Factors influencing the development of a personal tailored microbiota in the neonate, with particular emphasis on antibiotic therapy

References

• Lee YK, Manzmanian SK. Has the microbiota played a critical role in the evolution of the adaptive immune system? Science 2010;330:1768–73
   PubMed Web of Science ®Google Scholar
• Quin J, Li R, Raes J, et al. A human gut microbial gene catalogue established by metagenomic sequencing. Nature 2010;464:59–65
   PubMed Web of Science ®Google Scholar
• Johnson CL, Varsalovic J. The human microbiome and its potential importance to pediatrics. Pediatrics 2012;129:950–60
   PubMed Web of Science ®Google Scholar
• Blaser MJ. Who are we? Indigenous microbes and the ecology of human diseases. EMBO Reports 2006;7:956–60
   PubMed Web of Science ®Google Scholar
• Ottman N, Smidt H, de Vos WM, Belzer C. The function of our microbiota: who is out there and what do they do? Front Cell Infect Microbiol 2012;2:104
   PubMed Web of Science ®Google Scholar
• Mshvildadze M, Neu J. The infant intestinal microbiome: friend or foe? Early Hum Dev 2010;86:S67–71
   PubMed Web of Science ®Google Scholar
• Manichanh C, Reeder J, Gibert P, et al. Reshaping the gut microbiome with bacterial transplantation and antibiotic intake. Genome Res 2010;20:1411–9
   PubMed Web of Science ®Google Scholar
• Dominguez-Bello MG, Blaser MJ, Ley RE, Knight R. Development of the human gastrointestinal microbiota and insights from high-throughput sequencing. Gastroenterology 2011;140:1713–9
   PubMed Web of Science ®Google Scholar
• Muegge BD, Kuczynski J, Knights D, et al. Diet drives convergence in gut microbiome functions across mammalian phylogeny and within humans. Science 2011;332:970–4
   PubMed Web of Science ®Google Scholar
• Martin F-PJ, Collino S, Rezzi S, Kochhar S. Metabolomic application to decipher gut microbial metabolic influence in health and disease. Front Physiol 2012;3:113
   PubMedGoogle Scholar
• Penders J, Thijs C, Vink C, et al. Factors influencing the composition of the intestinal microbiota in early infancy. Pediatrics 2006;118:511–21
   PubMed Web of Science ®Google Scholar
• Turnbaugh PJ, Ley RE, Hamady M, et al. The human microbiome project. Nature 2007;449:804–10
   PubMed Web of Science ®Google Scholar
• Di Giulio DB. Source of infection leading to preterm death. J Perinat Med 2010;38:495–502
   PubMedGoogle Scholar
• Kramer MR, Hogue C. Place matters: variation in the black/white very preterm birth rate across U.S. metropolitan areas. 2002–2004. Public Health Rep 2008;123:576–85
   PubMed Web of Science ®Google Scholar
• Ackermann G, Thomalla S, Ackermann F, et al. Prevalence and characteristics of bacteria and host factors in an outbreak situation of antibiotic-associated diarrhoea. J Med Microbiol 2005;54:149–53
   PubMed Web of Science ®Google Scholar
• Donders G, Bellen G, Rezeberga D. Aerobic vaginitis in pregnancy. BJOG 2011;118:1163–70
   PubMed Web of Science ®Google Scholar
• Biasucci G, Benenati B, Morelli L, et al. Cesarean delivery may affect the early biodiversity of the intestinal bacteria. J Nutr 2008;138:1796S–800S
   PubMed Web of Science ®Google Scholar
• Biasucci G, Rubini M, Riboni S, et al. mode of delivery affects the bacterial community in the newborn gut. Early Hum Dev 2010;86:13–15
   PubMed Web of Science ®Google Scholar
• Gronlund MM, Lehtonen OP, Eerola E, Kero P. Fecal microflora in healthy infants born by different methods of delivery: permanent changes in intestinal flora after cesarean delivery. J Pediatr Gastroenterol Nutr 1999;28:19–25
   PubMed Web of Science ®Google Scholar
• Arboleya S, Binetti A, Salazar N, et al. Establishment and development of intestinal microbiota in preterm neonates. FEMS Microbiol Ecol 2012;79:763–72
   PubMed Web of Science ®Google Scholar
• Poroyko V, Morowitz M, Bell T, et al. Diet creates metabolic niches in the “immature gut” that shape microbial communities. Nutr Hosp 2011;26:1283–95
   PubMed Web of Science ®Google Scholar
• Zivkovic AM, German JB, Lebrilla CB, Mills DA. Human milk glycobiome and its impact on the infant gastrointestinal microbiota. PNAS 2011;108:4653–8
   PubMed Web of Science ®Google Scholar
• Bezirtzoglou E, Stavropoulou E. Immunology and probiotic impact of the newborn and young children intestinal microflora. Anaerobe 2011;17:369–74
   PubMed Web of Science ®Google Scholar
• Palmer C, Bik EM, Di Giulio DB, et al. Development of the human infant intestinal microbiota. PlosBiol 2007;5:e177
   PubMed Web of Science ®Google Scholar
• Ravel J, Gajer P, Abdo Z, et al. Vaginal microbiome of reproductive-age women. PNAS 2011;108:4680–7
   PubMed Web of Science ®Google Scholar
• Ishii M, Toda T, Ikarashi N, et al. Effects of intestinal flora on the expression of cytochrome P4503A in the liver. Yakugaku Zasshi 2012;132:301–10
   PubMed Web of Science ®Google Scholar
• Kinross JM, Darzi AW, Nicholson JK. Gut microbiome-host interactions in health and disease. Genome Med 2011;3:14
   PubMed Web of Science ®Google Scholar
• Rakoff-Nahoum S, Paglino J, Eslami-Varzaneh F, et al. Recognition microflora by toll-like receptors is required for intestinal homeostasis. Cell 2004;118:229–41
   PubMed Web of Science ®Google Scholar
• Rook GA, Brunet LR. Microbes immunoregulation and the gut. Gut 2005;54:317–20
   PubMed Web of Science ®Google Scholar
• Madara J. Building an intestine-architectural contributions of comensal bacteria. N Engl J Med 2004;351:1685–6
   PubMed Web of Science ®Google Scholar
• Collado MC, Cernada M, Bauerl C, et al. Microbial ecology and host-microbiota interactions during early life stages. Gut Microbes 2012;3:352–65
   PubMed Web of Science ®Google Scholar
• Rautava S, Luoto R, Salminen S, Isolauri E. Microbial contact during pregnancy, intestinal colonization and human disease. Nat Rev Gastroenetrol Hepatol 2012;9:565–76
   PubMed Web of Science ®Google Scholar
• Rohde CL, Bartolini V, Jones N. The use of probiotics in the prevention and treatment of antibiotic-associated diarrhea with special interest in Clostridium difficile-associated diarrhea. Nutr ClinPract 2009;24:33–40
   Google Scholar
• De La Cpchetière MF, Durand T, Lalande V, et al. Effect of antibiotic therapy on human fecal microbiota and the relation to the development of Clostridium difficile. Microb Ecol 2008;56:395–402
   PubMedGoogle Scholar
• Gorkiewicz G. Nosocomial and antibiotic-associated diarrhea caused by organisms other than Clostridium difficile. Int J Antimicrob Agents 2009;33:37–41
   PubMed Web of Science ®Google Scholar
• Son HJ, Lim YC, Ha KS, et al. Propofol and aminophylline antagonize each other during the mobilization of intracellular calcium in human umbilical vein endothelial cells. J Korean Med Sci 2010;25:222–7
   Google Scholar
• Johnston BC, Goldenberg JZ, Vandvik PO, et al. Probiotics for the prevention of pediatric antibiotic-associated diarrhea. Cochrane Database Syst Rev 2011;11:CD004827
   PubMedGoogle Scholar
• Schumann A, Nutten S, Donnicola D, et al. Neonatal antibiotic treatment alters gastrointestinal tract developmental gene expression and intestinal barrier transcriptome. Physiol Genomics 2005;23:309–18
   Google Scholar
• Mshvildadze M, Neu J, Schuster J, et al. Intestinal microbial ecology in premature infants assessed with non- culture- based techniques. J Pediatr 2010;156:20–5
   PubMed Web of Science ®Google Scholar
• Westerbeek EA, van den Berg A, Lafeber HN, et al. The intestinal bacterial colonization in preterm infants: a review of the literature. Clin Nutr 2006;25:361–8
   PubMed Web of Science ®Google Scholar
• Collignon A, Sandré C, Barc MC. Saccharomyces boulardii modulates dendritic cell properties and intestinal microbiota disruption after antimicrobic treatment. Gastroenterol Clin Biol 2010;34:71–8
   Google Scholar
• Khoruts A, Dicksved J, Jansson JK, Sadowsky MJ. Changes in the composition of the human fecal microbiome after bacteriotherapy for recurrent Clostridium difficile-asociate diarrhea. J Clin Gastroenterol 2010;44:354–60
   PubMed Web of Science ®Google Scholar
• Surawicz CM. The microbiota and infectious diarrhea. Gastroenterol Clin Biol 2010;34:29–36
   PubMedGoogle Scholar
• Toda T, Ohi K, Kudo T, et al. Antibiotics suppress Cyp3a in the mouse liver by reducing lithocholic acid-producing intestinal flora. Yakugaku Zasshi 2009;129:601–8
   PubMedGoogle Scholar
• Dethlefsen L, Relman DA. Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation. PNAS USA 2011;1:4554–61
   Google Scholar
• Buffie CG, Jarchum I, Equinda M, et al. Profound alterations of intestinal microbiota following a single dose of clindamycin results in sustained susceptibility to Clostridium difficile-induced colitis. Infect Immun 2012;80:62–73
   PubMed Web of Science ®Google Scholar
• Willing BP, Russell SL, Finlay BB. Shifting the balance: antibiotic effects on host-microbiota mutualism. Nat Rev Microbiol 2011;9:233–43
   PubMed Web of Science ®Google Scholar
• Relman DA. The human microbiome: ecosystem resilience and health. Netr Rev 2012;1:2–9
   Google Scholar
• Costello EK, Stagaman K, Dethlefsen L, et al. The application of ecological theory toward an understanding of the human microbiome. Science 2012;336:1255–62
   PubMed Web of Science ®Google Scholar
• Heinken A, Sahoo S, Fleming RMT, Thiele I. System-level characterization of a host-microbe metabolic symbiosis in the mammalian gut. Gut Microbes 2013;4:1–13
   Google Scholar
• Preidis GA, Versalovic J. Targeting the human microbiome with antibiotics, probiotics, and prebiotics: gastroenterology enters the metagenomics era. Gastroenterology 2009;136:2015–31
   PubMed Web of Science ®Google Scholar
• Grover S, Rashmi HM, Srivastava AK, Batish VK. Probiotics for human health. New innovations and emerging trends. Gut Pathogens 2012;4:15
   PubMed Web of Science ®Google Scholar
• Claus SP, Ellero SL, Berger B, et al. Colonization-induced host-gut microbial metabolic interaction. mBio 2011;2:e00271–10
   PubMed Web of Science ®Google Scholar