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The Importance of the Microbiome in the Gut

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Clinical Understanding of the Human Gut Microbiome

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Abstract

The recognition and study of microbes present throughout the human gastrointestinal tract is centuries old. Initially with an observational and descriptive approach, the field evolved via Koch’s postulates to emphasize the germ-theory approach to the roles of the gut microbiota in human health and disease. Two landmark advances in the field of microbiology during the twentieth Century catalyzed step-advances in our knowledge and approach to the study of the gut microbiota. First, the development of techniques for the cultivation and characterization of fastidious anaerobic bacteria expanded our awareness of the complex interplay between the host and both infectious as well as “commensal” microorganisms. Second, the development of high throughput DNA sequencing technologies expanded the scale and scope of our understanding of the human gut microbiota and with it, “microbiome research” brought about a broader acceptance of microbes as a community affecting health and disease. Here, we provide a brief overview of the evolution of gut microbiota research, resulting in a more clinically relevant definition of the term “microbiome” and how this research is providing new insights relevant to the improved understanding of the establishment of the gut microbiota and its links with the pathophysiology, diagnosis and treatment of digestive diseases and disorders.

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References

  1. Du H, Kuang T-T, Qiu S, Xu T, Gang Huan C-L, Fan G, et al. Fecal medicines used in traditional medical system of China: a systematic review of their names, original species, traditional uses, and modern investigations. Chin Med. 2019;14:31.

    Article  PubMed  PubMed Central  Google Scholar 

  2. de Groot PF, Frissen MN, de Clercq NC, Nieuwdorp M. Fecal microbiota transplantation in metabolic syndrome: history, present and future. Gut Microbes. 2017;8(3):253–67.

    Article  PubMed  PubMed Central  Google Scholar 

  3. Corliss JO. A salute to Antony van Leeuwenhoek of Delft, most versatile 17th century founding father of protistology. Protist. 2002;153(2):177–90.

    Article  PubMed  Google Scholar 

  4. Kyle RA, Steensma DP, Shampo MA. Barry James Marshall 2014; discovery of Helicobacter pylori as a cause of peptic ulcer. Mayo Clin Proc. 2016;91(5):e67–8.

    Article  PubMed  Google Scholar 

  5. Hacker J, Blum-Oehler G. In appreciation of Theodor Escherich. Nat Rev Microbiol. 2007;5(12):902.

    Article  CAS  Google Scholar 

  6. Savage DC. Microbial biota of the human intestine: a tribute to some pioneering scientists. Curr Issues Intest Microbiol. 2001;2(1):1–15.

    CAS  PubMed  Google Scholar 

  7. Grenham S, Clarke G, Cryan JF, Dinan TG. Brain-gut-microbe communication in health and disease. Front Physiol. 2011;2:94.

    Article  PubMed  PubMed Central  Google Scholar 

  8. Fessler J, Matson V, Gajewski TF. Exploring the emerging role of the microbiome in cancer immunotherapy. J Immunother Cancer. 2019;7(1):108.

    Article  PubMed  PubMed Central  Google Scholar 

  9. Farzi A, Fröhlich EE, Holzer P. Gut microbiota and the neuroendocrine system. Neurotherapeutics. 2018;15(1):5–22.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Schroeder BO, Bäckhed F. Signals from the gut microbiota to distant organs in physiology and disease. Nat Med. 2016;22(10):1079–89.

    Article  CAS  PubMed  Google Scholar 

  11. Hooper LV, Wong MH, Thelin A, Hansson L, Falk PG, Gordon JI. Molecular analysis of commensal host-microbial relationships in the intestine. Science. 2001;291(5505):881–4.

    Article  CAS  PubMed  Google Scholar 

  12. Stappenbeck TS, Hooper LV, Gordon JI. Developmental regulation of intestinal angiogenesis by indigenous microbes via Paneth cells. PNAS. 2002;99(24):15451–5.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Turnbaugh PJ, Ley RE, Mahowald MA, Magrini V, Mardis ER, Gordon JI. An obesity-associated gut microbiome with increased capacity for energy harvest. Nature. 2006;444(7122):1027–31.

    Article  PubMed  Google Scholar 

  14. Turnbaugh PJ, Ridaura VK, Faith JJ, Rey FE, Knight R, Gordon JI. The effect of diet on the human gut microbiome: a metagenomic analysis in humanized gnotobiotic mice. Sci Transl Med. 2009;1(6):6ra14.

    Article  PubMed  PubMed Central  Google Scholar 

  15. Ridaura VK, Faith JJ, Rey FE, Cheng J, Duncan AE, Kau AL, et al. Gut microbiota from twins discordant for obesity modulate metabolism in mice. Science. 2013;341(6150):1241214.

    Article  PubMed  Google Scholar 

  16. Ducarmon QR, Zwittink RD, Hornung BVH, van Schaik W, Young VB, Kuijper EJ. Gut microbiota and colonization resistance against bacterial enteric infection. Microbiol Mol Biol Rev. 2019;83(3):e00007-19.

    Article  PubMed  PubMed Central  Google Scholar 

  17. Becattini S, Littmann ER, Carter RA, Kim SG, Morjaria SM, Ling L, et al. Commensal microbes provide first line defense against Listeria monocytogenes infection. J Exp Med. 2017;214(7):1973–89.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Bhattarai Y, Kashyap PC. Germ-free mice model for studying host-microbial interactions. Methods Mol Biol. 2016;1438:123–35.

    Article  CAS  PubMed  Google Scholar 

  19. Walter J, Armet AM, Finlay BB, Shanahan F. Establishing or exaggerating causality for the gut microbiome: lessons from human microbiota-associated rodents. Cell. 2020;180(2):221–32.

    Article  CAS  PubMed  Google Scholar 

  20. Quigley EM. Basic definitions and concepts: organization of the gut microbiome. Gastroenterol Clin North Am. 2017;46(1):1–8.

    Article  PubMed  Google Scholar 

  21. Morgan XC, Huttenhower C. Chapter 12: Human microbiome analysis. PLoS Comput Biol. 2012;8(12):e1002808.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Malla MA, Dubey A, Kumar A, Yadav S, Hashem A, Abd_Allah EF. Exploring the human microbiome: the potential future role of next-generation sequencing in disease diagnosis and treatment. Front Immunol. 2019;9:2868.

    Google Scholar 

  23. Garmaeva S, Sinha T, Kurilshikov A, Fu J, Wijmenga C, Zhernakova A. Studying the gut virome in the metagenomic era: challenges and perspectives. BMC Biol. 2019;17(1):84.

    Article  PubMed  PubMed Central  Google Scholar 

  24. Coker OO, Nakatsu G, Dai RZ, Wu WKK, Wong SH, Ng SC, et al. Enteric fungal microbiota dysbiosis and ecological alterations in colorectal cancer. Gut. 2019;68(4):654–62.

    Article  CAS  PubMed  Google Scholar 

  25. Di Paola M, Rizzetto L, Stefanini I, Vitali F, Massi-Benedetti C, Tocci N, et al. Comparative immunophenotyping of Saccharomyces cerevisiae and Candida spp. strains from Crohn’s disease patients and their interactions with the gut microbiome. J Transl Autoimmun. 2020;3:100036.

    Article  PubMed  PubMed Central  Google Scholar 

  26. Tito RY, Chaffron S, Caenepeel C, Lima-Mendez G, Wang J, Vieira-Silva S, et al. Population-level analysis of Blastocystis subtype prevalence and variation in the human gut microbiota. Gut. 2019;68(7):1180–9.

    Article  CAS  PubMed  Google Scholar 

  27. Berg G, Rybakova D, Fischer D, Cernava T, Vergès M-CC, Charles T, et al. Microbiome definition re-visited: old concepts and new challenges. Microbiome. 2020;8(1):103.

    Article  PubMed  PubMed Central  Google Scholar 

  28. Proctor L, LoTempio J, Marquitz A, Daschner P, Xi D, Flores R, et al. A review of 10 years of human microbiome research activities at the US National Institutes of Health, Fiscal Years 2007-2016. Microbiome. 2019;7(1):31.

    Article  Google Scholar 

  29. Robles-Alonso V, Guarner F. From basic to applied research: lessons from the human microbiome projects. J Clin Gastroenterol. 2014;48(Suppl 1):S3–4.

    Article  PubMed  Google Scholar 

  30. Proctor LM, Creasy HH, Fettweis JM, Lloyd-Price J, Mahurkar A, Zhou W, et al. The integrative human microbiome project. Nature. 2019;569(7758):641–8.

    Article  Google Scholar 

  31. Hadrich D. Microbiome research is becoming the key to better understanding health and nutrition. Front Genet. 2018;9:212.

    Article  PubMed  PubMed Central  Google Scholar 

  32. Aagaard K, Ma J, Antony KM, Ganu R, Petrosino J, Versalovic J. The placenta harbors a unique microbiome. Sci Transl Med. 2014;6(237):237ra65.

    Article  PubMed  PubMed Central  Google Scholar 

  33. Theis KR, Romero R, Winters AD, Greenberg JM, Gomez-Lopez N, Alhousseini A, et al. Does the human placenta delivered at term have a microbiota? Results of cultivation, quantitative real-time PCR, 16S rRNA gene sequencing, and metagenomics. Am J Obstet Gynecol. 2019;220(3):267.e1–39.

    Article  CAS  PubMed  Google Scholar 

  34. Neuman H, Koren O. The pregnancy microbiome. Nestle Nutr Inst Workshop Ser. 2017;88:1–9.

    Article  PubMed  Google Scholar 

  35. Neu J, Rushing J. Cesarean versus vaginal delivery: long-term infant outcomes and the hygiene hypothesis. Clin Perinatol. 2011;38(2):321–31.

    Article  PubMed  PubMed Central  Google Scholar 

  36. Shao Y, Forster SC, Tsaliki E, Vervier K, Strang A, Simpson N, et al. Stunted microbiota and opportunistic pathogen colonization in caesarean-section birth. Nature. 2019;574(7776):117–21.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. Korpela K, Helve O, Kolho KL, Saisto T, Skogberg K, Dikareva E, et al. Maternal fecal microbiota transplantation in cesarean-born infants rapidly restores normal gut microbial development: a proof-of-concept study. Cell. 2020;183(2):324–34.e5.

    Article  CAS  PubMed  Google Scholar 

  38. Chong PP, Chin VK, Looi CY, Wong WF, Madhavan P, Yong VC. The microbiome and irritable bowel syndrome—a review on the pathophysiology, current research and future therapy. Front Microbiol. 2019;10:1136.

    Article  PubMed  PubMed Central  Google Scholar 

  39. Tap J, Derrien M, Tornblom H, Brazeilles R, Cools-Portier S, Dore J, et al. Identification of an intestinal microbiota signature associated with severity of irritable bowel syndrome. Gastroenterology. 2017;152(1):111–23.e8.

    Article  PubMed  Google Scholar 

  40. Rajilić-Stojanović M, Jonkers DM, Salonen A, Hanevik K, Raes J, Jalanka J, et al. Intestinal microbiota and diet in IBS: causes, consequences, or epiphenomena? Am J Gastroenterol. 2015;110(2):278–87.

    Article  PubMed  PubMed Central  Google Scholar 

  41. Pimentel M, Lembo A. Microbiome and its role in irritable bowel syndrome. Dig Dis Sci. 2020;65(3):829–39.

    Article  CAS  PubMed  Google Scholar 

  42. Pascal V, Pozuelo M, Borruel N, Casellas F, Campos D, Santiago A, et al. A microbial signature for Crohn’s disease. Gut. 2017;66(5):813–22.

    Article  CAS  PubMed  Google Scholar 

  43. Mondot S, Kang S, Furet JP, Aguirre de Carcer D, McSweeney C, Morrison M, et al. Highlighting new phylogenetic specificities of Crohn’s disease microbiota. Inflamm Bowel Dis. 2011;17(1):185–92.

    Article  CAS  PubMed  Google Scholar 

  44. Matijašić M, Meštrović T, Paljetak HČ, Perić M, Barešić A, Verbanac D. Gut microbiota beyond bacteria-mycobiome, virome, archaeome, and eukaryotic parasites in IBD. Int J Mol Sci. 2020;21(8):2668.

    Article  PubMed  PubMed Central  Google Scholar 

  45. Ungaro F, Massimino L, D’Alessio S, Danese S. The gut virome in inflammatory bowel disease pathogenesis: from metagenomics to novel therapeutic approaches. United European Gastroenterol J. 2019;7(8):999–1007.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  46. Lam S, Zuo T, Ho M, Chan FKL, Chan PKS, Ng SC. Review article: fungal alterations in inflammatory bowel diseases. Aliment Pharmacol Ther. 2019;50(11–12):1159–71.

    Article  PubMed  Google Scholar 

  47. Zuo T, Lu XJ, Zhang Y, Cheung CP, Lam S, Zhang F, et al. Gut mucosal virome alterations in ulcerative colitis. Gut. 2019;68(7):1169–79.

    Article  CAS  PubMed  Google Scholar 

  48. Halmos EP, Christophersen CT, Bird AR, Shepherd SJ, Gibson PR, Muir JG. Diets that differ in their FODMAP content alter the colonic luminal microenvironment. Gut. 2015;64(1):93–100.

    Article  CAS  PubMed  Google Scholar 

  49. Staudacher HM, Whelan K. Altered gastrointestinal microbiota in irritable bowel syndrome and its modification by diet: probiotics, prebiotics and the low FODMAP diet. Proc Nutr Soc. 2016;75(3):306–18.

    Article  CAS  PubMed  Google Scholar 

  50. Staudacher HM, Whelan K. The low FODMAP diet: recent advances in understanding its mechanisms and efficacy in IBS. Gut. 2017;66(8):1517–27.

    Article  CAS  PubMed  Google Scholar 

  51. Pigneur B, Lepage P, Mondot S, Schmitz J, Goulet O, Doré J, et al. Mucosal healing and bacterial composition in response to enteral nutrition vs steroid-based induction therapy—a randomised prospective clinical trial in children with Crohn’s disease. J Crohns Colitis. 2019;13(7):846–55.

    Article  PubMed  Google Scholar 

  52. Murtaza N, Cuív PÓ, Morrison M. Diet and the microbiome. Gastroenterol Clin North Am. 2017;46(1):49–60.

    Article  PubMed  Google Scholar 

  53. MacLellan A, Moore-Connors J, Grant S, Cahill L, Langille MGI, Van Limbergen J. The impact of exclusive enteral nutrition (EEN) on the gut microbiome in Crohn’s disease: a review. Nutrients. 2017;9(5):447.

    Article  PubMed  PubMed Central  Google Scholar 

  54. Kaakoush NO, Day AS, Leach ST, Lemberg DA, Nielsen S, Mitchell HM. Effect of exclusive enteral nutrition on the microbiota of children with newly diagnosed Crohn’s disease. Clin Transl Gastroenterol. 2015;6(1):e71.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  55. Gevers D, Kugathasan S, Denson LA, Vazquez-Baeza Y, Van Treuren W, Ren B, et al. The treatment-naive microbiome in new-onset Crohn’s disease. Cell Host Microbe. 2014;15(3):382–92.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  56. De Cruz P, Kang S, Wagner J, Buckley M, Sim WH, Prideaux L, et al. Association between specific mucosa-associated microbiota in Crohn’s disease at the time of resection and subsequent disease recurrence: a pilot study. J Gastroenterol Hepatol. 2015;30(2):268–78.

    Article  PubMed  Google Scholar 

  57. Sokol H, Pigneur B, Watterlot L, Lakhdari O, Bermudez-Humaran LG, Gratadoux JJ, et al. Faecalibacterium prausnitzii is an anti-inflammatory commensal bacterium identified by gut microbiota analysis of Crohn disease patients. Proc Natl Acad Sci U S A. 2008;105(43):16731–6.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  58. Lloyd-Price J, Arze C, Ananthakrishnan AN, Schirmer M, Avila-Pacheco J, Poon TW, et al. Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases. Nature. 2019;569(7758):655–62.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  59. Schirmer M, Franzosa EA, Lloyd-Price J, McIver LJ, Schwager R, Poon TW, et al. Dynamics of metatranscription in the inflammatory bowel disease gut microbiome. Nat Microbiol. 2018;3(3):337–46.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  60. Varela E, Manichanh C, Gallart M, Torrejon A, Borruel N, Casellas F, et al. Colonisation by Faecalibacterium prausnitzii and maintenance of clinical remission in patients with ulcerative colitis. Aliment Pharmacol Ther. 2013;38(2):151–61.

    Article  CAS  PubMed  Google Scholar 

  61. Miquel S, Leclerc M, Martin R, Chain F, Lenoir M, Raguideau S, et al. Identification of metabolic signatures linked to anti-inflammatory effects of Faecalibacterium prausnitzii. mBio. 2015;6(2):e00300-15.

    Article  PubMed  PubMed Central  Google Scholar 

  62. Quevrain E, Maubert MA, Michon C, Chain F, Marquant R, Tailhades J, et al. Identification of an anti-inflammatory protein from Faecalibacterium prausnitzii, a commensal bacterium deficient in Crohn’s disease. Gut. 2016;65(3):415–25.

    Article  CAS  PubMed  Google Scholar 

  63. Atarashi K, Tanoue T, Oshima K, Suda W, Nagano Y, Nishikawa H, et al. Treg induction by a rationally selected mixture of Clostridia strains from the human microbiota. Nature. 2013;500(7461):232–6.

    Article  CAS  PubMed  Google Scholar 

  64. Narushima S, Sugiura Y, Oshima K, Atarashi K, Hattori M, Suematsu M, et al. Characterization of the 17 strains of regulatory T cell-inducing human-derived Clostridia. Gut Microbes. 2014;5(3):333–9.

    Article  PubMed  PubMed Central  Google Scholar 

  65. Wright EK, Kamm MA, Wagner J, Teo SM, Cruz P, Hamilton AL, et al. Microbial factors associated with postoperative Crohn’s disease recurrence. J Crohns Colitis. 2017;11(2):191–203.

    Article  PubMed  Google Scholar 

  66. Zhang J, Hoedt EC, Liu Q, Berendsen E, Teh JJ, Hamilton A, et al. Elucidation of Proteus mirabilis as a key bacterium in Crohn’s disease inflammation. Gastroenterology. 2021;160(1):317–330.e11.

    Article  CAS  PubMed  Google Scholar 

  67. Mondot S, Lepage P, Seksik P, Allez M, Treton X, Bouhnik Y, et al. Structural robustness of the gut mucosal microbiota is associated with Crohn’s disease remission after surgery. Gut. 2016;65(6):954–62.

    Article  CAS  PubMed  Google Scholar 

  68. Ni J, Shen TD, Chen EZ, Bittinger K, Bailey A, Roggiani M, et al. A role for bacterial urease in gut dysbiosis and Crohn’s disease. Sci Transl Med. 2017;9(416):eaah6888.

    Article  PubMed  PubMed Central  Google Scholar 

  69. Lee D, Albenberg L, Compher C, Baldassano R, Piccoli D, Lewis JD, et al. Diet in the pathogenesis and treatment of inflammatory bowel diseases. Gastroenterology. 2015;148(6):1087–106.

    Article  CAS  PubMed  Google Scholar 

  70. Charlebois A, Rosenfeld G, Bressler B. The impact of dietary interventions on the symptoms of inflammatory bowel disease: a systematic review. Crit Rev Food Sci Nutr. 2016;56(8):1370–8.

    Article  CAS  PubMed  Google Scholar 

  71. Halmos EP, Gibson PR. Dietary management of IBD—insights and advice. Nat Rev Gastroenterol Hepatol. 2015;12(3):133–46.

    Article  CAS  PubMed  Google Scholar 

  72. Levine A, Sigall Boneh R, Wine E. Evolving role of diet in the pathogenesis and treatment of inflammatory bowel diseases. Gut. 2018;67(9):1726–38.

    Article  CAS  PubMed  Google Scholar 

  73. Weng YJ, Gan HY, Li X, Huang Y, Li ZC, Deng HM, et al. Correlation of diet, microbiota and metabolite networks in inflammatory bowel disease. J Dig Dis. 2019;20(9):447–59.

    Article  CAS  PubMed  Google Scholar 

  74. Ford AC, Lacy BE, Talley NJ. Irritable bowel syndrome. N Engl J Med. 2017;376(26):2566–78.

    Article  CAS  PubMed  Google Scholar 

  75. Drossman DA. Functional gastrointestinal disorders: what’s new for Rome IV? Lancet Gastroenterol Hepatol. 2016;1(1):6–8.

    Article  PubMed  Google Scholar 

  76. Talley NJ. Functional gastrointestinal disorders as a public health problem. Neurogastroenterol Motil. 2008;20(Suppl 1):121–9.

    Article  PubMed  Google Scholar 

  77. Keely S, Walker MM, Marks E, Talley NJ. Immune dysregulation in the functional gastrointestinal disorders. Eur J Clin Investig. 2015;45(12):1350–9.

    Article  Google Scholar 

  78. Talley NJ, Walker MM, Holtmann G. Functional dyspepsia. Curr Opin Gastroenterol. 2016;32(6):467–73.

    Article  CAS  PubMed  Google Scholar 

  79. Powell N, Walker MM, Talley NJ. The mucosal immune system: master regulator of bidirectional gut-brain communications. Nat Rev Gastroenterol Hepatol. 2017;14(3):143–59.

    Article  CAS  PubMed  Google Scholar 

  80. Burns G, Carroll G, Mathe A, Horvat J, Foster P, Walker MM, et al. Evidence for local and systemic immune activation in functional dyspepsia and the irritable bowel syndrome: a systematic review. Am J Gastroenterol. 2019;114(3):429–36.

    Article  PubMed  Google Scholar 

  81. Walker MM, Aggarwal KR, Shim LS, Bassan M, Kalantar JS, Weltman MD, et al. Duodenal eosinophilia and early satiety in functional dyspepsia: confirmation of a positive association in an Australian cohort. J Gastroenterol Hepatol. 2014;29(3):474–9.

    Article  PubMed  Google Scholar 

  82. Walker MM, Talley NJ, Prabhakar M, Pennaneac’h CJ, Aro P, Ronkainen J, et al. Duodenal mastocytosis, eosinophilia and intraepithelial lymphocytosis as possible disease markers in the irritable bowel syndrome and functional dyspepsia. Aliment Pharmacol Ther. 2009;29(7):765–73.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  83. Liebregts T, Adam B, Bredack C, Roth A, Heinzel S, Lester S, et al. Immune activation in patients with irritable bowel syndrome. Gastroenterology. 2007;132(3):913–20.

    Article  CAS  PubMed  Google Scholar 

  84. Spinedi E, Hadid R, Daneva T, Gaillard RC. Cytokines stimulate the CRH but not the vasopressin neuronal system: evidence for a median eminence site of interleukin-6 action. Neuroendocrinology. 1992;56(1):46–53.

    Article  CAS  PubMed  Google Scholar 

  85. Shanahan ER, Zhong L, Talley NJ, Morrison M, Holtmann G. Characterisation of the gastrointestinal mucosa-associated microbiota: a novel technique to prevent cross-contamination during endoscopic procedures. Aliment Pharmacol Ther. 2016;43(11):1186–96.

    Article  CAS  PubMed  Google Scholar 

  86. Shanahan ER, Shah A, Koloski N, Walker MM, Talley NJ, Morrison M, et al. Influence of cigarette smoking on the human duodenal mucosa-associated microbiota. Microbiome. 2018;6(1):150.

    Article  PubMed  PubMed Central  Google Scholar 

  87. Zhong L, Shanahan ER, Raj A, Koloski NA, Fletcher L, Morrison M, et al. Dyspepsia and the microbiome: time to focus on the small intestine. Gut. 2017;66(6):1168–9.

    Article  CAS  PubMed  Google Scholar 

  88. Shah A, Talley NJ, Koloski N, Macdonald GA, Kendall BJ, Shanahan ER, et al. Duodenal bacterial load as determined by quantitative polymerase chain reaction in asymptomatic controls, functional gastrointestinal disorders and inflammatory bowel disease. Aliment Pharmacol Ther. 2020;52:155–67.

    Article  CAS  PubMed  Google Scholar 

  89. Vandeputte D, Kathagen G, D’Hoe K, Vieira-Silva S, Valles-Colomer M, Sabino J, et al. Quantitative microbiome profiling links gut community variation to microbial load. Nature. 2017;551(7681):507–11.

    Article  CAS  PubMed  Google Scholar 

  90. Vieira-Silva S, Sabino J, Valles-Colomer M, Falony G, Kathagen G, Caenepeel C, et al. Quantitative microbiome profiling disentangles inflammation- and bile duct obstruction-associated microbiota alterations across PSC/IBD diagnoses. Nat Microbiol. 2019;4(11):1826–31.

    Article  CAS  PubMed  Google Scholar 

  91. Garrett WS. Cancer and the microbiota. Science. 2015;348(6230):80–6.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  92. Meng C, Bai C, Brown TD, Hood LE, Tian Q. Human gut microbiota and gastrointestinal cancer. Genomics Proteomics Bioinformatics. 2018;16(1):33–49.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  93. Ferreira RM, Pereira-Marques J, Pinto-Ribeiro I, Costa JL, Carneiro F, Machado JC, et al. Gastric microbial community profiling reveals a dysbiotic cancer-associated microbiota. Gut. 2018;67(2):226–36.

    Article  CAS  PubMed  Google Scholar 

  94. Coker OO, Dai Z, Nie Y, Zhao G, Cao L, Nakatsu G, et al. Mucosal microbiome dysbiosis in gastric carcinogenesis. Gut. 2018;67(6):1024–32.

    Article  CAS  PubMed  Google Scholar 

  95. Rajilic-Stojanovic M, Figueiredo C, Smet A, Hansen R, Kupcinskas J, Rokkas T, et al. Systematic review: gastric microbiota in health and disease. Aliment Pharmacol Ther. 2020;51(6):582–602.

    Article  PubMed  Google Scholar 

  96. Yu J, Feng Q, Wong SH, Zhang D, Liang QY, Qin Y, et al. Metagenomic analysis of faecal microbiome as a tool towards targeted non-invasive biomarkers for colorectal cancer. Gut. 2017;66(1):70–8.

    Article  CAS  PubMed  Google Scholar 

  97. Dai Z, Coker OO, Nakatsu G, Wu WKK, Zhao L, Chen Z, et al. Multi-cohort analysis of colorectal cancer metagenome identified altered bacteria across populations and universal bacterial markers. Microbiome. 2018;6(1):70.

    Article  PubMed  PubMed Central  Google Scholar 

  98. Liang JQ, Li T, Nakatsu G, Chen YX, Yau TO, Chu E, et al. A novel faecal Lachnoclostridium marker for the non-invasive diagnosis of colorectal adenoma and cancer. Gut. 2020;69(7):1248–57.

    Article  CAS  PubMed  Google Scholar 

  99. Münch NS, Fang HY, Ingermann J, Maurer HC, Anand A, Kellner V, et al. High-fat diet accelerates carcinogenesis in a mouse model of Barrett’s esophagus via interleukin 8 and alterations to the gut microbiome. Gastroenterology. 2019;157(2):492–506.e2.

    Article  PubMed  Google Scholar 

  100. Gopalakrishnan V, Helmink BA, Spencer CN, Reuben A, Wargo JA. The influence of the gut microbiome on cancer, immunity, and cancer immunotherapy. Cancer Cell. 2018;33(4):570–80.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  101. Helmink BA, Khan MAW, Hermann A, Gopalakrishnan V, Wargo JA. The microbiome, cancer, and cancer therapy. Nat Med. 2019;25(3):377–88.

    Article  CAS  PubMed  Google Scholar 

  102. Zitvogel L, Ma Y, Raoult D, Kroemer G, Gajewski TF. The microbiome in cancer immunotherapy: diagnostic tools and therapeutic strategies. Science (New York, NY). 2018;359(6382):1366–70.

    Article  CAS  Google Scholar 

  103. Guglielmi G. How gut microbes are joining the fight against cancer. Nature. 2018;557(7706):482–4.

    Article  CAS  PubMed  Google Scholar 

  104. Vetizou M, Pitt JM, Daillere R, Lepage P, Waldschmitt N, Flament C, et al. Anticancer immunotherapy by CTLA-4 blockade relies on the gut microbiota. Science. 2015;350(6264):1079–84.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  105. Sivan A, Corrales L, Hubert N, Williams JB, Aquino-Michaels K, Earley ZM, et al. Commensal Bifidobacterium promotes antitumor immunity and facilitates anti-PD-L1 efficacy. Science. 2015;350(6264):1084–9.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  106. Routy B, Le Chatelier E, Derosa L, Duong CPM, Alou MT, Daillere R, et al. Gut microbiome influences efficacy of PD-1-based immunotherapy against epithelial tumors. Science. 2018;359(6371):91–7.

    Article  CAS  PubMed  Google Scholar 

  107. Gopalakrishnan V, Spencer CN, Nezi L, Reuben A, Andrews MC, Karpinets TV, et al. Gut microbiome modulates response to anti-PD-1 immunotherapy in melanoma patients. Science. 2018;359(6371):97–103.

    Article  CAS  PubMed  Google Scholar 

  108. Matson V, Fessler J, Bao R, Chongsuwat T, Zha Y, Alegre ML, et al. The commensal microbiome is associated with anti-PD-1 efficacy in metastatic melanoma patients. Science. 2018;359(6371):104–8.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  109. Tanoue T, Morita S, Plichta DR, Skelly AN, Suda W, Sugiura Y, et al. A defined commensal consortium elicits CD8 T cells and anti-cancer immunity. Nature. 2019;565(7741):600–5.

    Article  CAS  PubMed  Google Scholar 

  110. Borody T, Fischer M, Mitchell S, Campbell J. Fecal microbiota transplantation in gastrointestinal disease: 2015 update and the road ahead. Expert Rev Gastroenterol Hepatol. 2015;9(11):1379–91.

    Article  CAS  PubMed  Google Scholar 

  111. Paramsothy S, Walsh AJ, Borody T, Samuel D, van den Bogaerde J, Leong RW, et al. Gastroenterologist perceptions of faecal microbiota transplantation. World J Gastroenterol. 2015;21(38):10907–14.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  112. Gough E, Shaikh H, Manges AR. Systematic review of intestinal microbiota transplantation (fecal bacteriotherapy) for recurrent Clostridium difficile infection. Clin Infect Dis. 2011;53(10):994–1002.

    Article  PubMed  Google Scholar 

  113. Quraishi MN, Widlak M, Bhala N, Moore D, Price M, Sharma N, et al. Systematic review with meta-analysis: the efficacy of faecal microbiota transplantation for the treatment of recurrent and refractory Clostridium difficile infection. Aliment Pharmacol Ther. 2017;46(5):479–93.

    Article  CAS  PubMed  Google Scholar 

  114. Lai CY, Sung J, Cheng F, Tang W, Wong SH, Chan PKS, et al. Systematic review with meta-analysis: review of donor features, procedures and outcomes in 168 clinical studies of faecal microbiota transplantation. Aliment Pharmacol Ther. 2019;49(4):354–63.

    Article  PubMed  Google Scholar 

  115. Narula N, Kassam Z, Yuan Y, Colombel JF, Ponsioen C, Reinisch W, et al. Systematic review and meta-analysis: fecal microbiota transplantation for treatment of active ulcerative colitis. Inflamm Bowel Dis. 2017;23(10):1702–9.

    Article  PubMed  Google Scholar 

  116. Costello SP, Soo W, Bryant RV, Jairath V, Hart AL, Andrews JM. Systematic review with meta-analysis: faecal microbiota transplantation for the induction of remission for active ulcerative colitis. Aliment Pharmacol Ther. 2017;46(3):213–24.

    Article  CAS  PubMed  Google Scholar 

  117. Sokol H, Landman C, Seksik P, Berard L, Montil M, Nion-Larmurier I, et al. Fecal microbiota transplantation to maintain remission in Crohn’s disease: a pilot randomized controlled study. Microbiome. 2020;8(1):12.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  118. Baxter M, Colville A. Adverse events in faecal microbiota transplant: a review of the literature. J Hosp Infect. 2016;92(2):117–27.

    Article  CAS  PubMed  Google Scholar 

  119. Wang S, Xu M, Wang W, Cao X, Piao M, Khan S, et al. Systematic review: adverse events of fecal microbiota transplantation. PLoS One. 2016;11(8):e0161174.

    Article  PubMed  PubMed Central  Google Scholar 

  120. Luo Y, Lucas AL, Grinspan AM. Fecal transplants by colonoscopy and capsules are cost-effective strategies for treating recurrent Clostridioides difficile infection. Dig Dis Sci. 2020;65(4):1125–33.

    Article  PubMed  Google Scholar 

  121. Mullish BH, Quraishi MN, Segal JP, McCune VL, Baxter M, Marsden GL, et al. The use of faecal microbiota transplant as treatment for recurrent or refractory Clostridium difficile infection and other potential indications: joint British Society of Gastroenterology (BSG) and Healthcare Infection Society (HIS) guidelines. Gut. 2018;67(11):1920–41.

    Article  PubMed  Google Scholar 

  122. Kelly CR, Yen EF, Grinspan AM, Kahn SA, Atreja A, Lewis JD, et al. Fecal microbiota transplantation is highly effective in real-world practice: initial results from the FMT National Registry. Gastroenterology. 2020;158:S-14–5.

    Article  Google Scholar 

  123. Paramsothy S, Paramsothy R, Rubin DT, Kamm MA, Kaakoush NO, Mitchell HM, et al. Faecal microbiota transplantation for inflammatory bowel disease: a systematic review and meta-analysis. J Crohns Colitis. 2017;11(10):1180–99.

    Article  PubMed  Google Scholar 

  124. Paramsothy S, Nielsen S, Kamm MA, Deshpande NP, Faith JJ, Clemente JC, et al. Specific bacteria and metabolites associated with response to fecal microbiota transplantation in patients with ulcerative colitis. Gastroenterology. 2019;156(5):1440–54.e2.

    Article  PubMed  Google Scholar 

  125. Moayyedi P, Surette MG, Kim PT, Libertucci J, Wolfe M, Onischi C, et al. Fecal microbiota transplantation induces remission in patients with active ulcerative colitis in a randomized controlled trial. Gastroenterology. 2015;149(1):102–9.e6.

    Article  PubMed  Google Scholar 

  126. Kong L, Lloyd-Price J, Vatanen T, Seksik P, Beaugerie L, Simon T, et al. Linking strain engraftment in fecal microbiota transplantation with maintenance of remission in Crohn’s disease. Gastroenterology. 2020;159(6):2193–202.e5.

    Article  CAS  PubMed  Google Scholar 

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Authors and Affiliations

  1. University of Queensland Frazer Institute, Faculty of Medicine, and NHMRC Centre for Digestive Health, University of Queensland, Saint Lucia, QLD, Australia

    Mark Morrison

  2. University of Queensland Frazer Institute, Faculty of Medicine, University of Queensland, Saint Lucia, QLD, Australia

    Nida Murtaza

  3. School of Medicine and Public Health, and NHMRC Centre for Digestive Health, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, NSW, Australia

    Nicholas J. Talley

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  1. Mark Morrison
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  2. Nida Murtaza
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Correspondence to Nicholas J. Talley .

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  1. Medically Associated Science and Technology (MAST) Program, Cedars-Sinai Medical Center, West Hollywood, CA, USA

    Mark Pimentel

  2. Medically Associated Science and Technology (MAST) Program, Cedars-Sinai Medical Center, West Hollywood, CA, USA

    Ruchi Mathur

  3. Medically Associated Science and Technology (MAST) Program, Cedars-Sinai Medical Center, West Hollywood, CA, USA

    Gillian M. Barlow

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Morrison, M., Murtaza, N., Talley, N.J. (2023). The Importance of the Microbiome in the Gut. In: Pimentel, M., Mathur, R., Barlow, G.M. (eds) Clinical Understanding of the Human Gut Microbiome. Springer, Cham. https://doi.org/10.1007/978-3-031-46712-7_1

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