1932

Abstract

The gut microbiome plays an integral role in health and disease, and diet is a major driver of its composition, diversity, and functional capacity. Given the dynamic development of the gut microbiome in infants and children, it is critical to address two major questions: () Can diet modify the composition, diversity, or function of the gut microbiome, and () will such modification affect functional/clinical outcomes including immune function, cognitive development, and overall health? We synthesize the evidence on the effect of nutritional interventions on the gut microbiome in infants and children across 26 studies. Findings indicate the need to study older children, assess the whole intestinal tract, and harmonize methods and interpretation of findings, which are critical for informing meaningful clinical and public health practice. These findings are relevant for precision health, may help identify windows of opportunity for intervention, and may inform the design and delivery of such interventions.

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2021-10-11
2024-12-05
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Literature Cited

  1. 1. 
    Aakko J, Grzeskowiak L, Asukas T, Paivansade E, Lehto KM et al. 2017. Lipid-based nutrient supplements do not affect gut Bifidobacterium microbiota in Malawian infants: a randomized trial. J. Pediatr. Gastroenterol. Nutr. 64:610–15
    [Google Scholar]
  2. 2. 
    Aly H, Said RN, Wali IE, Elwakkad A, Soliman Y et al. 2017. Medically graded honey supplementation formula to preterm infants as a prebiotic: a randomized controlled trial. J. Pediatr. Gastroenterol. Nutr. 64:966–70
    [Google Scholar]
  3. 3. 
    Amarri S, Benatti F, Callegari ML, Shahkhalili Y, Chauffard F et al. 2006. Changes of gut microbiota and immune markers during the complementary feeding period in healthy breast-fed infants. J. Pediatr. Gastroenterol. Nutr. 42:488–95
    [Google Scholar]
  4. 4. 
    Andrews SC, Robinson AK, Rodriguez-Quinones F. 2003. Bacterial iron homeostasis. FEMS Microbiol. Rev. 27:215–37
    [Google Scholar]
  5. 5. 
    Arimond M, Zeilani M, Jungjohann S, Brown KH, Ashorn P et al. 2015. Considerations in developing lipid-based nutrient supplements for prevention of undernutrition: experience from the International Lipid-Based Nutrient Supplements (iLiNS) Project. Matern. Child Nutr. 11:31–61
    [Google Scholar]
  6. 6. 
    Arrieta MC, Stiemsma LT, Amenyogbe N, Brown EM, Finlay B. 2014. The intestinal microbiome in early life: health and disease. Front. Immunol. 5:427
    [Google Scholar]
  7. 7. 
    Azad MB, Konya T, Maughan H, Guttman DS, Field CJ et al. 2013. Gut microbiota of healthy Canadian infants: profiles by mode of delivery and infant diet at 4 months. CMAJ 185:385–94
    [Google Scholar]
  8. 8. 
    Backhed 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
    [Google Scholar]
  9. 9. 
    Benn C, Fisker A, Napirna B, Roth A, Diness B et al. 2010. Vitamin A supplementation and BCG vaccination at birth in low birthweight neonates: two by two factorial randomised controlled trial. BMJ 340:c1101
    [Google Scholar]
  10. 10. 
    Benner M, Ferwerda G, Joosten I, van der Molen RG. 2018. How uterine microbiota might be responsible for a receptive, fertile endometrium. Hum. Reprod. Update 24:393–415
    [Google Scholar]
  11. 11. 
    Berding K, Holscher HD, Arthur AE, Donovan SM. 2018. Fecal microbiome composition and stability in 4- to 8-year old children is associated with dietary patterns and nutrient intake. J. Nutr. Biochem. 56:165–74
    [Google Scholar]
  12. 12. 
    Bhinder G, Allaire JM, Garcia C, Lau JT, Chan JM et al. 2017. Milk fat globule membrane supplementation in formula modulates the neonatal gut microbiome and normalizes intestinal development. Sci. Rep. 7:45274
    [Google Scholar]
  13. 13. 
    Biesalski HK. 2016. Nutrition meets the microbiome: micronutrients and the microbiota. Ann. N. Y. Acad. Sci. 1372:53–64
    [Google Scholar]
  14. 14. 
    Blanton LV, Charbonneau MR, Salih T, Barratt MJ, Venkatesh S et al. 2016. Gut bacteria that prevent growth impairments transmitted by microbiota from malnourished children. Science 351:6275aad3311
    [Google Scholar]
  15. 15. 
    Britton GJ, Contijoch EJ, Mogno I, Vennaro OH, Llewellyn SR et al. 2019. Microbiotas from humans with inflammatory bowel disease alter the balance of gut Th17 and RORγt+ regulatory T cells and exacerbate colitis in mice. Immunity 50:212–24.e4
    [Google Scholar]
  16. 16. 
    Butcher J, Unger S, Li J, Bando N, Romain G et al. 2018. Independent of birth mode or gestational age, very-low-birth-weight infants fed their mothers' milk rapidly develop personalized microbiotas low in Bifidobacterium. J. Nutr. 148:326–35
    [Google Scholar]
  17. 17. 
    Candido FG, Valente FX, Grzeskowiak LM, Moreira APB, Rocha D, Alfenas RCG. 2018. Impact of dietary fat on gut microbiota and low-grade systemic inflammation: mechanisms and clinical implications on obesity. Int. J. Food Sci. Nutr. 69:125–43
    [Google Scholar]
  18. 18. 
    Carmody RN, Bisanz JE, Bowen BP, Maurice CF, Lyalina S et al. 2019. Cooking shapes the structure and function of the gut microbiome. Nat. Microbiol. 4:2052–63
    [Google Scholar]
  19. 19. 
    Casals-Pascual C, Gonzalez A, Vazquez-Baeza Y, Song SJ, Jiang L, Knight R. 2020. Microbial diversity in clinical microbiome studies: sample size and statistical power considerations. Gastroenterology 158:1524–28
    [Google Scholar]
  20. 20. 
    Chatterton DE, Nguyen DN, Bering SB, Sangild PT. 2013. Anti-inflammatory mechanisms of bioactive milk proteins in the intestine of newborns. Int. J. Biochem. Cell Biol. 45:1730–47
    [Google Scholar]
  21. 21. 
    Chen RY, Mostafa I, Hibberd MC, Das S, Mahfuz M et al. 2021. A microbiota-directed food intervention for undernourished children. N. Engl. J. Med. 384:1517–28
    [Google Scholar]
  22. 22. 
    Cheung YB, Xu Y, Mangani C, Fan YM, Dewey KG et al. 2016. Gut microbiota in Malawian infants in a nutritional supplementation trial. Trop. Med. Int. Health 21:283–90
    [Google Scholar]
  23. 23. 
    Chi C, Xue Y, Lv N, Hao Y, Liu R et al. 2019. Longitudinal gut bacterial colonization and its influencing factors of low birth weight infants during the first 3 months of life. Front. Microbiol. 10:1105
    [Google Scholar]
  24. 24. 
    Clemente JC, Manasson J, Scher JU. 2018. The role of the gut microbiome in systemic inflammatory disease. BMJ 360:j5145
    [Google Scholar]
  25. 25. 
    Costello EK, Carlisle EM, Bik EM, Morowitz MJ, Relman DA. 2013. Microbiome assembly across multiple body sites in low-birthweight infants. mBio 4:e00782-13
    [Google Scholar]
  26. 26. 
    Culligan EP, Sleator RD, Marchesi JR, Hill C. 2014. Metagenomic identification of a novel salt tolerance gene from the human gut microbiome which encodes a membrane protein with homology to a brp/blh-family β-carotene 15,15′-monooxygenase. PLOS ONE 9:e103318
    [Google Scholar]
  27. 27. 
    Davis LM, Kakuda T, DiRita VJ. 2009. A Campylobacter jejuni znuA orthologue is essential for growth in low-zinc environments and chick colonization. J. Bacteriol. 191:1631–40
    [Google Scholar]
  28. 28. 
    De Filippo C, Cavalieri D, Di Paola M, Ramazzotti M, Poullet JB et al. 2010. Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa. PNAS 107:14691–96
    [Google Scholar]
  29. 29. 
    de Meij TG, Budding AE, de Groot EF, Jansen FM, Frank Kneepkens CM et al. 2016. Composition and stability of intestinal microbiota of healthy children within a Dutch population. FASEB J 30:1512–22
    [Google Scholar]
  30. 30. 
    de Weerth C, Fuentes S, Puylaert P, de Vos WM. 2013. Intestinal microbiota of infants with colic: development and specific signatures. Pediatrics 131:e550–550
    [Google Scholar]
  31. 31. 
    Derrien M, Alvarez AS, de Vos WM. 2019. The gut microbiota in the first decade of life. Trends Microbiol 27:997–1010
    [Google Scholar]
  32. 32. 
    Differding MK, Benjamin-Neelon SE, Hoyo C, Ostbye T, Mueller NT. 2020. Timing of complementary feeding is associated with gut microbiota diversity and composition and short chain fatty acid concentrations over the first year of life. BMC Microbiol 20:56
    [Google Scholar]
  33. 33. 
    Dinh DM, Ramadass B, Kattula D, Sarkar R, Braunstein P et al. 2016. Longitudinal analysis of the intestinal microbiota in persistently stunted young children in South India. PLOS ONE 11:e0155405
    [Google Scholar]
  34. 34. 
    Div. Commun. Dis. Control, Calif. Dep. Public Health 2019. Infant botulism treatment and prevention program. California Department of Public Health https://www.infantbotulism.org/parent/honey.php
    [Google Scholar]
  35. 35. 
    Dogra S, Sakwinska O, Soh SE, Ngom-Bru C, Bruck WM et al. 2015. Dynamics of infant gut microbiota are influenced by delivery mode and gestational duration and are associated with subsequent adiposity. mBio 6:1e02419-14
    [Google Scholar]
  36. 36. 
    Dominguez-Bello MG, Costello EK, Contreras M, Magris M, Hidalgo G et al. 2010. Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns. PNAS 107:11971–75
    [Google Scholar]
  37. 37. 
    Dostal A, Baumgartner J, Riesen N, Chassard C, Smuts CM et al. 2014. Effects of iron supplementation on dominant bacterial groups in the gut, faecal SCFA and gut inflammation: a randomised, placebo-controlled intervention trial in South African children. Br. J. Nutr. 112:547–56
    [Google Scholar]
  38. 38. 
    Enam F, Mansell TJ. 2019. Prebiotics: tools to manipulate the gut microbiome and metabolome. J. Ind. Microbiol. Biotechnol. 46:1445–59
    [Google Scholar]
  39. 39. 
    Erdman JW Jr., Macdonald IA, Zeisel SH 2012. Present Knowledge in Nutrition Oxford, UK: Wiley-Blackwell. , 10th ed..
    [Google Scholar]
  40. 40. 
    Fallani M, Amarri S, Uusijarvi A, Adam R, Khanna S et al. 2011. Determinants of the human infant intestinal microbiota after the introduction of first complementary foods in infant samples from five European centres. Microbiology 157:1385–92
    [Google Scholar]
  41. 41. 
    Flaherman VJ, Narayan NR, Hartigan-O'Connor D, Cabana MD, McCulloch CE, Paul IM 2018. The effect of early limited formula on breastfeeding, readmission, and intestinal microbiota: a randomized clinical trial. J. Pediatr. 196:84–90.e1
    [Google Scholar]
  42. 42. 
    Fragiadakis GK, Wastyk HC, Robinson JL, Sonnenburg ED, Sonnenburg JL, Gardner CD. 2020. Long-term dietary intervention reveals resilience of the gut microbiota despite changes in diet and weight. Am. J. Clin. Nutr. 111:1127–36
    [Google Scholar]
  43. 43. 
    Frame LA, Costa E, Jackson SA 2020. Current explorations of nutrition and the gut microbiome: a comprehensive evaluation of the review literature. Nutr. Rev. 78:10798–812
    [Google Scholar]
  44. 44. 
    Garrido D, Dallas DC, Mills DA. 2013. Consumption of human milk glycoconjugates by infant-associated bifidobacteria: mechanisms and implications. Microbiology 159:649–64
    [Google Scholar]
  45. 45. 
    Gehrig JL, Venkatesh S, Chang HW, Hibberd MC, Kung VL et al. 2019. Effects of microbiota-directed foods in gnotobiotic animals and undernourished children. Science 365:6449eaau4732
    [Google Scholar]
  46. 46. 
    Gentile CL, Weir TL. 2018. The gut microbiota at the intersection of diet and human health. Science 362:776–80
    [Google Scholar]
  47. 47. 
    Ghosh TS, Gupta SS, Bhattacharya T, Yadav D, Barik A et al. 2014. Gut microbiomes of Indian children of varying nutritional status. PLOS ONE 9:e95547
    [Google Scholar]
  48. 48. 
    Gibson GR, Hutkins R, Sanders ME, Prescott SL, Reimer RA et al. 2017. 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. 14:491–502
    [Google Scholar]
  49. 49. 
    Gilbert JA, Blaser MJ, Caporaso JG, Jansson JK, Lynch SV, Knight R. 2018. Current understanding of the human microbiome. Nat. Med. 24:392–400
    [Google Scholar]
  50. 50. 
    Gilbert JA, Jansson JK, Knight R. 2014. The Earth Microbiome project: successes and aspirations. BMC Biol 12:69
    [Google Scholar]
  51. 51. 
    Gonzalez A, Navas-Molina JA, Kosciolek T, McDonald D, Vazquez-Baeza Y et al. 2018. Qiita: rapid, web-enabled microbiome meta-analysis. Nat. Methods 15:796–98
    [Google Scholar]
  52. 52. 
    Griffiths J, Jenkins P, Vargova M, Bowler U, Juszczak E et al. 2018. Enteral lactoferrin to prevent infection for very preterm infants: the ELFIN RCT. Health Technol. Assess. 22:1–60
    [Google Scholar]
  53. 53. 
    Groer MW, Gregory KE, Louis-Jacques A, Thibeau S, Walker WA. 2015. The very low birth weight infant microbiome and childhood health. Birth Defects Res. C 105:252–64
    [Google Scholar]
  54. 54. 
    Groer MW, Miller EM, D'Agata A, Ho TTB, Dutra SV et al. 2020. Contributors to dysbiosis in very-low-birth-weight infants. J. Obstet. Gynecol. Neonatal Nurs. 49:232–42
    [Google Scholar]
  55. 55. 
    Grune T, Lietz G, Palou A, Ross AC, Stahl W et al. 2010. β-carotene is an important vitamin A source for humans. J. Nutr. 140:2268S–85S
    [Google Scholar]
  56. 56. 
    Grzeskowiak L, Collado MC, Mangani C, Maleta K, Laitinen K et al. 2012. Distinct gut microbiota in southeastern African and northern European infants. J. Pediatr. Gastroenterol. Nutr. 54:812–16
    [Google Scholar]
  57. 57. 
    Grzywacz K, Butcher J, Li J, Barrington K, Mohamed I, Stintzi A 2020. Bovine lactoferrin supplementation does not disrupt microbiota development in preterm infants receiving probiotics. J. Pediatr. Gastroenterol. Nutr. 71:216–22
    [Google Scholar]
  58. 58. 
    Gupta SS, Mohammed MH, Ghosh TS, Kanungo S, Nair GB, Mande SS. 2011. Metagenome of the gut of a malnourished child. Gut Pathog 3:7
    [Google Scholar]
  59. 59. 
    Harrison EH. 2012. Mechanisms involved in the intestinal absorption of dietary vitamin A and provitamin A carotenoids. Biochim. Biophys. Acta 1821:70–77
    [Google Scholar]
  60. 60. 
    Hascoët JM, Hubert C, Rochat F, Legagneur H, Gaga S et al. 2011. Effect of formula composition on the development of infant gut microbiota. J. Pediatr. Gastroenterol. Nutr. 52:756–62
    [Google Scholar]
  61. 61. 
    He X, Parenti M, Grip T, Lonnerdal B, Timby N et al. 2019. Fecal microbiome and metabolome of infants fed bovine MFGM supplemented formula or standard formula with breast-fed infants as reference: a randomized controlled trial. Sci. Rep. 9:11589
    [Google Scholar]
  62. 62. 
    He Y, Cao L, Yu J 2018. Prophylactic lactoferrin for preventing late-onset sepsis and necrotizing enterocolitis in preterm infants: a PRISMA-compliant systematic review and meta-analysis. Medicine 97:e11976
    [Google Scholar]
  63. 63. 
    Herman DR, Rhoades N, Mercado J, Argueta P, Lopez U, Flores GE. 2020. Dietary habits of 2- to 9-year-old American children are associated with gut microbiome composition. J. Acad. Nutr. Diet. 120:517–34
    [Google Scholar]
  64. 64. 
    Herrera E. 2002. Implications of dietary fatty acids during pregnancy on placental, fetal and postnatal development—a review. Placenta 23:Suppl. AS9–9
    [Google Scholar]
  65. 65. 
    Hibberd MC, Wu M, Rodionov DA, Li X, Cheng J et al. 2017. The effects of micronutrient deficiencies on bacterial species from the human gut microbiota. Sci. Transl. Med. 9:390eaal4069
    [Google Scholar]
  66. 66. 
    Hjelmsø MH, Shah SA, Thorsen J, Rasmussen M, Vestergaard G et al. 2020. Prenatal dietary supplements influence the infant airway microbiota in a randomized factorial clinical trial. Nat. Commun. 11:426
    [Google Scholar]
  67. 67. 
    Huda MN, Ahmad SM, Kalanetra KM, Taft DH, Alam MJ et al. 2019. Neonatal vitamin A supplementation and vitamin A status are associated with gut microbiome composition in Bangladeshi infants in early infancy and at 2 years of age. J. Nutr. 149:1075–88
    [Google Scholar]
  68. 68. 
    Huey SL, Jiang L, Fedarko MW, McDonald D, Martino C et al. 2020. Nutrition and the gut microbiota in 10- to 18-month-old children living in urban slums of Mumbai, India. mSphere 5:5e00731-20
    [Google Scholar]
  69. 69. 
    Imdad A, Nicholson MR, Tanner-Smith EE, Zackular JP, Gomez-Duarte OG et al. 2018. Fecal transplantation for treatment of inflammatory bowel disease. Cochrane Database Syst. Rev. 11:CD012774
    [Google Scholar]
  70. 70. 
    Jaeggi T, Kortman GA, Moretti D, Chassard C, Holding P et al. 2015. Iron fortification adversely affects the gut microbiome, increases pathogen abundance and induces intestinal inflammation in Kenyan infants. Gut 64:731–42
    [Google Scholar]
  71. 71. 
    Jakobsson HE, Abrahamsson TR, Jenmalm MC, Harris K, Quince C et al. 2014. Decreased gut microbiota diversity, delayed Bacteroidetes colonisation and reduced Th1 responses in infants delivered by Caesarean section. Gut 63:559–66
    [Google Scholar]
  72. 72. 
    Jones RB, Alderete TL, Kim JS, Millstein J, Gilliland FD, Goran MI. 2019. High intake of dietary fructose in overweight/obese teenagers associated with depletion of Eubacterium and Streptococcus in gut microbiome. Gut Microbes 10:712–19
    [Google Scholar]
  73. 73. 
    Kamng'ona AW, Young R, Arnold CD, Patson N, Jorgensen JM et al. 2020. Provision of lipid-based nutrient supplements to mothers during pregnancy and 6 months postpartum and to their infants from 6 to 18 months promotes infant gut microbiota diversity at 18 months of age but not microbiota maturation in a rural Malawian setting: secondary outcomes of a randomized trial. J. Nutr. 150:918–28
    [Google Scholar]
  74. 74. 
    Kau AL, Planer JD, Liu J, Rao S, Yatsunenko T et al. 2015. Functional characterization of IgA-targeted bacterial taxa from undernourished Malawian children that produce diet-dependent enteropathy. Sci. Transl. Med. 7:276ra24
    [Google Scholar]
  75. 75. 
    Koenig JE, Spor A, Scalfone N, Fricker AD, Stombaugh J et al. 2011. Succession of microbial consortia in the developing infant gut microbiome. PNAS 108:Suppl. 14578–85
    [Google Scholar]
  76. 76. 
    Koleva PT, Tun HM, Konya T, Guttman DS, Becker AB et al. 2017. Sex-specific impact of asthma during pregnancy on infant gut microbiota. Eur. Respir. J. 50:1700280
    [Google Scholar]
  77. 77. 
    Kolho KL, Korpela K, Jaakkola T, Pichai MV, Zoetendal EG et al. 2015. Fecal microbiota in pediatric inflammatory bowel disease and its relation to inflammation. Am. J. Gastroenterol. 110:921–30
    [Google Scholar]
  78. 78. 
    Kolodziejczyk AA, Zheng D, Elinav E. 2019. Diet-microbiota interactions and personalized nutrition. Nat. Rev. Microbiol. 17:742–53
    [Google Scholar]
  79. 79. 
    Konieczna P, Ferstl R, Ziegler M, Frei R, Nehrbass D et al. 2013. Immunomodulation by Bifidobacterium infantis 35624 in the murine lamina propria requires retinoic acid-dependent and independent mechanisms. PLOS ONE 8:e62617
    [Google Scholar]
  80. 80. 
    Kortman GA, Raffatellu M, Swinkels DW, Tjalsma H. 2014. Nutritional iron turned inside out: intestinal stress from a gut microbial perspective. FEMS Microbiol. Rev. 38:1202–34
    [Google Scholar]
  81. 81. 
    Kostic AD, Gevers D, Siljander H, Vatanen T, Hyotylainen T et al. 2015. The dynamics of the human infant gut microbiome in development and in progression toward type 1 diabetes. Cell Host Microbe 17:260–73
    [Google Scholar]
  82. 82. 
    Krebs NF, Sherlock LG, Westcott J, Culbertson D, Hambidge KM et al. 2013. Effects of different complementary feeding regimens on iron status and enteric microbiota in breastfed infants. J. Pediatr. 163:416–23
    [Google Scholar]
  83. 83. 
    Kundu P, Blacher E, Elinav E, Pettersson S. 2017. Our gut microbiome: the evolving inner self. Cell 171:1481–93
    [Google Scholar]
  84. 84. 
    Kunz C, Rudloff S, Baier W, Klein N, Strobel S. 2000. Oligosaccharides in human milk: structural, functional, and metabolic aspects. Annu. Rev. Nutr. 20:699–722
    [Google Scholar]
  85. 85. 
    Le Huerou-Luron I, Bouzerzour K, Ferret-Bernard S, Menard O, Le Normand L et al. 2018. A mixture of milk and vegetable lipids in infant formula changes gut digestion, mucosal immunity and microbiota composition in neonatal piglets. Eur. J. Nutr. 57:463–76
    [Google Scholar]
  86. 86. 
    Lee H, Padhi E, Hasegawa Y, Larke J, Parenti M et al. 2018. Compositional dynamics of the milk fat globule and its role in infant development. Front. Pediatr. 6:313
    [Google Scholar]
  87. 87. 
    Lee MJ, Kang MJ, Lee SY, Lee E, Kim K et al. 2018. Perturbations of gut microbiome genes in infants with atopic dermatitis according to feeding type. J. Allergy Clin. Immunol. 141:1310–19
    [Google Scholar]
  88. 88. 
    Leiby JS, McCormick K, Sherrill-Mix S, Clarke EL, Kessler LR et al. 2018. Lack of detection of a human placenta microbiome in samples from preterm and term deliveries. Microbiome 6:196
    [Google Scholar]
  89. 89. 
    Levine A, El-Matary W, Van Limbergen J. 2020. A case-based approach to new directions in dietary therapy of Crohn's disease: food for thought. Nutrients 12:3880
    [Google Scholar]
  90. 90. 
    Levine A, Wine E, Assa A, Sigall Boneh R, Shaoul R et al. 2019. Crohn's disease exclusion diet plus partial enteral nutrition induces sustained remission in a randomized controlled trial. Gastroenterology 157:440–50.e8
    [Google Scholar]
  91. 91. 
    Lewis JD, Abreu MT. 2017. Diet as a trigger or therapy for inflammatory bowel diseases. Gastroenterology 152:398–414.e6
    [Google Scholar]
  92. 92. 
    Lewis ZT, Sidamonidze K, Tsaturyan V, Tsereteli D, Khachidze N et al. 2017. The fecal microbial community of breast-fed infants from Armenia and Georgia. Sci. Rep 7:40932
    [Google Scholar]
  93. 93. 
    Li M, Wang M, Donovan SM. 2014. Early development of the gut microbiome and immune-mediated childhood disorders. Semin. Reprod. Med. 32:74–86
    [Google Scholar]
  94. 94. 
    Liang G, Zhao C, Zhang H, Mattei L, Sherrill-Mix S et al. 2020. The stepwise assembly of the neonatal virome is modulated by breastfeeding. Nature 581:470–74
    [Google Scholar]
  95. 95. 
    Liedtke J, Vahjen W. 2012. In vitro antibacterial activity of zinc oxide on a broad range of reference strains of intestinal origin. Vet. Microbiol. 160:251–55
    [Google Scholar]
  96. 96. 
    Ma N, Tian Y, Wu Y, Ma X. 2017. Contributions of the interaction between dietary protein and gut microbiota to intestinal health. Curr. Protein Pept. Sci. 18:795–808
    [Google Scholar]
  97. 97. 
    Macfarlane GT, Cummings JH, Allison C 1986. Protein degradation by human intestinal bacteria. J. Gen. Microbiol. 132:1647–56
    [Google Scholar]
  98. 98. 
    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 170:212–19
    [Google Scholar]
  99. 99. 
    Maher SE, O'Brien EC, Moore RL, Byrne DF, Geraghty AA et al. 2020. The association between the maternal diet and the maternal and infant gut microbiome: a systematic review. Br. J. Nutr In press. https://doi.org/10.1017/S0007114520000847
    [Crossref] [Google Scholar]
  100. 100. 
    Marcobal A, Sonnenburg JL. 2012. Human milk oligosaccharide consumption by intestinal microbiota. Clin. Microbiol. Infect. 18:Suppl. 412–15
    [Google Scholar]
  101. 101. 
    McGuire MK, McGuire MA. 2017. Got bacteria? The astounding, yet not-so-surprising, microbiome of human milk. Curr. Opin. Biotechnol. 44:63–68
    [Google Scholar]
  102. 102. 
    Mehta S, Finkelstein JL, Venkatramanan S, Huey SL, Udipi SA et al. 2017. Effect of iron and zinc-biofortified pearl millet consumption on growth and immune competence in children aged 12–18 months in India: study protocol for a randomised controlled trial. BMJ Open 7:e017631
    [Google Scholar]
  103. 103. 
    Milajerdi A, Sadeghi O, Siadat SD, Keshavarz SA, Sima A et al. 2020. A randomized controlled trial investigating the effect of a diet low in fermentable oligosaccharides, disaccharides, monosaccharides, and polyols on the intestinal microbiome and inflammation in patients with ulcerative colitis: study protocol for a randomized controlled trial. Trials 21:201
    [Google Scholar]
  104. 104. 
    Million M, Diallo A, Raoult D. 2017. Gut microbiota and malnutrition. Microb. Pathog. 106:127–38
    [Google Scholar]
  105. 105. 
    Million M, Tomas J, Wagner C, Lelouard H, Raoult D, Gorvel J-P. 2018. New insights in gut microbiota and mucosal immunity of the small intestine. Hum. Microbiome J. 7–8:23–32
    [Google Scholar]
  106. 106. 
    Mirpuri J, Raetz M, Sturge CR, Wilhelm CL, Benson A et al. 2014. Proteobacteria-specific IgA regulates maturation of the intestinal microbiota. Gut Microbes 5:28–39
    [Google Scholar]
  107. 107. 
    Miyazawa T, Burdeos GC, Itaya M, Nakagawa K, Miyazawa T. 2019. Vitamin E: regulatory redox interactions. IUBMB Life 71:430–41
    [Google Scholar]
  108. 108. 
    Mohan A, Quek S-Y, Gutierrez-Maddox N, Gao Y, Shu Q. 2017. Effect of honey in improving the gut microbial balance. Food Q. Saf. 1:107–15
    [Google Scholar]
  109. 109. 
    Monira S, Nakamura S, Gotoh K, Izutsu K, Watanabe H et al. 2011. Gut microbiota of healthy and malnourished children in Bangladesh. Front. Microbiol. 2:228
    [Google Scholar]
  110. 110. 
    Moossavi S, Sepehri S, Robertson B, Bode L, Goruk S et al. 2019. Composition and variation of the human milk microbiota are influenced by maternal and early-life factors. Cell Host Microbe 25:324–35.e4
    [Google Scholar]
  111. 111. 
    Mostafa I, Nahar NN, Islam MM, Huq S, Mustafa M et al. 2020. Proof-of-concept study of the efficacy of a microbiota-directed complementary food formulation (MDCF) for treating moderate acute malnutrition. BMC Public Health 20:242
    [Google Scholar]
  112. 112. 
    Muhlhofer A, Buhler-Ritter B, Frank J, Zoller WG, Merkle P et al. 2003. Carotenoids are decreased in biopsies from colorectal adenomas. Clin. Nutr. 22:65–70
    [Google Scholar]
  113. 113. 
    Murphy K, Curley D, O'Callaghan TF, O'Shea CA, Dempsey EM et al. 2017. The composition of human milk and infant faecal microbiota over the first three months of life: a pilot study. Sci. Rep. 7:40597
    [Google Scholar]
  114. 114. 
    Nealon NJ, Parker KD, Lahaie P, Ibrahim H, Maurya AK et al. 2019. Bifidobacterium longum-fermented rice bran and rice bran supplementation affects the gut microbiome and metabolome. Benef. Microbes 10:823–39
    [Google Scholar]
  115. 115. 
    O'Callaghan A, van Sinderen D. 2016. Bifidobacteria and their role as members of the human gut microbiota. Front. Microbiol. 7:925
    [Google Scholar]
  116. 116. 
    Oliphant K, Allen-Vercoe E 2019. Macronutrient metabolism by the human gut microbiome: major fermentation by-products and their impact on host health. Microbiome 7:91
    [Google Scholar]
  117. 117. 
    Ordiz MI, Janssen S, Humphrey G, Ackermann G, Stephenson K et al. 2020. The effect of legume supplementation on the gut microbiota in rural Malawian infants aged 6 to 12 months. Am. J. Clin. Nutr. 111:884–92
    [Google Scholar]
  118. 118. 
    Orozco MN, Solomons NW, Schumann K, Friel JK, de Montenegro AL. 2010. Antioxidant-rich oral supplements attenuate the effects of oral iron on in situ oxidation susceptibility of human feces. J. Nutr. 140:1105–10
    [Google Scholar]
  119. 119. 
    Paganini D, Jaeggi T, Cercamondi C, Kujinga P, Moretti D, Zimmermann M. 2016. Anemia and iron status are predictors of gut microbiome composition and metabolites in infants and children in rural Kenya. FASEB J 30:S1296.2
    [Google Scholar]
  120. 120. 
    Paganini D, Uyoga MA, Kortman GAM, Boekhorst J, Schneeberger S et al. 2019a. Maternal human milk oligosaccharide profile modulates the impact of an intervention with iron and galacto-oligosaccharides in Kenyan infants. Nutrients 11:2596
    [Google Scholar]
  121. 121. 
    Paganini D, Uyoga MA, Kortman GAM, Cercamondi CI, Moretti D et al. 2017. Prebiotic galacto-oligosaccharides mitigate the adverse effects of iron fortification on the gut microbiome: a randomised controlled study in Kenyan infants. Gut 66:1956–67
    [Google Scholar]
  122. 122. 
    Paganini D, Uyoga MA, Kortman GAM, Cercamondi CI, Winkler HC et al. 2019b. Iron-containing micronutrient powders modify the effect of oral antibiotics on the infant gut microbiome and increase post-antibiotic diarrhoea risk: a controlled study in Kenya. Gut 68:645–53
    [Google Scholar]
  123. 123. 
    Pannaraj PS, Li F, Cerini C, Bender JM, Yang S et al. 2017. Association between breast milk bacterial communities and establishment and development of the infant gut microbiome. JAMA Pediatr 171:647–54
    [Google Scholar]
  124. 124. 
    Peng M, Bitsko E, Biswas D. 2015. Functional properties of peanut fractions on the growth of probiotics and foodborne bacterial pathogens. J. Food Sci. 80:M635–635
    [Google Scholar]
  125. 125. 
    Qasem W, Azad MB, Hossain Z, Azad E, Jorgensen S et al. 2017. Assessment of complementary feeding of Canadian infants: effects on microbiome & oxidative stress, a randomized controlled trial. BMC Pediatr 17:54
    [Google Scholar]
  126. 126. 
    Rampelli S, Guenther K, Turroni S, Wolters M, Veidebaum T et al. 2018. Pre-obese children's dysbiotic gut microbiome and unhealthy diets may predict the development of obesity. Commun. Biol 1:222
    [Google Scholar]
  127. 127. 
    Redondo-Useros N, Nova E, Gonzalez-Zancada N, Diaz LE, Gomez-Martinez S, Marcos A 2020. Microbiota and lifestyle: a special focus on diet. Nutrients 12:1776
    [Google Scholar]
  128. 128. 
    Reed S, Neuman H, Moscovich S, Glahn RP, Koren O, Tako E. 2015. Chronic zinc deficiency alters chick gut microbiota composition and function. Nutrients 7:9768–84
    [Google Scholar]
  129. 129. 
    Ridlon JM, Kang DJ, Hylemon PB. 2006. Bile salt biotransformations by human intestinal bacteria. J. Lipid Res. 47:241–59
    [Google Scholar]
  130. 130. 
    Rinninella E, Cintoni M, Raoul P, Lopetuso LR, Scaldaferri F et al. 2019. Food components and dietary habits: keys for a healthy gut microbiota composition. Nutrients 11:2393
    [Google Scholar]
  131. 131. 
    Round JL, Palm NW. 2018. Causal effects of the microbiota on immune-mediated diseases. Sci. Immunol. 3:20eaao1603
    [Google Scholar]
  132. 132. 
    Rowland I, Gibson G, Heinken A, Scott K, Swann J et al. 2018. Gut microbiota functions: metabolism of nutrients and other food components. Eur. J. Nutr. 57:1–24
    [Google Scholar]
  133. 133. 
    Salas AA, Kabani N, Travers CP, Phillips V, Ambalavanan N, Carlo WA 2017. Short versus extended duration of trophic feeding to reduce time to achieve full enteral feeding in extremely preterm infants: an observational study. Neonatology 112:211–16
    [Google Scholar]
  134. 134. 
    Salazar N, Arboleya S, Fernandez-Navarro T, de Los Reyes-Gavilan CG, Gonzalez S, Gueimonde M. 2019. Age-associated changes in gut microbiota and dietary components related with the immune system in adulthood and old age: a cross-sectional study. Nutrients 11:1765
    [Google Scholar]
  135. 135. 
    Salvatore S, Pensabene L, Borrelli O, Saps M, Thapar N et al. 2018. Mind the gut: probiotics in paediatric neurogastroenterology. Benef. Microbes 9:883–98
    [Google Scholar]
  136. 136. 
    Savage JH, Lee-Sarwar KA, Sordillo JE, Lange NE, Zhou Y et al. 2018. Diet during pregnancy and infancy and the infant intestinal microbiome. J. Pediatr. 203:47–54.e4
    [Google Scholar]
  137. 137. 
    Scholmerich J, Freudemann A, Kottgen E, Wietholtz H, Steiert B et al. 1987. Bioavailability of zinc from zinc-histidine complexes. I. Comparison with zinc sulfate in healthy men. Am. J. Clin. Nutr. 45:1480–86
    [Google Scholar]
  138. 138. 
    Schumann K, Kroll S, Weiss G, Frank J, Biesalski HK et al. 2005. Monitoring of hematological, inflammatory and oxidative reactions to acute oral iron exposure in human volunteers: preliminary screening for selection of potentially-responsive biomarkers. Toxicology 212:10–23
    [Google Scholar]
  139. 139. 
    Sender R, Fuchs S, Milo R 2016. Are we really vastly outnumbered? Revisiting the ratio of bacterial to host cells in humans. Cell 164:337–40
    [Google Scholar]
  140. 140. 
    Serban DE. 2015. Microbiota in inflammatory bowel disease pathogenesis and therapy: Is it all about diet?. Nutr. Clin. Pract. 30:760–79
    [Google Scholar]
  141. 141. 
    Shinn LM, Li Y, Mansharamani A, Auvil LS, Welge ME et al. 2021. Fecal bacteria as biomarkers for predicting food intake in healthy adults. J. Nutr. 151:423–33
    [Google Scholar]
  142. 142. 
    Smith AH, Zoetendal E, Mackie RI. 2005. Bacterial mechanisms to overcome inhibitory effects of dietary tannins. Microb. Ecol. 50:197–205
    [Google Scholar]
  143. 143. 
    Smith EA, Macfarlane GT. 1996. Enumeration of human colonic bacteria producing phenolic and indolic compounds: effects of pH, carbohydrate availability and retention time on dissimilatory aromatic amino acid metabolism. J. Appl. Bacteriol. 81:288–302
    [Google Scholar]
  144. 144. 
    Smith MI, Yatsunenko T, Manary MJ, Trehan I, Mkakosya R et al. 2013. Gut microbiomes of Malawian twin pairs discordant for kwashiorkor. Science 339:548–54
    [Google Scholar]
  145. 145. 
    Sommer A, Tarwotjo I, Djunaedi E, West K, Loeden A et al. 1986. Impact of vitamin A supplementation on childhood mortality: a randomised controlled community trial. Lancet 327:1169–73
    [Google Scholar]
  146. 146. 
    Soofi S, Cousens S, Iqbal SP, Akhund T, Khan J et al. 2013. Effect of provision of daily zinc and iron with several micronutrients on growth and morbidity among young children in Pakistan: a cluster-randomised trial. Lancet 382:29–40
    [Google Scholar]
  147. 147. 
    Sordillo J, Zhou Y, McGeachie M, Ziniti J, Lange N et al. 2017. Factors influencing the infant gut microbiome at age 3–6 months: findings from the ethnically diverse Vitamin D Antenatal Asthma Reduction Trial (VDAART). J. Allergy Clin. Immunol. 139:482–91.e14
    [Google Scholar]
  148. 148. 
    Starke IC, Pieper R, Neumann K, Zentek J, Vahjen W. 2014. The impact of high dietary zinc oxide on the development of the intestinal microbiota in weaned piglets. FEMS Microbiol. Ecol. 87:416–27
    [Google Scholar]
  149. 149. 
    Subramanian S, Huq S, Yatsunenko T, Haque R, Mahfuz M et al. 2014. Persistent gut microbiota immaturity in malnourished Bangladeshi children. Nature 510:417–21
    [Google Scholar]
  150. 150. 
    Talsness CE, Penders J, Jansen E, Damoiseaux J, Thijs C, Mommers M. 2017. Influence of vitamin D on key bacterial taxa in infant microbiota in the KOALA Birth Cohort Study. PLOS ONE 12:e0188011
    [Google Scholar]
  151. 151. 
    Tang M, Frank DN, Hendricks AE, Ir D, Esamai F et al. 2017. Iron in micronutrient powder promotes an unfavorable gut microbiota in Kenyan infants. Nutrients 9:776
    [Google Scholar]
  152. 152. 
    Tang M, Frank DN, Sherlock L, Ir D, Robertson CE, Krebs NF. 2016. Effect of vitamin E with therapeutic iron supplementation on iron repletion and gut microbiome in U.S. iron deficient infants and toddlers. J. Pediatr. Gastroenterol. Nutr. 63:3379–85
    [Google Scholar]
  153. 153. 
    The Human Microbiome Proj. Consort., Huttenhower C, Gevers D, Knight R, Abubucker S et al. 2012. Structure, function and diversity of the healthy human microbiome. Nature 486:207–14
    [Google Scholar]
  154. 154. 
    Thompson AL, Monteagudo-Mera A, Cadenas MB, Lampl ML, Azcarate-Peril MA. 2015. 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. 5:3
    [Google Scholar]
  155. 155. 
    Townsend GE 2nd, Han W, Schwalm ND 3rd, Raghavan V, Barry NA et al. 2019. Dietary sugar silences a colonization factor in a mammalian gut symbiont. PNAS 116:233–38
    [Google Scholar]
  156. 156. 
    Truong DT, Tett A, Pasolli E, Huttenhower C, Segata N. 2017. Microbial strain-level population structure and genetic diversity from metagenomes. Genome Res 27:626–38
    [Google Scholar]
  157. 157. 
    Turnbaugh PJ. 2017. Microbes and diet-induced obesity: fast, cheap, and out of control. Cell Host Microbe 21:278–81
    [Google Scholar]
  158. 158. 
    Turnbaugh PJ, Ley RE, Hamady M, Fraser-Liggett CM, Knight R, Gordon JI. 2007. The human microbiome project. Nature 449:804–10
    [Google Scholar]
  159. 159. 
    Vahjen W, Pieper R, Zentek J. 2011. Increased dietary zinc oxide changes the bacterial core and enterobacterial composition in the ileum of piglets. J. Anim. Sci. 89:2430–39
    [Google Scholar]
  160. 160. 
    Van den Abbeele P, Belzer C, Goossens M, Kleerebezem M, De Vos WM et al. 2013. Butyrate-producing Clostridium cluster XIVa species specifically colonize mucins in an in vitro gut model. ISME J 7:949–61
    [Google Scholar]
  161. 161. 
    van den Berg A, van Elburg RM, Westerbeek EAM, van der Linde EGM, Knol J et al. 2007. The effect of glutamine-enriched enteral nutrition on intestinal microflora in very low birth weight infants: a randomized controlled trial. Clin. Nutr. 26:430–39
    [Google Scholar]
  162. 162. 
    van Zwol A, van den Berg A, Knol J, Twisk J, Fetter W, van Elburg R. 2010. Intestinal microbiota in allergic and nonallergic 1-year-old very low birthweight infants after neonatal glutamine supplementation. Acta Paediatr 99:1868–74
    [Google Scholar]
  163. 163. 
    Varkey A, Devi S, Mukhopadhyay A, Kamat NG, Pauline M et al. 2020. Metabolome and microbiome alterations related to short-term feeding of a micronutrient-fortified, high-quality legume protein-based food product to stunted school age children: a randomized controlled pilot trial. Clin. Nutr. 39:3251–61
    [Google Scholar]
  164. 164. 
    Veldhoen M, Brucklacher-Waldert V. 2012. Dietary influences on intestinal immunity. Nat. Rev. Immunol. 12:696–708
    [Google Scholar]
  165. 165. 
    Wampach L, Heintz-Buschart A, Hogan A, Muller EEL, Narayanasamy S et al. 2017. Colonization and succession within the human gut microbiome by archaea, bacteria, and microeukaryotes during the first year of life. Front. Microbiol 8:738
    [Google Scholar]
  166. 166. 
    WHO Multicent. Growth Ref. Study Group, de Onis M 2006. WHO Child Growth Standards based on length/height, weight and age. Acta Paediatr. 95:S45076–85
    [Google Scholar]
  167. 167. 
    Wu G. 2016. Dietary protein intake and human health. Food Funct 7:1251–65
    [Google Scholar]
  168. 168. 
    Xiang R, Tang Q, Chen XQ, Li MY, Yang MX et al. 2019. Effects of zinc combined with probiotics on antibiotic-associated diarrhea secondary to childhood pneumonia. J. Trop. Pediatr. 65:421–26
    [Google Scholar]
  169. 169. 
    Ximenez C, Torres J. 2017. Development of microbiota in infants and its role in maturation of gut mucosa and immune system. Arch. Med. Res. 48:666–80
    [Google Scholar]
  170. 170. 
    Yang I, Corwin EJ, Brennan PA, Jordan S, Murphy JR, Dunlop A. 2016. The infant microbiome: implications for infant health and neurocognitive development. Nurs. Res. 65:76–88
    [Google Scholar]
  171. 171. 
    Yatsunenko T, Rey FE, Manary MJ, Trehan I, Dominguez-Bello MG et al. 2012. Human gut microbiome viewed across age and geography. Nature 486:222–27
    [Google Scholar]
  172. 172. 
    Yilmaz B, Li H. 2018. Gut microbiota and iron: the crucial actors in health and disease. Pharmaceuticals 11:498
    [Google Scholar]
  173. 173. 
    Yoon BK, Jackman JA, Valle-Gonzalez ER, Cho NJ. 2018. Antibacterial free fatty acids and monoglycerides: biological activities, experimental testing, and therapeutic applications. Int. J. Mol. Sci. 19:41114
    [Google Scholar]
  174. 174. 
    Young VB. 2017. The role of the microbiome in human health and disease: an introduction for clinicians. BMJ 356:j831
    [Google Scholar]
  175. 175. 
    Younge N, Yang Q, Seed PC. 2017. Enteral high fat-polyunsaturated fatty acid blend alters the pathogen composition of the intestinal microbiome in premature infants with an enterostomy. J. Pediatr. 181:93–101.e6
    [Google Scholar]
  176. 176. 
    Zackular JP, Moore JL, Jordan AT, Juttukonda LJ, Noto MJ et al. 2016. Dietary zinc alters the microbiota and decreases resistance to Clostridium difficile infection. Nat. Med. 22:1330–34
    [Google Scholar]
  177. 177. 
    Zambrana LE, McKeen S, Ibrahim H, Zarei I, Borresen EC et al. 2019. Rice bran supplementation modulates growth, microbiota and metabolome in weaning infants: a clinical trial in Nicaragua and Mali. Sci. Rep. 9:13919
    [Google Scholar]
  178. 178. 
    Zeevi D, Korem T, Zmora N, Israeli D, Rothschild D et al. 2015. Personalized nutrition by prediction of glycemic responses. Cell 163:1079–94
    [Google Scholar]
  179. 179. 
    Zhao J, Zhang X, Liu H, Brown MA, Qiao S. 2019. Dietary protein and gut microbiota composition and function. Curr. Protein Pept. Sci. 20:145–54
    [Google Scholar]
  180. 180. 
    Zhou Y, Shan G, Sodergren E, Weinstock G, Walker WA, Gregory KE. 2015. Longitudinal analysis of the premature infant intestinal microbiome prior to necrotizing enterocolitis: a case-control study. PLOS ONE 10:e0118632
    [Google Scholar]
  181. 181. 
    Zimmermann MB, Chassard C, Rohner F, N'Goran EK, Nindjin C et al. 2010. The effects of iron fortification on the gut microbiota in African children: a randomized controlled trial in Cote d'Ivoire. Am. J. Clin. Nutr. 92:1406–15
    [Google Scholar]
  182. 182. 
    Zivkovic AM, German JB, Lebrilla CB, Mills DA 2011. Human milk glycobiome and its impact on the infant gastrointestinal microbiota. PNAS 108:Suppl. 14653–58
    [Google Scholar]
  183. 183. 
    Zlotkin S, Newton S, Aimone AM, Azindow I, Amenga-Etego S et al. 2013. Effect of iron fortification on malaria incidence in infants and young children in Ghana: a randomized trial. JAMA 310:938–47
    [Google Scholar]
  184. 184. 
    Zmora N, Suez J, Elinav E. 2019. You are what you eat: diet, health and the gut microbiota. Nat. Rev. Gastroenterol. Hepatol. 16:35–56
    [Google Scholar]
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