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The Gut Microbiota: A Clinically Impactful Factor in Patient Health and Disease

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Abstract

The gut microbiota, often referred to as the body’s virtual organ, is a complex ecosystem made up of trillions of microorganisms that interact with host physiology in a myriad of ways. This lifelong interaction begins in the early stages of life, and it is subject to alterations exerted by environmental factors, especially those that characterise modern societies such as ultra-processed foods and pharmaceutical interventions, amongst others. These alterations, in turn, carry with them implications for host health and disease. Due to this putative role in human health and the fact that study of the gut microbiota is now rapidly evolving, it is of paramount importance that all clinicians be aware of the most up-to-date literature in this field. Herein, we present a state-of-the-art review which aims to outline the most relevant pre-clinical and clinical knowledge around the gut microbiota-host interaction. This review focuses primarily on the development and key functions of the gut microbiota with respect to host health and disease, but also addresses the basic concept of gut dysbiosis.

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References

  1. Young VB. The role of the microbiome in human health and disease: an introduction for clinicians. BMJ. 2017;356.

  2. Cani PD. Human gut microbiome: Hopes, threats and promises. Gut. 2018:1716–25.

  3. Valdes AM, Walter J, Segal E, Spector TD. Role of the gut microbiota in nutrition and health. BMJ. 2018;361.

  4. Thursby E, Juge N. Introduction to the human gut microbiota. Biochem J. 2017;474(11):1823–36.

    CAS  PubMed  PubMed Central  Google Scholar 

  5. G. Francisco, Probiotics and prebiotics, World Gastroenterol. Organ. Glob. Guidel., no. February, 2017.

  6. Sender R, Fuchs S, Milo R. Revised estimates for the number of human and bacteria cells in the body. PLoS Biol. 2016;14(8):1–14.

    Google Scholar 

  7. Matamoros S, Gras-Leguen C, Le Vacon F, Potel G, De La Cochetiere MF. Development of intestinal microbiota in infants and its impact on health. Trends Microbiol. 2013;21(4):167–73.

    CAS  PubMed  Google Scholar 

  8. Tanaka M, Nakayama J. Development of the gut microbiota in infancy and its impact on health in later life. Allergol Int. 2017;66(4):515–22.

    CAS  PubMed  Google Scholar 

  9. Monica F, et al. Changes of intestinal microbiota in early life. J Matern Neonatal Med. 2018;7058:1–11.

    Google Scholar 

  10. J. M. Allen et al., Exercise alters gut microbiota composition and function in lean and obese humans, vol. 50, no 4. 2018.

  11. Y. Vallès and M. P. Francino, Air pollution, early life microbiome, and development, Curr. Environ. Heal. Reports, 2018.

  12. Castaner O, Goday A, Park YM, Lee SH, Magkos F, Shiow SATE, et al. The gut Microbiome profile in obesity: a systematic review. Int J Endocrinol. 2018;2018:1–9.

    Google Scholar 

  13. Clemente JC, Manasson J, Scher JU. The role of the gut microbiome in systemic inflammatory disease. Bmj. 2018:j5145.

  14. Gao R, Gao Z, Huang L, Qin H. Gut microbiota and colorectal cancer. Eur J Clin Microbiol Infect Dis. 2017;36(5):757–69.

    CAS  PubMed  PubMed Central  Google Scholar 

  15. Lee YY, Hassan SA, Ismail IH, Chong SY, Raja Ali RA, Amin Nordin S, et al. Gut microbiota in early life and its influence on health and disease: a position paper by the Malaysian Working Group on Gastrointestinal Health. J Paediatr Child Health. 2017;53(12):1152–8.

    PubMed  Google Scholar 

  16. Perez-Muñoz ME, Arrieta MC, Ramer-Tait AE, Walter J. A critical assessment of the ‘sterile womb’ and ‘in utero colonization’ hypotheses: implications for research on the pioneer infant microbiome. Microbiome. 2017;5(1):1–19.

    Google Scholar 

  17. R. W. Walker, J. C. Clemente, I. Peter, and R. J. F. Loos, The prenatal gut microbiome: are we colonized with bacteria in utero?, Pediatr Obes, vol 12, no June, pp. 3–17, 2017.

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

  19. M. C. Collado, S. Rautava, J. Aakko, E. Isolauri, and S. Salminen, Human gut colonisation may be initiated in utero by distinct microbial communities in the placenta and amniotic fluid, Sci Rep, vol 6, no October 2015, pp. 1–13, 2016.

  20. Rodríguez JM, et al. The composition of the gut microbiota throughout life, with an emphasis on early life. Microb Ecol Heal Dis. 2015;26(0):1–17.

    Google Scholar 

  21. Ferretti P, et al. Mother-to-infant microbial transmission from different body sites shapes the developing infant gut microbiome. Cell Host Microbe. 2018;24(1):133–145.e5.

    CAS  PubMed  Google Scholar 

  22. Gomez-Arango LF, Barrett HL, McIntyre HD, Callaway LK, Morrison M, Nitert MD. Contributions of the maternal oral and gut microbiome to placental microbial colonization in overweight and obese pregnant women. Sci Rep. 2017;7(1).

  23. Parnell LA, Briggs CM, Cao B, Delannoy-Bruno O, Schrieffer AE, Mysorekar IU. Microbial communities in placentas from term normal pregnancy exhibit spatially variable profiles. Sci Rep. 2017;7(1):1–11.

    Google Scholar 

  24. Guarino A, Ashkenazi S, Gendrel D, Lo Vecchio A, Shamir R, Szajewska H. European society for pediatric gastroenterology, hepatology, and nutrition/european society for pediatric infectious diseases evidence-based guidelines for the management of acute gastroenteritis in children in Europe: update 2014. J Pediatr Gastroenterol Nutr. 2014;59(1):132–52.

    PubMed  Google Scholar 

  25. V. Y. Peeters Linde, Daelemans Siel, Antibiotic treatment in infants: effect on the gastro-intestinal microbiome and long-term consequences, vol. 9, no. 1, pp. 40–52, 2018.

  26. Penders J, Thijs C, Vink C, Stelma FF, Snijders B, Kummeling I, et al. Factors influencing the composition of the intestinal microbiota in early infancy. Pediatrics. 2006;118(2):511–21.

    PubMed  Google Scholar 

  27. Stewart CJ, Ajami NJ, O’Brien JL, Hutchinson DS, Smith DP, Wong MC, et al. Temporal development of the gut microbiome in early childhood from the TEDDY study. Nature. 2018;562(7728):583–8.

    CAS  PubMed  Google Scholar 

  28. Cox LM, Yamanishi S, Sohn J, Alekseyenko AV, Leung JM, Cho I, et al. Altering the intestinal microbiota during a critical developmental window has lasting metabolic consequences. Cell. 2014;158(4):705–21.

    CAS  PubMed  PubMed Central  Google Scholar 

  29. Gibson MK, Crofts TS, Dantas G. Antibiotics and the developing infant gut microbiota and resistome. Curr Opin Microbiol. 2015;27:51–6.

    CAS  PubMed  PubMed Central  Google Scholar 

  30. Odamaki T, et al. Age-related changes in gut microbiota composition from newborn to centenarian: a cross-sectional study. BMC Microbiol. 2016;16(1):1–12.

    Google Scholar 

  31. Rutayisire E, Huang K, Liu Y, Tao F. The mode of delivery affects the diversity and colonization pattern of the gut microbiota during the first year of infants’ life: a systematic review. BMC Gastroenterol. 2016;16(1):1–12.

    Google Scholar 

  32. L. F. Stinson, M. S. Payne, and J. A. Keelan, A critical review of the bacterial baptism hypothesis and the impact of cesarean delivery on the infant microbiome, Front. Med., vol. 5, no. May, 2018.

  33. Goulet O. Potential role of the intestinal microbiota in programming health and disease. Nutr Rev. 2015;73:32–40.

    PubMed  Google Scholar 

  34. Bokulich NA, et al. Antibiotics, birth mode, and diet shape microbiome maturation during early life. Sci Transl Med. 2016;8(343):1–14.

    Google Scholar 

  35. Ximenez C, Torres J. Development of microbiota in infants and its role in maturation of gut mucosa and immune system. Arch Med Res. 2017;48(8):666–80.

    PubMed  Google Scholar 

  36. Hill CJ, et al. Evolution of gut microbiota composition from birth to 24 weeks in the INFANTMET cohort. Microbiome. 2017;5(1):1–18.

    Google Scholar 

  37. Z. Liwen, W. Yu, X. Kaihong, and C. Baojin, A low abundance of bi fi dobacterium but not Lactobacillius in the feces of Chinese children with wheezing diseases, vol. 40, no. September, pp. 0–5, 2018.

  38. C. J. Stewart, N. D. Embleton, E. Clements, P. N. Luna, D. P. Smith, T. Y. Fofanova, A. Nelson, G. Taylor, C. H. Orr, J. F. Petrosino, J. E. Berrington, S. P. Cummings, Cesarean or vaginal birth does not impact the longitudinal development of the gut microbiome in a cohort of exclusively preterm infants, Front Microbiol, vol. 8, no. JUN, 2017.

  39. Cassir N, Simeoni U, La Scola B. Gut microbiota and the pathogenesis of necrotizing enterocolitis in preterm neonates. Future Microbiol. Feb. 2016;11(2):273–92.

    CAS  PubMed  Google Scholar 

  40. Pammi M, et al. Intestinal dysbiosis in preterm infants preceding necrotizing enterocolitis: a systematic review and meta-analysis. Microbiome. 2017;5(1):1–15.

    Google Scholar 

  41. Mai V, et al. Distortions in development of intestinal microbiota associated with late onset sepsis in preterm infants. PLoS One. 2013;8(1):1–9.

    Google Scholar 

  42. Wandro S, Osborne S, Enriquez C, Bixby C, Arrieta A, Whiteson K. The microbiome and metabolome of preterm infant stool are personalized and not driven by health outcomes, including necrotizing enterocolitis and late-onset Sepsis. mSphere. 2018;3(3).

  43. Stewart CJ, Embleton ND, Marrs ECL, Smith DP, Fofanova T, Nelson A, et al. Longitudinal development of the gut microbiome and metabolome in preterm neonates with late onset sepsis and healthy controls. Microbiome. 2017;5(1):75.

    PubMed  PubMed Central  Google Scholar 

  44. Aceti A, et al. Probiotics prevent late-onset sepsis in human milk-fed, very low birth weight preterm infants: systematic review and meta-analysis. Nutrients. 2017;9(8):1–21.

    Google Scholar 

  45. Wilkins T, Sequoia J. Probiotics for gastrointestinal conditions: a summary of the evidence. Am Fam Physician. 2017;96(3):170–8.

    PubMed  Google Scholar 

  46. Deshpande G, Athalye-Jape G, Patole S. Para-probiotics for preterm neonates—the next frontier. Nutrients. 2018;10(7):1–9.

    Google Scholar 

  47. Korpela K, Blakstad EW, Moltu SJ, Strømmen K, Nakstad B, Rønnestad AE, et al. Intestinal microbiota development and gestational age in preterm neonates. Sci Rep. 2018;8(1):2453.

    PubMed  PubMed Central  Google Scholar 

  48. Andreas NJ, Kampmann B, Mehring Le-Doare K. Human breast milk: a review on its composition and bioactivity. Early Hum Dev. 2015;91(11):629–35.

    CAS  PubMed  Google Scholar 

  49. Gibson GR, et al. Expert consensus document: the International Scientific Association for Probiotics and Prebiotics (ISAPP) consensus statement on the definition and scope of prebiotics. Nat Rev Gastroenterol Hepatol. 2017;14(8):491–502.

    PubMed  Google Scholar 

  50. Fernández L, Langa S, Martín V, Maldonado A, Jiménez E, Martín R, et al. The human milk microbiota: origin and potential roles in health and disease. Pharmacol Res. 2013;69(1):1–10.

    PubMed  Google Scholar 

  51. Lundgren SN, et al. Maternal diet during pregnancy is related with the infant stool microbiome in a delivery mode-dependent manner. Microbiome. 2018;6(1):1–11.

    Google Scholar 

  52. Zinöcker MK, Lindseth IA. The western diet–microbiome-host interaction and its role in metabolic disease. Nutrients. 2018;10(3):1–15.

    Google Scholar 

  53. De Filippo C, et al. Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa. Proc Natl Acad Sci. 2010;107(33):14691–6.

    PubMed  Google Scholar 

  54. Graf D, et al. Contribution of diet to the composition of the human gut microbiota. Microb. Ecol. Heal. Dis. 2015;26(0):1–11.

    Google Scholar 

  55. Vangay P, et al. US Immigration westernizes the human gut microbiome. Cell. 2018;175(4):962–972.e10.

    CAS  PubMed  Google Scholar 

  56. Mancabelli L, Milani C, Lugli GA, Turroni F, Ferrario C, van Sinderen D, et al. Meta-analysis of the human gut microbiome from urbanized and pre-agricultural. Environ Microbiol. 2017;19(4):1379–90.

    PubMed  Google Scholar 

  57. González-garay AG, Romo-romo A, Serralde-zúñiga AE. Review of recommendations for the use of caloric sweeteners by adults review of recommendations for the use of caloric sweeteners by adults and children. In: no. May; 2018.

    Google Scholar 

  58. Nettleton JE, Reimer RA, Shearer J. Reshaping the gut microbiota: impact of low calorie sweeteners and the link to insulin resistance? Physiol Behav. 2016;164:488–93.

    CAS  PubMed  Google Scholar 

  59. Duda-Chodak A, Tarko T, Satora P, Sroka P. Interaction of dietary compounds, especially polyphenols, with the intestinal microbiota: a review. Eur J Nutr. 2015;54(3):325–41.

    CAS  PubMed  PubMed Central  Google Scholar 

  60. Ventola CL. The antibiotic resistance crisis: part 1: causes and threats. P T A peer-reviewed J Formul Manag. 2015;40(4):277–83.

    Google Scholar 

  61. Seedat F, et al. Adverse events in women and children who have received intrapartum antibiotic prophylaxis treatment: a systematic review. BMC Pregnancy Childbirth. 2017;17(1):1–14.

    Google Scholar 

  62. Palleja A, Mikkelsen KH, Forslund SK, Kashani A, Allin KH, Nielsen T, et al. Recovery of gut microbiota of healthy adults following antibiotic exposure. Nat Microbiol. 2018;3(11):1255–65.

    CAS  PubMed  Google Scholar 

  63. Imhann F, Bonder MJ, Vich Vila A, Fu J, Mujagic Z, Vork L, et al. Proton pump inhibitors affect the gut microbiome. Gut. 2016;65(5):740–8.

    CAS  PubMed  Google Scholar 

  64. Reveles KR, Ryan CN, Chan L, Cosimi RA, Haynes WL. Proton pump inhibitor use associated with changes in gut microbiota composition. Gut. 2018;67(7):1369–70.

    CAS  PubMed  Google Scholar 

  65. De La Cuesta-Zuluaga J, et al. Metformin is associated with higher relative abundance of mucin-degrading akkermansia muciniphila and several short-chain fatty acid-producing microbiota in the gut. Diabetes Care. 2017;40(1):54–62.

    PubMed  Google Scholar 

  66. Lee H, Ko G, Microbiome E, National S. Effect of metformin on metabolic improvement and gut microbiota. Appl Environ Microbiol. 2014;80(19):5935–43.

    PubMed  PubMed Central  Google Scholar 

  67. Falony G, et al. Population-level analysis of gut microbiome variation. Science (80). 2016;352(6285):560–4.

    CAS  Google Scholar 

  68. Jackson MA, Verdi S, Maxan ME, Shin CM, Zierer J, Bowyer RCE, et al. Gut microbiota associations with common diseases and prescription medications in a population-based cohort. Nat Commun. 2018;9(1):2655.

    PubMed  PubMed Central  Google Scholar 

  69. Bai J, Behera M, Bruner DW. The gut microbiome, symptoms, and targeted interventions in children with cancer: a systematic review. Support Care Cancer. 2017.

  70. Spanogiannopoulos P, Bess EN, Carmody RN, Turnbaugh PJ. The microbial pharmacists within us: a metagenomic view of xenobiotic metabolism. Nat Rev Microbiol. 2016;14(5):273–87.

    CAS  PubMed  PubMed Central  Google Scholar 

  71. Sousa T, Paterson R, Moore V, Carlsson A, Abrahamsson B, Basit AW. The gastrointestinal microbiota as a site for the biotransformation of drugs. Int J Pharm. 2008;363(1–2):1–25.

    CAS  PubMed  Google Scholar 

  72. Haiser HJ, Seim KL, Balskus EP, Turnbaugh PJ. Mechanistic insight into digoxin inactivation by Eggerthella lenta augments our understanding of its pharmacokinetics. Gut Microbes. 2014;5(2):37–41.

    Google Scholar 

  73. Enright EF, Griffin BT, Gahan CGM, Joyce SA. Microbiome-mediated bile acid modification: role in intestinal drug absorption and metabolism. Pharmacol Res. 2018;133:170–86.

    CAS  PubMed  Google Scholar 

  74. Enright EF, Joyce SA, Gahan CGM, Griffin BT. Impact of gut microbiota-mediated bile acid metabolism on the solubilization capacity of bile salt micelles and drug solubility. Mol Pharm. 2017;14(4):1251–63.

    CAS  PubMed  Google Scholar 

  75. Mitchell CM, Davy BM, Hulver MW, Neilson AP, Bennett BJ, Davy KP. Does exercise alter gut microbial composition?—a systematic review. August. 2018.

  76. Barton W, et al. The microbiome of professional athletes differs from that of more sedentary subjects in composition and particularly at the functional metabolic level. Gut. 2018;67(4):625–33.

    CAS  PubMed  Google Scholar 

  77. Wells JM, Rossi O, Meijerink M, van Baarlen P. Epithelial crosstalk at the microbiota-mucosal interface. Proc. Natl. Acad. Sci. 2011;108(Supplement_1):4607–14.

    CAS  PubMed  Google Scholar 

  78. Rowland I, Gibson G, Heinken A, Scott K, Swann J, Thiele I, et al. Gut microbiota functions: metabolism of nutrients and other food components. Eur J Nutr. 2018;57(1):1–24.

    CAS  PubMed  Google Scholar 

  79. Sayin SI, et al. Gut microbiota regulates bile acid metabolism by reducing the levels of tauro-beta-muricholic acid, a naturally occurring FXR antagonist. Cell Metab. 2013;17(2):225–35.

    CAS  PubMed  Google Scholar 

  80. Stappenbeck TS, Hooper LV, Gordon JI. Developmental regulation of intestinal angiogenesis by indigenous microbes via Paneth cells. Proc Natl Acad Sci U S A. 2002;99(24):15451–5.

    CAS  PubMed  PubMed Central  Google Scholar 

  81. Cecal enlargement in germ-free animals. Nutr Rev. 1960;18(10):313–4.

    Google Scholar 

  82. Neufeld KM, Kang N, Bienenstock J, Foster JA. Reduced anxiety-like behavior and central neurochemical change in germ-free mice. Neurogastroenterol Motil. 2011;23(3):255–65.

    CAS  PubMed  Google Scholar 

  83. Cebra JJ. Influences of microbiota on intestinal immune system development. Am J Clin Nutr. 1999;69(5):1046s–51s.

    CAS  PubMed  Google Scholar 

  84. Karl JP, Meydani M, Barnett JB, Vanegas SM, Barger K, Fu X, et al. Fecal concentrations of bacterially derived vitamin K forms are associated with gut microbiota composition but not plasma or fecal cytokine concentrations in healthy adults. Am J Clin Nutr. 2017;106(4):1052–61.

    CAS  PubMed  PubMed Central  Google Scholar 

  85. Wu GD, et al. Linking long-term dietary patterns with gut microbial enterotypes. Science (80). 2011;334(6052):105–8.

    CAS  Google Scholar 

  86. Louis Petra FHJ. Formation of propionate and butyrate by the human colonic microbiota. Environ Microbiol. 2017;19(1):29–41.

    CAS  PubMed  Google Scholar 

  87. Zambell KL, Fitch MD, Fleming SE. Acetate and butyrate are the major substrates for de novo lipogenesis in rat colonic epithelial cells. J Nutr. 2003;133(11):3509–15.

    CAS  PubMed  Google Scholar 

  88. Frost G, et al. The short-chain fatty acid acetate reduces appetite via a central homeostatic mechanism. Nat Commun. 2014;5:1–11.

    CAS  Google Scholar 

  89. Canani RB, Di Costanzo M, Leone L, Pedata M, Meli R, Calignano A. Potential beneficial effects of butyrate in intestinal and extraintestinal diseases. World J Gastroenterol. 2011;17(12):1519–28.

    CAS  PubMed  PubMed Central  Google Scholar 

  90. Anderson JW, Bridges SR. Short-chain fatty acid fermentation products of plant fiber affect glucose metabolism of isolated rat hepatocytes. Exp Biol Med. 1984;177(2):372–6.

    CAS  Google Scholar 

  91. Tazoe H, Otomo Y, Kaji I, Tanaka R, Karaki SI, Kuwahara A. Roles of short-chain fatty acids receptors, GPR41 and GPR43 on colonic functions. J Physiol Pharmacol. 2008;59(SUPPL.2):251–62.

    PubMed  Google Scholar 

  92. Everard A, Cani PD. Gut microbiota and GLP-1. Rev Endocr Metab Disord. 2014;15(3):189–96.

    CAS  PubMed  Google Scholar 

  93. Cani PD, Bibiloni R, Knauf C, Neyrinck AM, Delzenne NM. Changes in gut microbiota control metabolic diet–induced obesity and diabetes in mice. Diabetes. 2008;57(6):1470–81.

    CAS  PubMed  Google Scholar 

  94. Stellwag EJ, Hylemon PB. 7alpha-Dehydroxylation of cholic acid and chenodeoxycholic acid by Clostridium leptum. J Lipid Res. 1979;20:325–33.

    CAS  PubMed  Google Scholar 

  95. Jones BV, Begley M, Hill C, Gahan CGM, Marchesi JR. Functional and comparative metagenomic analysis of bile salt hydrolase activity in the human gut microbiome. Proc Natl Acad Sci U S A. 2008;105(36):13580–5.

    CAS  PubMed  PubMed Central  Google Scholar 

  96. Martin FPJ, Dumas ME, Wang Y, Legido-Quigley C, Yap IKS, Tang H, et al. A top-down systems biology view of microbiome-mammalian metabolic interactions in a mouse model. Mol Syst Biol. 2007;3(112).

  97. Fiorucci S, Mencarelli A, Palladino G, Cipriani S. Bile-acid-activated receptors: targeting TGR5 and farnesoid-X-receptor in lipid and glucose disorders. Trends Pharmacol Sci. 2009;30(11):570–80.

    CAS  PubMed  Google Scholar 

  98. Ryan PM, Stanton C, Caplice NM. Bile acids at the cross-roads of gut microbiome-host cardiometabolic interactions. Diabetol Metab Syndr. 2017;9(1):1–12.

    Google Scholar 

  99. Thomas C, Gioiello A, Noriega L, Strehle A, Oury J, Rizzo G, et al. TGR5-mediated bile acid sensing controls glucose homeostasis. Cell Metab. 2009;10(3):167–77.

    CAS  PubMed  PubMed Central  Google Scholar 

  100. Neuschwander-Tetri BA, Loomba R, Sanyal AJ, Lavine JE, van Natta ML, Abdelmalek MF, et al. Farnesoid X nuclear receptor ligand obeticholic acid for non-cirrhotic, non-alcoholic steatohepatitis (FLINT): a multicentre, randomised, placebo-controlled trial. Lancet. 2015;385(9972):956–65.

    CAS  PubMed  Google Scholar 

  101. Govindarajan K, MacSharry J, Casey PG, Shanahan F, Joyce SA, Gahan CGM. Unconjugated bile acids influence expression of circadian genes: a potential mechanism for microbe-host crosstalk. PLoS One. 2016;11(12):1–13.

    Google Scholar 

  102. Agus A, Planchais J, Sokol H. Gut microbiota regulation of tryptophan metabolism in health and disease. Cell Host Microbe. 2018;23(6):716–24.

    CAS  PubMed  Google Scholar 

  103. R. Mazzoli and E. Pessione, The neuro-endocrinological role of microbial glutamate and GABA signaling, Front Microbiol, vol 7, no NOV, pp. 1–17, 2016.

  104. De Vadder F, et al. Gut microbiota regulates maturation of the adult enteric nervous system via enteric serotonin networks. Proc Natl Acad Sci. 2018;115(25):6458–63.

    CAS  PubMed  Google Scholar 

  105. Bonaz B, Bazin T, Pellissier S. The vagus nerve at the interface of the microbiota-gut-brain axis. Front Neurosci, vol 12, no FEB. 2018:1–9.

  106. Hoyles L, et al. Microbiome–host systems interactions: protective effects of propionate upon the blood–brain barrier. DoiOrg, p. 170548:2017.

  107. D. J. Reis, S. S. Ilardi, and S. E. W. Punt, The anxiolytic effect of probiotics: a systematic review and meta-analysis of the clinical and preclinical literature, PLoS One, vol. 13, no. 6, p. e0199041, 2018.

  108. Allen AP, et al. Bifidobacterium longum 1714 as a translational psychobiotic: modulation of stress, electrophysiology and neurocognition in healthy volunteers. Transl Psychiatry. 2016;11:6.

    Google Scholar 

  109. Bravo JA, Forsythe P, Chew MV, Escaravage E, Savignac HM, Dinan TG, et al. Ingestion of lactobacillus strain regulates emotional behavior and central GABA receptor expression in a mouse via the vagus nerve. Proc Natl Acad Sci. 2011;108(38):16050–5.

    CAS  PubMed  Google Scholar 

  110. Belkaid Y, Hand TW. Role of the microbiota in immunity and inflammation. Cell. 2014;157(1):121–41.

    CAS  PubMed  PubMed Central  Google Scholar 

  111. Vatanen T, Kostic AD, d’Hennezel E, Siljander H, Franzosa EA, Yassour M, et al. Variation in Microbiome LPS immunogenicity contributes to autoimmunity in humans. Cell. 2016;165(4):842–53.

    CAS  PubMed  PubMed Central  Google Scholar 

  112. Song SJ, et al. Cohabiting family members share microbiota with one another and with their dogs. Elife. 2013;2013(2):1–22.

    Google Scholar 

  113. Tun HM, et al. Exposure to household furry pets influences the gut microbiota of infants at 3–4 months following various birth scenarios. Microbiome. 2017;5(1):1–14.

    Google Scholar 

  114. Fall T, et al. Early exposure to dogs and farm animals and the risk of childhood asthma. JAMA Pediatr. 2015;169(11):e153219.

    PubMed  Google Scholar 

  115. Azad MB, et al. Infant gut microbiota and the hygiene hypothesis of allergic disease: impact of household pets and siblings on microbiota composition and diversity. Allergy, Asthma Clin. Immunol. 2013;9(1):15.

    Google Scholar 

  116. Romagnami S. Human TH1 and TH2 subsets: regulation of differentiation and role in protection and immunopathology. Int Arch Allergy Immunol. 1992;98(4):279–85.

    Google Scholar 

  117. Ivanov II, Frutos RL, Manel N, Yoshinaga K, Rifkin DB, Sartor RB, et al. Specific microbiota direct the differentiation of IL-17-producing T-helper cells in the mucosa of the small intestine. Cell Host Microbe. 2008;4(4):337–49.

    CAS  PubMed  PubMed Central  Google Scholar 

  118. Bloomfield SF, Rook GAW, Scott EA, Shanahan F, Stanwell-Smith R, Turner P. Time to abandon the hygiene hypothesis: new perspectives on allergic disease, the human microbiome, infectious disease prevention and the role of targeted hygiene. Perspect Public Health. 2016;136(4):213–24.

    PubMed  PubMed Central  Google Scholar 

  119. M. J. Ege, The hygiene hypothesis in the age of the microbiome, Ann Am Thorac Soc, vol. 14, no. November, pp. S348–S353, 2017, 14.

  120. Corbett AJ, Eckle SBG, Birkinshaw RW, Liu L, Patel O, Mahony J, et al. T-cell activation by transitory neo-antigens derived from distinct microbial pathways. Nature. 2014;509(7500):361–5.

    CAS  PubMed  Google Scholar 

  121. Martinez FO, Gordon S. The M1 and M2 paradigm of macrophage activation: time for reassessment. F1000Prime Rep. 2014;6(March):1–13.

    CAS  Google Scholar 

  122. Wang N, Liang H, Zen K. Molecular mechanisms that influence the macrophage M1-M2 polarization balance. Front Immunol. 2014;5(NOV):1–9.

    Google Scholar 

  123. Libby P, Lichtman AH, Hansson GK. Immune effector mechanisms implicated in atherosclerosis: from mice to humans. Immunity. 2013;38(6):1092–104.

    CAS  PubMed  PubMed Central  Google Scholar 

  124. Round JL, Mazmanian SK. Inducible Foxp3+ regulatory T-cell development by\na commensal bacterium of the intestinal microbiota. Proc Natl Acad Sci U S A. 2010;107(27):12204–9.

    CAS  PubMed  PubMed Central  Google Scholar 

  125. Abdi K, Singh NJ, Matzinger P. Lipopolysaccharide-activated dendritic cells: ‘exhausted’ or alert and waiting? J Immunol. 2012;188(12):5981–9.

    CAS  PubMed  PubMed Central  Google Scholar 

  126. Macatonia SE, et al. Dendritic cells produce IL-12 and direct the development of Th1 cells from naive CD4+ T cells. J Immunol. 1995;154(10):5071–9.

    CAS  PubMed  Google Scholar 

  127. Iebba V, et al. Eubiosis and dysbiosis: the two sides of the microbiota. New Microbiol. 2016;39(1):1–12.

    CAS  PubMed  Google Scholar 

  128. Hooks KB, A M. O’Malley, Dysbiosis and its discontents. MBio. 2017;8(5):1–11.

    Google Scholar 

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Authors and Affiliations

  1. Pediatric Nutrition and Gastroenterology Department, Instituto Nacional de Pediatría, Mexico City, Mexico

    David Avelar Rodriguez, Rubén Peña Vélez, Erick Manuel Toro Monjaraz & Jaime Ramirez Mayans

  2. School of Medicine, University College Cork, Cork, Ireland

    Paul MacDaragh Ryan

Authors
  1. David Avelar Rodriguez
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  2. Rubén Peña Vélez
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  3. Erick Manuel Toro Monjaraz
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  4. Jaime Ramirez Mayans
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  5. Paul MacDaragh Ryan
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Correspondence to David Avelar Rodriguez.

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Avelar Rodriguez, D., Peña Vélez, R., Toro Monjaraz, E.M. et al. The Gut Microbiota: A Clinically Impactful Factor in Patient Health and Disease. SN Compr. Clin. Med. 1, 188–199 (2019). https://doi.org/10.1007/s42399-018-0036-1

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  • DOI: https://doi.org/10.1007/s42399-018-0036-1

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