.1002\/hep.30036","volume":"69","author":"FR Ponziani","year":"2019","unstructured":"Ponziani FR, Bhoori S, Castelli C, Putignani L, Rivoltini L, Del Chierico F, Sanguinetti M, Morelli D, Paroni Sterbini F, Petito V, Reddel S, Calvani R, Camisaschi C, Picca A, Tuccitto A, Gasbarrini A, Pompili M, Mazzaferro V (2019) Hepatocellular carcinoma is associated with gut microbiota profile and inflammation in nonalcoholic fatty liver disease. Hepatology 69(1):107\u2013120","journal-title":"Hepatology"},{"issue":"2","key":"1129_CR41","doi-asserted-by":"publisher","first-page":"315","DOI":"10.1016\/j.jhep.2024.08.028","volume":"82","author":"B Sangro","year":"2025","unstructured":"Sangro B et al (2025) EASL clinical practice guidelines on the management of hepatocellular carcinoma. J Hepatol 82(2):315\u2013374","journal-title":"J Hepatol"},{"issue":"2","key":"1129_CR42","doi-asserted-by":"publisher","first-page":"230","DOI":"10.1016\/j.jhep.2019.08.016","volume":"72","author":"RF Schwabe","year":"2020","unstructured":"Schwabe RF, Greten TF (2020) Gut microbiome in HCC - Mechanisms, diagnosis and therapy. J Hepatol 72(2):230\u2013238","journal-title":"J Hepatol"},{"issue":"32","key":"1129_CR43","doi-asserted-by":"publisher","first-page":"19376","DOI":"10.1073\/pnas.2000047117","volume":"117","author":"SA Scott","year":"2020","unstructured":"Scott SA, Fu J, Chang PV (2020) Microbial tryptophan metabolites regulate gut barrier function via the aryl hydrocarbon receptor. Proc Natl Acad Sci U S A 117(32):19376\u201319387","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"11","key":"1129_CR44","doi-asserted-by":"publisher","first-page":"2498","DOI":"10.1101\/gr.1239303","volume":"13","author":"P Shannon","year":"2003","unstructured":"Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T (2003) Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 13(11):2498\u20132504","journal-title":"Genome Res"},{"issue":"11","key":"1129_CR45","doi-asserted-by":"publisher","first-page":"1700","DOI":"10.1016\/j.cmet.2022.09.017","volume":"34","author":"H Tilg","year":"2022","unstructured":"Tilg H, Adolph TE, Trauner M (2022) Gut-liver axis: pathophysiological concepts and clinical implications. Cell Metab 34(11):1700\u20131718","journal-title":"Cell Metab"},{"issue":"2","key":"1129_CR46","doi-asserted-by":"publisher","first-page":"100223","DOI":"10.1016\/j.jhepr.2020.100223","volume":"3","author":"JC To","year":"2021","unstructured":"To JC, Chiu AP, Tschida BR, Lo LH, Chiu CH, Li XX, Kuka TP, Linden MA, Amin K, Chan WC, Bell JB, Moriarity BS, Largaespada DA, Keng VW (2021) ZBTB20 regulates WNT\/CTNNB1 signalling pathway by suppressing PPARG during hepatocellular carcinoma tumourigenesis. JHEP Rep 3(2):100223","journal-title":"JHEP Rep"},{"issue":"7","key":"1129_CR47","doi-asserted-by":"publisher","first-page":"397","DOI":"10.1038\/s41575-018-0011-z","volume":"15","author":"A Tripathi","year":"2018","unstructured":"Tripathi A, Debelius J, Brenner DA, Karin M, Loomba R, Schnabl B, Knight R (2018) The gut-liver axis and the intersection with the microbiome. Nat Rev Gastroenterol Hepatol 15(7):397\u2013411","journal-title":"Nat Rev Gastroenterol Hepatol"},{"issue":"1","key":"1129_CR48","doi-asserted-by":"publisher","first-page":"4","DOI":"10.1038\/s41423-020-00592-6","volume":"18","author":"R Wang","year":"2021","unstructured":"Wang R, Tang R, Li B, Ma X, Schnabl B, Tilg H (2021) Gut microbiome, liver immunology, and liver diseases. Cell Mol Immunol 18(1):4\u201317","journal-title":"Cell Mol Immunol"},{"key":"1129_CR49","doi-asserted-by":"publisher","first-page":"1467197","DOI":"10.3389\/fcimb.2025.1467197","volume":"15","author":"X Wang","year":"2025","unstructured":"Wang X, Zhang B, Jiang R (2025a) Microbiome interplays in the gut-liver axis: implications for liver cancer pathogenesis and therapeutic insights. Front Cell Infect Microbiol 15:1467197","journal-title":"Front Cell Infect Microbiol"},{"issue":"1","key":"1129_CR50","doi-asserted-by":"publisher","first-page":"105","DOI":"10.1080\/21691401.2025.2475088","volume":"53","author":"Y Wang","year":"2025","unstructured":"Wang Y, Peng X, Qian B, Wang L, Wang J (2025b) The integration of metabolites from Forsythia suspensa and gut microbiota ameliorates drug-induced liver injury: network pharmacology and molecular docking studies. Artif Cells Nanomed Biotechnol 53(1):105\u2013121","journal-title":"Artif Cells Nanomed Biotechnol"},{"issue":"1","key":"1129_CR51","doi-asserted-by":"publisher","first-page":"92","DOI":"10.1186\/s40643-025-00933-1","volume":"12","author":"Y Wang","year":"2025","unstructured":"Wang Y, Wang X, Zhang X, Pan M, Sun M, Chen Z, Song Y (2025c) Utilizing network pharmacology and other tools to examine active components and mechanism of action of Magnolia officinalis rheum rhabarbarum decoction in treating Streptococcus pyogenes skin infections. Bioresour Bioprocess 12(1):92","journal-title":"Bioresour Bioprocess"},{"key":"1129_CR52","doi-asserted-by":"publisher","first-page":"19","DOI":"10.2147\/JIR.S394503","volume":"16","author":"J Xia","year":"2023","unstructured":"Xia J, Ding H, Liu S, An R, Shi X, Chen M, Ren H (2023) C-type lectin receptors-triggered antifungal immunity may synergize with and optimize the effects of immunotherapy in hepatocellular carcinoma. J Inflamm Res 16:19\u201333","journal-title":"J Inflamm Res"},{"issue":"1","key":"1129_CR53","doi-asserted-by":"publisher","first-page":"2473504","DOI":"10.1080\/19490976.2025.2473504","volume":"17","author":"J Yao","year":"2025","unstructured":"Yao J, Ning B, Ding J (2025) The gut microbiota: an emerging modulator of drug resistance in hepatocellular carcinoma. Gut Microbes 17(1):2473504","journal-title":"Gut Microbes"},{"issue":"1","key":"1129_CR54","doi-asserted-by":"publisher","first-page":"94","DOI":"10.1186\/s40643-026-01083-8","volume":"13","author":"W Yao","year":"2026","unstructured":"Yao W, Huo J, Liu K, Tao P (2026) Unveiling the therapeutic potential of gut microbiota metabolites for the treatment of renal fibrosis based on network pharmacology study. Bioresour Bioprocess 13(1):94","journal-title":"Bioresour Bioprocess"},{"issue":"3","key":"1129_CR55","doi-asserted-by":"publisher","first-page":"173","DOI":"10.1038\/s41575-024-01021-z","volume":"22","author":"YH Yeo","year":"2025","unstructured":"Yeo YH, Abdelmalek M, Khan S, Moylan CA, Rodriquez L, Villanueva A, Yang JD (2025) Current and emerging strategies for the prevention of hepatocellular carcinoma. Nat Rev Gastroenterol Hepatol 22(3):173\u2013190","journal-title":"Nat Rev Gastroenterol Hepatol"},{"issue":"1","key":"1129_CR56","doi-asserted-by":"publisher","first-page":"131","DOI":"10.1016\/j.chom.2023.11.011","volume":"32","author":"J Yu","year":"2024","unstructured":"Yu J, Zhu P, Shi L, Gao N, Li Y, Shu C, Xu Y, Yu Y, He J, Guo D, Zhang X, Wang X, Shao S, Dong W, Wang Y, Zhang W, Zhang W, Chen WH, Chen X, Liu Z, Yang X, Zhang B (2024) Bifidobacterium longum promotes postoperative liver function recovery in patients with hepatocellular carcinoma. Cell Host Microbe 32(1):131-144 e136","journal-title":"Cell Host Microbe"},{"issue":"1","key":"1129_CR57","doi-asserted-by":"publisher","first-page":"30","DOI":"10.1186\/s40643-025-00869-6","volume":"12","author":"Q Yu","year":"2025","unstructured":"Yu Q, Zhu L, Ding X, Lou Y (2025) Integration of network pharmacology and experimental validation to explore the pharmacological mechanism of andrographolide against asthma. Bioresour Bioprocess 12(1):30","journal-title":"Bioresour Bioprocess"},{"issue":"2","key":"1129_CR58","doi-asserted-by":"publisher","first-page":"225","DOI":"10.1002\/cac2.12388","volume":"43","author":"X Zhan","year":"2023","unstructured":"Zhan X, Wu R, Kong XH, You Y, He K, Sun XY, Huang Y, Chen WX, Duan L (2023) Elevated neutrophil extracellular traps by HBV-mediated S100A9-TLR4\/RAGE-ROS cascade facilitate the growth and metastasis of hepatocellular carcinoma. Cancer Commun (Lond) 43(2):225\u2013245","journal-title":"Cancer Commun (Lond)"},{"issue":"4","key":"1129_CR59","doi-asserted-by":"publisher","first-page":"761","DOI":"10.1136\/gutjnl-2019-319664","volume":"70","author":"X Zhang","year":"2021","unstructured":"Zhang X, Coker OO, Chu ES, Fu K, Lau HCH, Wang YX, Chan AWH, Wei H, Yang X, Sung JJY, Yu J (2021) Dietary cholesterol drives fatty liver-associated liver cancer by modulating gut microbiota and metabolites. Gut 70(4):761\u2013774","journal-title":"Gut"},{"key":"1129_CR60","doi-asserted-by":"publisher","first-page":"116306","DOI":"10.1016\/j.jep.2023.116306","volume":"309","author":"L Zhao","year":"2023","unstructured":"Zhao L, Zhang H, Li N, Chen J, Xu H, Wang Y, Liang Q (2023) Network pharmacology, a promising approach to reveal the pharmacology mechanism of Chinese medicine formula. J Ethnopharmacol 309:116306","journal-title":"J Ethnopharmacol"}],"container-title":["Bioresources and Bioprocessing"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s40643-026-01129-x.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1186\/s40643-026-01129-x","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s40643-026-01129-x.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,9,12]],"date-time":"2026-09-12T05:02:26Z","timestamp":1789189346000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1186\/s40643-026-01129-x"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,9,12]]},"references-count":60,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2026,12]]}},"alternative-id":["1129"],"URL":"https:\/\/doi.org\/10.1186\/s40643-026-01129-x","relation":{},"ISSN":["2197-4365"],"issn-type":[{"value":"2197-4365","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,9,12]]},"assertion":[{"value":"24 May 2026","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"24 August 2026","order":2,"name":"revised","label":"Revised","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"30 August 2026","order":3,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"12 September 2026","order":4,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"Not applicable.","order":1,"name":"Ethics","label":"Ethics approval and consent to participate","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"Not applicable, this manuscript does not include any details, images, or videos relating to an individual person.","order":2,"name":"Ethics","label":"Consent for publication","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"The authors declare that no Gen AI was used in the creation of this manuscript.","order":3,"name":"Ethics","label":"Generative AI statement","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"The authors declare that they have no competing interests.","order":4,"name":"Ethics","label":"Competing interests","group":{"name":"EthicsHeading","label":"Declarations"}}],"article-number":"133"}}