Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Review Article
  • Published:

Gut–liver axis: barriers and functional circuits

Abstract

The gut and the liver are characterized by mutual interactions between both organs, the microbiome, diet and other environmental factors. The sum of these interactions is conceptualized as the gut–liver axis. In this Review we discuss the gut–liver axis, concentrating on the barriers formed by the enterohepatic tissues to restrict gut-derived microorganisms, microbial stimuli and dietary constituents. In addition, we discuss the establishment of barriers in the gut and liver during development and their cooperative function in the adult host. We detail the interplay between microbial and dietary metabolites, the intestinal epithelium, vascular endothelium, the immune system and the various host soluble factors, and how this interplay establishes a homeostatic balance in the healthy gut and liver. Finally, we highlight how this balance is disrupted in diseases of the gut and liver, outline the existing therapeutics and describe the cutting-edge discoveries that could lead to the development of novel treatment approaches.

Key points

  • The concept of a ‘gut–liver axis’ emphasizes the clinically relevant link between gut and liver diseases, and the reciprocal interactions between both organs and the microbiome.

  • The enterohepatic tissues form a series of semi-permissive physical, chemical and immunological barriers that limit dissemination of gut content including live microorganisms.

  • Gut epithelial barriers do not simply exclude luminal antigen; they enable a regulated uptake tailored to support different requirements of the tissue at different ages, and different anatomical sites.

  • The liver limits dissemination of gut material via blood whereas gut-draining lymph nodes restrict lymphogenic spread and induce homeostatic immune responses.

  • Microbial and dietary metabolites and the immune system tune barriers of the gut–liver axis to establish a homeostatic balance in the healthy gut and liver.

  • Microbiome-based strategies such as use of antimicrobials, prebiotics, probiotics, synbiotics, bacteriophage therapy and faecal microbiota transplantation aim to restore intestinal homeostasis in liver diseases.

This is a preview of subscription content, access via your institution

Access options

Buy this article

Prices may be subject to local taxes which are calculated during checkout

Fig. 1: Gut–liver axis barriers and anatomical connections.
Fig. 2: Functional interactions between the immune cells of the gut, liver and gut microbiota.
Fig. 3: Gut microbiota dynamics throughout life and disease onset or progression.
Fig. 4: Alterations of the gut–liver axis in chronic liver disease.

Similar content being viewed by others

References

  1. Hornef, M. W. & Torow, N. ‘Layered immunity’ and the ‘neonatal window of opportunity’ – timed succession of non-redundant phases to establish mucosal host–microbial homeostasis after birth. Immunology 159, 15–25 (2020).

    Article  CAS  PubMed  Google Scholar 

  2. Volta, U. et al. IgA antibodies to dietary antigens in liver cirrhosis. Ric. Clin. Lab. 17, 235–242 (1987).

    Article  CAS  PubMed  Google Scholar 

  3. Tripathi, A. et al. The gut–liver axis and the intersection with the microbiome. Nat. Rev. Gastroenterol. Hepatol. 15, 397–411 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Trebicka, J., Bork, P., Krag, A. & Arumugam, M. Utilizing the gut microbiome in decompensated cirrhosis and acute-on-chronic liver failure. Nat. Rev. Gastroenterol. Hepatol. 18, 167–180 (2021).

    Article  PubMed  Google Scholar 

  5. Buckley, A. & Turner, J. R. Cell biology of tight junction barrier regulation and mucosal disease. Cold Spring Harb. Perspect. Biol. 10, a029314 (2018).

    Article  PubMed  PubMed Central  Google Scholar 

  6. Volynets, V. et al. Assessment of the intestinal barrier with five different permeability tests in healthy C57BL/6J and BALB/cJ mice. Dig. Dis. Sci. 61, 737–746 (2016).

    Article  CAS  PubMed  Google Scholar 

  7. Mowat, A. M., Scott, C. L. & Bain, C. C. Barrier-tissue macrophages: functional adaptation to environmental challenges. Nat. Med. 23, 1258–1270 (2017).

    Article  CAS  PubMed  Google Scholar 

  8. Frazer, L. C. & Good, M. Intestinal epithelium in early life. Mucosal Immunol. 15, 1181–1187 (2022).

    Article  CAS  PubMed  Google Scholar 

  9. Muncan, V. et al. Blimp1 regulates the transition of neonatal to adult intestinal epithelium. Nat. Commun. 2, 452 (2011).

    Article  PubMed  Google Scholar 

  10. Westrom, B., Arevalo Sureda, E., Pierzynowska, K., Pierzynowski, S. G. & Perez-Cano, F. J. The immature gut barrier and its importance in establishing immunity in newborn mammals. Front. Immunol. 11, 1153 (2020).

    Article  PubMed  PubMed Central  Google Scholar 

  11. Clarke, R. M. & Hardy, R. N. An analysis of the mechanism of cessation of uptake of macromolecular substances by the intestine of the young rat (‘closure’). J. Physiol. 204, 127–134 (1969).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. He, W. et al. FcRn-mediated antibody transport across epithelial cells revealed by electron tomography. Nature 455, 542–546 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Zheng, W. et al. Microbiota-targeted maternal antibodies protect neonates from enteric infection. Nature 577, 543–548 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Sanidad, K. Z. et al. Maternal gut microbiome-induced IgG regulates neonatal gut microbiome and immunity. Sci. Immunol. 7, eabh3816 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Arevalo Sureda, E., Westrom, B., Pierzynowski, S. G. & Prykhodko, O. Maturation of the intestinal epithelial barrier in neonatal rats coincides with decreased FcRn expression, replacement of vacuolated enterocytes and changed Blimp-1 expression. PLoS ONE 11, e0164775 (2016).

    Article  PubMed  PubMed Central  Google Scholar 

  16. Gomez de Aguero, M. et al. The maternal microbiota drives early postnatal innate immune development. Science 351, 1296–1302 (2016).

    Article  PubMed  Google Scholar 

  17. Park, J. et al. Lysosome-rich enterocytes mediate protein absorption in the vertebrate gut. Dev. Cell 51, 7–20.e6 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Remis, N. N. et al. Mucolipin co-deficiency causes accelerated endolysosomal vacuolation of enterocytes and failure-to-thrive from birth to weaning. PLoS Genet. 10, e1004833 (2014).

    Article  PubMed  PubMed Central  Google Scholar 

  19. Kolyva, S., Triga, M., Kritikou, D. & Chrysis, D. The effect of feeding patterns on serum zonulin levels in infants at 3-4 months of age. Eur. J. Pediatr. 180, 3273–3278 (2021).

    Article  CAS  PubMed  Google Scholar 

  20. Renz, H., Brandtzaeg, P. & Hornef, M. The impact of perinatal immune development on mucosal homeostasis and chronic inflammation. Nat. Rev. Immunol. 12, 9–23 (2011).

    Article  PubMed  Google Scholar 

  21. Nakamura, Y., Kimura, S. & Hase, K. M cell-dependent antigen uptake on follicle-associated epithelium for mucosal immune surveillance. Inflamm. Regen. 38, 15 (2018).

    Article  PubMed  PubMed Central  Google Scholar 

  22. Gustafsson, J. K. et al. Intestinal goblet cells sample and deliver lumenal antigens by regulated endocytic uptake and transcytosis. Elife 10, e67292 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Jinnohara, T. et al. IL-22BP dictates characteristics of Peyer’s patch follicle-associated epithelium for antigen uptake. J. Exp. Med. 214, 1607–1618 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Johansson, M. E. et al. The inner of the two Muc2 mucin-dependent mucus layers in colon is devoid of bacteria. Proc. Natl Acad. Sci. USA 105, 15064–15069 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Constant, D. A., Nice, T. J. & Rauch, I. Innate immune sensing by epithelial barriers. Curr. Opin. Immunol. 73, 1–8 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Vaishnava, S. et al. The antibacterial lectin RegIIIγ promotes the spatial segregation of microbiota and host in the intestine. Science 334, 255–258 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. Birchenough, G. M., Johansson, M. E., Gustafsson, J. K., Bergstrom, J. H. & Hansson, G. C. New developments in goblet cell mucus secretion and function. Mucosal Immunol. 8, 712–719 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Sellin, M. E. et al. Epithelium-intrinsic NAIP/NLRC4 inflammasome drives infected enterocyte expulsion to restrict Salmonella replication in the intestinal mucosa. Cell Host Microbe 16, 237–248 (2014).

    Article  CAS  PubMed  Google Scholar 

  29. Fulde, M. et al. Neonatal selection by Toll-like receptor 5 influences long-term gut microbiota composition. Nature 560, 489–493 (2018).

    Article  CAS  PubMed  Google Scholar 

  30. Al Nabhani, Z. et al. A weaning reaction to microbiota is required for resistance to immunopathologies in the adult. Immunity 50, 1276–1288.e5 (2019).

    Article  CAS  PubMed  Google Scholar 

  31. Scharschmidt, T. C. et al. A wave of regulatory T cells into neonatal skin mediates tolerance to commensal microbes. Immunity 43, 1011–1021 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  32. Boothby, I. C. et al. Early-life inflammation primes a T helper 2 cell-fibroblast niche in skin. Nature 599, 667–672 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Gola, A. et al. Commensal-driven immune zonation of the liver promotes host defence. Nature 589, 131–136 (2021).

    Article  CAS  PubMed  Google Scholar 

  34. Li, M. et al. A wave of Foxp3(+) regulatory T cell accumulation in the neonatal liver plays unique roles in maintaining self-tolerance. Cell Mol. Immunol. 17, 507–518 (2020).

    Article  PubMed  Google Scholar 

  35. Maria, A., English, K. A. & Gorham, J. D. Appropriate development of the liver Treg compartment is modulated by the microbiota and requires TGF-β and MyD88. J. Immunol. Res. 2014, 279736 (2014).

    Article  PubMed  PubMed Central  Google Scholar 

  36. Tilg, H., Adolph, T. E. & Trauner, M. Gut–liver axis: pathophysiological concepts and clinical implications. Cell Metab. 34, 1700–1718 (2022).

    Article  CAS  PubMed  Google Scholar 

  37. Luciani, C., Hager, F. T., Cerovic, V. & Lelouard, H. Dendritic cell functions in the inductive and effector sites of intestinal immunity. Mucosal Immunol. 15, 40–50 (2022).

    Article  CAS  PubMed  Google Scholar 

  38. Atarashi, K. et al. ATP drives lamina propria T(H)17 cell differentiation. Nature 455, 808–812 (2008).

    Article  CAS  PubMed  Google Scholar 

  39. Hadis, U. et al. Intestinal tolerance requires gut homing and expansion of FoxP3+ regulatory T cells in the lamina propria. Immunity 34, 237–246 (2011).

    Article  CAS  PubMed  Google Scholar 

  40. Houston, S. A. et al. The lymph nodes draining the small intestine and colon are anatomically separate and immunologically distinct. Mucosal Immunol. 9, 468–478 (2016).

    Article  CAS  PubMed  Google Scholar 

  41. Esterhazy, D. et al. Compartmentalized gut lymph node drainage dictates adaptive immune responses. Nature 569, 126–130 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  42. Macpherson, A. J. & Smith, K. Mesenteric lymph nodes at the center of immune anatomy. J. Exp. Med. 203, 497–500 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  43. Hammerschmidt, S. I. et al. Stromal mesenteric lymph node cells are essential for the generation of gut-homing T cells in vivo. J. Exp. Med. 205, 2483–2490 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  44. Cording, S. et al. The intestinal micro-environment imprints stromal cells to promote efficient Treg induction in gut-draining lymph nodes. Mucosal Immunol. 7, 359–368 (2014).

    Article  CAS  PubMed  Google Scholar 

  45. Muschaweck, M. et al. Cognate recognition of microbial antigens defines constricted CD4+ T cell receptor repertoires in the inflamed colon. Immunity 54, 2565–2577.e6 (2021).

    Article  CAS  PubMed  Google Scholar 

  46. Song, X. et al. Microbial bile acid metabolites modulate gut RORγ+ regulatory T cell homeostasis. Nature 577, 410–415 (2020).

    Article  CAS  PubMed  Google Scholar 

  47. Pabst, O. & Slack, E. IgA and the intestinal microbiota: the importance of being specific. Mucosal Immunol. 13, 12–21 (2020).

    Article  CAS  PubMed  Google Scholar 

  48. Rollenske, T. et al. Parallelism of intestinal secretory IgA shapes functional microbial fitness. Nature 598, 657–661 (2021).

    Article  CAS  PubMed  Google Scholar 

  49. Nakajima, A. et al. IgA regulates the composition and metabolic function of gut microbiota by promoting symbiosis between bacteria. J. Exp. Med. 215, 2019–2034 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  50. Corthesy, B. Multi-faceted functions of secretory IgA at mucosal surfaces. Front. Immunol. 4, 185 (2013).

    Article  PubMed  PubMed Central  Google Scholar 

  51. Magri, G. et al. Human secretory IgM emerges from plasma cells clonally related to gut memory B cells and targets highly diverse commensals. Immunity 47, 118–134.e8 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  52. Catanzaro, J. R. et al. IgA-deficient humans exhibit gut microbiota dysbiosis despite secretion of compensatory IgM. Sci. Rep. 9, 13574 (2019).

    Article  PubMed  PubMed Central  Google Scholar 

  53. Chen, K., Magri, G., Grasset, E. K. & Cerutti, A. Rethinking mucosal antibody responses: IgM, IgG and IgD join IgA. Nat. Rev. Immunol. 20, 427–441 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  54. Moro-Sibilot, L. et al. Mouse and human liver contain immunoglobulin A-secreting cells originating from Peyer’s patches and directed against intestinal antigens. Gastroenterology 151, 311–323 (2016).

    Article  CAS  PubMed  Google Scholar 

  55. Spadoni, I. et al. A gut-vascular barrier controls the systemic dissemination of bacteria. Science 350, 830–834 (2015).

    Article  CAS  PubMed  Google Scholar 

  56. Mouries, J. et al. Microbiota-driven gut vascular barrier disruption is a prerequisite for non-alcoholic steatohepatitis development. J. Hepatol. 71, 1216–1228 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  57. Bertocchi, A. et al. Gut vascular barrier impairment leads to intestinal bacteria dissemination and colorectal cancer metastasis to liver. Cancer Cell 39, 708–724.e11 (2021).

    Article  CAS  PubMed  Google Scholar 

  58. Han, Y. H. et al. Enterically derived high-density lipoprotein restrains liver injury through the portal vein. Science 373, eabe6729 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  59. Balmer, M. L. et al. The liver may act as a firewall mediating mutualism between the host and its gut commensal microbiota. Sci. Transl Med. 6, 237ra266 (2014).

    Article  Google Scholar 

  60. Liang, Y. et al. Temporal analyses of postnatal liver development and maturation by single-cell transcriptomics. Dev. Cell 57, 398–414.e5 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  61. Almeida, J. I. et al. Hallmarks of the human intestinal microbiome on liver maturation and function. J. Hepatol. 76, 694–725 (2022).

    Article  PubMed  Google Scholar 

  62. De Simone, G. et al. Identification of a Kupffer cell subset capable of reverting the T cell dysfunction induced by hepatocellular priming. Immunity 54, 2089–2100.e8 (2021).

    Article  PubMed  PubMed Central  Google Scholar 

  63. Guilliams, M. et al. Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches. Cell https://doi.org/10.1016/j.cell.2021.12.018 (2022).

    Article  PubMed  PubMed Central  Google Scholar 

  64. Bonnardel, J. et al. Stellate cells, hepatocytes, and endothelial cells imprint the Kupffer cell identity on monocytes colonizing the liver macrophage niche. Immunity 51, 638–654.e9 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  65. Volckmar, J. et al. Targeted antigen delivery to dendritic cells elicits robust antiviral T cell-mediated immunity in the liver. Sci. Rep. 7, 43985 (2017).

    Article  PubMed  PubMed Central  Google Scholar 

  66. Wiggins, B. G. et al. The human liver microenvironment shapes the homing and function of CD4+ T-cell populations. Gut 71, 1399–1411 (2022).

    Article  CAS  PubMed  Google Scholar 

  67. Dudek, M. et al. Auto-aggressive CXCR6+ CD8 T cells cause liver immune pathology in NASH. Nature 592, 444–449 (2021).

    Article  CAS  PubMed  Google Scholar 

  68. Deczkowska, A. et al. XCR1+ type 1 conventional dendritic cells drive liver pathology in non-alcoholic steatohepatitis. Nat. Med. 27, 1043–1054 (2021).

    Article  CAS  PubMed  Google Scholar 

  69. Zundler, S. et al. Gut immune cell trafficking: inter-organ communication and immune-mediated inflammation. Nat. Rev. Gastroenterol. Hepatol. https://doi.org/10.1038/s41575-022-00663-1 (2022).

    Article  PubMed  Google Scholar 

  70. van Best, N. et al. Bile acids drive the newborn’s gut microbiota maturation. Nat. Commun. 11, 3692 (2020).

    Article  PubMed  PubMed Central  Google Scholar 

  71. Trindade, B. C. et al. The cholesterol metabolite 25-hydroxycholesterol restrains the transcriptional regulator SREBP2 and limits intestinal IgA plasma cell differentiation. Immunity 54, 2273–2287.e6 (2021).

    Article  PubMed  PubMed Central  Google Scholar 

  72. Emgard, J. et al. Oxysterol sensing through the receptor GPR183 promotes the lymphoid-tissue-inducing function of innate lymphoid cells and colonic inflammation. Immunity 48, 120–132.e8 (2018).

    Article  PubMed  PubMed Central  Google Scholar 

  73. Kennedy, K. M. et al. Questioning the fetal microbiome illustrates pitfalls of low-biomass microbial studies. Nature 613, 639–649 (2023).

    Article  CAS  PubMed  Google Scholar 

  74. Lagkouvardos, I. et al. Early life gut microbiota profiles linked to synbiotic formula effects: a randomized clinical trial in European infants. Am. J. Clin. Nutr. https://doi.org/10.1016/j.ajcnut.2022.11.012 (2022).

    Article  PubMed  Google Scholar 

  75. Koenig, J. E. et al. Succession of microbial consortia in the developing infant gut microbiome. Proc. Natl Acad. Sci. USA 108, 4578–4585 (2011).

    Article  CAS  PubMed  Google Scholar 

  76. Macpherson, A. J., de Aguero, M. G. & Ganal-Vonarburg, S. C. How nutrition and the maternal microbiota shape the neonatal immune system. Nat. Rev. Immunol. 17, 508–517 (2017).

    Article  CAS  PubMed  Google Scholar 

  77. Galazzo, G. et al. Development of the microbiota and associations with birth mode, diet, and atopic disorders in a longitudinal analysis of stool samples, collected from infancy through early childhood. Gastroenterology 158, 1584–1596 (2020).

    Article  CAS  PubMed  Google Scholar 

  78. Nguyen, L. H. et al. Antibiotic use and the development of inflammatory bowel disease: a national case-control study in Sweden. Lancet Gastroenterol. Hepatol. 5, 986–995 (2020).

    Article  PubMed  PubMed Central  Google Scholar 

  79. Agrawal, M. et al. Early life exposures and the risk of inflammatory bowel disease: systematic review and meta-analyses. EClinicalMedicine 36, 100884 (2021).

    Article  PubMed  PubMed Central  Google Scholar 

  80. Yoon, H. et al. Increased pancreatic protease activity in response to antibiotics impairs gut barrier and triggers colitis. Cell Mol. Gastroenterol. Hepatol. 6, 370–388.e3 (2018).

    Article  PubMed  PubMed Central  Google Scholar 

  81. Sender, R., Fuchs, S. & Milo, R. Revised estimates for the number of human and bacteria cells in the body. PLoS Biol. 14, e1002533 (2016).

    Article  PubMed  PubMed Central  Google Scholar 

  82. Chu, H. et al. The Candida albicans exotoxin candidalysin promotes alcohol-associated liver disease. J. Hepatol. 72, 391–400 (2020).

    Article  CAS  PubMed  Google Scholar 

  83. Lemoinne, S. et al. Fungi participate in the dysbiosis of gut microbiota in patients with primary sclerosing cholangitis. Gut 69, 92–102 (2020).

    Article  CAS  PubMed  Google Scholar 

  84. Duan, Y. et al. Bacteriophage targeting of gut bacterium attenuates alcoholic liver disease. Nature 575, 505–511 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  85. Zheng, Y. et al. Gut microbiome affects the response to anti-PD-1 immunotherapy in patients with hepatocellular carcinoma. J. Immunother. Cancer 7, 193 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  86. Mao, J. et al. Gut microbiome is associated with the clinical response to anti-PD-1 based immunotherapy in hepatobiliary cancers. J. Immunother. Cancer 9, e003334 (2021).

    Article  PubMed  PubMed Central  Google Scholar 

  87. Martin-Gallausiaux, C., Marinelli, L., Blottiere, H. M., Larraufie, P. & Lapaque, N. SCFA: mechanisms and functional importance in the gut. Proc. Nutr. Soc. 80, 37–49 (2021).

    Article  CAS  PubMed  Google Scholar 

  88. Lee, Y. S. et al. Microbiota-derived lactate accelerates intestinal stem-cell-mediated epithelial development. Cell Host Microbe 24, 833–846.e6 (2018).

    Article  CAS  PubMed  Google Scholar 

  89. Metidji, A. et al. The environmental sensor AHR protects from inflammatory damage by maintaining intestinal stem cell homeostasis and barrier integrity. Immunity 49, 353–362.e5 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  90. Sorrentino, G. et al. Bile acids signal via TGR5 to activate intestinal stem cells and epithelial regeneration. Gastroenterology 159, 956–968.e8 (2020).

    Article  CAS  PubMed  Google Scholar 

  91. Kelly, C. J. et al. Crosstalk between microbiota-derived short-chain fatty acids and intestinal epithelial HIF augments tissue barrier function. Cell Host Microbe 17, 662–671 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  92. Leonardi, I. et al. Mucosal fungi promote gut barrier function and social behavior via type 17 immunity. Cell 185, 831–846.e14 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  93. Chang, P. V., Hao, L., Offermanns, S. & Medzhitov, R. The microbial metabolite butyrate regulates intestinal macrophage function via histone deacetylase inhibition. Proc. Natl Acad. Sci. USA 111, 2247–2252 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  94. Scott, N. A. et al. Antibiotics induce sustained dysregulation of intestinal T cell immunity by perturbing macrophage homeostasis. Sci. Transl Med. 10, eaao4755 (2018).

    Article  PubMed  PubMed Central  Google Scholar 

  95. Morita, N. et al. GPR31-dependent dendrite protrusion of intestinal CX3CR1+ cells by bacterial metabolites. Nature 566, 110–114 (2019).

    Article  CAS  PubMed  Google Scholar 

  96. Guo, C. et al. Bile acids control inflammation and metabolic disorder through inhibition of NLRP3 inflammasome. Immunity 45, 802–816 (2016).

    Article  CAS  PubMed  Google Scholar 

  97. Hang, S. et al. Bile acid metabolites control TH17 and Treg cell differentiation. Nature 576, 143–148 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  98. Campbell, C. et al. Bacterial metabolism of bile acids promotes generation of peripheral regulatory T cells. Nature 581, 475–479 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  99. Paik, D. et al. Human gut bacteria produce TH17-modulating bile acid metabolites. Nature 603, 907–912 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  100. Li, W. et al. A bacterial bile acid metabolite modulates Treg activity through the nuclear hormone receptor NR4A1. Cell Host Microbe 29, 1366–1377.e9 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  101. Wang, Z. et al. Non-lethal inhibition of gut microbial trimethylamine production for the treatment of atherosclerosis. Cell 163, 1585–1595 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  102. Devlin, A. S. et al. Modulation of a circulating uremic solute via rational genetic manipulation of the gut microbiota. Cell Host Microbe 20, 709–715 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  103. Costa, D. et al. Systemic inflammation increases across distinct stages of advanced chronic liver disease and correlates with decompensation and mortality. J. Hepatol. 74, 819–828 (2021).

    Article  CAS  PubMed  Google Scholar 

  104. Arroyo, V. et al. The systemic inflammation hypothesis: towards a new paradigm of acute decompensation and multiorgan failure in cirrhosis. J. Hepatol. 74, 670–685 (2021).

    Article  CAS  PubMed  Google Scholar 

  105. Yuan, J. et al. Fatty liver disease caused by high-alcohol-producing Klebsiella pneumoniae. Cell Metab. 30, 675–688.e7 (2019).

    Article  CAS  PubMed  Google Scholar 

  106. Seo, B. et al. Roseburia spp. abundance associates with alcohol consumption in humans and its administration ameliorates alcoholic fatty liver in mice. Cell Host Microbe 27, 25–40.e6 (2020).

    Article  CAS  PubMed  Google Scholar 

  107. Maccioni, L. et al. Intestinal permeability, microbial translocation, changes in duodenal and fecal microbiota, and their associations with alcoholic liver disease progression in humans. Gut Microbes 12, 1782157 (2020).

    Article  PubMed  PubMed Central  Google Scholar 

  108. Sorribas, M. et al. FXR modulates the gut-vascular barrier by regulating the entry sites for bacterial translocation in experimental cirrhosis. J. Hepatol. 71, 1126–1140 (2019).

    Article  CAS  PubMed  Google Scholar 

  109. Haderer, M. et al. Novel pathomechanism for spontaneous bacterial peritonitis: disruption of cell junctions by cellular and bacterial proteases. Gut 71, 580–592 (2022).

    Article  CAS  PubMed  Google Scholar 

  110. Colombel, J. F. et al. Jejunal immunoglobulin secretion in alcoholic patients with and without cirrhosis. J. Hepatol. 12, 145–149 (1991).

    Article  CAS  PubMed  Google Scholar 

  111. Pelletier, G., Briantais, M. J., Buffet, C., Pillot, J. & Etienne, J. P. Serum and intestinal secretory IgA in alcoholic cirrhosis of the liver. Gut 23, 475–480 (1982).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  112. Yan, A. W. et al. Enteric dysbiosis associated with a mouse model of alcoholic liver disease. Hepatology 53, 96–105 (2011).

    Article  CAS  PubMed  Google Scholar 

  113. Teltschik, Z. et al. Intestinal bacterial translocation in rats with cirrhosis is related to compromised Paneth cell antimicrobial host defense. Hepatology 55, 1154–1163 (2012).

    Article  PubMed  Google Scholar 

  114. Wiest, R., Lawson, M. & Geuking, M. Pathological bacterial translocation in liver cirrhosis. J. Hepatol. 60, 197–209 (2014).

    Article  PubMed  Google Scholar 

  115. Du Plessis, J. et al. Activated intestinal macrophages in patients with cirrhosis release NO and IL-6 that may disrupt intestinal barrier function. J. Hepatol. 58, 1125–1132 (2013).

    Article  PubMed  Google Scholar 

  116. Wang, L. et al. Intestinal REG3 lectins protect against alcoholic steatohepatitis by reducing mucosa-associated microbiota and preventing bacterial translocation. Cell Host Microbe 19, 227–239 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  117. Duan, Y. et al. CRIg on liver macrophages clears pathobionts and protects against alcoholic liver disease. Nat. Commun. 12, 7172 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  118. Yang, Y. et al. Within-host evolution of a gut pathobiont facilitates liver translocation. Nature 607, 563–570 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  119. Luther, J. et al. Hepatic gap junctions amplify alcohol liver injury by propagating cGAS-mediated IRF3 activation. Proc. Natl Acad. Sci. USA 117, 11667–11673 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  120. Henao-Mejia, J. et al. Inflammasome-mediated dysbiosis regulates progression of NAFLD and obesity. Nature 482, 179–185 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  121. Haussinger, D. et al. Hepatic encephalopathy. Nat. Rev. Dis. Primers 8, 43 (2022).

    Article  PubMed  Google Scholar 

  122. Craven, L. et al. Allogenic fecal microbiota transplantation in patients with nonalcoholic fatty liver disease improves abnormal small intestinal permeability: a randomized control trial. Am. J. Gastroenterol. 115, 1055–1065 (2020).

    Article  PubMed  Google Scholar 

  123. Witjes, J. J. et al. Donor fecal microbiota transplantation alters gut microbiota and metabolites in obese individuals with steatohepatitis. Hepatol. Commun. 4, 1578–1590 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  124. Vrieze, A. et al. Transfer of intestinal microbiota from lean donors increases insulin sensitivity in individuals with metabolic syndrome. Gastroenterology 143, 913–916.e7 (2012).

    Article  CAS  PubMed  Google Scholar 

  125. Bajaj, J. S. et al. Fecal microbial transplant capsules are safe in hepatic encephalopathy: a phase 1, randomized, placebo-controlled trial. Hepatology 70, 1690–1703 (2019).

    Article  CAS  PubMed  Google Scholar 

  126. Bajaj, J. S. et al. Fecal microbiota transplant from a rational stool donor improves hepatic encephalopathy: a randomized clinical trial. Hepatology 66, 1727–1738 (2017).

    Article  CAS  PubMed  Google Scholar 

  127. Philips, C. A., Phadke, N., Ganesan, K., Ranade, S. & Augustine, P. Corticosteroids, nutrition, pentoxifylline, or fecal microbiota transplantation for severe alcoholic hepatitis. Indian J. Gastroenterol. 37, 215–225 (2018).

    Article  PubMed  Google Scholar 

  128. Philips, C. A., Ahamed, R., Rajesh, S., Abduljaleel, J. K. P. & Augustine, P. Long-term outcomes of stool transplant in alcohol-associated hepatitis – analysis of clinical outcomes, relapse, gut microbiota and comparisons with standard care. J. Clin. Exp. Hepatol. 12, 1124–1132 (2022).

    Article  CAS  PubMed  Google Scholar 

  129. Sharma, A. et al. Fecal microbiota transplantation in alcohol-associated acute-on-chronic liver failure: an open-label clinical trial. Hepatol. Int. 16, 433–446 (2022).

    Article  PubMed  Google Scholar 

  130. Marcella, C. et al. Systematic review: the global incidence of faecal microbiota transplantation-related adverse events from 2000 to 2020. Aliment. Pharmacol. Ther. 53, 33–42 (2021).

    PubMed  Google Scholar 

  131. Olmedo, M. et al. Is it reasonable to perform fecal microbiota transplantation for recurrent Clostridium difficile infection in patients with liver cirrhosis? Rev. Esp. Quimioter. 32, 205–207 (2019).

    CAS  PubMed  PubMed Central  Google Scholar 

  132. Mehta, R. et al. Preliminary experience with single fecal microbiota transplant for treatment of recurrent overt hepatic encephalopathy – a case series. Indian J. Gastroenterol. 37, 559–562 (2018).

    Article  PubMed  Google Scholar 

  133. DeFilipp, Z. et al. Drug-resistant E. coli bacteremia transmitted by fecal microbiota transplant. N. Engl. J. Med. 381, 2043–2050 (2019).

    Article  PubMed  Google Scholar 

  134. Keller, J. J. et al. A standardised model for stool banking for faecal microbiota transplantation: a consensus report from a multidisciplinary UEG working group. United Eur. Gastroenterol. J. 9, 229–247 (2021).

    Article  Google Scholar 

  135. Mucke, M. M. et al. Efficacy of norfloxacin prophylaxis to prevent spontaneous bacterial peritonitis: a systematic review and meta-analysis. Clin. Transl Gastroenterol. 11, e00223 (2020).

    Article  PubMed  PubMed Central  Google Scholar 

  136. Goel, A., Rahim, U., Nguyen, L. H., Stave, C. & Nguyen, M. H. Systematic review with meta-analysis: rifaximin for the prophylaxis of spontaneous bacterial peritonitis. Aliment. Pharmacol. Ther. 46, 1029–1036 (2017).

    Article  CAS  PubMed  Google Scholar 

  137. Bass, N. M. et al. Rifaximin treatment in hepatic encephalopathy. N. Engl. J. Med. 362, 1071–1081 (2010).

    Article  CAS  PubMed  Google Scholar 

  138. Kang, D. J. et al. Rifaximin exerts beneficial effects independent of its ability to alter microbiota composition. Clin. Transl Gastroenterol. 7, e187 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  139. Bajaj, J. S. et al. Modulation of the metabiome by rifaximin in patients with cirrhosis and minimal hepatic encephalopathy. PLoS ONE 8, e60042 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  140. Patel, V. C. et al. Rifaximin-α reduces gut-derived inflammation and mucin degradation in cirrhosis and encephalopathy: RIFSYS randomised controlled trial. J. Hepatol. 76, 332–342 (2022).

    Article  CAS  PubMed  Google Scholar 

  141. Dalal, R., McGee, R. G., Riordan, S. M. & Webster, A. C. Probiotics for people with hepatic encephalopathy. Cochrane Database Syst. Rev. 2, CD008716 (2017).

    PubMed  Google Scholar 

  142. Liu, L., Li, P., Liu, Y. & Zhang, Y. Efficacy of probiotics and synbiotics in patients with nonalcoholic fatty liver disease: a meta-analysis. Dig. Dis. Sci. 64, 3402–3412 (2019).

    Article  PubMed  Google Scholar 

  143. Depommier, C. et al. Supplementation with Akkermansia muciniphila in overweight and obese human volunteers: a proof-of-concept exploratory study. Nat. Med. 25, 1096–1103 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  144. Juanola, O. et al. Circulating levels of butyrate are inversely related to portal hypertension, endotoxemia, and systemic inflammation in patients with cirrhosis. FASEB J. 33, 11595–11605 (2019).

    Article  CAS  PubMed  Google Scholar 

  145. Jin, M. et al. Faecal microbiota from patients with cirrhosis has a low capacity to ferment non-digestible carbohydrates into short-chain fatty acids. Liver Int. 39, 1437–1447 (2019).

    Article  CAS  PubMed  Google Scholar 

  146. Smirnova, E. et al. Fecal microbiome distinguishes alcohol consumption from alcoholic hepatitis but does not discriminate disease severity. Hepatology 72, 271–286 (2020).

    Article  CAS  PubMed  Google Scholar 

  147. Roychowdhury, S., Glueck, B., Han, Y., Mohammad, M. A. & Cresci, G. A. M. A designer synbiotic attenuates chronic-binge ethanol-induced gut–liver injury in mice. Nutrients 11, 97 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  148. Cresci, G. A. et al. Prophylactic tributyrin treatment mitigates chronic-binge ethanol-induced intestinal barrier and liver injury. J. Gastroenterol. Hepatol. 32, 1587–1597 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  149. Sheng, L. et al. Hepatic inflammation caused by dysregulated bile acid synthesis is reversible by butyrate supplementation. J. Pathol. 243, 431–441 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  150. Wang, Q. et al. Oral administration of PEGylated TLR7 ligand ameliorates alcohol-associated liver disease via the induction of IL-22. Proc. Natl Acad. Sci. USA 118, e2020868118 (2021).

    Article  CAS  PubMed  Google Scholar 

  151. Hendrikx, T. et al. Bacteria engineered to produce IL-22 in intestine induce expression of REG3G to reduce ethanol-induced liver disease in mice. Gut 68, 1504–1515 (2019).

    Article  CAS  PubMed  Google Scholar 

  152. Brandl, K. et al. Dysregulation of serum bile acids and FGF19 in alcoholic hepatitis. J. Hepatol. 69, 396–405 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  153. Axelson, M. & Sjovall, J. Potential bile acid precursors in plasma – possible indicators of biosynthetic pathways to cholic and chenodeoxycholic acids in man. J. Steroid Biochem. 36, 631–640 (1990).

    Article  CAS  PubMed  Google Scholar 

  154. Vlahcevic, Z. R., Goldman, M., Schwartz, C. C., Gustafsson, J. & Swell, L. Bile acid metabolism in cirrhosis. VII. Evidence for defective feedback control of bile acid synthesis. Hepatology 1, 146–150 (1981).

    Article  CAS  PubMed  Google Scholar 

  155. Ponz de Leon, M., Loria, P., Iori, R. & Carulli, N. Cholesterol absorption in cirrhosis: the role of total and individual bile acid pool size. Gastroenterology 80, 1428–1437 (1981).

    Article  CAS  PubMed  Google Scholar 

  156. Kakiyama, G. et al. Modulation of the fecal bile acid profile by gut microbiota in cirrhosis. J. Hepatol. 58, 949–955 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  157. Kakiyama, G. et al. Colonic inflammation and secondary bile acids in alcoholic cirrhosis. Am. J. Physiol. Gastrointest. Liver Physiol. 306, G929–G937 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  158. Naugler, W. E. et al. Fibroblast growth factor signaling controls liver size in mice with humanized livers. Gastroenterology 149, 728–740.e15 (2015).

    Article  CAS  PubMed  Google Scholar 

  159. Li, Z. et al. Circulating FGF19 closely correlates with bile acid synthesis and cholestasis in patients with primary biliary cirrhosis. PLoS ONE 12, e0178580 (2017).

    Article  PubMed  PubMed Central  Google Scholar 

  160. Wunsch, E. et al. Expression of hepatic fibroblast growth factor 19 is enhanced in primary biliary cirrhosis and correlates with severity of the disease. Sci. Rep. 5, 13462 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  161. Schneider, K. M. et al. Gut microbiota depletion exacerbates cholestatic liver injury via loss of FXR signalling. Nat. Metab. 3, 1228–1241 (2021).

    Article  CAS  PubMed  Google Scholar 

  162. Min, H. K. et al. Increased hepatic synthesis and dysregulation of cholesterol metabolism is associated with the severity of nonalcoholic fatty liver disease. Cell Metab. 15, 665–674 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  163. Jiao, N. et al. Suppressed hepatic bile acid signalling despite elevated production of primary and secondary bile acids in NAFLD. Gut 67, 1881–1891 (2018).

    Article  CAS  PubMed  Google Scholar 

  164. McGlone, E. R., Tan, T., Bloom, S. R. & Walters, J. R. F. What can we learn from mouse models about bile acid-mediated changes after bariatric surgery? Gastroenterology 157, 4–8 (2019).

    Article  PubMed  Google Scholar 

  165. Thakare, R., Alamoudi, J. A., Gautam, N., Rodrigues, A. D. & Alnouti, Y. Species differences in bile acids I. Plasma and urine bile acid composition. J. Appl. Toxicol. 38, 1323–1335 (2018).

    Article  CAS  PubMed  Google Scholar 

  166. Hofmann, A. F. The continuing importance of bile acids in liver and intestinal disease. Arch. Intern. Med. 159, 2647–2658 (1999).

    Article  CAS  PubMed  Google Scholar 

  167. de Boer, J. F. et al. A human-like bile acid pool induced by deletion of hepatic Cyp2c70 modulates effects of FXR activation in mice. J. Lipid Res. 61, 291–305 (2020).

    Article  PubMed  Google Scholar 

  168. Simbrunner, B., Trauner, M. & Reiberger, T. Review article: therapeutic aspects of bile acid signalling in the gut–liver axis. Aliment. Pharmacol. Ther. 54, 1243–1262 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  169. Fiorucci, S., Biagioli, M., Sepe, V., Zampella, A. & Distrutti, E. Bile acid modulators for the treatment of nonalcoholic steatohepatitis (NASH). Expert Opin. Investig. Drugs 29, 623–632 (2020).

    Article  CAS  PubMed  Google Scholar 

  170. Nevens, F. et al. A placebo-controlled trial of obeticholic acid in primary biliary cholangitis. N. Engl. J. Med. 375, 631–643 (2016).

    Article  CAS  PubMed  Google Scholar 

  171. Esan, O., Viljoen, A. & Wierzbicki, A. S. Colesevelam – a bile acid sequestrant for treating hypercholesterolemia and improving hyperglycemia. Expert Opin. Pharmacother. 23, 1363–1370 (2022).

    Article  CAS  PubMed  Google Scholar 

  172. Thompson, R. J. et al. Odevixibat treatment in progressive familial intrahepatic cholestasis: a randomised, placebo-controlled, phase 3 trial. Lancet Gastroenterol. Hepatol. 7, 830–842 (2022).

    Article  PubMed  Google Scholar 

  173. Harrison, S. A. et al. NGM282 for treatment of non-alcoholic steatohepatitis: a multicentre, randomised, double-blind, placebo-controlled, phase 2 trial. Lancet 391, 1174–1185 (2018).

    Article  CAS  PubMed  Google Scholar 

  174. Harrison, S. A. et al. NGM282 improves liver fibrosis and histology in 12 weeks in patients with nonalcoholic steatohepatitis. Hepatology 71, 1198–1212 (2020).

    Article  CAS  PubMed  Google Scholar 

  175. Harrison, S. A. et al. Efficacy and safety of aldafermin, an engineered FGF19 analog, in a randomized, double-blind, placebo-controlled trial of patients with nonalcoholic steatohepatitis. Gastroenterology 160, 219–231.e1 (2021).

    Article  CAS  PubMed  Google Scholar 

  176. Harrison, S. A. et al. Aldafermin in patients with non-alcoholic steatohepatitis (ALPINE 2/3): a randomised, double-blind, placebo-controlled, phase 2b trial. Lancet Gastroenterol. Hepatol. 7, 603–616 (2022).

    Article  PubMed  Google Scholar 

  177. Younossi, Z. M. et al. Obeticholic acid for the treatment of non-alcoholic steatohepatitis: interim analysis from a multicentre, randomised, placebo-controlled phase 3 trial. Lancet 394, 2184–2196 (2019).

    Article  CAS  PubMed  Google Scholar 

  178. Ubeda, M. et al. Obeticholic acid reduces bacterial translocation and inhibits intestinal inflammation in cirrhotic rats. J. Hepatol. 64, 1049–1057 (2016).

    Article  CAS  PubMed  Google Scholar 

  179. Hao, H. et al. Farnesoid X receptor regulation of the NLRP3 inflammasome underlies cholestasis-associated sepsis. Cell Metab. 25, 856–867.e5 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  180. John, B. V. et al. Impact of obeticholic acid exposure on decompensation and mortality in primary biliary cholangitis and cirrhosis. Hepatol. Commun. 5, 1426–1436 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  181. Dapito, D. H. et al. Promotion of hepatocellular carcinoma by the intestinal microbiota and TLR4. Cancer Cell 21, 504–516 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  182. Schneider, K. M. et al. Imbalanced gut microbiota fuels hepatocellular carcinoma development by shaping the hepatic inflammatory microenvironment. Nat. Commun. 13, 3964 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  183. Yoshimoto, S. et al. Obesity-induced gut microbial metabolite promotes liver cancer through senescence secretome. Nature 499, 97–101 (2013).

    Article  CAS  PubMed  Google Scholar 

  184. Zhang, X. et al. Dietary cholesterol drives fatty liver-associated liver cancer by modulating gut microbiota and metabolites. Gut 70, 761–774 (2021).

    Article  CAS  PubMed  Google Scholar 

  185. Singh, V. et al. Dysregulated microbial fermentation of soluble fiber induces cholestatic liver cancer. Cell 175, 679–694.e22 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  186. Ma, C. et al. Gut microbiome-mediated bile acid metabolism regulates liver cancer via NKT cells. Science 360, eaan5931 (2018).

    Article  PubMed  PubMed Central  Google Scholar 

  187. Li, J. et al. Probiotics modulated gut microbiota suppresses hepatocellular carcinoma growth in mice. Proc. Natl Acad. Sci. USA 113, E1306–E1315 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  188. Ponziani, F. R. et al. Hepatocellular carcinoma is associated with gut microbiota profile and inflammation in nonalcoholic fatty liver disease. Hepatology 69, 107–120 (2019).

    Article  CAS  PubMed  Google Scholar 

  189. Behary, J. et al. Gut microbiota impact on the peripheral immune response in non-alcoholic fatty liver disease related hepatocellular carcinoma. Nat. Commun. 12, 187 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  190. Su, G. L., Hoesel, L. M., Bayliss, J., Hemmila, M. R. & Wang, S. C. Lipopolysaccharide binding protein inhibitory peptide protects against acetaminophen-induced hepatotoxicity. Am. J. Physiol. Gastrointest. Liver Physiol. 299, G1319–G1325 (2010).

    Article  CAS  PubMed  Google Scholar 

  191. Chen, T., Li, R. & Chen, P. Gut microbiota and chemical-induced acute liver injury. Front. Physiol. 12, 688780 (2021).

    Article  PubMed  PubMed Central  Google Scholar 

  192. Schneider, K. M. et al. Intestinal dysbiosis amplifies acetaminophen-induced acute liver injury. Cell Mol. Gastroenterol. Hepatol. 11, 909–933 (2021).

    Article  CAS  PubMed  Google Scholar 

  193. Yip, L. Y. et al. The liver–gut microbiota axis modulates hepatotoxicity of tacrine in the rat. Hepatology 67, 282–295 (2018).

    Article  CAS  PubMed  Google Scholar 

  194. Clayton, T. A., Baker, D., Lindon, J. C., Everett, J. R. & Nicholson, J. K. Pharmacometabonomic identification of a significant host–microbiome metabolic interaction affecting human drug metabolism. Proc. Natl Acad. Sci. USA 106, 14728–14733 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  195. Chou, H. H. et al. Age-related immune clearance of hepatitis B virus infection requires the establishment of gut microbiota. Proc. Natl Acad. Sci. USA 112, 2175–2180 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  196. Wu, T. et al. CD4+ T cells play a critical role in microbiota-maintained anti-HBV immunity in a mouse model. Front. Immunol. 10, 927 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  197. Sandler, N. G. et al. Host response to translocated microbial products predicts outcomes of patients with HBV or HCV infection. Gastroenterology 141, 1220–1230 (2011).

    Article  PubMed  Google Scholar 

  198. Ali, R. O. et al. Longitudinal multi-omics analyses of the gut–liver axis reveals metabolic dysregulation in hepatitis C infection and cirrhosis. Nat. Microbiol. https://doi.org/10.1038/s41564-022-01273-y (2022).

    Article  PubMed  Google Scholar 

  199. Ponziani, F. R. et al. Influence of hepatitis C virus eradication with direct-acting antivirals on the gut microbiota in patients with cirrhosis. Aliment. Pharmacol. Ther. 48, 1301–1311 (2018).

    Article  CAS  PubMed  Google Scholar 

  200. Oh, T. G. et al. A universal gut-microbiome-derived signature predicts cirrhosis. Cell Metab. 32, 878–888.e6 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  201. Mzava, O. et al. A metagenomic DNA sequencing assay that is robust against environmental DNA contamination. Nat. Commun. 13, 4197 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  202. Han, G., Luong, H. & Vaishnava, S. Low abundance members of the gut microbiome exhibit high immunogenicity. Gut Microbes 14, 2104086 (2022).

    Article  PubMed  PubMed Central  Google Scholar 

  203. Le Roy, T. et al. Intestinal microbiota determines development of non-alcoholic fatty liver disease in mice. Gut 62, 1787–1794 (2013).

    Article  PubMed  Google Scholar 

  204. Llopis, M. et al. Intestinal microbiota contributes to individual susceptibility to alcoholic liver disease. Gut 65, 830–839 (2016).

    Article  CAS  PubMed  Google Scholar 

  205. Walter, J., Armet, A. M., Finlay, B. B. & Shanahan, F. Establishing or exaggerating causality for the gut microbiome: lessons from human microbiota-associated rodents. Cell 180, 221–232 (2020).

    Article  CAS  PubMed  Google Scholar 

  206. Thomas, A. M. & Segata, N. Multiple levels of the unknown in microbiome research. BMC Biol. 17, 48 (2019).

    Article  PubMed  PubMed Central  Google Scholar 

  207. van der Lelie, D. et al. Rationally designed bacterial consortia to treat chronic immune-mediated colitis and restore intestinal homeostasis. Nat. Commun. 12, 3105 (2021).

    Article  PubMed  PubMed Central  Google Scholar 

  208. Miller, B. M., Liou, M. J., Lee, J. Y. & Baumler, A. J. The longitudinal and cross-sectional heterogeneity of the intestinal microbiota. Curr. Opin. Microbiol. 63, 221–230 (2021).

    Article  CAS  PubMed  Google Scholar 

  209. Koh, A., De Vadder, F., Kovatcheva-Datchary, P. & Backhed, F. From dietary fiber to host physiology: short-chain fatty acids as key bacterial metabolites. Cell 165, 1332–1345 (2016).

    Article  CAS  PubMed  Google Scholar 

  210. Bui, T. P. et al. Production of butyrate from lysine and the Amadori product fructoselysine by a human gut commensal. Nat. Commun. 6, 10062 (2015).

    Article  CAS  PubMed  Google Scholar 

  211. Lee, J. Y., Tsolis, R. M. & Baumler, A. J. The microbiome and gut homeostasis. Science 377, eabp9960 (2022).

    Article  CAS  PubMed  Google Scholar 

  212. Canfora, E. E., Jocken, J. W. & Blaak, E. E. Short-chain fatty acids in control of body weight and insulin sensitivity. Nat. Rev. Endocrinol. 11, 577–591 (2015).

    Article  CAS  PubMed  Google Scholar 

  213. Zhao, S. et al. Dietary fructose feeds hepatic lipogenesis via microbiota-derived acetate. Nature 579, 586–591 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  214. Kindt, A. et al. The gut microbiota promotes hepatic fatty acid desaturation and elongation in mice. Nat. Commun. 9, 3760 (2018).

    Article  PubMed  PubMed Central  Google Scholar 

  215. Arpaia, N. et al. Metabolites produced by commensal bacteria promote peripheral regulatory T-cell generation. Nature 504, 451–455 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  216. Duscha, A. et al. Propionic acid shapes the multiple sclerosis disease course by an immunomodulatory mechanism. Cell 180, 1067–1080.e16 (2020).

    Article  CAS  PubMed  Google Scholar 

  217. Perino, A., Demagny, H., Velazquez-Villegas, L. & Schoonjans, K. Molecular physiology of bile acid signaling in health, disease, and aging. Physiol. Rev. 101, 683–731 (2021).

    Article  CAS  PubMed  Google Scholar 

  218. Ridlon, J. M., Harris, S. C., Bhowmik, S., Kang, D. J. & Hylemon, P. B. Consequences of bile salt biotransformations by intestinal bacteria. Gut Microbes 7, 22–39 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  219. Marion, S. et al. Biogeography of microbial bile acid transformations along the murine gut. J. Lipid Res. 61, 1450–1463 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  220. Fuchs, C. D. & Trauner, M. Role of bile acids and their receptors in gastrointestinal and hepatic pathophysiology. Nat. Rev. Gastroenterol. Hepatol. 19, 432–450 (2022).

    Article  CAS  PubMed  Google Scholar 

  221. Keitel, V., Stindt, J. & Haussinger, D. Bile acid-activated receptors: GPBAR1 (TGR5) and other G protein-coupled receptors. Handb. Exp. Pharmacol. 256, 19–49 (2019).

    Article  CAS  PubMed  Google Scholar 

  222. Leonhardt, J. et al. Circulating bile acids in liver failure activate TGR5 and induce monocyte dysfunction. Cell Mol. Gastroenterol. Hepatol. 12, 25–40 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  223. Schaap, F. G., Trauner, M. & Jansen, P. L. Bile acid receptors as targets for drug development. Nat. Rev. Gastroenterol. Hepatol. 11, 55–67 (2014).

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgements

The authors were supported by the German Research Foundation (DFG) Project-ID 403224013 – SFB 1382.

Author information

Authors and Affiliations

Authors

Contributions

The authors contributed equally to all aspects of the article.

Corresponding author

Correspondence to Oliver Pabst.

Ethics declarations

Competing interests

The authors declare no competing interests.

Peer review

Peer review information

Nature Reviews Gastroenterology & Hepatology thanks Harry Sokol, Reiner Wiest and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

Additional information

Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Rights and permissions

Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Pabst, O., Hornef, M.W., Schaap, F.G. et al. Gut–liver axis: barriers and functional circuits. Nat Rev Gastroenterol Hepatol 20, 447–461 (2023). https://doi.org/10.1038/s41575-023-00771-6

Download citation

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/s41575-023-00771-6

This article is cited by

Search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing