The Journal of Pediatrics
Volume 156, Issue 1 , Pages 20-25 , January 2010

Intestinal Microbial Ecology in Premature Infants Assessed with Non–Culture-Based Techniques

  • Maka Mshvildadze, MD

      Affiliations

    • Chachava Scientific-Research Institute of Perinatal Medicine Obstetrics and Gynecology, Tbilisi, Georgia
    • Department of Pediatrics, University of Florida, Gainesville, FL
  • ,
  • Josef Neu, MD

      Affiliations

    • Department of Pediatrics, University of Florida, Gainesville, FL
    • Corresponding Author InformationReprint requests: Josef Neu, Department of Pediatrics, University of Florida, 1600 SW Archer Rd, Human Development Building Rm HD 513, Gainesville, FL 32610.
  • ,
  • Jonathan Shuster, PhD

      Affiliations

    • Departments of Epidemiology and Health Policy Research, University of Florida, Gainesville, FL
    • General Clinical Research Center, University of Florida, Gainesville, FL
  • ,
  • Douglas Theriaque, MS

      Affiliations

    • General Clinical Research Center, University of Florida, Gainesville, FL
  • ,
  • Nan Li, MS, MD

      Affiliations

    • Department of Pediatrics, University of Florida, Gainesville, FL
  • ,
  • Volker Mai, MPH, PhD

      Affiliations

    • Microbiology and Cell Sciences and Emerging Pathogens Institute, University of Florida, Gainesville, FL

Received 9 March 2009 ,Revised 15 May 2009 ,Accepted 26 June 2009.

References 

  1. Hattori M, Taylor TD. The human intestinal microbiome: a new frontier of human biology. DNA Res. 2009;16:1–12
  2. Dethlefsen L, Eckburg PB, Bik EM, Relman DA. Assembly of the human intestinal microbiota. Trends Ecol Evol. 2006;21:517–523
  3. Dethlefsen L, McFall-Ngai M, Relman DA. An ecological and evolutionary perspective on human-microbe mutualism and disease. Nature. 2007;449:811–818
  4. Turnbaugh PJ, Ley RE, Hamady M, Fraser-Liggett CM, Knight R, Gordon JI. The human microbiome project. Nature. 2007;449:804–810
  5. Hooper LV, Gordon JI. Commensal host-bacterial relationships in the gut. Science. 2001;292:1115–1118
  6. Hooper LV. Bacterial contributions to mammalian gut development. Trends Microbiol. 2004;12:129–134
  7. Caicedo RA, Schanler RJ, Li N, Neu J. The developing intestinal ecosystem: implications for the neonate. Pediatr Res. 2005;58:625–628
  8. Riesenfeld CS, Schloss PD, Handelsman J. Metagenomics: genomic analysis of microbial communities. Annu Rev Genet. 2004;38:525–552
  9. Frank DN, Pace NR. Gastrointestinal microbiology enters the metagenomics era. Curr Opin Gastroenterol. 2008;24:4–10
  10. Claud EC, Walker WA. Hypothesis: inappropriate colonization of the premature intestine can cause neonatal necrotizing enterocolitis. FASEB J. 2001;15:1398–1403
  11. Gewolb IH, Schwalbe RS, Taciak VL, Harrison TS, Panigrahi P. Stool microflora in extremely low birthweight infants. Arch Dis Child Fetal Neonatal Ed. 1999;80:F167–F173
  12. Butel MJ, Suau A, Campeotto F, Magne F, Aires J, Ferraris L, et al. Conditions of bifidobacterial colonization in preterm infants: a prospective analysis. J Pediatr Gastroenterol Nutr. 2007;44:577–582
  13. Magne F, Abély M, Boyer F, Morville P, Pochart P, Suau A. Low species diversity and high interindividual variability in faeces of preterm infants as revealed by sequences of 16S rRNA genes and PCR-temporal temperature gradient gel electrophoresis profiles. FEMS Microbiol Ecol. 2006;57:128–138
  14. Mshvildadze M, Neu J, Mai V. Intestinal microbiota development in the premature neonate: establishment of a lasting commensal relationship?. Nutr Rev. 2008;66:658–663
  15. Neu J, Douglas-Escobar M, Lopez M. Microbes and the developing gastrointestinal tract. Nutr Clin Prac. 2007;22:174–182
  16. Neu J. Functional development of the fetal gastrointestinal tract. Semin Perinatol. 1989;13:224–235
  17. Neu J. Gastrointestinal development and meeting the nutritional needs of premature infants. Am J Clin Nutr. 2007;85:629-34S
  18. Neu J, Mackey AD. Neonatal gastrointestinal innate immunity. NeoReviews. 2003;4:14–18
  19. Nanthakumar NN, Fusunyan RD, Sanderson I, Walker WA. Inflammation in the developing human intestine: a possible pathophysiologic contribution to necrotizing enterocolitis. Proc Natl Acad Sci U S A. 2000;97:6043–6048
  20. Mai V, Greenwald B, Morris JG, Raufman JP, Stine OC. Effect of bowel preparation and colonoscopy on post-procedure intestinal microbiota composition. Gut. 2006;55:1822–1823
  21. Zoetendal EG, Ben-Amor K, Akkermans AD, Abee T, de Vos WM. DNA isolation protocols affect the detection limit of PCR approaches of bacteria in samples from the human gastrointestinal tract. Syst Appl Microbiol. 2001;24:405–410
  22. Begon M, Harper JL, Townsend CR Ecology: individuals, populations, and communities. 3rd ed. Cambridge, MA: Blackwell Science Ltd.; 1996.
  23. Hamady M, Walker JJ, Harris JK, Gold NJ, Knight R. Error-correcting barcoded primers for pyrosequencing hundreds of samples in multiplex. Nat Methods. 2008;5:235–237
  24. Lozupone C, Knight R. UniFrac: a new phylogenetic method for comparing microbial communities. Appl Environ Microbiol. 2005;71:8228–8235
  25. Lozupone C, Hamady M, Knight R. UniFrac—an online tool for comparing microbial community diversity in a phylogenetic context. BMC Bioinformatics. 2006;7:371
  26. Millar MR, Linton CJ, Cade A, Glancy D, Hall M, Jalal H. Application of 16S rRNA gene PCR to study bowel flora of preterm infants with and without necrotizing enterocolitis. J Clin Microbiol. 1996;34:2506–2510
  27. de la Cochetiere MF, Piloquet H, des Robert C, Darmaun D, Galmiche JP, Roze JC. Early intestinal bacterial colonization and necrotizing enterocolitis in premature infants: the putative role of Clostridium. Pediatr Res. 2004;56:366–370
  28. DiGiulio DB, Romero R, Amogan HP, Kusanovic JP, Bik EM, Gotsch F, et al. Microbial prevalence, diversity and abundance in amniotic fluid during preterm labor: a molecular and culture-based investigation. PLoS ONE. 2008;3:33056
  29. Goldenberg RL, Culhane JF, Iams JD, Romero R. Epidemiology and causes of preterm birth. Lancet. 2008;371:75–84
  30. Fanaro S, Chierici R, Guerrini P, Vigi V. Intestinal microflora in early infancy: composition and development. Acta Paediatr Suppl. 2003;91:48–55
  31. Cotten CM, Taylor S, Stoll B, Goldberg RN, Hansen NI, Sánchez PJ, et al. Prolonged duration of initial empirical antibiotic treatment is associated with increased rates of necrotizing enterocolitis and death for extremely low birth weight infants. Pediatrics. 2009;123:58–66

 Supported in part by grants from the National Institute of Research Resources, National Institutes of Health (RO1 HD 059143 and M01RR00082) and an educational grant (M.M.) from the European Society for Pediatric Research. The authors declare no conflicts of interest.

PII: S0022-3476(09)00623-4

doi: 10.1016/j.jpeds.2009.06.063

The Journal of Pediatrics
Volume 156, Issue 1 , Pages 20-25 , January 2010