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International Journal of Clinical Nutrition & Dietetics Volume 4 (2018), Article ID 4:IJCND-132, 10 pages
https://doi.org/10.15344/2456-8171/2018/132
Review Article
Creation of the World: Regulation of Development of Host Immunity by Microbiota from Birth Onwards

Ger T. Rijkers1,2*, Ciska Lindelauf1, Wieke Kagenaar1, Nicole B. Rutten3* and Frans J. van Overveld1

1Department of Science, University College Roosevelt, Middelburg, The Netherlands
2Laboratory for Medical Microbiology and Immunology, St Antonius Hospital, Nieuwegein, The Netherlands
3Department of Pediatrics, St Antonius Hospital, Nieuwegein, The Netherlands
Prof. Ger T. Rijkers, Department of Sciences, University College Roosevelt, P.O. Box 94 4330 AB Middelburg, The Netherlands, Tel: +31 (0)118 655 500, Fax: +31 (0)118 655 508; E-mail: anna.scottodabusco@uniroma1.it
Dr. Nicole B. Rutten, Department of General Practice, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands; E-mail: b.rutten@maastrichtuniversity.nl
06 April 2018; 28 June 2018; 30 June 2018
Rijkers GT, Lindelauf C, Kagenaar W, Rutten NB, van Overveld FJ, et al. (2018) Creation of the World: Regulation of Development of Host Immunity by Microbiota from Birth Onwards. Int J Clin Nutr Diet 4: 132. doi: https://doi.org/10.15344/2456-8171/2018/132

References

  1. Sender R, Fuchs S, Milo R (2016) Revised Estimates for the Number of Human and Bacteria Cells in the Body. PLoS Biol 14: e1002533 [CrossRef] [Google Scholar] [PubMed]
  2. Savage DC (1977) Microbial ecology of the gastrointestinal tract. Annu Rev Microbiol 31: 107-133 [CrossRef] [Google Scholar] [PubMed]
  3. Vaishampayan PA, Kuehl JV, Froula JL, Morgan JL, Ochman H, et al. (2010) Comparative metagenomics and population dynamics of the gut microbiota in mother and infant. Genome Biol Evol 2: 53-66 [CrossRef] [Google Scholar] [PubMed]
  4. Lepage P, Leclerc MC, Joossens M, Mondot S, Blottière HM, et al. (2013) A metagenomic insight into our gut's microbiome. Gut 62: 146-158 [CrossRef] [Google Scholar] [PubMed]
  5. Gill SR, Pop M, Deboy RT, Eckburg PB, Turnbaugh PJ, et al. (2006) Metagenomic analysis of the human distal gut microbiome. Science 312: 1355-1359 [CrossRef] [Google Scholar] [PubMed]
  6. Bik EM (2009) Composition and function of the human-associated microbiota. Nutr Rev Suppl 2: 164-171 [CrossRef] [Google Scholar] [PubMed]
  7. Castanys-Muñoz E, Martin MJ, Vazquez E (2016) Building a Beneficial Microbiome from Birth. Adv Nutr 7: 323-330 [CrossRef] [Google Scholar] [PubMed]
  8. Hugon P, Dufour JC, Colson P, Fournier PE, Sallah K, et al. (2015) A comprehensive repertoire of prokaryotic species identified in human beings. Lancet Infect Dis 15: 1211-1219 [CrossRef] [Google Scholar] [PubMed]
  9. Qin J, Li R, Raes J, Arumugam M, Solvsten K, et al. (2010) A human gut microbial gene catalogue established by metagenomics sequencing. Nature 464: 59-65 [CrossRef] [Google Scholar] [PubMed]
  10. Fraher MH, O’Toole PW, Quigley EMM (2012) Techniques used to characterize the gut microbiota: a guide for the clinician. Nat Rev Gastroenterol Hepatol 9: 312-322 [CrossRef] [Google Scholar] [PubMed]
  11. Zoetendal EG, Rajilic-Stojanovic M, de Vos WM (2008) High-throughput diversity and functionality analysis of the gastrointestinal tract microbiota. Gut 57: 1605-1615 [CrossRef] [Google Scholar] [PubMed]
  12. Clemente JC, Ursell LK, Parfrey LW, Knight R (2012) The impact of the gut microbiota on human health: an integrative view. Cell 148: 1258-1270 [CrossRef] [Google Scholar] [PubMed]
  13. Blaser MJ (2014) The microbiome revolution. J Clin Invest 124: 4162-4165 [CrossRef] [Google Scholar] [PubMed]
  14. Lynch SV, Pedersen O (2016) The Human Intestinal Microbiome in Health and Disease. N Engl J Med 375: 2369-2379 [CrossRef] [Google Scholar] [PubMed]
  15. Chen TS, Chen PS (1989) Intestinal autointoxication: a medical leitmotif. J Clin Gastroenterol 11: 434-441 [CrossRef] [Google Scholar] [PubMed]
  16. Metchnikoff E (1907) The prolongation of life; optimistic studies. G. P. Putnam’s Sons, New York & London [Google Scholar]
  17. Lederberg J, McCray A (2001) Ome sweet ’omics: A genealogical treasury of words. Science 15: 8 [Google Scholar]
  18. Goulet O (2015) Potential role of the intestinal microbiota in programming health and disease. Nutr Rev Suppl 1: 32-40 [CrossRef] [Google Scholar] [PubMed]
  19. Petrosino JF, Highlander S, Luna RA, Gibbs RA, Versalovic J, et al. (2009) Metagenomic pyrosequencing and microbial identification. Clin Chem 55: 856-866 [CrossRef] [Google Scholar] [PubMed]
  20. Ottman N, Smidt H, de Vos WM, Belzer C (2012) The function of our microbiota: who is out there and what do they do? Front Cell Infect Microbiol 2: 104 [CrossRef] [Google Scholar] [PubMed]
  21. Li J, Jia H, Cai X, Zhong H, Feng Q, et al. (2014) An integrated catalog of reference genes in the human gut microbiome. Nat Biotechnol 32: 834-841 [CrossRef] [Google Scholar] [PubMed]
  22. MGC Project Team, Temple G, Gerhard DS, Rasooly R, Feingold EA, et al. (2009) The completion of the Mammalian Gene Collection (MGC). Genome Res 19: 2324-2333 [CrossRef] [Google Scholar] [PubMed]
  23. Woese CR, Fox GE (1977) Phylogenetic structure of the prokaryotic domain: the primary kingdoms. Proc Natl Acad Sci USA 74: 5088-5090 [CrossRef] [Google Scholar] [PubMed]
  24. Hattori M, Taylor TD (2009) The human intestinal microbiome: a new frontier of human biology. DNA Res 16: 1-12 [CrossRef] [Google Scholar] [PubMed]
  25. Fraher MH, O’Toole PW, Quigley EMM (2012) Techniques used to characterize the gut microbiota: a guide for the clinician. Nat Rev Gastroenterol Hepatol 9: 312-322 [CrossRef] [Google Scholar] [PubMed]
  26. Mahowald MA, Rey FE, Seedorf H, Turnbaugh PJ, Fulton RS, et al. (2009) Characterizing a model human gut microbiota composed of members of its two dominant bacterial phyla. Proc Natl Acad Sci USA 106: 5859-5864 [CrossRef] [Google Scholar] [PubMed]
  27. Tap J, Mondot S, Levenez F, Pelletier E, Caron C, et al. (2009) Towards the human intestinal microbiota phylogenetic core. Environ Microbiol 11: 2574-2584 [CrossRef] [Google Scholar] [PubMed]
  28. Aagaard K, Ma J, Antony KM, Ganu R, Petrosino J, et al. (2014) The placenta harbors a unique microbiome. Sci Transl Med 6: 237ra65 [CrossRef] [Google Scholar] [PubMed]
  29. Collado MC, Rautava S, Aakko J, Isolauri E, Salminen S, et al. (2016) Human gut colonisation may be initiated in utero by distinct microbial communities in the placenta and amniotic fluid. Sci Rep 6: 23129 [Google Scholar]
  30. Ardissone AN, de la Cruz DM, Davis-Richardson AG, Rechcigl KT, Li N, et al. (2014) Meconium microbiome analysis identifies bacteria correlated with premature birth. PLoS One 9: 90784 [CrossRef] [Google Scholar] [PubMed]
  31. Lauder AP, Roche AM, Sherrill-Mix S, Bailey A, Laughlin AL, et al. (2016) Comparison of placenta samples with contamination controls does not provide evidence for a distinct placenta microbiota. Microbiome 4: 29 [CrossRef] [Google Scholar] [PubMed]
  32. Kurokawa K, Itoh T, Kuwahara T, Oshima K, Toh H, et al. (2007) Comparative metagenomics revealed commonly enriched gene sets in human gut microbiomes. DNA Res14: 169-181 [CrossRef] [Google Scholar] [PubMed]
  33. Gensollen T, Iyer SS, Kasper DL, Blumberg RS (2016) How colonization by microbiota in early life shapes the immune system. Science 352: 539-544 [CrossRef] [Google Scholar] [PubMed]
  34. Koenig JE, Spor A, Scalfone N, Fricker AD, Stombaugh J, et al. (2011) Succession of microbial consortia in the developing infant gut microbiome. Proc Natl Acad Sci USA 108: 4578-4585 [CrossRef] [Google Scholar] [PubMed]
  35. Palmer C, Bik EM, DiGiulio DB, Relman DA, Brown PO, et al. (2007) Development of the human infant intestinal microbiota. PLoS Biol 5: e177 [CrossRef] [Google Scholar] [PubMed]
  36. Bäckhed F, Roswall J, Peng Y, Feng Q, Jia H, et al. (2015) Dynamics and Stabilization of the Human Gut Microbiome during the First Year of Life. Cell Host Microbe 17: 690-703 [CrossRef] [Google Scholar] [PubMed]
  37. Ringel-Kulka T, Cheng J, Ringel Y, Salojärvi J, Carroll I, et al. (2013) Intestinal microbiota in healthy U.S. young children and adults-a high throughput microarray analysis. PLoS One 8: e64315 [CrossRef] [Google Scholar] [PubMed]
  38. Yatsunenko T, Rey FE, Manary MJ, Trehan I, Dominguez-Bello MG, et al. (2012) Human gut microbiome viewed across age and geography. Nature 486: 222-227 [CrossRef] [Google Scholar] [PubMed]
  39. Cheng J, Ringel-Kulka T, Heikamp-de Jong I, Ringel Y, Carroll I, et al. (2016) Discordant temporal development of bacterial phyla and the emergence of core in the fecal microbiota of young children. ISME J 10: 1002-1014 [CrossRef] [Google Scholar] [PubMed]
  40. Matamoros S, Gras-Leguen C, Le Vacon F, Potel G, de La Cochetiere MF, et al. (2013) Development of intestinal microbiota in infants and its impact on health. Trends Microbiol 21: 167-173 [CrossRef] [Google Scholar] [PubMed]
  41. Lozupone CA, Stombaugh JI, Gordon JI, Jansson JK, Knight R, et al. (2012) Diversity, stability and resilience of the human gut microbiota. Nature 489: 220-230 [CrossRef] [Google Scholar] [PubMed]
  42. Turnbaugh PJ, Hamady M, Yatsunenko T, Cantarel BL, Duncan A, et al. (2009) A core gut microbiome in obese and lean twins. Nature 457: 480- 484 [CrossRef] [Google Scholar] [PubMed]
  43. Adlerberth I, Wold AE (2009) Establishment of the gut microbiota in Western infants. Acta Paediatr 98: 229-238 [CrossRef] [Google Scholar] [PubMed]
  44. Lloyd-Price J, Abu-Ali G, Huttenhower C (2016) The healthy human microbiome. Genome Med 8: 51 [CrossRef] [Google Scholar] [PubMed]
  45. Tamburini S, Shen N, Wu HC, Clemente JC (2016) The microbiome in early life: implications for health outcomes. Nat Med 22:713-722 [CrossRef] [Google Scholar] [PubMed]
  46. Penders J, Thijs C, Vink C, Stelma FF, Snijders B, et al. (2006) Factors influencing the composition of the intestinal microbiota in early infancy. Pediatrics 118: 511-521 [CrossRef] [Google Scholar] [PubMed]
  47. Arrieta MC, Stiemsma LT, Amenyogbe N, Brown EM, Finlay B, et al. (2014) The Intestinal Microbiome in Early Life: Health and Disease. Front Immunol 5: 427 [CrossRef] [Google Scholar] [PubMed]
  48. Madan JC, Hoen AG, Lundgren SN, Farzan SF, Cottingham KL, et al. (2016) Association of Cesarean Delivery and Formula Supplementation With the Intestinal Microbiome of 6-Week-Old Infants. JAMA Pediatr 170: 212-219 [CrossRef] [Google Scholar] [PubMed]
  49. Biasucci G, Benenati B, Morelli L, Bessi E, Boehm G, et al. (2008) Cesarean delivery may affect the early biodiversity of intestinal bacteria. J Nutr 138: 1796-1800 [CrossRef] [Google Scholar] [PubMed]
  50. Mangin I, Suau A, Gotteland M, Brunser O, Pochart P, et al. (2010) Amoxicillin treatment modifies the composition of Bifidobacterium species in infant intestinal microbiota. Anaerobe 16: 433-438 [CrossRef] [Google Scholar] [PubMed]
  51. Yassour M, Vatanen T, Siljander H, Hämäläinen AM, Härkönen T, et al. (2016) Natural history of the infant gut microbiome and impact of antibiotic treatment on bacterial strain diversity and stability. Sci Transl Med 8: 343ra81 [CrossRef] [Google Scholar] [PubMed]
  52. Dominguez-Bello MG, Costello EK, Contreras M, et al. (2010) Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns. Proc Natl Acad Sci USA 107: 11971- 11975 [CrossRef] [Google Scholar] [PubMed]
  53. Rutayisire E, Huang K, Liu Y, Tao F (2016) 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 16: 86 [CrossRef] [Google Scholar] [PubMed]
  54. Stokholm J, Thorsen J, Chawes BL, Schjørring S, Krogfelt KA, et al. (2016) Cesarean section changes neonatal gut colonization. J Allergy Clin Immunol 138: 881-889 [CrossRef] [Google Scholar] [PubMed]
  55. Madan JC, Hoen AG, Lundgren SN, Farzan SF, Cottingham KL, et al. (2016) Association of Cesarean Delivery and Formula Supplementation With the Intestinal Microbiome of 6-Week-Old Infants. JAMA Pediatr 170: 212-219 [CrossRef] [Google Scholar] [PubMed]
  56. Power SE, O'Toole PW, Stanton C, Ross RP, Fitzgerald GF, et al. (2014) Intestinal microbiota, diet and health. Br J Nutr 111: 387–402 [CrossRef] [Google Scholar] [PubMed]
  57. Bezirtzoglou E, Stavropoulou E (2011) Immunology and probiotic impact of the newborn and young children intestinal microflora. Anaerobe 17: 369- 374 [CrossRef] [Google Scholar] [PubMed]
  58. Jernberg C, Löfmark S, Edlund C, Jansson JK (2007) Long-term ecological impacts of antibiotic administration on the human intestinal microbiota. ISME J 1: 56-66 [CrossRef] [Google Scholar] [PubMed]
  59. Zou ZH, Liu D, Li HD, Zhu DP, He Y, et al. (2018) Prenatal and postnatal antibiotic exposure influences the gut microbiota of preterm infants in neonatal intensive care units. Ann Clin Microbiol Antimicrob 17: 9 [CrossRef] [Google Scholar] [PubMed]
  60. Tanaka S, Kobayashi T, Songjinda P, Tateyama A, Tsubouchi M, et al. (2009) Influence of antibiotic exposure in the early postnatal period on the development of intestinal microbiota. FEMS Immunol Med Microbiol 56: 80-87 [CrossRef] [Google Scholar] [PubMed]
  61. Savino F, Roana J, Mandras N, Tarasco V, Locatelli E, et al. (2011) Faecal microbiota in breast-fed infants after antibiotic therapy. Acta Paediatr 100: 75-78 [CrossRef] [Google Scholar] [PubMed]
  62. Francino MP (2016) Antibiotics and the Human Gut Microbiome: Dysbioses and Accumulation of Resistances. Front Microbiol 6: 1543 [CrossRef] [Google Scholar] [PubMed]
  63. Penders J, Thijs C, van den Brandt PA, Kummeling I, Snijders B, et al.(2007) Gut microbiota composition and development of atopic manifestations in infancy: the KOALA Birth Cohort Study. Gut 56: 661-667 [CrossRef] [Google Scholar] [PubMed]
  64. Rutten NB, Rijkers GT, Meijssen CB, Crijns CE, Oudshoorn JH, et al. (2015) Intestinal microbiota composition after antibiotic treatment in early life: the INCA study. BMC Pediatr 15: 204 [CrossRef] [Google Scholar] [PubMed]
  65. Oosterloo BC, van Elburg RM, Rutten NB, Bunkers CM, Crijns CE, et al. (2018) Wheezing and infantile colic are associated with neonatal antibiotic treatment. Pediatr Allergy Immunol 29: 151-158 [CrossRef] [Google Scholar] [PubMed]
  66. Blaser MJ, Bello MG (2014) Maternal antibiotic use and risk of asthma in offspring. Lancet Respir Med 2: e16 [CrossRef] [Google Scholar] [PubMed]
  67. Kemppainen KM, Vehik K, Lynch KF, Larsson HE, Canepa RJ, et al. (2017) Association Between Early-Life Antibiotic Use and the Risk of Islet or Celiac Disease Autoimmunity. JAMA Pediatr 171: 1217-1225 [CrossRef] [Google Scholar] [PubMed]
  68. Blaser MJ (2016) Antibiotic use and its consequences for the normal microbiome. Science 352: 544-545 [CrossRef] [Google Scholar] [PubMed]
  69. Cox LM, Blaser MJ (2015) Antibiotics in early life and obesity. Nat RevEndocrinol 11: 182-190 [CrossRef] [Google Scholar] [PubMed]
  70. Schmidt TSB, Raes J, Bork P (2018) The Human Gut Microbiome: From Association to Modulation. Cell 172: 1198-215 [CrossRef] [Google Scholar] [PubMed]
  71. Goodrich JK, Davenport ER, Beaumont M, Jackson MA, Knight R, et al. (2016) Genetic Determinants of the Gut Microbiome in UK Twins. Cell Host Microbe 19: 731-743 [CrossRef] [Google Scholar] [PubMed]
  72. Xie H, Guo R, Zhong H, Feng Q, Lan Z, et al. (2016) Shotgun Metagenomics of 250 Adult Twins Reveals Genetic and Environmental Impacts on the Gut Microbiome. Cell Syst 3: 572-584 [CrossRef] [Google Scholar] [PubMed]
  73. Marietta E, Rishi A, Taneja V (2015) Immunogenetic control of the intestinal microbiota. Immunology 145: 313-322 [CrossRef] [Google Scholar] [PubMed]
  74. Chong CYL, Bloomfield FH, O’Sullivan JM (2018) Factors Affecting Gastrointestinal Microbiome Development in Neonates. Nutrients 10: 274 [CrossRef] [Google Scholar] [PubMed]
  75. Li M, Wang M, Donovan SM (2014) Early development of the gut microbiome and immune-mediated childhood disorders. SeminReprod Med 32: 74-86 [CrossRef] [Google Scholar] [PubMed]
  76. Sjögren YM, Tomicic S, Lundberg A, Böttcher MF, Björkstén B, et al. (2009) Influence of early gut microbiota on the maturation of childhood mucosal and systemic immune responses. Clin Exp Allergy 39: 1842-1851 [CrossRef] [Google Scholar] [PubMed]
  77. Indrio F, Martini S, Francavilla R, Corvaglia L, Cristofori F, et al. (2017) Epigenetic Matters: The Link between Early Nutrition, Microbiome, and Long-term Health Development. Front Pediatr 5: 178 [CrossRef] [Google Scholar] [PubMed]
  78. Bäckhed F, Ley RE, Sonnenburg JL, Peterson DA, Gordon JI, et al. (2005) Host-bacterial mutualism in the human intestine. Science 307: 1915-1920. [CrossRef] [Google Scholar] [PubMed]
  79. Schaible UE, Kaufmann SH (2005) A nutritive view on the host-pathogen interplay. Trends Microbiol 3: 373-380. [CrossRef] [Google Scholar] [PubMed]
  80. Feng Q, Chen WD, Wang YD (2018) Gut Microbiota: An Integral Moderator in Health and Disease. Front Microbiol 9: 151 [CrossRef] [Google Scholar] [PubMed]
  81. Guilloteau P, Martin L, Eeckhaut V, Ducatelle R, Zabielski R, et al. (2010) From the gut to the peripheral tissues: the multiple effects of butyrate. Nutr Res Rev 23: 366-384 [CrossRef] [Google Scholar] [PubMed]
  82. Kasubuchi M, Hasegawa S, Hiramatsu T, Ichimura A, Kimura I, et al. (2015) Dietary gut microbial metabolites, short-chain fatty acids, and host metabolic regulation. Nutrients 7: 2839-2849 [CrossRef] [Google Scholar] [PubMed]
  83. Rechavi E, Lev A, Lee YN, Simon AJ, Yinon Y, et al. (2015) Timely and spatially regulated maturation of B and T cell repertoire during human fetal development. Science Transl Med 7: 276ra25 [CrossRef] [Google Scholar] [PubMed]
  84. Ygberg S, Nilsson A (2012) The developing immune system-from foetus to toddler. Acta Paediatrica 101: 120-127 [CrossRef] [Google Scholar] [PubMed]
  85. Kuper CF, van Bilsen J, Cnossen H, Houben G, Garthoff J, et al. (2016) Development of immune organs and functioning in humans and test animals: Implications for immune intervention studies. Reprod Toxicol 64: 180-190 [CrossRef] [Google Scholar] [PubMed]
  86. Granato A, Chen Y, Wesemann DR (2015) Primary immunoglobulin repertoire development: time and space matter. CurrOpin Immunol 33: 126-131 [CrossRef] [Google Scholar] [PubMed]
  87. Brugman S, Perdijk O, van Neerven RJ, Savelkoul HF (2015) Mucosal Immune Development in Early Life: Setting the Stage. Arch Immunol Ther Exp (Warsz) 63: 251-68 [CrossRef] [Google Scholar] [PubMed]
  88. Parker A, Lawson MAE, Vaux L, Pin C (2017) Host-microbe interaction in the gastrointestinal tract. Environ Microbiol [CrossRef] [Google Scholar] [PubMed]
  89. Gury-BenAri M, Thaiss CA, Serafini N, Winter DR, Giladi A, et al. (2016) The Spectrum and Regulatory Landscape of Intestinal Innate Lymphoid Cells Are Shaped by the Microbiome. Cell. 166: 1231-1246 [CrossRef] [Google Scholar] [PubMed]
  90. Buela KA, Omenetti S, Pizarro TT (2015) Cross-talk between type 3 innate lymphoid cells and the gut microbiota in inflammatory bowel disease. Curr Opin Gastroenterol 31: 449-455 [CrossRef] [Google Scholar] [PubMed]
  91. Farkas AM, Ivanov II (2015) Escaping Negative Selection: ILC You in the Gut. Immunity 43:12-14 [CrossRef] [Google Scholar] [PubMed]
  92. Hooper LV, Littman DR, Macpherson AJ (2012) Interactions between the microbiota and the immune system. Science 336: 1268-1273 [CrossRef] [Google Scholar] [PubMed]
  93. Hug H, Mohajeri MH, La Fata G (2018) Toll-Like Receptors: Regulators of the Immune Response in the Human Gut. Nutrients 10: 203 [CrossRef] [Google Scholar] [PubMed]
  94. Menckeberg CL, Hol J, Simons-Oosterhuis Y, Raatgeep HR, de Ruiter LF, et al. (2015) Human buccal epithelium acquires microbial hyporesponsiveness at birth, a role for secretory leukocyte protease inhibitor. Gut 64: 884-893 [CrossRef] [Google Scholar] [PubMed]
  95. Tanoue T, Honda K (2012) Induction of Treg cells in the mouse colonic mucosa: a central mechanism to maintain host-microbiota homeostasis. Semin Immunol 24: 50-57 [CrossRef] [Google Scholar] [PubMed]
  96. Mazmanian SK, Liu CH, Tzianabos AO, Kasper KL (2005) An immunomodulatorymolecule of symbiotic bacteria directs maturation of the host immune system. Cell 122: 107-118 [CrossRef] [Google Scholar] [PubMed]
  97. Mazmanian SK, Round JL, Kasper DL (2008) A microbial symbiosis factor prevents intestinal inflammatory disease. Nature 453: 620-625 [Google Scholar]
  98. Erturk-Hasdemir D, Kasper DL (2018) Finding a needle in a haystack: Bacteroides fragilis polysaccharide A as the archetypical symbiosis factor. Ann N Y Acad Sci 1417: 116-129 [CrossRef] [Google Scholar] [PubMed]
  99. Hevia A, Delgado S., Sánchez B, Margolles A (2015) Molecular players involved in the interaction between beneficial bacteria and the immune system. Front Microbiol 6: 1285 [CrossRef] [Google Scholar] [PubMed]
  100. Fouhy F, Ross RP, Fitzgerald GF, Stanton C, Cotter PD, et al. (2012) Composition of the early intestinal microbiota: Knowledge, knowledge gaps and the use of high throughput sequencing to address these gaps. Landes Bioscience 3: 203-220 [CrossRef] [Google Scholar] [PubMed]
  101. Frosali S, Pagliari D, Gambassi G, Landolfi R, Pandolfi F, et al. (2015) How the Intricate Interaction among Toll-Like Receptors, Microbiota, and Intestinal Immunity Can Influence Gastrointestinal Pathology. J Immunol Res 2015: 489821 [CrossRef] [Google Scholar]
  102. Patterson AM, Mulder IE, Travis AJ, Lan A, Cerf-Bensussan N, et al. (2017) Human Gut Symbiont Roseburia hominis Promotes and Regulates Innate Immunity. Front Immunol 8: 1166 [CrossRef] [Google Scholar] [PubMed]
  103. 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: 232-236 [CrossRef] [Google Scholar] [PubMed]
  104. 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: 446-450 [CrossRef] [Google Scholar] [PubMed]
  105. 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: 451-455 [CrossRef] [Google Scholar] [PubMed]
  106. Kaisar MMM, Pelgrom LR, van der Ham AJ, Yazdanbakhsh M, Everts B, et al. (2017) Butyrate Conditions Human Dendritic Cells to Prime Type 1 Regulatory T Cells via both Histone Deacetylase Inhibition and G Protein- Coupled Receptor 109A Signaling. Front Immunol 8: 1429 [CrossRef] [Google Scholar] [PubMed]
  107. Schnupf P, Gaboriau-Routhiau V, Gros M, Friedman R, Moya-Nilges M, et al. (2015) Growth and host interaction of mouse segmented filamentous bacteria in vitro. Nature 520: 99-103 [CrossRef] [Google Scholar] [PubMed]
  108. Lin L, Zhang J (2017) Role of intestinal microbiota and metabolites on gut homeostasis and human diseases. BMC Immunol 18: 2 [CrossRef] [Google Scholar] [PubMed]
  109. Hansen CH, Krych L, Nielsen DS, Vogensen FK, Hansen LH, et al. (2012) Early life treatment with vancomycin propagates Akkermansiamuciniphila and reduces diabetes incidence in the NOD mouse. Diabetologia 55: 2285- 2294 [CrossRef] [Google Scholar] [PubMed]
  110. Wang L, Christophersen CT, Sorich MJ, Gerber JP, Angley MT, et al. (2011) Low relative abundances of the mucolytic bacterium Akkermansia muciniphila and bifidobacterium spp. in feces of children with autism. Appl Environ Microbiol 77: 6718-6721 [CrossRef] [Google Scholar] [PubMed]
  111. Derrien, M, Belzer C, de Vos WM (2016) Akkermansia muciniphila and its role in regulating host functions. MicrobPathog 106: 171-181 [CrossRef] [Google Scholar] [PubMed]
  112. Ottman N, Geerlings SY, Aalvink S, de Vos WM, Belzer C, et al. (2017) Action and function of Akkermansia muciniphila in microbiome ecology, health and disease. Best Pract Res Clin Gastroenterol 31: 637-642 [CrossRef] [Google Scholar]
  113. Sokol H, Seksik P, Furet JP, Firmesse O, Nion-Larmurier I, et al. (2009) Low counts of Faecalibacterium prausnitzii in colitis microbiota. Inflamm Bowel Dis 15: 1183-1189 [CrossRef] [Google Scholar] [PubMed]
  114. Lopez-Siles M, Duncan SH, Garcia-Gil LJ, Martinez-Medina M (2017) Faecalibacterium prausnitzii: from microbiology to diagnostics and prognostics. ISME J 11: 841-851 [CrossRef] [Google Scholar] [PubMed]
  115. Quévrain E, Maubert MA, Michon C, Chain F, Marquant R, et al. (2016) Identification of an anti-inflammatory protein from Faecalibacteriumprausnitzii, a commensal bacteriumdeficient in crohn's disease. Gut 65: 415-425 [CrossRef] [Google Scholar] [PubMed]
  116. Wang Y, Ma R, Liu F, Lee SA, Zhang L, et al. (2018) Modulation of Gut Microbiota: A Novel Paradigm of Enhancing the Efficacy of Programmed Death-1 and Programmed Death Ligand-1 Blockade Therapy. Front Immunol 9: 374 [CrossRef] [Google Scholar] [PubMed]
  117. Humphries A, Daud A (2018) The gut microbiota and immune checkpoint inhibitors. Hum VaccinImmunother 1: 1-14 [CrossRef] [Google Scholar] [PubMed]
  118. Uribe-Herranz M, Bittinger K, Rafail S, Guedan S, Pierini S, et al. (2018) Gut microbiota modulates adoptive cell therapy via CD8α dendritic cells and IL-12. JCI Insight 3: 94952 [CrossRef] [Google Scholar] [PubMed]
  119. Cremonesi E, Governa V, Garzon JFG, Mele V, Amicarella F, et al. (2018) Gut microbiota modulate T cell trafficking into human colorectal cancer. Gut [CrossRef] [Google Scholar] [PubMed]
  120. Hampton T (2018) Gut Microbes May Shape Response to Cancer Immunotherapy. JAMA 319: 430-431 [CrossRef] [Google Scholar] [PubMed]
  121. Kroemer G, Zitvogel L (2018) Cancer immunotherapy in 2017: The breakthrough of the microbiota. Nat Rev Immunol 18: 87-88 [CrossRef] [Google Scholar] [PubMed]
  122. Kaiser J (2017) Gut microbes shape response to cancer immunotherapy. Science 358: 573 [CrossRef] [Google Scholar] [PubMed]
  123. Björkstén B, Sepp E, Julge K, Voor T, Mikelsaar M (2001) Allergy development and the intestinal microflora during the first year of life. J Allergy Clin Immunol108: 516-520 [CrossRef] [Google Scholar] [PubMed]
  124. Abrahamsson TR, Jakobsson HE, Andersson AF, Björkstén B, Engstrand L, et al. (2014) Low gut microbiota diversity in early infancy precedes asthma at school age. Clin Exp Allergy 44: 842-850 [CrossRef] [Google Scholar] [PubMed]
  125. Bisgaard H, Li N, Bonnelykke K, Chawes BL, Skov T, et al. (2011) Reduced diversity of the intestinal microbiota during infancy is associated with increased risk of allergic disease at school age. J Allergy Clin Immunol 128: 646-652 [CrossRef] [Google Scholar] [PubMed]
  126. Wold AE (1998) The hygiene hypothesis revised: is the rising frequency of allergy due to changes in the intestinal flora? Allergy 53: 20-25 [CrossRef] [Google Scholar] [PubMed]
  127. Bae JM (2018) Interpretation of epigenetic epidemiology for allergic diseases. Epidemiol Health [CrossRef] [PubMed]
  128. Ferrandiz-Mont D, Wahyuniati N, Chen HJ, Mulyadi M, Zanaria TM, et al. (2018) Hygiene practices: Are they protective factors for eczema symptoms? ImmunInflamm Dis 6: 297-306 [CrossRef] [Google Scholar] [PubMed]
  129. Haahtela T, Holgate S, Pawankar R, Akdis CA, Benjaponpitak S, et al. (2013) The biodiversity hypothesis and allergic disease: world allergy organization position statement. World Allergy Organ J 6:3 [CrossRef] [Google Scholar] [PubMed]
  130. van Tilburg Bernardes E, Arrieta MC (2017) Hygiene Hypothesis in Asthma Development: Is Hygiene to Blame? Arch Med Res 48: 717-726 [CrossRef] [Google Scholar] [PubMed]
  131. Alm B, Erdes L, Möllborg P, Pettersson R, Norvenius SG, et al. (2008) Neonatal antibiotic treatment is a risk factor for early wheezing. Pediatrics 121: 697-702 [CrossRef] [Google Scholar] [PubMed]
  132. Verhulst SL, Vael C, Beunckens C, Nelen V, Goossens H, et al. (2008) A longitudinal analysis on the association between antibiotic use, intestinal microflora, and wheezing during the first year of life. J Asthma 45: 828-832 [CrossRef] [Google Scholar] [PubMed]
  133. Kalliomäki M, Collado MC, Salminen S, Isolauri E (2008) Early differences in fecal microbiota composition in children may predict overweight. Am J Clin Nutr 87: 534-538 [CrossRef] [Google Scholar] [PubMed]
  134. Reinhardt C, Reigstad CS, Bäckhed F (2009) Intestinal microbiota during infancy and its implications for obesity. J Pediatr Gastroenterol Nutr 48: 249-256 [CrossRef] [Google Scholar] [PubMed]
  135. Musso G, Gambino R, Cassader M (2011) Interactions between gut microbiota and host metabolism predisposing to obesity and diabetes. Annu Rev Med 62:361-380 [CrossRef] [Google Scholar] [PubMed]
  136. Abraham C, Medzhitov R (2011) Interactions between the host innate immune system andmicrobes in inflammatory bowel disease. Gastroenterology 140: 1729-1737 [CrossRef] [Google Scholar] [PubMed]
  137. Echarri PP, Graciá CM, Berruezo GR, Vives I, Ballesta M, et al. (2011) Assessment of intestinal microbiota of full-term breast-fed infants from two different geographical locations. Early Hum Dev 87: 511-513 [CrossRef] [Google Scholar] [PubMed]
  138. Marques TM, Wall R, Ross RP, Fitzgerald GF, Ryan CA, et al. (2010) Programming infant gut microbiota: influence of dietary and environmental factors. CurrOpin Biotechnol 21: 149-156 [CrossRef] [Google Scholar] [PubMed]
  139. Markowiak P, Śliżewska K (2017) Effects of Probiotics, Prebiotics, and Synbiotics on Human Health. Nutrients 9: 201 [CrossRef] [Google Scholar] [PubMed]
  140. Roberfroid M, Gibson GR, Hoyles L, McCartney AL, Rastall R, et al. (2010) Prebiotic effects: metabolic and health benefits. Br J Nutr 104: 1-63 [CrossRef] [Google Scholar] [PubMed]
  141. Hill C, Guarner F, Reid G, Gibson GR, Merenstein DJ, et al. (2014) Expert consensus document: The International Scientific Association for Probiotics and Prebiotics consensus statement on the scope and appropriate use of the term probiotic. Nat Rev Gastroenterol Hepatol 11: 506-514 [CrossRef] [Google Scholar] [PubMed]
  142. Goldenberg JZ, Yap C, Lytvyn L, Lo CK, Beardsley J, et al. (2017) Probiotics for the prevention of Clostridium difficile-associated diarrhea in adults and children. Cochrane Database Syst Rev. 12: CD006095 [CrossRef] [Google Scholar] [PubMed]
  143. Goldenberg JZ, Lytvyn L, Steurich J, et al. (2011) Probiotics for the prevention of pediatric antibiotic-associated diarrhea. Cochrane Database Syst Rev 19: CD004827 [CrossRef] [Google Scholar] [PubMed]
  144. Hao Q, Lu Z, Dong BR, Huang CQ, Wu T, et al. (2015) Probiotics for preventing acute upper respiratory tract infections. Cochrane Database Syst Rev 2:CD006895 [CrossRef] [Google Scholar] [PubMed]
  145. Bo L, Li J, Tao T, Bai Y, Ye X,, et al. (2014) Probiotics for preventing ventilator-associated pneumonia. Cochrane Database Syst Rev 10: CD009066 [CrossRef] [Google Scholar] [PubMed]
  146. Dalal R, McGee RG, Riordan SM, Webster AC (2017) Probiotics for people with hepatic encephalopathy. Cochrane Database Syst Rev 2: CD008716 [CrossRef] [Google Scholar] [PubMed]
  147. Singh S, Stroud AM, Holubar SD, Pardi DS (2015) Treatment and prevention of pouchitis after ileal pouch-anal anastomosis for chronic ulcerative colitis. Cochrane Database Syst Rev 16: CD001176 [CrossRef] [Google Scholar] [PubMed]
  148. AlFaleh K, Anabrees J (2014) Probiotics for prevention of necrotizing enterocolitisin preterm infants. Cochrane Database Syst Rev 4: CD005496 [CrossRef] [Google Scholar] [PubMed]
  149. Ismail IH, Licciardi P V, Tang ML (2013) Probiotic effects in allergic disease. J Paediatr Child Health 49: 709-715 [CrossRef] [Google Scholar] [PubMed]
  150. Niers L, Martín R, Rijkers G, Sengers F, Timmerman H, et al. (2009) The effects of selected probiotic strains on the development of eczema (the PandA study). Allergy 64: 1349-1358 [CrossRef] [Google Scholar] [PubMed]
  151. Osborn DA, Sinn JKH (2007) Probiotics in infants for prevention of allergic disease and food hypersensitivity. Cochrane Database Syst Rev 4: CD006475 [CrossRef] [Google Scholar] [PubMed]
  152. Boyle RJ, Bath-Hextall FJ, Leonardi-Bee J, Murrell DF, Tang ML, et al. (2008) Probiotics for treating eczema. Cochrane Database Syst Rev 4: CD006135 [CrossRef] [Google Scholar] [PubMed]
  153. Zuccotti G, Meneghin F, Aceti A, Barone G, Callegari ML, et al. (2015) Probiotics for prevention of atopic diseases ininfants: systematic review and meta-analysis. Allergy 70: 1356-1371 [CrossRef] [Google Scholar] [PubMed]
  154. West CE (2014) Gut microbiota and allergic disease: new findings. CurrOpin Clin NutrMetab Care 17: 261-266 [CrossRef] [Google Scholar] [PubMed]
  155. Garcia-Larsen V, Ierodiakonou D, Jarrold K, Cunha S, Chivinge J, et al. (2018) Diet during pregnancy and infancy and risk of allergic or autoimmune disease: A systematic review and meta-analysis. PLoS Med 15: e1002507 [CrossRef] [Google Scholar] [PubMed]
  156. Umu ÖCO, Rudi K, Diep DB (2017) Modulation of the gut microbiota by prebiotic fibres and bacteriocins. MicrobEcol Health Dis. 28: 1348886 [CrossRef] [Google Scholar] [PubMed]
  157. Wilson B, Whelan K (2017) Prebiotic inulin-type fructans and galactooligosaccharides: definition, specificity, function, and application in gastrointestinal disorders. J Gastroenterol Hepatol. Suppl 1: 64-68 [CrossRef] [Google Scholar] [PubMed]
  158. Deehan EC, Duar RM, Armet AM, Perez-Muñoz ME, Jin M, et al. (2017) Modulation ofthe Gastrointestinal Microbiome with Nondigestible Fermentable Carbohydrates ToImprove Human Health. Microbiol Spectr [CrossRef] [Google Scholar] [PubMed]
  159. Watkins C, Stanton C, Ryan CA, Ross RP (2017) Microbial Therapeutics Designed for Infant Health. Front Nutr 4: 48 [CrossRef] [Google Scholar] [PubMed]
  160. Kim HK, Rutten NB, Besseling-van der Vaart I, Niers LE, Choi YH, et al. (2015) Probiotic supplementation influences faecal short chain fatty acids in infants at high risk for eczema. Benef Microbes 6: 783-790 [CrossRef] [Google Scholar] [PubMed]
  161. Barouki R, Gluckman PD, Grandjean P, Hanson M, Heindel JJ, et al. (2012) Developmental origins of non-communicable disease: implications for research and public health. Environ Health 11: 42 [CrossRef] [Google Scholar] [PubMed]
  162. Butel MJ, Waligora-Dupriet AJ, Wydau-Dematteis S (2018) The developing gut microbiota and its consequences for health. J Dev Orig Health Dis. Mar 22: 1-8 [CrossRef] [Google Scholar] [PubMed]
  163. Subramanian S, Huq S, Yatsunenko T, Haque R, Mahfuz M, et al. (2014) Persistent gut microbiota immaturity in malnourished Bangladeshi children. Nature 510: 417-421 [CrossRef] [Google Scholar] [PubMed]