[ 1 ] British Thoracic Society Scottish Intercollegiate Guidelines Network. British guideline on the management of asthma. Thorax 2014;69(Suppl 1):1–192. link1

[ 2 ] Chiang JL, Maahs DM, Garvey KC, Hood KK, Laffel LM, Weinzimer SA, et al. Type 1 diabetes in children and adolescents: a position statement by the American Diabetes Association. Diabetes Care 2018;41(9):2026–44. link1

[ 3 ] Koletzko S, Niggemann B, Arato A, Dias JA, Heuschkel R, Husby S, et al. European Society of Pediatric Gastroenterology, Hepatology, and Nutrition. Diagnostic approach and management of cow’s-milk protein allergy in infants and children: ESPGHAN GI Committee practical guidelines. J Pediatr Gastroenterol Nutr 2012;55(2):221–9. link1

[ 4 ] Afshin A, Forouzanfar MH, Reitsma MB, Sur P, Estep K, Lee A, et al. GBD 2015 Obesity Collaborators. Health effects of overweight and obesity in 195 countries over 25 years. N Engl J Med 2017;377(1):13–27. link1

[ 5 ] Zwaigenbaum L, Brian JA, Ip A. Early detection for autism spectrum disorder in young children. Paediatr Child Health 2019;24(7):424–43. link1

[ 6 ] Devaraj S, Hemarajata P, Versalovic J. The human gut microbiome and body metabolism: implications for obesity and diabetes. Clin Chem 2013;59 (4):617–28. link1

[ 7 ] Achenbach P, Bonifacio E, Koczwara K, Ziegler AG. Natural history of type 1 diabetes. Diabetes 2005;54(Suppl 2):S25–31. link1

[ 8 ] Lin CH, Lin WD, Chou IC, Lee IC, Hong SY. Epilepsy and neurodevelopmental outcomes in children with etiologically diagnosed central nervous system infections: a retrospective cohort study. Front Neurol 2019;10:528. link1

[ 9 ] Mustonen N, Siljander H, Peet A, Tillmann V, Härkönen T, Ilonen J, et al. DIABIMMUNE Study Group. Early childhood infections precede development of b-cell autoimmunity and type 1 diabetes in children with HLA-conferred disease risk. Pediatr Diabetes 2018;19(2):293–9. link1

[10] Esposito S, Preti V, Consolo S, Nazzari E, Principi N. Adenovirus 36 infection and obesity. J Clin Virol 2012;55(2):95–100. link1

[11] Fitas AL, Martins C, Borrego LM, Lopes L, Jörns A, Lenzen S, et al. Immune cell and cytokine patterns in children with type 1 diabetes mellitus undergoing a remission phase: a longitudinal study. Pediatr Diabetes 2018;19(5):963–71. link1

[12] Kelishadi R, Roufarshbaf M, Soheili S, Payghambarzadeh F, Masjedi M. Association of childhood obesity and the immune system: a systematic review of reviews. Child Obes 2017;13(4):332–46. link1

[13] Upton J, Nowak-Wegrzyn A. The impact of baked egg and baked milk diets on IgE- and non-IgE-mediated allergy. Clin Rev Allergy Immunol 2018;55 (2):118–38. link1

[14] Galowitz S, Chang C. Immunobiology of critical pediatric asthma. Clin Rev Allergy Immunol 2015;48(1):84–96. link1

[15] Han H, Li Y, Fang J, Liu G, Yin J, Li T, et al. Gut microbiota and type 1 diabetes. Int J Mol Sci 2018;19(4):995. link1

[16] Everard A, Belzer C, Geurts L, Ouwerkerk JP, Druart C, Bindels LB, et al. Crosstalk between Akkermansia muciniphila and intestinal epithelium controls diet-induced obesity. Proc Natl Acad Sci USA 2013;110(22):9066–71. link1

[17] Dominguez-Bello MG, Godoy-Vitorino F, Knight R, Blaser MJ. Role of the microbiome in human development. Gut 2019;68(6):1108–14. link1

[18] Wang B, Yao M, Lv L, Ling Z, Li L. The human microbiota in health and disease. Engineering 2017;3(1):71–82. link1

[19] Milani C, Duranti S, Bottacini F, Casey E, Turroni F, Mahony J, et al. The first microbial colonizers of the human gut: composition, activities, and health implications of the infant gut microbiota. Microbiol Mol Biol Rev 2017;81(4): e00036–17. link1

[20] Zhu D, Xiao S, Yu J, Ai Q, He Y, Cheng C, et al. Effects of one-week empirical antibiotic therapy on the early development of gut microbiota and metabolites in preterm infants. Sci Rep 2017;7(1):8025. link1

[21] Chen K, Chen H, Faas MM, de Haan BJ, Li J, Xiao P, et al. Specific inulin-type fructan fibers protect against autoimmune diabetes by modulating gut immunity, barrier function, and microbiota homeostasis. Mol Nutr Food Res. Epub 2017 Mar 24.

[22] Spacova I, Petrova MI, Fremau A, Pollaris L, Vanoirbeek J, Ceuppens JL, et al. Intranasal administration of probiotic Lactobacillus rhamnosus GG prevents birch pollen-induced allergic asthma in a murine model. Allergy 2019;74 (1):100–10. link1

[23] Huang CF, Chie WC, Wang IJ. Efficacy of Lactobacillus administration in school-age children with asthma: a randomized, placebo-controlled trial. Nutrients 2018;10(11):10. link1

[24] Sanders ME, Merenstein DJ, Reid G, Gibson GR, Rastall RA. Probiotics and prebiotics in intestinal health and disease: from biology to the clinic. Nat Rev Gastroenterol Hepatol 2019;16:605–16. link1

[25] Sanders ME, Shane AL, Merenstein DJ. Advancing probiotic research in humans in the United States: challenges and strategies. Gut Microbes 2016;7 (2):97–100. link1

[26] Shane AL, Cabana MD, Vidry S, Merenstein D, Hummelen R, Ellis CL, et al. Guide to designing, conducting, publishing and communicating results of clinical studies involving probiotic applications in human participants. Gut Microbes 2010;1(4):243–53. link1

[27] Hollister EB, Riehle K, Luna RA, Weidler EM, Rubio-Gonzales M, Mistretta TA, et al. Structure and function of the healthy pre-adolescent pediatric gut microbiome. Microbiome 2015;3(1):36. link1

[28] Koenig JE, Spor A, Scalfone N, Fricker AD, Stombaugh J, Knight R, et al. Succession of microbial consortia in the developing infant gut microbiome. Proc Natl Acad Sci USA 2011;108(Suppl 1):4578–85. link1

[29] Palmer C, Bik EM, DiGiulio DB, Relman DA, Brown PO. Development of the human infant intestinal microbiota. PLoS Biol 2007;5(7):e177. link1

[30] Dugas LR, Lie L, Plange-Rhule J, Bedu-Addo K, Bovet P, Lambert EV, et al. Gut microbiota, short chain fatty acids, and obesity across the epidemiologic transition: the METS-Microbiome study protocol. BMC Public Health 2018;18 (1):978. link1

[31] Gavin PG, Hamilton-Williams EE. The gut microbiota in type 1 diabetes: friend or foe? Curr Opin Endocrinol Diabetes Obes 2019;26(4):207–12. link1

[32] Dzidic M, Abrahamsson TR, Artacho A, Collado MC, Mira A, Jenmalm MC. Oral microbiota maturation during the first 7 years of life in relation to allergy development. Allergy 2018;73(10):2000–11. link1

[33] Martínez-González AE, Andreo-Martínez P. The role of gut microbiota in gastrointestinal symptoms of children with ASD. Medicina 2019;55 (8):55. link1

[34] Hirata Y, Ihara S, Koike K. Targeting the complex interactions between microbiota, host epithelial and immune cells in inflammatory bowel disease. Pharmacol Res 2016;113(Pt A):574–84. link1

[35] Borre YE, O’Keeffe GW, Clarke G, Stanton C, Dinan TG, Cryan JF. Microbiota and neurodevelopmental windows: implications for brain disorders. Trends Mol Med 2014;20(9):509–18. link1

[36] Osadchiy V, Martin CR, Mayer EA. The gut–brain axis and the microbiome: mechanisms and clinical implications. Clin Gastroenterol Hepatol 2019;17 (2):322–32. link1

[37] Goehler LE, Park SM, Opitz N, Lyte M, Gaykema RP. Campylobacter jejuni infection increases anxiety-like behavior in the holeboard: possible anatomical substrates for viscerosensory modulation of exploratory behavior. Brain Behav Immun 2008;22(3):354–66. link1

[38] Bilbo SD, Levkoff LH, Mahoney JH, Watkins LR, Rudy JW, Maier SF. Neonatal infection induces memory impairments following an immune challenge in adulthood. Behav Neurosci 2005;119(1):293–301. link1

[39] Ceppa F, Mancini A, Tuohy K. Current evidence linking diet to gut microbiota and brain development and function. Int J Food Sci Nutr 2019;70(1):1–19. link1

[40] Erny D, Hrabeˇ de Angelis AL, Jaitin D, Wieghofer P, Staszewski O, David E, et al. Host microbiota constantly control maturation and function of microglia in the CNS. Nat Neurosci 2015;18(7):965–77. link1

[41] Keunen K, van Elburg RM, van Bel F, Benders MJ. Impact of nutrition on brain development and its neuroprotective implications following preterm birth. Pediatr Res 2015;77(1–2):148–55. link1

[42] Li M, Wang B, Zhang M, Rantalainen M, Wang S, Zhou H, et al. Symbiotic gut microbes modulate human metabolic phenotypes. Proc Natl Acad Sci USA 2008;105(6):2117–22. link1

[43] Yassour M, Vatanen T, Siljander H, Hämäläinen AM, Härkönen T, Ryhänen SJ, et al. DIABIMMUNE Study Group. Natural history of the infant gut microbiome and impact of antibiotic treatment on bacterial strain diversity and stability. Sci Transl Med 2016;8(343):343ra81. link1

[44] Kostic AD, Gevers D, Siljander H, Vatanen T, Hyötyläinen T, Hämäläinen AM, et al. DIABIMMUNE Study Group. The dynamics of the human infant gut microbiome in development and in progression toward type 1 diabetes. Cell Host Microbe 2015;17(2):260–73. link1

[45] Subramanian S, Huq S, Yatsunenko T, Haque R, Mahfuz M, Alam MA, et al. Persistent gut microbiota immaturity in malnourished Bangladeshi children. Nature 2014;510(7505):417–21. link1

[46] Bergström A, Skov TH, Bahl MI, Roager HM, Christensen LB, Ejlerskov KT, et al. Establishment of intestinal microbiota during early life: a longitudinal, explorative study of a large cohort of Danish infants. Appl Environ Microbiol 2014;80(9):2889–900. link1

[47] 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. link1

[48] Yatsunenko T, Rey FE, Manary MJ, Trehan I, Dominguez-Bello MG, Contreras M, et al. Human gut microbiome viewed across age and geography. Nature 2012;486(7402):222–7. link1

[49] Ringel-Kulka T, Cheng J, Ringel Y, Salojärvi J, Carroll I, Palva A, et al. Intestinal microbiota in healthy US young children and adults—a high throughput microarray analysis. PLoS One 2013;8(5):e64315. link1

[50] Black MM. Effects of vitamin B12 and folate deficiency on brain development in children. Food Nutr Bull 2008;29(2 Suppl 1):S126–31. link1

[51] Le Chatelier E, Nielsen T, Qin J, Prifti E, Hildebrand F, Falony G, et al. MetaHIT Consortium. Richness of human gut microbiome correlates with metabolic markers. Nature 2013;500(7464):541–6. link1

[52] Cani PD, Amar J, Iglesias MA, Poggi M, Knauf C, Bastelica D, et al. Metabolic endotoxemia initiates obesity and insulin resistance. Diabetes 2007;56 (7):1761–72. link1

[53] Goulet O. Potential role of the intestinal microbiota in programming health and disease. Nutr Rev 2015;73(Suppl 1):32–40. link1

[54] 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. link1

[55] 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):86. link1

[56] Vandenplas Y, Carnielli VP, Ksiazyk J, Luna MS, Migacheva N, Mosselmans JM, et al. Factors affecting early-life intestinal microbiota development. Nutrition 2020;78:110812. link1

[57] Dominguez-Bello MG, Costello EK, Contreras M, Magris M, Hidalgo G, Fierer N, et al. Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns. Proc Natl Acad Sci USA 2010;107(26):11971–5. link1

[58] Bokulich NA, Chung J, Battaglia T, Henderson N, Jay M, Li H, et al. Antibiotics, birth mode, and diet shape microbiome maturation during early life. Sci Transl Med 2016;8(343):343ra82. link1

[59] Adlercreutz EH, Wingren CJ, Vincente RP, Merlo J, Agardh D. Perinatal risk factors increase the risk of being affected by both type 1 diabetes and coeliac disease. Acta Paediatr 2015;104(2):178–84. link1

[60] Kuhle S, Tong OS, Woolcott CG. Association between caesarean section and childhood obesity: a systematic review and meta-analysis. Obes Rev 2015;16 (4):295–303. link1

[61] Black M, Bhattacharya S, Philip S, Norman JE, McLernon DJ. Planned cesarean delivery at term and adverse outcomes in childhood health. JAMA 2015;314 (21):2271–9. link1

[62] Bäckhed F, Roswall J, Peng Y, Feng Q, Jia H, Kovatcheva-Datchary P, et al. Dynamics and stabilization of the human gut microbiome during the first year of life. Cell Host Microbe 2015;17(5):690–703. link1

[63] Planer JD, Peng Y, Kau AL, Blanton LV, Ndao IM, Tarr PI, et al. Development of the gut microbiota and mucosal IgA responses in twins and gnotobiotic mice. Nature 2016;534(7606):263–6. link1

[64] Schwarzenberg SJ, Georgieff MK; Committee on Nutrition. Advocacy for improving nutrition in the first 1000 days to support childhood development and adult health. Pediatrics 2018;141(2):e20173716. link1

[65] Bode L. Human milk oligosaccharides: prebiotics and beyond. Nutr Rev 2009;67(Suppl 2):S183–91. link1

[66] Chouraqui JP. Does the contribution of human milk oligosaccharides to the beneficial effects of breast milk allow us to hope for an improvement in infant formulas? Crit Rev Food Sci Nutr. Epub 2020 May 12.

[67] Diaz HR. Fetal, neonatal, and infant microbiome: perturbations and subsequent effects on brain development and behavior. Semin Fetal Neonatal Med 2016;21(6):410–7. link1

[68] Savage JH, Lee-Sarwar KA, Sordillo JE, Lange NE, Zhou Y, O’Connor GT, et al. Diet during pregnancy and infancy and the infant intestinal microbiome. J Pediatr 2018;203:47–54. link1

[69] Baumann-Dudenhoeffer AM, D’Souza AW, Tarr PI, Warner BB, Dantas G. Infant diet and maternal gestational weight gain predict early metabolic maturation of gut microbiomes. Nat Med 2018;24(12):1822–9. link1

[70] Thompson AL, Monteagudo-Mera A, Cadenas MB, Lampl ML, Azcarate-Peril MA. Milk- and solid-feeding practices and daycare attendance are associated with differences in bacterial diversity, predominant communities, and metabolic and immune function of the infant gut microbiome. Front Cell Infect Microbiol 2015;5:3. link1

[71] Leong C, Haszard JJ, Lawley B, Otal A, Taylor RW, Szymlek-Gay EA, et al. Mediation analysis as a means of identifying dietary components that differentially affect the fecal microbiota of infants weaned by modified babyled and traditional approaches. Appl Environ Microbiol 2018;84(18):1–14. link1

[72] Nobel YR, Cox LM, Kirigin FF, Bokulich NA, Yamanishi S, Teitler I, et al. Metabolic and metagenomic outcomes from early-life pulsed antibiotic treatment. Nat Commun 2015;6(1):7486. link1

[73] 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. link1

[74] Kaliannan K, Wang B, Li XY, Bhan AK, Kang JX. Omega-3 fatty acids prevent early-life antibiotic exposure-induced gut microbiota dysbiosis and later-life obesity. Int J Obes 2016;40(6):1039–42. link1

[75] Chelimo C, Camargo Jr CA, Morton SMB, Grant CC. Association of repeated antibiotic exposure up to age 4 years with body mass at age 4.5 years. JAMA Netw Open 2020;3(1):e1917577. link1

[76] Livanos AE, Greiner TU, Vangay P, Pathmasiri W, Stewart D, McRitchie S, et al. Antibiotic-mediated gut microbiome perturbation accelerates development of type 1 diabetes in mice. Nat Microbiol 2016;1(11):16140. link1

[77] Korpela K, Salonen A, Virta LJ, Kekkonen RA, Forslund K, Bork P, et al. Intestinal microbiome is related to lifetime antibiotic use in Finnish preschool children. Nat Commun 2016;7(1):10410. link1

[78] Jacobi SK, Odle J. Nutritional factors influencing intestinal health of the neonate. Adv Nutr 2012;3(5):687–96. link1

[79] Wagner CL, Taylor SN, Johnson D. Host factors in amniotic fluid and breast milk that contribute to gut maturation. Clin Rev Allergy Immunol 2008;34 (2):191–204. link1

[80] Kayama H, Takeda K. Functions of innate immune cells and commensal bacteria in gut homeostasis. J Biochem 2016;159(2):141–9. link1

[81] Hooper LV. Bacterial contributions to mammalian gut development. Trends Microbiol 2004;12(3):129–34. link1

[82] Schnupf P, Gaboriau-Routhiau V, Cerf-Bensussan N. Host interactions with segmented filamentous bacteria: an unusual trade-off that drives the postnatal maturation of the gut immune system. Semin Immunol 2013;25 (5):342–51. link1

[83] Schnupf P, Gaboriau-Routhiau V, Gros M, Friedman R, Moya-Nilges M, Nigro G, et al. Growth and host interaction of mouse segmented filamentous bacteria in vitro. Nature 2015;520(7545):99–103. link1

[84] Gaboriau-Routhiau V, Rakotobe S, Lécuyer E, Mulder I, Lan A, Bridonneau C, et al. The key role of segmented filamentous bacteria in the coordinated maturation of gut helper T cell responses. Immunity 2009;31(4):677–89. link1

[85] Ivanov II, Atarashi K, Manel N, Brodie EL, Shima T, Karaoz U, et al. Induction of intestinal Th17 cells by segmented filamentous bacteria. Cell 2009;139 (3):485–98. link1

[86] Eklund KK, Niemi K, Kovanen PT. Immune functions of serum amyloid A. Crit Rev Immunol 2012;32(4):335–48. link1

[87] Zhang H, Wang L, Chu Y. Reactive oxygen species: the signal regulator of B cell. Free Radic Biol Med 2019;142:16–22. link1

[88] Atarashi K, Tanoue T, Ando M, Kamada N, Nagano Y, Narushima S, et al. Th17 Cell induction by adhesion of microbes to intestinal epithelial cells. Cell 2015;163(2):367–80. link1

[89] Furusawa Y, Obata Y, Hase K. Commensal microbiota regulates T cell fate decision in the gut. Semin Immunopathol 2015;37(1):17–25. link1

[90] Singh N, Gurav A, Sivaprakasam S, Brady E, Padia R, Shi H, et al. Activation of GPR109A, receptor for niacin and the commensal metabolite butyrate, suppresses colonic inflammation and carcinogenesis. Immunity 2014;40 (1):128–39. link1

[91] Zhou L, Sonnenberg GF. Essential immunologic orchestrators of intestinal homeostasis. Sci Immunol 2018;3(20):eaao1605. link1

[92] Talham GL, Jiang HQ, Bos NA, Cebra JJ. Segmented filamentous bacteria are potent stimuli of a physiologically normal state of the murine gut mucosal immune system. Infect Immun 1999;67(4):1992–2000. link1

[93] Nagashima K, Sawa S, Nitta T, Tsutsumi M, Okamura T, Penninger JM, et al. Identification of subepithelial mesenchymal cells that induce IgA and diversify gut microbiota. Nat Immunol 2017;18(6):675–82. link1

[94] Kau AL, Ahern PP, Griffin NW, Goodman AL, Gordon JI. Human nutrition, the gut microbiome and the immune system. Nature 2011;474 (7351):327–36. link1

[95] Burrin DG, Stoll B. Key nutrients and growth factors for the neonatal gastrointestinal tract. Clin Perinatol 2002;29(1):65–96. link1

[96] Samuel BS, Shaito A, Motoike T, Rey FE, Backhed F, Manchester JK, et al. Effects of the gut microbiota on host adiposity are modulated by the shortchain fatty-acid binding G protein-coupled receptor, GPR41. Proc Natl Acad Sci USA 2008;105(43):16767–72. link1

[97] Maslowski KM, Vieira AT, Ng A, Kranich J, Sierro F, Yu D, et al. Regulation of inflammatory responses by gut microbiota and chemoattractant receptor GPR43. Nature 2009;461(7268):1282–6. link1

[98] Park J, Kim M, Kang SG, Jannasch AH, Cooper B, Patterson J, et al. Short-chain fatty acids induce both effector and regulatory T cells by suppression of histone deacetylases and regulation of the mTOR-S6K pathway. Mucosal Immunol 2015;8(1):80–93. link1

[99] Fukuda S, Toh H, Hase K, Oshima K, Nakanishi Y, Yoshimura K, et al. Bifidobacteria can protect from enteropathogenic infection through production of acetate. Nature 2011;469(7331):543–7. link1

[100] Steimle A, Autenrieth IB, Frick JS. Structure and function: lipid A modifications in commensals and pathogens. Int J Med Microbiol 2016;306 (5):290–301. link1

[101] Gronbach K, Flade I, Holst O, Lindner B, Ruscheweyh HJ, Wittmann A, et al. Endotoxicity of lipopolysaccharide as a determinant of T-cell-mediated colitis induction in mice. Gastroenterology 2014;146(3):765–75. link1

[102] Bainbridge BW, Coats SR, Pham TT, Reife RA, Darveau RP. Expression of a Porphyromonas gingivalis lipid A palmitylacyltransferase in Escherichia coli yields a chimeric lipid A with altered ability to stimulate interleukin-8 secretion. Cell Microbiol 2006;8(1):120–9. link1

[103] Hrncir T, Stepankova R, Kozakova H, Hudcovic T, Tlaskalova-Hogenova H. Gut microbiota and lipopolysaccharide content of the diet influence development of regulatory T cells: studies in germ-free mice. BMC Immunol 2008;9(1):65. link1

[104] Mason KL, Huffnagle GB, Noverr MC, Kao JY. Overview of gut immunology. Adv Exp Med Biol 2008;635:1–14. link1

[105] Magalhaes JG, Tattoli I, Girardin SE. The intestinal epithelial barrier: how to distinguish between the microbial flora and pathogens. Semin Immunol 2007;19(2):106–15. link1

[106] Crawley JN. Behavioral phenotyping strategies for mutant mice. Neuron 2008;57(6):809–18. link1

[107] Gareau MG, Wine E, Rodrigues DM, Cho JH, Whary MT, Philpott DJ, et al. Bacterial infection causes stress-induced memory dysfunction in mice. Gut 2011;60(3):307–17. link1

[108] Neufeld KM, Kang N, Bienenstock J, Foster JA. Reduced anxiety-like behavior and central neurochemical change in germ-free mice. Neurogastroenterol Motil 2011;23:255–64. link1

[109] Shohamy D. Learning and motivation in the human striatum. Curr Opin Neurobiol 2011;21(3):408–14. link1

[110] Diaz Heijtz R, Wang S, Anuar F, Qian Y, Björkholm B, Samuelsson A, et al. Normal gut microbiota modulates brain development and behavior. Proc Natl Acad Sci USA 2011;108(7):3047–52. link1

[111] Sudo N, Chida Y, Aiba Y, Sonoda J, Oyama N, Yu XN, et al. Postnatal microbial colonization programs the hypothalamic–pituitary–adrenal system for stress response in mice. J Physiol 2004;558(Pt 1):263–75. link1

[112] Mayer EA. Gut feelings: the emerging biology of gut–brain communication. Nat Rev Neurosci 2011;12(8):453–66. link1

[113] Gasperotti M, Passamonti S, Tramer F, Masuero D, Guella G, Mattivi F, et al. Fate of microbial metabolites of dietary polyphenols in rats: is the brain their target destination? ACS Chem Neurosci 2015;6(8):1341–52. link1

[114] Ridaura V, Belkaid Y. Gut microbiota: the link to your second brain. Cell 2015;161(2):193–4. link1

[115] Nayak D, Roth TL, McGavern DB. Microglia development and function. Annu Rev Immunol 2014;32(1):367–402. link1

[116] Nayak D, Zinselmeyer BH, Corps KN, McGavern DB. In vivo dynamics of innate immune sentinels in the CNS. Intravital 2012;1(2):95–106. link1

[117] Haghikia A, Jörg S, Duscha A, Berg J, Manzel A, Waschbisch A, et al. Dietary fatty acids directly impact central nervous system autoimmunity via the small intestine. Immunity 2015;43(4):817–29. link1

[118] Yano JM, Yu K, Donaldson GP, Shastri GG, Ann P, Ma L, et al. Indigenous bacteria from the gut microbiota regulate host serotonin biosynthesis. Cell 2015;161(2):264–76. link1

[119] Ridlon JM, Kang DJ, Hylemon PB. Bile salt biotransformations by human intestinal bacteria. J Lipid Res 2006;47(2):241–59. link1

[120] Benarroch EE. Histamine in the CNS: multiple functions and potential neurologic implications. Neurology 2010;75(16):1472–9. link1

[121] Vanhala A, Yamatodani A, Panula P. Distribution of histamine-, 5- hydroxytryptamine-, and tyrosine hydroxylase-immunoreactive neurons and nerve fibers in developing rat brain. J Comp Neurol 1994;347(1):101–14. link1

[122] Barcik W, Wawrzyniak M, Akdis CA, O’Mahony L. Immune regulation by histamine and histamine-secreting bacteria. Curr Opin Immunol 2017;48:108–13. link1

[123] Barcik W, Pugin B, Westermann P, Perez NR, Ferstl R, Wawrzyniak M, et al. Histamine-secreting microbes are increased in the gut of adult asthma patients. J Allergy Clin Immunol 2016;138(5):1491–4. link1

[124] Zhu J, Qu C, Lu X, Zhang S. Activation of microglia by histamine and substance P. Cell Physiol Biochem 2014;34(3):768–80. link1

[125] Khakh BS, Sofroniew MV. Diversity of astrocyte functions and phenotypes in neural circuits. Nat Neurosci 2015;18(7):942–52. link1

[126] Homberg JR, Kolk SM, Schubert D. Editorial perspective of the research topic ‘‘Deciphering serotonin’s role in neurodevelopment”. Front Cell Neurosci 2013;7:212. link1

[127] Gaspar P, Cases O, Maroteaux L. The developmental role of serotonin: news from mouse molecular genetics. Nat Rev Neurosci 2003;4(12):1002–12. link1

[128] Golubeva AV, Joyce SA, Moloney G, Burokas A, Sherwin E, Arboleya S, et al. Microbiota-related changes in bile acid and tryptophan metabolism are associated with gastrointestinal dysfunction in a mouse model of autism. EBioMedicine 2017;24:166–78. link1

[129] Li W, Dowd SE, Scurlock B, Acosta-Martinez V, Lyte M. Memory and learning behavior in mice is temporally associated with diet-induced alterations in gut bacteria. Physiol Behav 2009;96(4–5):557–67. link1

[130] Burks AW, Tang M, Sicherer S, Muraro A, Eigenmann PA, Ebisawa M, et al. ICON: food allergy. J Allergy Clin Immunol 2012;129(4):906–20. link1

[131] Ng M, Fleming T, Robinson M, Thomson B, Graetz N, Margono C, et al. Global, regional, and national prevalence of overweight and obesity in children and adults during 1980–2013: a systematic analysis for the Global Burden of Disease Study 2013. Lancet 2014;384(9945):766–81. link1

[132] Di Cesare M, Soric´ M, Bovet P, Miranda JJ, Bhutta Z, Stevens GA, et al. The epidemiological burden of obesity in childhood: a worldwide epidemic requiring urgent action. BMC Med 2019;17(1):212. link1

[133] Wild SH, Byrne CD. Risk factors for diabetes and coronary heart disease. BMJ 2006;333(7576):1009–11. link1

[134] Korpela K, Renko M, Vänni P, Paalanne N, Salo J, Tejesvi MV, et al. Microbiome of the first stool and overweight at age 3 years: a prospective cohort study. Pediatr Obes 2020;15(11):e12680. link1

[135] Bervoets L, Van Hoorenbeeck K, Kortleven I, Van Noten C, Hens N, Vael C, et al. Differences in gut microbiota composition between obese and lean children: a cross-sectional study. Gut Pathog 2013;5:10. link1

[136] Korpela K, Zijlmans MA, Kuitunen M, Kukkonen K, Savilahti E, Salonen A, et al. Childhood BMI in relation to microbiota in infancy and lifetime antibiotic use. Microbiome 2017;5(1):26. link1

[137] Stanislawski MA, Dabelea D, Wagner BD, Iszatt N, Dahl C, Sontag MK, et al. Gut microbiota in the first 2 years of life and the association with body mass index at age 12 in a Norwegian birth cohort. MBio 2018;9(5): e01751–18. link1

[138] Benítez-Páez A, Gómez Del Pugar EM, López-Almela I, Moya-Pérez Á, Codoñer-Franch P, Sanz Y. Depletion of Blautia species in the microbiota of obese children relates to intestinal inflammation and metabolic phenotype worsening. mSystems 2020;5(2):e00857–19. link1

[139] Brown AJ, Goldsworthy SM, Barnes AA, Eilert MM, Tcheang L, Daniels D, et al. The orphan G protein-coupled receptors GPR41 and GPR43 are activated by propionate and other short chain carboxylic acids. J Biol Chem 2003;278 (13):11312–9. link1

[140] Blaut M. Gut microbiota and energy balance: role in obesity. Proc Nutr Soc 2015;74(3):227–34. link1

[141] Slavin JL. Dietary fiber and body weight. Nutrition 2005;21(3):411–8. link1

[142] Sun L, Ma L, Ma Y, Zhang F, Zhao C, Nie Y. Insights into the role of gut microbiota in obesity: pathogenesis, mechanisms, and therapeutic perspectives. Protein Cell 2018;9(5):397–403. link1

[143] Tazoe H, Otomo Y, Kaji I, Tanaka R, Karaki SI, Kuwahara A. Roles of shortchain fatty acids receptors, GPR41 and GPR43 on colonic functions. J Physiol Pharmacol 2008;59(Suppl 2):251–62. link1

[144] Lin HC, Neevel C, Chen JH. Slowing intestinal transit by PYY depends on serotonergic and opioid pathways. Am J Physiol Gastrointest Liver Physiol 2004;286(4):G558–63. link1

[145] Murugesan S, Nirmalkar K, Hoyo-Vadillo C, García-Espitia M, RamírezSánchez D, García-Mena J. Gut microbiome production of short-chain fatty acids and obesity in children. Eur J Clin Microbiol Infect Dis 2018;37 (4):621–5. link1

[146] Hersoug LG, Møller P, Loft S. Role of microbiota-derived lipopolysaccharide in adipose tissue inflammation, adipocyte size and pyroptosis during obesity. Nutr Res Rev 2018;31(2):153–63. link1

[147] Li F, Jiang C, Krausz KW, Li Y, Albert I, Hao H, et al. Microbiome remodelling leads to inhibition of intestinal farnesoid X receptor signalling and decreased obesity. Nat Commun 2013;4(1):2384. link1

[148] Vatanen T, Franzosa EA, Schwager R, Tripathi S, Arthur TD, Vehik K, et al. The human gut microbiome in early-onset type 1 diabetes from the TEDDY study. Nature 2018;562(7728):589–94. link1

[149] Rhys Williams SC, Reem A, Pablo AM, Abdul B, David B, Stéphane B, et al. IDF diabetes atlas. 9th ed. Brussels: International Diabetes Federation; 2019. link1

[150] Craig ME, Kim KW, Isaacs SR, Penno MA, Hamilton-Williams EE, Couper JJ, et al. Early-life factors contributing to type 1 diabetes. Diabetologia 2019;62 (10):1823–34. link1

[151] Leiva-Gea I, Sánchez-Alcoholado L, Martín-Tejedor B, Castellano-Castillo D, Moreno-Indias I, Urda-Cardona A, et al. Gut microbiota differs in composition and functionality between children with type 1 diabetes and MODY2 and healthy control subjects: a case-control study. Diabetes Care 2018;41 (11):2385–95. link1

[152] De Goffau MC, Luopajärvi K, Knip M, Ilonen J, Ruohtula T, Härkönen T, et al. Fecal microbiota composition differs between children with b-cell autoimmunity and those without. Diabetes 2013;62(4):1238–44. link1

[153] Mariño E, Richards JL, McLeod KH, Stanley D, Yap YA, Knight J, et al. Gut microbial metabolites limit the frequency of autoimmune T cells and protect against type 1 diabetes. Nat Immunol 2017;18(5):552–62. link1

[154] Chen B, Sun L, Zhang X. Integration of microbiome and epigenome to decipher the pathogenesis of autoimmune diseases. J Autoimmun 2017;83:31–42. link1

[155] Li B, Selmi C, Tang R, Gershwin ME, Ma X. The microbiome and autoimmunity: a paradigm from the gut-liver axis. Cell Mol Immunol 2018;15(6):595–609. link1

[156] Davis-Richardson AG, Triplett EW. A model for the role of gut bacteria in the development of autoimmunity for type 1 diabetes. Diabetologia 2015;58 (7):1386–93. link1

[157] Arrieta MC, Stiemsma LT, Dimitriu PA, Thorson L, Russell S, Yurist-Doutsch S, et al. CHILD Study Investigators. Early infancy microbial and metabolic alterations affect risk of childhood asthma. Sci Transl Med 2015;7 (307):307ra152. link1

[158] Iweala OI, Nagler CR. The microbiome and food allergy. Annu Rev Immunol 2019;37(1):377–403. link1

[159] Shreiner A, Huffnagle GB, Noverr MC. The ‘‘microflora hypothesis” of allergic disease. Adv Exp Med Biol 2008;635:113–34. link1

[160] Zimmermann P, Messina N, Mohn WW, Finlay BB, Curtis N. Association between the intestinal microbiota and allergic sensitization, eczema, and asthma: a systematic review. J Allergy Clin Immunol 2019;143(2):467–85. link1

[161] Fujimura KE, Sitarik AR, Havstad S, Lin DL, Levan S, Fadrosh D, et al. Neonatal gut microbiota associates with childhood multisensitized atopy and T cell differentiation. Nat Med 2016;22(10):1187–91. link1

[162] Levan SR, Stamnes KA, Lin DL, Panzer AR, Fukui E, McCauley K, et al. Elevated faecal 12,13-diHOME concentration in neonates at high risk for asthma is produced by gut bacteria and impedes immune tolerance. Nat Microbiol 2019;4(11):1851–61. link1

[163] Sicherer SH. Epidemiology of food allergy. J Allergy Clin Immunol 2011;127 (3):594–602. link1

[164] Berni Canani R, Sangwan N, Stefka AT, Nocerino R, Paparo L, Aitoro R, et al. Lactobacillus rhamnosus GG-supplemented formula expands butyrateproducing bacterial strains in food allergic infants. ISME J 2016;10 (3):742–50. link1

[165] Bunyavanich S, Shen N, Grishin A, Wood R, Burks W, Dawson P, et al. Earlylife gut microbiome composition and milk allergy resolution. J Allergy Clin Immunol 2016;138(4):1122–30. link1

[166] Caminero A, Meisel M, Jabri B, Verdu EF. Mechanisms by which gut microorganisms influence food sensitivities. Nat Rev Gastroenterol Hepatol 2019;16(1):7–18. link1

[167] Verdu EF, Galipeau HJ, Jabri B. Novel players in coeliac disease pathogenesis: role of the gut microbiota. Nat Rev Gastroenterol Hepatol 2015;12 (9):497–506. link1

[168] Bouziat R, Hinterleitner R, Brown JJ, Stencel-Baerenwald JE, Ikizler M, Mayassi T, et al. Reovirus infection triggers inflammatory responses to dietary antigens and development of celiac disease. Science 2017;356(6333):44–50. link1

[169] Morrison DJ, Preston T. Formation of short chain fatty acids by the gut microbiota and their impact on human metabolism. Gut Microbes 2016;7 (3):189–200. link1

[170] Lamas B, Richard ML, Leducq V, Pham HP, Michel ML, Da Costa G, et al. CARD9 impacts colitis by altering gut microbiota metabolism of tryptophan into aryl hydrocarbon receptor ligands. Nat Med 2016;22(6):598–605. link1

[171] Hadis U, Wahl B, Schulz O, Hardtke-Wolenski M, Schippers A, Wagner N, et al. Intestinal tolerance requires gut homing and expansion of FoxP3+ regulatory T cells in the lamina propria. Immunity 2011;34(2):237–46. link1

[172] Smith PM, Howitt MR, Panikov N, Michaud M, Gallini CA, Bohlooly-Y M, et al. The microbial metabolites, short-chain fatty acids, regulate colonic Treg cell homeostasis. Science 2013;341(6145):569–73. link1

[173] Hamer HM, Jonkers D, Venema K, Vanhoutvin S, Troost FJ, Brummer RJ. Review article: the role of butyrate on colonic function. Aliment Pharmacol Ther 2008;27(2):104–19. link1

[174] UNICEF, WHO, World Bank Group. Joint child malnutrition estimates—levels and trends in child malnutrition. Global report. New York: UNICEF; 2019.

[175] Acosta AM, De Burga RR, Chavez CB, Flores JT, Olortegui MP, Pinedo SR, et al; MAL-ED Network Investigators. Relationship between growth and illness, enteropathogens and dietary intakes in the first 2 years of life: findings from the MAL-ED birth cohort study. BMJ Glob Health 2017;2(4):e000370. link1

[176] Vonaesch P, Morien E, Andrianonimiadana L, Sanke H, Mbecko JR, Huus KE, et al; Afribiota Investigators. Stunted childhood growth is associated with decompartmentalization of the gastrointestinal tract and overgrowth of oropharyngeal taxa. Proc Natl Acad Sci USA 2018;115(36):E8489–98. link1

[177] Dinh DM, Ramadass B, Kattula D, Sarkar R, Braunstein P, Tai A, et al. Longitudinal analysis of the intestinal microbiota in persistently stunted young children in South India. PLoS ONE 2016;11(5):e0155405. link1

[178] Harper KM, Mutasa M, Prendergast AJ, Humphrey J, Manges AR. Environmental enteric dysfunction pathways and child stunting: a systematic review. PLoS Negl Trop Dis 2018;12(1):e0006205. link1

[179] Weisz AJ, Manary MJ, Stephenson K, Agapova S, Manary FG, Thakwalakwa C, et al. Abnormal gut integrity is associated with reduced linear growth in rural Malawian children. J Pediatr Gastroenterol Nutr 2012;55(6):747–50. link1

[180] Rakoff-Nahoum S, Paglino J, Eslami-Varzaneh F, Edberg S, Medzhitov R. Recognition of commensal microflora by Toll-like receptors is required for intestinal homeostasis. Cell 2004;118(2):229–41. link1

[181] Piccirillo CA. Regulatory T cells in health and disease. Cytokine 2008;43 (3):395–401. link1

[182] Slack E, Hapfelmeier S, Stecher B, Velykoredko Y, Stoel M, Lawson MA, et al. Innate and adaptive immunity cooperate flexibly to maintain host– microbiota mutualism. Science 2009;325(5940):617–20. link1

[183] Vaarala O, Atkinson MA, Neu J. The ‘‘perfect storm” for type 1 diabetes: the complex interplay between intestinal microbiota, gut permeability, and mucosal immunity. Diabetes 2008;57(10):2555–62. link1

[184] Kelly P, Menzies I, Crane R, Zulu I, Nickols C, Feakins R, et al. Responses of small intestinal architecture and function over time to environmental factors in a tropical population. Am J Trop Med Hyg 2004;70(4):412–9. link1

[185] Gehrig JL, Venkatesh S, Chang HW, Hibberd MC, Kung VL, Cheng J, et al. Effects of microbiota-directed foods in gnotobiotic animals and undernourished children. Science 2019;365(6449):eaau4732. link1

[186] McAllister AK. Immune contributions to cause and effect in autism spectrum disorder. Biol Psychiatry 2017;81(5):380–2. link1

[187] Wang M, Wan J, Rong H, He F, Wang H, Zhou J, et al. Alterations in gut glutamate metabolism associated with changes in gut microbiota composition in children with autism spectrum disorder. mSystems 2019;4 (1):e00321–18. link1

[188] Sun X, Allison C, Matthews FE, Sharp SJ, Auyeung B, Baron-Cohen S, et al. Prevalence of autism in mainland China, Hong Kong and Taiwan: a systematic review and meta-analysis. Mol Autism 2013;4(1):1–13. link1

[189] Bauman ML. Medical comorbidities in autism: challenges to diagnosis and treatment. Neurotherapeutics 2010;7(3):320–7. link1

[190] Zhang M, Ma W, Zhang J, He Y, Wang J. Analysis of gut microbiota profiles and microbe-disease associations in children with autism spectrum disorders in China. Sci Rep 2018;8(1):13981. link1

[191] Ding HT, Taur Y, Walkup JT. Gut microbiota and autism: key concepts and findings. J Autism Dev Disord 2017;47(2):480–9. link1

[192] Sandler RH, Finegold SM, Bolte ER, Buchanan CP, Maxwell AP, Väisänen ML, et al. Short-term benefit from oral vancomycin treatment of regressive-onset autism. J Child Neurol 2000;15(7):429–35. link1

[193] Frick LR, Williams K, Pittenger C. Microglial dysregulation in psychiatric disease. Clin Dev Immunol 2013;2013:1–10. link1

[194] Chang PV, Hao L, Offermanns S, Medzhitov R. The microbial metabolite butyrate regulates intestinal macrophage function via histone deacetylase inhibition. Proc Natl Acad Sci USA 2014;111(6):2247–52. link1

[195] Dalile B, Van Oudenhove L, Vervliet B, Verbeke K. The role of short-chain fatty acids in microbiota–gut–brain communication. Nat Rev Gastroenterol Hepatol 2019;16(8):461–78. link1

[196] Benchimol EI, Fortinsky KJ, Gozdyra P, Van den Heuvel M, Van Limbergen J, Griffiths AM. Epidemiology of pediatric inflammatory bowel disease: a systematic review of international trends. Inflamm Bowel Dis 2011;17 (1):423–39. link1

[197] Abramson O, Durant M, Mow W, Finley A, Kodali P, Wong A, et al. Incidence, prevalence, and time trends of pediatric inflammatory bowel disease in northern California, 1996 to 2006. J Pediatr 2010;157(2):233–9. link1

[198] Oliveira SB, Monteiro IM. Diagnosis and management of inflammatory bowel disease in children. BMJ 2017;357:j2083. link1

[199] Peloquin JM, Goel G, Villablanca EJ, Xavier RJ. Mechanisms of pediatric inflammatory bowel disease. Annu Rev Immunol 2016;34(1):31–64. link1

[200] Knoll RL, Forslund K, Kultima JR, Meyer CU, Kullmer U, Sunagawa S, et al. Gut microbiota differs between children with inflammatory bowel disease and healthy siblings in taxonomic and functional composition: a metagenomic analysis. Am J Physiol Gastrointest Liver Physiol 2017;312(4): G327–39. link1

[201] Gevers D, Kugathasan S, Denson LA, Vázquez-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. link1

[202] Zhang X, Deeke SA, Ning Z, Starr AE, Butcher J, Li J, et al. Metaproteomics reveals associations between microbiome and intestinal extracellular vesicle proteins in pediatric inflammatory bowel disease. Nat Commun 2018;9 (1):2873. link1

[203] Gonçalves P, Araújo JR, Di Santo JP. A cross-talk between microbiota-derived short-chain fatty acids and the host mucosal immune system regulates intestinal homeostasis and inflammatory bowel disease. Inflamm Bowel Dis 2018;24(3):558–72. link1

[204] Lepage P, Häsler R, Spehlmann ME, Rehman A, Zvirbliene A, Begun A, et al. Twin study indicates loss of interaction between microbiota and mucosa of patients with ulcerative colitis. Gastroenterology 2011;141 (1):227–36. link1

[205] Sokol H, Pigneur B, Watterlot L, Lakhdari O, Bermúdez-Humarán 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 USA 2008;105(43):16731–6. link1

[206] Nicolucci AC, Hume MP, Martínez I, Mayengbam S, Walter J, Reimer RA. Prebiotics reduce body fat and alter intestinal microbiota in children who are overweight or with obesity. Gastroenterology 2017;153(3):711–22. link1

[207] Grimaldi R, Gibson GR, Vulevic J, Giallourou N, Castro-Mejía JL, Hansen LH, et al. A prebiotic intervention study in children with autism spectrum disorders (ASDs). Microbiome 2018;6(1):133. link1

[208] Savilahti E, Härkönen T, Savilahti EM, Kukkonen K, Kuitunen M, Knip M. Probiotic intervention in infancy is not associated with development of b cell autoimmunity and type 1 diabetes. Diabetologia 2018;61(12):2668–70. link1

[209] Buffington SA, Di Prisco GV, Auchtung TA, Ajami NJ, Petrosino JF, CostaMattioli M. Microbial reconstitution reverses maternal diet-induced social and synaptic deficits in offspring. Cell 2016;165(7):1762–75. link1

[210] Gibson GR, Hutkins R, Sanders ME, Prescott SL, Reimer RA, Salminen SJ, et al. 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. link1

[211] Hill C, Guarner F, Reid G, Gibson GR, Merenstein DJ, Pot B, et al. The international scientific association for probiotics and prebiotics consensus statement on the scope and appropriate use of the term probiotic. Nat Rev Gastroenterol Hepatol 2014;11(8):506–14. link1

[212] Wang Y, Li N, Yang JJ, Zhao DM, Chen B, Zhang GQ, et al. Probiotics and fructooligosaccharide intervention modulate the microbiota–gut–brain axis to improve autism spectrum reducing also the hyper-serotonergic state and the dopamine metabolism disorder. Pharmacol Res 2020;157:104784. link1

[213] Saran S, Gopalan S, Krishna TP. Use of fermented foods to combat stunting and failure to thrive. Nutrition 2002;18(5):393–6. link1

[214] Sanders ME, Akkermans LMA, Haller D, Hammerman C, Heimbach J, Hörmannsperger G, et al. Safety assessment of probiotics for human use. Gut Microbes 2010;1(3):164–85. link1

[215] Kunz AN, Noel JM, Fairchok MP. Two cases of Lactobacillus bacteremia during probiotic treatment of short gut syndrome. J Pediatr Gastroenterol Nutr 2004;38(4):457–8. link1

[216] Land MH, Rouster-Stevens K, Woods CR, Cannon ML, Cnota J, Shetty AK. Lactobacillus sepsis associated with probiotic therapy. Pediatrics 2005;115 (1):178–81. link1

[217] Kalliomäki M, Salminen S, Arvilommi H, Kero P, Koskinen P, Isolauri E. Probiotics in primary prevention of atopic disease: a randomised placebocontrolled trial. Lancet 2001;357(9262):1076–9. link1

[218] Kopp MV, Hennemuth I, Heinzmann A, Urbanek R. Randomized, doubleblind, placebo-controlled trial of probiotics for primary prevention: no clinical effects of Lactobacillus GG supplementation. Pediatrics 2008;121(4): e850–6. link1

[219] Taylor AL, Dunstan JA, Prescott SL. Probiotic supplementation for the first 6 months of life fails to reduce the risk of atopic dermatitis and increases the risk of allergen sensitization in high-risk children: a randomized controlled trial. J Allergy Clin Immunol 2007;119(1):184–91. link1

[220] Honeycutt TCB, El Khashab M, Wardrop 3rd RM, McNeal-Trice K, Honeycutt ALB, Christy CG, et al. Probiotic administration and the incidence of nosocomial infection in pediatric intensive care: a randomized placebocontrolled trial. Pediatr Crit Care Med 2007;8(5):452–8. link1

[221] Doron S, Snydman DR. Risk and safety of probiotics. Clin Infect Dis 2015;60 (Suppl 2):S129–34. link1

[222] Masco L, Huys G, De Brandt E, Temmerman R, Swings J. Culture-dependent and culture-independent qualitative analysis of probiotic products claimed to contain bifidobacteria. Int J Food Microbiol 2005;102(2):221–30. link1

[223] Kang DW, Adams JB, Gregory AC, Borody T, Chittick L, Fasano A, et al. Microbiota transfer therapy alters gut ecosystem and improves gastrointestinal and autism symptoms: an open-label study. Microbiome 2017;5(1):10. link1

[224] Karolewska-Bochenek K, Grzesiowski P, Banaszkiewicz A, Gawronska A, Kotowska M, Dziekiewicz M, et al. A two-week fecal microbiota transplantation course in pediatric patients with inflammatory bowel disease. Adv Exp Med Biol 2018;1047:81–7. link1

[225] Chen B, Avinashi V, Dobson S. Fecal microbiota transplantation for recurrent clostridium difficile infection in children. J Infect 2017;74(Suppl 1):S120–7. link1

[226] Zhong S, Zeng J, Deng Z, Jiang L, Zhang B, Yang K, et al. Fecal microbiota transplantation for refractory diarrhea in immunocompromised diseases: a pediatric case report. Ital J Pediatr 2019;45(1):116. link1

[227] 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. link1

[228] Butler ÉM, Chiavaroli V, Derraik JGB, Grigg CP, Wilson BC, Walker N, et al. Maternal bacteria to correct abnormal gut microbiota in babies born by Csection. Medicine 2020;99(30):e21315. link1

[229] Zellmer C, Sater MRA, Huntley MH, Osman M, Olesen SW, Ramakrishna B. Shiga toxin-producing Escherichia coli transmission via fecal microbiota transplant. Clin Infect Dis. In press.

[230] Arumugam M, Raes J, Pelletier E, Le Paslier D, Yamada T, Mende DR, et al; MetaHIT Consortium. Enterotypes of the human gut microbiome. Nature 2011;473(7346):174–80. link1

[231] Richard ML, Lamas B, Liguori G, Hoffmann TW, Sokol H. Gut fungal microbiota: the Yin and Yang of inflammatory bowel disease. Inflamm Bowel Dis 2015;21(3):656–65. link1

[232] Strati F, Cavalieri D, Albanese D, De Felice C, Donati C, Hayek J, et al. New evidences on the altered gut microbiota in autism spectrum disorders. Microbiome 2017;5(1):24. link1

[233] Goldman DL, Chen Z, Shankar V, Tyberg M, Vicencio A, Burk R. Lower airway microbiota and mycobiota in children with severe asthma. J Allergy Clin Immunol 2018;141(2):808–11. link1

[234] Reynolds LA, Finlay BB. Early life factors that affect allergy development. Nat Rev Immunol 2017;17(8):518–28. link1

[235] Mar Rodríguez M, Pérez D, Javier Chaves F, Esteve E, Marin-Garcia P, Xifra G, et al. Obesity changes the human gut mycobiome. Sci Rep 2015;5 (1):14600. link1

[236] Honkanen J, Vuorela A, Muthas D, Orivuori L, Luopajärvi K, Tejesvi MVG, et al. Fungal dysbiosis and intestinal inflammation in children with b-cell autoimmunity. Front Immunol 2020;11:468. link1

[237] Kernbauer E, Ding Y, Cadwell K. An enteric virus can replace the beneficial function of commensal bacteria. Nature 2014;516(7529):94–8. link1

[238] Yeung WCG, Rawlinson WD, Craig ME. Enterovirus infection and type 1 diabetes mellitus: systematic review and meta-analysis of observational molecular studies. BMJ 2011;342:d35. link1

[239] Anagandula M, Richardson SJ, Oberste MS, Sioofy-Khojine AB, Hyöty H, Morgan NG, et al. Infection of human islets of langerhans with two strains of Coxsackie B virus serotype 1: assessment of virus replication, degree of cell death and induction of genes involved in the innate immunity pathway. J Med Virol 2014;86(8):1402–11. link1

[240] Krogvold L, Edwin B, Buanes T, Frisk G, Skog O, Anagandula M, et al. Detection of a low-grade enteroviral infection in the islets of langerhans of living patients newly diagnosed with type 1 diabetes. Diabetes 2015;64 (5):1682–7. link1

[241] Onderdonk AB, Hecht JL, McElrath TF, Delaney ML, Allred EN, Leviton A. Colonization of second-trimester placenta parenchyma. Am J Obstet Gynecol 2008;199(1):52.e1–10. link1

[242] Collado MC, Rautava S, Aakko J, Isolauri E, Salminen S. Human gut colonisation may be initiated in utero by distinct microbial communities in the placenta and amniotic fluid. Sci Rep 2016;6(1):23129. link1

[243] Pelzer E, Gomez-Arango LF, Barrett HL, Nitert MD. Review: maternal health and the placental microbiome. Placenta 2017;54:30–7. link1

[244] Jiménez E, Marín ML, Martín R, Odriozola JM, Olivares M, Xaus J, et al. Is meconium from healthy newborns actually sterile? Res Microbiol 2008;159 (3):187–93. link1

[245] Han YW, Redline RW, Li M, Yin L, Hill GB, McCormick TS. Fusobacterium nucleatum induces premature and term stillbirths in pregnantmice: implication of oral bacteria in preterm birth. Infect Immun 2004;72(4):2272–9. link1

[246] De Goffau MC, Lager S, Sovio U, Gaccioli F, Cook E, Peacock SJ, et al. Human placenta has no microbiome but can contain potential pathogens. Nature 2019;572(7769):329–34. link1

[247] Leiby JS, McCormick K, Sherrill-Mix S, Clarke EL, Kessler LR, Taylor LJ, et al. Lack of detection of a human placenta microbiome in samples from preterm and term deliveries. Microbiome 2018;6(1):196. link1

[248] Wong AC, Levy M. New approaches to microbiome-based therapies. mSystems 2019;4(3):e00122–19. link1

[249] Zmora N, Soffer E, Elinav E. Transforming medicine with the microbiome. Sci Transl Med 2019;11(477):eaaw1815. link1

[250] Perdijk O, Marsland BJ. The microbiome: toward preventing allergies and asthma by nutritional intervention. Curr Opin Immunol 2019;60:10–8. link1

[251] Van der Lelie D, Taghavi S, Henry C, Gilbert JA. The microbiome as a source of new enterprises and job creation: considering clinical faecal and synthetic microbiome transplants and therapeutic regulation. Microb Biotechnol 2017;10(1):4–5. link1

[252] Bafeta A, Koh M, Riveros C, Ravaud P. Harms reporting in randomized controlled trials of interventions aimed at modifying microbiota: a systematic review. Ann Intern Med 2018;169(4):240–7. link1

[253] Shan Y, Segre JA, Chang EB. Responsible stewardship for communicating microbiome research to the press and public. Nat Med 2019;25(6):872–4. link1

[254] Gwinn M, MacCannell D, Armstrong GL. Next-generation sequencing of infectious pathogens. JAMA 2019;321(9):893–4. link1

[255] Jansson JK, Baker ES. A multi-omic future for microbiome studies. Nat Microbiol 2016;1(5):16049. link1

[256] Lagier JC, Dubourg G, Million M, Cadoret F, Bilen M, Fenollar F, et al. Culturing the human microbiota and culturomics. Nat Rev Microbiol 2018;16 (9):540–50. link1

[257] Marx V. Engineers embrace microbiome messiness. Nat Methods 2019;16 (7):581–4. link1