1932

Abstract

It is known that the gut microbiota, the numerically vast and taxonomically diverse microbial communities that thrive in a symbiotic fashion within our alimentary tract, can affect the normal physiology of the gastrointestinal tract and liver. Further, disturbances of the microbiota community structure from both endogenous and exogenous influences as well as the failure of host responsive mechanisms have been implicated in a variety of disease processes. Mechanistically, alterations in intestinal permeability and dysbiosis of the microbiota can result in inflammation, immune activation, and exposure to xenobiotic influences. Additionally, the gut and liver are continually exposed to small molecule products of the microbiota with proinflammatory, gene regulatory, and oxidative properties. Long-term coevolution has led to tolerance and incorporation of these influences into normal physiology and homeostasis; conversely, changes in this equilibrium from either the host or the microbial side can result in a wide variety of immune, inflammatory, metabolic, and neoplastic intestinal and hepatic disorders.

Loading

Article metrics loading...

/content/journals/10.1146/annurev-pathol-030320-095722
2021-01-24
2024-04-18
Loading full text...

Full text loading...

/deliver/fulltext/pathmechdis/16/1/annurev-pathol-030320-095722.html?itemId=/content/journals/10.1146/annurev-pathol-030320-095722&mimeType=html&fmt=ahah

Literature Cited

  1. 1. 
    Virchow R. 1858. Cellular Pathology London: John Churchill
  2. 2. 
    de Bary HA. 1879. Die Erscheinung der Symbiose Strassburg: Verlag von Karl J. Trubner
  3. 3. 
    Bosch TCG, Guillemin K, McFall-Ngai M 2019. Evolutionary “experiments” in symbiosis: the study of model animals provides insights into the mechanisms underlying the diversity of host-microbe interactions. BioEssays 41:e1800256
    [Google Scholar]
  4. 4. 
    Geva-Zatorsky N, Elinav E, Pettersson S 2019. When cultures meet: the landscape of “social” interactions between the host and its indigenous microbes. BioEssays 41:e1900002
    [Google Scholar]
  5. 5. 
    Warnecke F, Luginbuhl P, Ivanova N, Ghassemian M, Richardson TH et al. 2007. Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite. Nature 450:560–65
    [Google Scholar]
  6. 6. 
    Flint HJ. 1997. The rumen microbial ecosystem—some recent developments. Trends Microbiol 5:483–88
    [Google Scholar]
  7. 7. 
    Neish AS. 2009. Microbes in gastrointestinal health and disease. Gastroenterology 136:65–80
    [Google Scholar]
  8. 8. 
    Vyas U, Ranganathan N. 2012. Probiotics, prebiotics, and synbiotics: gut and beyond. Gastroenterol. Res. Pract. 2012:872716
    [Google Scholar]
  9. 9. 
    Hollister EB, Gao C, Versalovic J 2014. Compositional and functional features of the gastrointestinal microbiome and their effects on human health. Gastroenterology 146:1449–58
    [Google Scholar]
  10. 10. 
    Gilbert JA, Quinn RA, Debelius J, Xu ZZ, Morton J et al. 2016. Microbiome-wide association studies link dynamic microbial consortia to disease. Nature 535:94–103
    [Google Scholar]
  11. 11. 
    Bach JF. 2018. The hygiene hypothesis in autoimmunity: the role of pathogens and commensals. Nat. Rev. Immunol. 18:105–20
    [Google Scholar]
  12. 12. 
    Cholapranee A, Ananthakrishnan AN. 2016. Environmental hygiene and risk of inflammatory bowel diseases: a systematic review and meta-analysis. Inflamm. Bowel Dis. 22:2191–99
    [Google Scholar]
  13. 13. 
    Ng SC, Shi HY, Hamidi N, Underwood FE, Tang W et al. 2018. Worldwide incidence and prevalence of inflammatory bowel disease in the 21st century: a systematic review of population-based studies. Lancet 390:2769–78
    [Google Scholar]
  14. 14. 
    Macpherson AJ, McCoy KD. 2015. Standardised animal models of host microbial mutualism. Mucosal Immunol 8:476–86
    [Google Scholar]
  15. 15. 
    Falk PG, Hooper LV, Midtvedt T, Gordon JI 1998. Creating and maintaining the gastrointestinal ecosystem: what we know and need to know from gnotobiology. Microbiol. Mol. Biol. Rev. 62:1157–70
    [Google Scholar]
  16. 16. 
    Smith K, McCoy KD, Macpherson AJ 2007. Use of axenic animals in studying the adaptation of mammals to their commensal intestinal microbiota. Semin. Immunol. 19:59–69
    [Google Scholar]
  17. 17. 
    Turnbaugh PJ, Ley RE, Hamady M, Fraser-Liggett CM, Knight R, Gordon JI 2007. The human microbiome project. Nature 449:804–10
    [Google Scholar]
  18. 18. 
    Gilbert JA, Blaser MJ, Caporaso JG, Jansson JK, Lynch SV, Knight R 2018. Current understanding of the human microbiome. Nat. Med. 24:392–400
    [Google Scholar]
  19. 19. 
    Hum. Microbiome Proj. Consort 2012. Structure, function and diversity of the healthy human microbiome. Nature 486:207–14
    [Google Scholar]
  20. 20. 
    Lozupone CA, Stombaugh JI, Gordon JI, Jansson JK, Knight R 2012. Diversity, stability and resilience of the human gut microbiota. Nature 489:220–30
    [Google Scholar]
  21. 21. 
    Chen F, Stappenbeck TS. 2019. Microbiome control of innate reactivity. Curr. Opin. Immunol. 56:107–13
    [Google Scholar]
  22. 22. 
    Schroeder BO, Backhed F. 2016. Signals from the gut microbiota to distant organs in physiology and disease. Nat. Med. 22:1079–89
    [Google Scholar]
  23. 23. 
    Dominguez-Bello MG, Godoy-Vitorino F, Knight R, Blaser MJ 2019. Role of the microbiome in human development. Gut 68:1108–14
    [Google Scholar]
  24. 24. 
    Tamburini S, Shen N, Wu HC, Clemente JC 2016. The microbiome in early life: implications for health outcomes. Nat. Med. 22:713–22
    [Google Scholar]
  25. 25. 
    David LA, Maurice CF, Carmody RN, Gootenberg DB, Button JE et al. 2014. Diet rapidly and reproducibly alters the human gut microbiome. Nature 505:559–63
    [Google Scholar]
  26. 26. 
    Sonnenburg ED, Smits SA, Tikhonov M, Higginbottom SK, Wingreen NS, Sonnenburg JL 2016. Diet-induced extinctions in the gut microbiota compound over generations. Nature 529:212–15
    [Google Scholar]
  27. 27. 
    Sonnenburg JL, Backhed F. 2016. Diet-microbiota interactions as moderators of human metabolism. Nature 535:56–64
    [Google Scholar]
  28. 28. 
    Kriss M, Hazleton KZ, Nusbacher NM, Martin CG, Lozupone CA 2018. Low diversity gut microbiota dysbiosis: drivers, functional implications and recovery. Curr. Opin. Microbiol. 44:34–40
    [Google Scholar]
  29. 29. 
    Modi SR, Collins JJ, Relman DA 2014. Antibiotics and the gut microbiota. J. Clin. Investig. 124:4212–18
    [Google Scholar]
  30. 30. 
    Maurice CF, Haiser HJ, Turnbaugh PJ 2013. Xenobiotics shape the physiology and gene expression of the active human gut microbiome. Cell 152:39–50
    [Google Scholar]
  31. 31. 
    Peterson LW, Artis D. 2014. Intestinal epithelial cells: regulators of barrier function and immune homeostasis. Nat. Rev. Immunol. 14:141–53
    [Google Scholar]
  32. 32. 
    Odenwald MA, Turner JR. 2017. The intestinal epithelial barrier: a therapeutic target. Nat. Rev. Gastroenterol. Hepatol. 14:9–21
    [Google Scholar]
  33. 33. 
    Luissint AC, Parkos CA, Nusrat A 2016. Inflammation and the intestinal barrier: leukocyte-epithelial cell interactions, cell junction remodeling, and mucosal repair. Gastroenterology 151:616–32
    [Google Scholar]
  34. 34. 
    Ivanov II, Honda K. 2012. Intestinal commensal microbes as immune modulators. Cell Host Microbe 12:496–508
    [Google Scholar]
  35. 35. 
    Jones RM, Neish AS. 2011. Recognition of bacterial pathogens and mucosal immunity. Cell Microbiol 13:670–76
    [Google Scholar]
  36. 36. 
    Johansson ME, Hansson GC. 2016. Immunological aspects of intestinal mucus and mucins. Nat. Rev. Immunol. 16:639–49
    [Google Scholar]
  37. 37. 
    Pastorelli L, De Salvo C, Mercado JR, Vecchi M, Pizarro TT 2013. Central role of the gut epithelial barrier in the pathogenesis of chronic intestinal inflammation: lessons learned from animal models and human genetics. Front. Immunol. 4:280
    [Google Scholar]
  38. 38. 
    Donaldson GP, Lee SM, Mazmanian SK 2016. Gut biogeography of the bacterial microbiota. Nat. Rev. Microbiol. 14:20–32
    [Google Scholar]
  39. 39. 
    Martinez-Guryn K, Leone V, Chang EB 2019. Regional diversity of the gastrointestinal microbiome. Cell Host Microbe 26:314–24
    [Google Scholar]
  40. 40. 
    Stappenbeck TS, Hooper LV, Gordon JI 2002. Developmental regulation of intestinal angiogenesis by indigenous microbes via Paneth cells. PNAS 99:15451–55
    [Google Scholar]
  41. 41. 
    Chandrasekharan B, Saeedi BJ, Alam A, Houser M, Srinivasan S et al. 2019. Interactions between commensal bacteria and enteric neurons, via FPR1 induction of ROS, increase gastrointestinal motility in mice. Gastroenterology 157:179–92.e2
    [Google Scholar]
  42. 42. 
    Abreu MT. 2010. Toll-like receptor signalling in the intestinal epithelium: how bacterial recognition shapes intestinal function. Nat. Rev. Immunol. 10:131–44
    [Google Scholar]
  43. 43. 
    Rakoff-Nahoum S, Paglino J, Eslami-Varzaneh F, Edberg S, Medzhitov R 2004. Recognition of commensal microflora by toll-like receptors is required for intestinal homeostasis. Cell 118:229–41
    [Google Scholar]
  44. 44. 
    Li X, Yang T, Sun Z 2019. Hormesis in health and chronic diseases. Trends Endocrinol. Metab. 30:944–58
    [Google Scholar]
  45. 45. 
    Lambeth JD, Neish AS. 2014. Nox enzymes and new thinking on reactive oxygen: a double-edged sword revisited. Annu. Rev. Pathol. Mech. Dis. 9:119–45
    [Google Scholar]
  46. 46. 
    Taylor CT, Colgan SP. 2017. Regulation of immunity and inflammation by hypoxia in immunological niches. Nat. Rev. Immunol. 17:774–85
    [Google Scholar]
  47. 47. 
    Alam A, Leoni G, Quiros M, Wu H, Desai C et al. 2016. The microenvironment of injured murine gut elicits a local pro-restitutive microbiota. Nat. Microbiol. 1:15021
    [Google Scholar]
  48. 48. 
    Jones RM, Neish AS. 2017. Redox signaling mediated by the gut microbiota. Free Radic. Biol. Med. 105:41–47
    [Google Scholar]
  49. 49. 
    Grasberger H, Gao J, Nagao-Kitamoto H, Kitamoto S, Zhang M et al. 2015. Increased expression of DUOX2 is an epithelial response to mucosal dysbiosis required for immune homeostasis in mouse intestine. Gastroenterology 149:1849–59
    [Google Scholar]
  50. 50. 
    Wentworth CC, Alam A, Jones RM, Nusrat A, Neish AS 2011. Enteric commensal bacteria induce extracellular signal-regulated kinase pathway signaling via formyl peptide receptor-dependent redox modulation of dual specific phosphatase 3. J. Biol. Chem. 286:38448–55
    [Google Scholar]
  51. 51. 
    Collier-Hyams LS, Sloane V, Batten BC, Neish AS 2005. Cutting edge: bacterial modulation of epithelial signaling via changes in neddylation of cullin-1. J. Immunol. 175:4194–98
    [Google Scholar]
  52. 52. 
    Swanson PA II, Kumar A, Samarin S, Vijay-Kumar M, Kundu K et al. 2011. Enteric commensal bacteria potentiate epithelial restitution via reactive oxygen species-mediated inactivation of focal adhesion kinase phosphatases. PNAS 108:8803–8
    [Google Scholar]
  53. 53. 
    Jones RM, Desai C, Darby TM, Luo L, Wolfarth AA et al. 2015. Lactobacilli modulate epithelial cytoprotection through the Nrf2 pathway. Cell Rep 12:1217–25
    [Google Scholar]
  54. 54. 
    Donohoe DR, Garge N, Zhang X, Sun W, O'Connell TM et al. 2011. The microbiome and butyrate regulate energy metabolism and autophagy in the mammalian colon. Cell Metab 13:517–26
    [Google Scholar]
  55. 55. 
    Sun M, Wu W, Liu Z, Cong Y 2017. Microbiota metabolite short chain fatty acids, GPCR, and inflammatory bowel diseases. J. Gastroenterol. 52:1–8
    [Google Scholar]
  56. 56. 
    Chang PV, Hao L, Offermanns S, Medzhitov R 2014. The microbial metabolite butyrate regulates intestinal macrophage function via histone deacetylase inhibition. PNAS 111:2247–52
    [Google Scholar]
  57. 57. 
    Schneider C, O'Leary CE, von Moltke J, Liang HE, Ang QY et al. 2018. A metabolite-triggered tuft cell-ILC2 circuit drives small intestinal remodeling. Cell 174:271–84.e14
    [Google Scholar]
  58. 58. 
    Levy M, Thaiss CA, Zeevi D, Dohnalova L, Zilberman-Schapira G et al. 2015. Microbiota-modulated metabolites shape the intestinal microenvironment by regulating NLRP6 inflammasome signaling. Cell 163:1428–43
    [Google Scholar]
  59. 59. 
    Jain U, Lai CW, Xiong S, Goodwin VM, Lu Q et al. 2018. Temporal regulation of the bacterial metabolite deoxycholate during colonic repair is critical for crypt regeneration. Cell Host Microbe 24:353–63.e5
    [Google Scholar]
  60. 60. 
    Cervantes-Barragan L, Chai JN, Tianero MD, Di Luccia B, Ahern PP et al. 2017. Lactobacillus reuteri induces gut intraepithelial CD4+CD8αα+ T cells. Science 357:806–10
    [Google Scholar]
  61. 61. 
    Venkatesh M, Mukherjee S, Wang H, Li H, Sun K et al. 2014. Symbiotic bacterial metabolites regulate gastrointestinal barrier function via the xenobiotic sensor PXR and Toll-like receptor 4. Immunity 41:296–310
    [Google Scholar]
  62. 62. 
    Taguchi K, Kensler TW. 2020. Nrf2 in liver toxicology. Arch. Pharm. Res. 43:337–49
    [Google Scholar]
  63. 63. 
    Wlodarska M, Luo C, Kolde R, d'Hennezel E, Annand JW et al. 2017. Indoleacrylic acid produced by commensal Peptostreptococcus species suppresses inflammation. Cell Host Microbe 22:25–37.e6
    [Google Scholar]
  64. 64. 
    Jones RM, Luo L, Ardita CS, Richardson AN, Kwon YM et al. 2013. Symbiotic lactobacilli stimulate gut epithelial proliferation via Nox-mediated generation of reactive oxygen species. EMBO J 32:3017–28
    [Google Scholar]
  65. 65. 
    Iatsenko I, Boquete JP, Lemaitre B 2018. Microbiota-derived lactate activates production of reactive oxygen species by the intestinal NADPH oxidase Nox and shortens Drosophila lifespan. Immunity 49:929–42.e5
    [Google Scholar]
  66. 66. 
    Reedy AR, Luo L, Neish AS, Jones RM 2019. Commensal microbiota-induced redox signaling activates proliferative signals in the intestinal stem cell microenvironment. Development 146:dev171520
    [Google Scholar]
  67. 67. 
    Storelli G, Defaye A, Erkosar B, Hols P, Royet J, Leulier F 2011. Lactobacillus plantarum promotes Drosophila systemic growth by modulating hormonal signals through TOR-dependent nutrient sensing. Cell Metab 14:403–14
    [Google Scholar]
  68. 68. 
    Brazil JC, Quiros M, Nusrat A, Parkos CA 2019. Innate immune cell-epithelial crosstalk during wound repair. J. Clin. Investig. 129:2983–93
    [Google Scholar]
  69. 69. 
    Matthews JD, Owens JA, Naudin CR, Saeedi BJ, Alam A et al. 2019. Neutrophil-derived reactive oxygen orchestrates epithelial cell signaling events during intestinal repair. Am. J. Pathol. 189:2221–32
    [Google Scholar]
  70. 70. 
    Pull SL, Doherty JM, Mills JC, Gordon JI, Stappenbeck TS 2005. Activated macrophages are an adaptive element of the colonic epithelial progenitor niche necessary for regenerative responses to injury. PNAS 102:99–104
    [Google Scholar]
  71. 71. 
    Alam A, Leoni G, Wentworth CC, Kwal JM, Wu H et al. 2014. Redox signaling regulates commensal-mediated mucosal homeostasis and restitution and requires formyl peptide receptor 1. Mucosal Immunol 7:645–55
    [Google Scholar]
  72. 72. 
    Kelly CJ, Zheng L, Campbell EL, Saeedi B, Scholz CC et al. 2015. Crosstalk between microbiota-derived short-chain fatty acids and intestinal epithelial HIF augments tissue barrier function. Cell Host Microbe 17:662–71
    [Google Scholar]
  73. 73. 
    Kaiko GE, Ryu SH, Koues OI, Collins PL, Solnica-Krezel L et al. 2016. The colonic crypt protects stem cells from microbiota-derived metabolites. Cell 165:1708–20
    [Google Scholar]
  74. 74. 
    Noto JM, Peek RM Jr 2017. The gastric microbiome, its interaction with Helicobacter pylori, and its potential role in the progression to stomach cancer. PLOS Pathog 13:e1006573
    [Google Scholar]
  75. 75. 
    Kommineni S, Bretl DJ, Lam V, Chakraborty R, Hayward M et al. 2015. Bacteriocin production augments niche competition by enterococci in the mammalian gastrointestinal tract. Nature 526:719–22
    [Google Scholar]
  76. 76. 
    Messaoudi S, Manai M, Kergourlay G, Prevost H, Connil N et al. 2013. Lactobacillus salivarius: bacteriocin and probiotic activity. Food Microbiol 36:296–304
    [Google Scholar]
  77. 77. 
    O'Shea EF, O'Connor PM, Raftis EJ, O'Toole PW, Stanton C et al. 2011. Production of multiple bacteriocins from a single locus by gastrointestinal strains of Lactobacillus salivarius. J. . Bacteriol 193:6973–82
    [Google Scholar]
  78. 78. 
    Slingerland AE, Schwabkey Z, Wiesnoski DH, Jenq RR 2017. Clinical evidence for the microbiome in inflammatory diseases. Front. Immunol. 8:400
    [Google Scholar]
  79. 79. 
    Halfvarson J, Brislawn CJ, Lamendella R, Vazquez-Baeza Y, Walters WA et al. 2017. Dynamics of the human gut microbiome in inflammatory bowel disease. Nat. Microbiol. 2:17004
    [Google Scholar]
  80. 80. 
    Gevers D, Kugathasan S, Denson LA, Vazquez-Baeza Y, Van Treuren W et al. 2014. The treatment-naive microbiome in new-onset Crohn's disease. Cell Host Microbe 15:382–92
    [Google Scholar]
  81. 81. 
    Mueller C, Macpherson AJ. 2006. Layers of mutualism with commensal bacteria protect us from intestinal inflammation. Gut 55:276–84
    [Google Scholar]
  82. 82. 
    McGovern DPB, Kugathasan S, Cho JH 2015. Genetics of inflammatory bowel diseases. Gastroenterology 149:1163–76.e2
    [Google Scholar]
  83. 83. 
    Artis D. 2008. Epithelial-cell recognition of commensal bacteria and maintenance of immune homeostasis in the gut. Nat. Rev. Immunol. 8:411–20
    [Google Scholar]
  84. 84. 
    Denning TL, Wang YC, Patel SR, Williams IR, Pulendran B 2007. Lamina propria macrophages and dendritic cells differentially induce regulatory and interleukin 17-producing T cell responses. Nat. Immunol. 8:1086–94
    [Google Scholar]
  85. 85. 
    Lee JS, Tato CM, Joyce-Shaikh B, Gulen MF, Cayatte C et al. 2015. Interleukin-23-independent IL-17 production regulates intestinal epithelial permeability. Immunity 43:727–38
    [Google Scholar]
  86. 86. 
    Yen D, Cheung J, Scheerens H, Poulet F, McClanahan T et al. 2006. IL-23 is essential for T cell-mediated colitis and promotes inflammation via IL-17 and IL-6. J. Clin. Investig. 116:1310–16
    [Google Scholar]
  87. 87. 
    Mohammadnia-Afrouzi M, Zavaran Hosseini A, Khalili A, Abediankenari S, Hosseini V, Maleki I 2015. Decrease of CD4+ CD25+ CD127low FoxP3+ regulatory T cells with impaired suppressive function in untreated ulcerative colitis patients. Autoimmunity 48:556–61
    [Google Scholar]
  88. 88. 
    Round JL, Mazmanian SK. 2010. Inducible Foxp3+ regulatory T-cell development by a commensal bacterium of the intestinal microbiota. PNAS 107:12204–9
    [Google Scholar]
  89. 89. 
    Furusawa Y, Obata Y, Fukuda S, Endo TA, Nakato G et al. 2013. Commensal microbe-derived butyrate induces the differentiation of colonic regulatory T cells. Nature 504:446–50
    [Google Scholar]
  90. 90. 
    Atarashi K, Tanoue T, Oshima K, Suda W, Nagano Y et al. 2013. Treg induction by a rationally selected mixture of Clostridia strains from the human microbiota. Nature 500:232–26
    [Google Scholar]
  91. 91. 
    Smith PM, Howitt MR, Panikov N, Michaud M, Gallini CA et al. 2013. The microbial metabolites, short-chain fatty acids, regulate colonic Treg cell homeostasis. Science 341:569–73
    [Google Scholar]
  92. 92. 
    Arpaia N, Campbell C, Fan X, Dikiy S, van der Veeken J et al. 2013. Metabolites produced by commensal bacteria promote peripheral regulatory T-cell generation. Nature 504:451–55
    [Google Scholar]
  93. 93. 
    Kudelka MR, Hinrichs BH, Darby T, Moreno CS, Nishio H et al. 2016. Cosmc is an X-linked inflammatory bowel disease risk gene that spatially regulates gut microbiota and contributes to sex-specific risk. PNAS 113:14787–92
    [Google Scholar]
  94. 94. 
    Geerlings SY, Kostopoulos I, de Vos WM, Belzer C 2018. Akkermansia muciniphila in the human gastrointestinal tract: when, where, and how. Microorganisms 6:75
    [Google Scholar]
  95. 95. 
    Song M, Chan AT. 2019. Environmental factors, gut microbiota, and colorectal cancer prevention. Clin. Gastroenterol. Hepatol. 17:275–89
    [Google Scholar]
  96. 96. 
    Scott AJ, Alexander JL, Merrifield CA, Cunningham D, Jobin C et al. 2019. International Cancer Microbiome Consortium consensus statement on the role of the human microbiome in carcinogenesis. Gut 68:1624–32
    [Google Scholar]
  97. 97. 
    Yachida S, Mizutani S, Shiroma H, Shiba S, Nakajima T et al. 2019. Metagenomic and metabolomic analyses reveal distinct stage-specific phenotypes of the gut microbiota in colorectal cancer. Nat. Med. 25:968–76
    [Google Scholar]
  98. 98. 
    Kostic AD, Gevers D, Pedamallu CS, Michaud M, Duke F et al. 2012. Genomic analysis identifies association of Fusobacterium with colorectal carcinoma. Genome Res 22:292–98
    [Google Scholar]
  99. 99. 
    Mima K, Nishihara R, Qian ZR, Cao Y, Sukawa Y et al. 2016. Fusobacterium nucleatum in colorectal carcinoma tissue and patient prognosis. Gut 65:1973–80
    [Google Scholar]
  100. 100. 
    Boleij A, Hechenbleikner EM, Goodwin AC, Badani R, Stein EM et al. 2015. The Bacteroides fragilis toxin gene is prevalent in the colon mucosa of colorectal cancer patients. Clin. Infect. Dis. 60:208–15
    [Google Scholar]
  101. 101. 
    Purcell RV, Pearson J, Aitchison A, Dixon L, Frizelle FA, Keenan JI 2017. Colonization with enterotoxigenic Bacteroides fragilis is associated with early-stage colorectal neoplasia. PLOS ONE 12:e0171602
    [Google Scholar]
  102. 102. 
    Bonnet M, Buc E, Sauvanet P, Darcha C, Dubois D et al. 2014. Colonization of the human gut by E. coli and colorectal cancer risk. Clin. Cancer Res. 20:859–67
    [Google Scholar]
  103. 103. 
    Dejea CM, Fathi P, Craig JM, Boleij A, Taddese R et al. 2018. Patients with familial adenomatous polyposis harbor colonic biofilms containing tumorigenic bacteria. Science 359:592–97
    [Google Scholar]
  104. 104. 
    Abdulamir AS, Hafidh RR, Abu Bakar F 2011. The association of Streptococcus bovis/gallolyticus with colorectal tumors: the nature and the underlying mechanisms of its etiological role. J. Exp. Clin. Cancer Res. 30:11
    [Google Scholar]
  105. 105. 
    Mughini-Gras L, Schaapveld M, Kramers J, Mooij S, Neefjes-Borst EA et al. 2018. Increased colon cancer risk after severe Salmonella infection. PLOS ONE 13:e0189721
    [Google Scholar]
  106. 106. 
    Butt J, Varga MG, Blot WJ, Teras L, Visvanathan K et al. 2019. Serologic response to Helicobacter pylori proteins associated with risk of colorectal cancer among diverse populations in the United States. Gastroenterology 156:175–86.e2
    [Google Scholar]
  107. 107. 
    Chen HM, Yu YN, Wang JL, Lin YW, Kong X et al. 2013. Decreased dietary fiber intake and structural alteration of gut microbiota in patients with advanced colorectal adenoma. Am. J. Clin. Nutr. 97:1044–52
    [Google Scholar]
  108. 108. 
    Thomas AM, Manghi P, Asnicar F, Pasolli E, Armanini F et al. 2019. Metagenomic analysis of colorectal cancer datasets identifies cross-cohort microbial diagnostic signatures and a link with choline degradation. Nat. Med. 25:667–78
    [Google Scholar]
  109. 109. 
    Dawson PA, Karpen SJ. 2015. Intestinal transport and metabolism of bile acids. J. Lipid Res. 56:1085–99
    [Google Scholar]
  110. 110. 
    Bayerdorffer E, Mannes GA, Ochsenkuhn T, Dirschedl P, Wiebecke B, Paumgartner G 1995. Unconjugated secondary bile acids in the serum of patients with colorectal adenomas. Gut 36:268–73
    [Google Scholar]
  111. 111. 
    Cross AJ, Moore SC, Boca S, Huang WY, Xiong X et al. 2014. A prospective study of serum metabolites and colorectal cancer risk. Cancer 120:3049–57
    [Google Scholar]
  112. 112. 
    Islam KBMS, Fukiya S, Hagio M, Fujii N, Ishizuka S et al. 2011. Bile acid is a host factor that regulates the composition of the cecal microbiota in rats. Gastroenterology 141:1773–81
    [Google Scholar]
  113. 113. 
    Wirbel J, Pyl PT, Kartal E, Zych K, Kashani A et al. 2019. Meta-analysis of fecal metagenomes reveals global microbial signatures that are specific for colorectal cancer. Nat. Med. 25:679–89
    [Google Scholar]
  114. 114. 
    Zeng HW, Umar S, Rust B, Lazarova D, Bordonaro M 2019. Secondary bile acids and short chain fatty acids in the colon: a focus on colonic microbiome, cell proliferation, inflammation, and cancer. Int. J. Mol. Sci. 20:1214
    [Google Scholar]
  115. 115. 
    Macpherson AJ, Heikenwalder M, Ganal-Vonarburg SC 2016. The liver at the nexus of host-microbial interactions. Cell Host Microbe 20:561–71
    [Google Scholar]
  116. 116. 
    Tripathi A, Debelius J, Brenner DA, Karin M, Loomba R et al. 2018. The gut-liver axis and the intersection with the microbiome. Nat. Rev. Gastroenterol. Hepatol. 15:397–411
    [Google Scholar]
  117. 117. 
    Klaassen CD, Cui JY. 2015. Review: mechanisms of how the intestinal microbiota alters the effects of drugs and bile acids. Drug Metab. Dispos. 43:1505–21
    [Google Scholar]
  118. 118. 
    Sayin SI, Wahlstrom A, Felin J, Jantti S, Marschall HU et al. 2013. Gut microbiota regulates bile acid metabolism by reducing the levels of tauro-beta-muricholic acid, a naturally occurring FXR antagonist. Cell Metab 17:225–35
    [Google Scholar]
  119. 119. 
    Wahlstrom A, Sayin SI, Marschall HU, Backhed F 2016. Intestinal crosstalk between bile acids and microbiota and its impact on host metabolism. Cell Metab 24:41–50
    [Google Scholar]
  120. 120. 
    Jia W, Xie G, Jia W 2018. Bile acid–microbiota crosstalk in gastrointestinal inflammation and carcinogenesis. Nat. Rev. Gastroenterol. Hepatol. 15:111–28
    [Google Scholar]
  121. 121. 
    Spadoni I, Zagato E, Bertocchi A, Paolinelli R, Hot E et al. 2015. A gut-vascular barrier controls the systemic dissemination of bacteria. Science 350:830–34
    [Google Scholar]
  122. 122. 
    Balmer ML, Slack E, de Gottardi A, Lawson MA, Hapfelmeier S et al. 2014. The liver may act as a firewall mediating mutualism between the host and its gut commensal microbiota. Sci. Transl. Med. 6:237ra66
    [Google Scholar]
  123. 123. 
    Wikoff WR, Anfora AT, Liu J, Schultz PG, Lesley SA et al. 2009. Metabolomics analysis reveals large effects of gut microflora on mammalian blood metabolites. PNAS 106:3698–703
    [Google Scholar]
  124. 124. 
    Wu KC, Cui JY, Klaassen CD 2012. Effect of graded Nrf2 activation on phase-I and -II drug metabolizing enzymes and transporters in mouse liver. PLOS ONE 7:e39006
    [Google Scholar]
  125. 125. 
    Okawa H, Motohashi H, Kobayashi A, Aburatani H, Kensler TW, Yamamoto M 2006. Hepatocyte-specific deletion of the keap1 gene activates Nrf2 and confers potent resistance against acute drug toxicity. Biochem. Biophys. Res. Commun. 339:79–88
    [Google Scholar]
  126. 126. 
    Enomoto A, Itoh K, Nagayoshi E, Haruta J, Kimura T et al. 2001. High sensitivity of Nrf2 knockout mice to acetaminophen hepatotoxicity associated with decreased expression of ARE-regulated drug metabolizing enzymes and antioxidant genes. Toxicol. Sci. 59:169–77
    [Google Scholar]
  127. 127. 
    Ke B, Shen X-D, Zhang Y, Ji H, Gao F et al. 2013. KEAP1-NRF2 complex in ischemia-induced hepatocellular damage of mouse liver transplants. J. Hepatol. 59:1200–7
    [Google Scholar]
  128. 128. 
    Saeedi BJ, Liu KH, Owens AO, Hunter-Chang S, Camacho MC et al. 2020. Gut resident Lactobacilli activate hepatic Nrf2 and protect against oxidative injury. Cell Metab 31:956–68.e5
    [Google Scholar]
  129. 129. 
    Hartmann P, Seebauer CT, Schnabl B 2015. Alcoholic liver disease: the gut microbiome and liver cross talk. Alcohol Clin. Exp. Res. 39:763–75
    [Google Scholar]
  130. 130. 
    Shao T, Zhao C, Li F, Gu Z, Liu L et al. 2018. Intestinal HIF-1α deletion exacerbates alcoholic liver disease by inducing intestinal dysbiosis and barrier dysfunction. J. Hepatol. 69:886–95
    [Google Scholar]
  131. 131. 
    Hartmann P, Chen P, Wang HJ, Wang L, McCole DF et al. 2013. Deficiency of intestinal mucin-2 ameliorates experimental alcoholic liver disease in mice. Hepatology 58:108–19
    [Google Scholar]
  132. 132. 
    Wang L, Fouts DE, Starkel P, Hartmann P, Chen P et al. 2016. Intestinal REG3 lectins protect against alcoholic steatohepatitis by reducing mucosa-associated microbiota and preventing bacterial translocation. Cell Host Microbe 19:227–39
    [Google Scholar]
  133. 133. 
    Qin N, Yang F, Li A, Prifti E, Chen Y et al. 2014. Alterations of the human gut microbiome in liver cirrhosis. Nature 513:59–64
    [Google Scholar]
  134. 134. 
    Loomba R, Seguritan V, Li W, Long T, Klitgord N et al. 2017. Gut microbiome-based metagenomic signature for non-invasive detection of advanced fibrosis in human nonalcoholic fatty liver disease. Cell Metab 25:1054–62.e5
    [Google Scholar]
  135. 135. 
    Rahman K, Desai C, Iyer SS, Thorn NE, Kumar P et al. 2016. Loss of junctional adhesion molecule a promotes severe steatohepatitis in mice on a diet high in saturated fat, fructose, and cholesterol. Gastroenterology 151:733–46.e12
    [Google Scholar]
  136. 136. 
    Henao-Mejia J, Elinav E, Jin C, Hao L, Mehal WZ et al. 2012. Inflammasome-mediated dysbiosis regulates progression of NAFLD and obesity. Nature 482:179–85
    [Google Scholar]
  137. 137. 
    Kummen M, Hov JR. 2019. The gut microbial influence on cholestatic liver disease. Liver Int 39:1186–96
    [Google Scholar]
  138. 138. 
    Nakamoto N, Sasaki N, Aoki R, Miyamoto K, Suda W et al. 2019. Gut pathobionts underlie intestinal barrier dysfunction and liver T helper 17 cell immune response in primary sclerosing cholangitis. Nat. Microbiol. 4:492–503
    [Google Scholar]
  139. 139. 
    Liao L, Schneider KM, Galvez EJC, Frissen M, Marschall HU et al. 2019. Intestinal dysbiosis augments liver disease progression via NLRP3 in a murine model of primary sclerosing cholangitis. Gut 68:1477–92
    [Google Scholar]
  140. 140. 
    Singh V, Yeoh BS, Chassaing B, Xiao X, Saha P et al. 2018. Dysregulated microbial fermentation of soluble fiber induces cholestatic liver cancer. Cell 175:679–94.e22
    [Google Scholar]
  141. 141. 
    Yoshimoto S, Loo TM, Atarashi K, Kanda H, Sato S et al. 2013. Obesity-induced gut microbial metabolite promotes liver cancer through senescence secretome. Nature 499:97–101
    [Google Scholar]
  142. 142. 
    Dapito DH, Mencin A, Gwak GY, Pradere JP, Jang MK et al. 2012. Promotion of hepatocellular carcinoma by the intestinal microbiota and TLR4. Cancer Cell 21:504–16
    [Google Scholar]
/content/journals/10.1146/annurev-pathol-030320-095722
Loading
/content/journals/10.1146/annurev-pathol-030320-095722
Loading

Data & Media loading...

  • Article Type: Review Article
This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error