The human gut microbiota: A dynamic interplay with the host from birth to senescence settled during childhood

Pediatric Research

Volumn 76, Issue 1, 2014, Pages 2-10

  Putignani, Lorenza ^a   Del Chierico, Federica ^a   Petrucca, Andrea ^a,b   Vernocchi, Pamela ^a,c   Dallapiccola, Bruno ^a  

^a BAMBINO GESÙ CHILDREN S HOSPITAL   (Italy)

^b SAPIENZA UNIVERSITY OF ROME   (Italy)

^c UNIVERSITY OF BOLOGNA   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

ADULTHOOD; BIRTH; CHILD DEVELOPMENT; CHILDHOOD; CLINICAL RESEARCH; DISEASE COURSE; DYSBIOSIS; GENETIC VARIABILITY; HOST; HUMAN; INTESTINE FLORA; MICROBIAL COMMUNITY; MICROBIOLOGY; MOTHER CHILD RELATION; PRIORITY JOURNAL; REVIEW; SENESCENCE; SYMBIOSIS;

BACTERIA; BREAST FEEDING; CHILD; FEMALE; GASTROINTESTINAL TRACT; GENOMICS; HUMANS; IMMUNE SYSTEM; INFANT; INFANT, NEWBORN; MATERNAL-FETAL EXCHANGE; METABOLOMICS; MICROBIOTA; PHENOTYPE; PREGNANCY; PROBIOTICS; PROTEOMICS; SYSTEMS BIOLOGY;

EID: 84902673930     PISSN: 00313998     EISSN: 15300447     Source Type: Journal    
DOI: 10.1038/pr.2014.49     Document Type: Review

References (80)

1. Del Chierico F, Vernocchi P, Bonizzi L, et al. Early-life gut microbiota under physiological and pathological conditions: the central role of combined meta-omics-based approaches. J Proteomics 2012;75:4580-7.
2. Stanghellini V, Barbara G, Cremon C, et al. Gut microbiota and related diseases: clinical features. Intern Emerg Med 2010;5:S57-63.
3. Putignani L, Carsetti R, Signore F, Manco M. Additional maternal and nonmaternal factors contribute to microbiota shaping in newborns. Proc Natl Acad Sci USA 2010;107:E159; author reply E160.
4. Lederberg J. The dawning of molecular genetics. Trends Microbiol 2000;8:194-5.
5. Arpaia N, Campbell C, Fan X, et al. Metabolites produced by commensal bacteria promote peripheral regulatory T-cell generation. Nature 2013;504:451-5.
6. Bäckhed F, Ding H, Wang T, et al. The gut microbiota as an environmental factor that regulates fat storage. Proc Natl Acad Sci USA 2004;101:15718-23.
7. Turnbaugh PJ, Ley RE, Mahowald MA, Magrini V, Mardis ER, Gordon JI. An obesity-Associated gut microbiome with increased capacity for energy harvest. Nature 2006;444:1027-31.
8. Ley RE, Bäckhed F, Turnbaugh P, Lozupone CA, Knight RD, Gordon JI. Obesity alters gut microbial ecology. Proc Natl Acad Sci USA 2005;102:11070-5.
9. Ley RE, Turnbaugh PJ, Klein S, Gordon JI. Microbial ecology: human gut microbes associated with obesity. Nature 2006;444:1022-3.
10. Burcelin R, Crivelli V, Dacosta A, Roy-Tirelli A, Thorens B. Heterogeneous metabolic adaptation of C57BL/6J mice to high-fat diet. Am J Physiol Endocrinol Metab 2002;282:E834-42.
11. Murphy EF, Cotter PD, Hogan A, et al. Divergent metabolic outcomes arising from targeted manipulation of the gut microbiota in diet-induced obesity. Gut 2013;62:220-6.
12. Wu X, Ma C, Han L, et al. Molecular characterisation of the faecal microbiota in patients with type II diabetes. Curr Microbiol 2010;61:69-78.
13. Abu-Shanab A, Quigley EM. The role of the gut microbiota in nonalcoholic fatty liver disease. Nat Rev Gastroenterol Hepatol 2010;7:691-701.
14. Henao-Mejia J, Elinav E, Jin C, et al. Inflammasome-mediated dysbiosis regulates progression of NAFLD and obesity. Nature 2012;482:179-85.
15. Vijay-Kumar M, Carvalho FA, Aitken JD, Fifadara NH, Gewirtz AT. TLR5 or NLRC4 is necessary and sufficient for promotion of humoral immunity by flagellin. Eur J Immunol 2010;40:3528-34.
16. Picardi PK, Caricilli AM, de Abreu LL, Carvalheira JB, Velloso LA, Saad MJ. Modulation of hypothalamic PTP1B in the TNF-Alpha-induced insulin and leptin resistance. FEBS Lett 2010;584:3179-84.
17. Mehal WZ. The Gordian Knot of dysbiosis, obesity and NAFLD. Nat Rev Gastroenterol Hepatol 2013;10:637-44.
18. Zhu L, Baker SS, Gill C, et al. Characterization of gut microbiomes in nonalcoholic steatohepatitis (NASH) patients: a connection between endogenous alcohol and NASH. Hepatology 2013;57:601-9.
19. Feuerer M, Herrero L, Cipolletta D, et al. Lean, but not obese, fat is enriched for a unique population of regulatory T cells that affect metabolic parameters. Nat Med 2009;15:930-9.
20. Hotamisligil GS, Peraldi P, Budavari A, Ellis R, White MF, Spiegelman BM. IRS-1-mediated inhibition of insulin receptor tyrosine kinase activity in TNF-Alpha- and obesity-induced insulin resistance. Science 1996;271:665-8.
21. Bouloumié A, Curat CA, Sengenès C, Lolmède K, Miranville A, Busse R. Role of macrophage tissue infiltration in metabolic diseases. Curr Opin Clin Nutr Metab Care 2005;8:347-54.
22. Cani PD, Amar J, Iglesias MA, et al. Metabolic endotoxemia initiates obesity and insulin resistance. Diabetes 2007;56:1761-72.
23. Lee RP, Lin NT, Chao YF, Lin CC, Harn HJ, Chen HI. High-density lipoprotein prevents organ damage in endotoxemia. Res Nurs Health 2007;30:250-60.
24. Mann ER, Landy JD, Bernardo D, et al. Intestinal dendritic cells: their role in intestinal inflammation, manipulation by the gut microbiota and differences between mice and men. Immunol Lett 2013;150:30-40.
25. Moreira AP, Texeira TF, Ferreira AB, Peluzio Mdo C, Alfenas Rde C. Influence of a high-fat diet on gut microbiota, intestinal permeability and metabolic endotoxaemia. Br J Nutr 2012;108:801-9.
26. Amar J, Chabo C, Waget A, et al. Intestinal mucosal adherence and translocation of commensal bacteria at the early onset of type 2 diabetes: molecular mechanisms and probiotic treatment. EMBO Mol Med 2011;3:559-72.
27. Garn H, Neves JF, Blumberg RS, Renz H. Effect of barrier microbes on organ-based inflammation. J Allergy Clin Immunol 2013;131:1465-78.
28. Börnigen D, Morgan XC, Franzosa EA, et al. Functional profiling of the gut microbiome in disease-Associated inflammation. Genome Med 2013;5:65.
29. Lê Cao KA, Rossouw D, Robert-Granié C, Besse P. A sparse PLS for variable selection when integrating omics data. Stat Appl Genet Mol Biol 2008;7:Article 35.
30. Qin J, Li Y, Cai Z, et al. A metagenome-wide association study of gut microbiota in type 2 diabetes. Nature 2012;490:55-60.
31. Han JC, Lawlor DA, Kimm SY. Childhood obesity. Lancet 2010;375:1737-48.
32. Petrof EO, Claud EC, Gloor GB, Allen-Vercoe E. Microbial ecosystems therapeutics: a new paradigm in medicine? Benef Microbes 2013;4:53-65.
33. Everard A, Cani PD. Diabetes, obesity and gut microbiota. Best Pract Res Clin Gastroenterol 2013;27:73-83.
34. Larsen N, Vogensen FK, van den Berg FW, et al. Gut microbiota in human adults with type 2 diabetes differs from non-diabetic adults. PLoS One 2010;5:e9085.
35. Raman M, Ahmed I, Gillevet PM, et al. Fecal microbiome and volatile organic compound metabolome in obese humans with nonalcoholic fatty liver disease. Clin Gastroenterol Hepatol 2013;11:868-75.
36. Collins SM, Bercik P. Gut microbiota: intestinal bacteria influence brain activity in healthy humans. Nat Rev Gastroenterol Hepatol 2013;10:326-7.
37. Finegold SM, Dowd SE, Gontcharova V, et al. Pyrosequencing study of fecal microflora of autistic and control children. Anaerobe 2010;16:444-53.
38. Nylund L, Satokari R, Nikkilä J, et al. Microarray analysis reveals marked intestinal microbiota aberrancy in infants having eczema compared to healthy children in at-risk for atopic disease. BMC Microbiol 2013;13:12.
39. Sjögren YM, Jenmalm MC, Böttcher MF, Björkstén B, Sverremark- Ekström E. Altered early infant gut microbiota in children developing allergy up to 5 years of age. Clin Exp Allergy 2009;39:518-26.
40. Burcelin R, Serino M, Chabo C, et al. Metagenome and metabolism: the tissue microbiota hypothesis. Diabetes Obes Metab 2013;15: Suppl 3:61-70.
41. Farrel GC, van Rooyan D, Gan L, Chitturi S. NASH is an inflammatory disorder pathogenic, prognostic and therapeutic. Gut Liver 2012;6:149-71.
42. Shim JO. Gut microbiota in inflammatory bowel disease. Pediatr Gastroenterol Hepatol Nutr 2013;16:17-21.
43. Carlisle EM, Morowitz MJ. The intestinal microbiome and necrotizing enterocolitis. Curr Opin Pediatr 2013;25:382-7.
44. Torrazza RM, Neu J. The altered gut microbiome and necrotizing enterocolitis. Clin Perinatol 2013;40:93-108.
45. Manco M. Gut microbiota and developmental programming of the brain: from evidence in behavioral endophenotypes to novel perspective in obesity. Front Cell Infect Microbiol 2012;2:109.
46. Hochberg Z, Feil R, Constancia M, et al. Child health, developmental plasticity, and epigenetic programming. Endocr Rev 2011;32:159-224.
47. Manco M, Putignani L, Bottazzo GF. Gut microbiota, lipopolysaccharides, and innate immunity in the pathogenesis of obesity and cardiovascular risk. Endocr Rev 2010;31:817-44.
48. Kang DW, Park JG, Ilhan ZE, et al. Reduced incidence of Prevotella and other fermenters in intestinal microflora of autistic children. PLoS One 2013;8:e68322.
49. Diaz Heijtz R, Wang S, Anuar F, et al. Normal gut microbiota modulates brain development and behavior. Proc Natl Acad Sci USA 2011;108:3047-52.
50. DiGiulio DB. Diversity of microbes in amniotic fluid. Semin Fetal Neonatal Med 2012;17:2-11.
51. Gosalbes MJ, Llop S, Vallès Y, Moya A, Ballester F, Francino MP. Meconium microbiota types dominated by lactic acid or enteric bacteria are differentially associated with maternal eczema and respiratory problems in infants. Clin Exp Allergy 2013;43:198-211.
52. Matamoros S, Gras-Leguen C, Le Vacon F, Potel G, de La Cochetiere MF. Development of intestinal microbiota in infants and its impact on health. Trends Microbiol 2013;21:167-73.
53. Azad MB, Konya T, Maughan H, et al. Gut microbiota of healthy Canadian infants: profiles by mode of delivery and infant diet at 4 months. CMAJ 2013;185:385-94.
54. Penders J, Thijs C, Vink C, et al. Factors influencing the composition of the intestinal microbiota in early infancy. Pediatrics 2006;118:511-21.
55. Watson J, Jones RC, Cortes C, et al. Community-Associated methicillinresistant Staphylococcus aureus infection among healthy newborns - Chicago and Los Angeles County, 2004. MMWR Morb Mortal Wkly Rep 2006;55:329-32.
56. Madan JC, Farzan SF, Hibberd PL, Karagas MR. Normal neonatal microbiome variation in relation to environmental factors, infection and allergy. Curr Opin Pediatr 2012;24:753-9.
57. Pessione E. Lactic acid bacteria contribution to gut microbiota complexity: lights and shadows. Front Cell Infect Microbiol 2012;2:86.
58. Koren O, Goodrich JK, Cullender TC, et al. Host remodeling of the gut microbiome and metabolic changes during pregnancy. Cell 2012;150:470-80.
59. Chung H, Pamp SJ, Hill JA, et al. Gut immune maturation depends on colonization with a host-specific microbiota. Cell 2012;149:1578-93.
60. Santacruz A, Collado MC, Garcia-Valdés L, et al. Gut microbiota composition is associated with body weight, weight gain and biochemical parameters in pregnant women. Br J Nutr 2010;104:83-92.
61. Collado MC, Cernada M, Baerl C, Vento M, Pérez-Martinez G. Microbial ecology and host-microbiota interactions during early life stages. Gut Microbes 2012;3:352-65.
62. Smaill FM, Gyte GM. Antibiotic prophylaxis versus no prophylaxis for preventing infection after cesarean section. Cochrane Database Syst Rev 2010;(1):CD007482.
63. Donnet-Hughes A, Perez PF, Doré J, et al. Potential role of the intestinal microbiota of the mother in neonatal immune education. Proc Nutr Soc 2010;69:407-15.
64. Dai D, Walker WA. Protective nutrients and bacterial colonization in the immature human gut. Adv Pediatr 1999;46:353-82.
65. Frimodt-Mller N. The mouse peritonitis model: present and future use. J Antimicrob Chemother 1993;31:Suppl D:55-60.
66. Salminen S, Isolauri E. Opportunities for improving the health and nutrition of the human infant by probiotics. Nestle Nutr Workshop Ser Pediatr Program 2008;62:223-33.
67. Kuitunen M, Kukkonen K, Juntunen-Backman K, et al. Probiotics prevent IgE-Associated allergy until age 5 years in cesarean-delivered children but not in the total cohort. J Allergy Clin Immunol 2009;123:335-41.
68. Rougé C, Goldenberg O, Ferraris L, et al. Investigation of the intestinal microbiota in preterm infants using different methods. Anaerobe 2010;16:362-70.
69. Connell JH, Slatyer RO. Mechanisms of succession in natural communities and their role in community stability and organization. Am Nat 1977;111:1119-44.
70. Palmer C, Bik EM, DiGiulio DB, Relman DA, Brown PO. Development of the human infant intestinal microbiota. PLoS Biol 2007;5:e177.
71. Koenig JE, Spor A, Scalfone N, et al. Succession of microbial consortia in the developing infant gut microbiome. Proc Natl Acad Sci USA 2011;108:4578-85.
72. White RA, Bjrnholt JV, Baird DD, et al. Novel developmental analyses identify longitudinal patterns of early gut microbiota that affect infant growth. PLoS Comput Biol 2013;9:e1003042.
73. Dominguez-Bello MG, Costello EK, Contreras M, 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;107:11971-5.
74. Costello EK, Lauber CL, Hamady M, Fierer N, Gordon JI, Knight R. Bacterial community variation in human body habitats across space and time. Science 2009;326:1694-7.
75. Turnbaugh PJ, Hamady M, Yatsunenko T, et al. A core gut microbiome in obese and lean twins. Nature 2009;457:480-4.
76. Vaishampayan PA, Kuehl JV, Froula JL, Morgan JL, Ochman H, Francino MP. Comparative metagenomics and population dynamics of the gut microbiota in mother and infant. Genome Biol Evol 2010;2:53-66.
77. Macarthur RH, Wison EO. The Theory of Island Biogeography. Princeton, NJ: Princeton University Press, 1967:1-224.
78. De Filippo C, Cavalieri D, Di Paola M, et al. Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa. Proc Natl Acad Sci USA 2010;107:14691-6.
79. Bäckhed F. Programming of host metabolism by the gut microbiota. Ann Nutr Metab 2011;58:Suppl 2:44-52.
80. Ravel J, Gajer P, Abdo Z, et al. Vaginal microbiome of reproductive-Age women. Proc Natl Acad Sci USA 2011;108:4680-7.