Pyrosequencing-based molecular monitoring of the intestinal bacterial colonization in preterm infants

Journal of Pediatric Gastroenterology and Nutrition

Volumn 53, Issue 5, 2011, Pages 512-519

  Chang, Ju Y ^a   Shin, Son M ^b   Chun, Jongsik ^a   Lee, Jae Hak ^a   Seo, Jeong Kee ^c  

^a Seoul National University   (South Korea)

^b Kwandong University College of Medicine   (South Korea)

^c Seoul National University Children's Hospital   (South Korea)

Author keywords

Intestinal microbiota; Preterm infants; Pyrosequencing

Indexed keywords

DNA 16S;

ACINETOBACTER; ARTICLE; BACTERIAL COLONIZATION; BACTEROIDES; CITROBACTER; CLINICAL ARTICLE; CLOSTRIDIUM DIFFICILE; CLOSTRIDIUM PERFRINGENS; DNA SEQUENCE; ENTEROBACTER; ENTEROCOCCUS; ESCHERICHIA COLI; FECES ANALYSIS; FIRMICUTES; HAEMOPHILUS; HIGH THROUGHPUT SEQUENCING; HUMAN; INFANT; INTESTINE FLORA; KOREA; LACTOBACILLUS; MICROBIAL COMMUNITY; MICROBIAL DIVERSITY; MICROBIOME; NONHUMAN; PERINATAL PERIOD; PREMATURITY; PRIORITY JOURNAL; PSEUDOMONAS; SERRATIA; STAPHYLOCOCCUS; STREPTOCOCCUS; VEILLONELLA; VERY LOW BIRTH WEIGHT;

ASIAN CONTINENTAL ANCESTRY GROUP; CLOSTRIDIUM; ENTEROBACTERIACEAE; ENTEROCOLITIS, NECROTIZING; FECES; GAMMAPROTEOBACTERIA; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; INFANT, NEWBORN; INFANT, PREMATURE; INFANT, VERY LOW BIRTH WEIGHT; INTESTINES; METAGENOME; PILOT PROJECTS; REPUBLIC OF KOREA; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA;

ACINETOBACTER; BACILLI (CLASS); BACTERIA (MICROORGANISMS); BACTEROIDES; BACTEROIDETES; CITROBACTER; CLOSTRIDIA; CLOSTRIDIUM DIFFICILE; ENTEROBACTER; ENTEROCOCCUS; ESCHERICHIA; FAECALIBACTERIUM; GAMMAPROTEOBACTERIA; ROSEBURIA; SERRATIA; STAPHYLOCOCCUS; STREPTOCOCCUS; VEILLONELLA;

EID: 80255138325     PISSN: 02772116     EISSN: 15364801     Source Type: Journal    
DOI: 10.1097/MPG.0b013e318227e518     Document Type: Article

References (34)

1. Furrie E. A molecular revolution in the study of intestinal microflora. Gut 2006;55:141-3. (Pubitemid 43117264)
2. Zoetendal EG, Collier CT, Koike S, et al. Molecular ecological analysis of the gastrointestinal microbiota: a review. J Nutr 2004;134:465-72. (Pubitemid 38141834)
3. Dethlefsen L, Eckburg PB, Bik EM, et al. Assembly of the human intestinal microbiota. Trends Ecol Evol 2006;21:517-23. (Pubitemid 44233957)
4. Sogin ML, Morrison HG, Huber JA, et al. Microbial diversity in the deep sea and the underexplored "rare biosphere." Proc Natl Acad Sci U S A 2006;103:12115-20. (Pubitemid 44215820)
5. Andersson AF, Lindberg M, Jakobsson H, et al. Comparative analysis of human gut microbiota by barcoded pyrosequencing. PLoS One 2008;3:e2836.
6. Fanaro S, Chierici R, Guerrini P, et al. Intestinal microflora in early infancy: composition and development. Acta Paediatr Suppl 2003; 91:48-55. (Pubitemid 37239252)
7. Magne F, Abely M, Boyer F, et al. 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; 57:128-38. (Pubitemid 43880249)
8. Millar MR, Linton CJ, Cade A, et al. Application of 16S rRNA gene PCR to study bowel flora of preterm infants with and without necrotizing enterocolitis. J Clin Microbiol 1996;34:2506-10. (Pubitemid 26307802)
9. Ley RE, Backhed F, Turnbaugh P, et al. Obesity alters gut microbial ecology. Proc Natl Acad Sci U S A 2005;102:11070-5. (Pubitemid 41105994)
10. Kalliomaki M, Collado MC, Salminen S, et al. Early differences in fecal microbiota composition in children may predict overweight. Am J Clin Nutr 2008;87:534-8. (Pubitemid 351364532)
11. Penders J, Thijs C, Vink C, et al. Factors influencing the composition of the intestinal microbiota in early infancy. Pediatrics 2006;118:511-21. (Pubitemid 46085405)
12. Blakey JL, Lubitz L, Barnes GL, et al. Development of gut colonisation in pre-term neonates. J Med Microbiol 1982;15:519-29. (Pubitemid 13196463)
13. Sakata H, Yoshioka H, Fujita K. Development of the intestinal flora in very low birth weight infants compared to normal full-term newborns. Eur J Pediatr 1985;144:186-90. (Pubitemid 15007000)
14. Gewolb IH, Schwalbe RS, Taciak VL, et al. Stool microflora in extremely low birthweight infants. Arch Dis Child Fetal Neonatal Ed 1999;80:F167-73. (Pubitemid 29453033)
15. Wang Y, Hoenig JD, Malin KJ, et al. 16S rRNA gene-based analysis of fecal microbiota from preterm infants with and without necrotizing enterocolitis. ISME J 2009;3:944-54.
16. Mshvildadze M, Neu J, Shuster J, et al. Intestinal microbial ecology in premature infants assessed with non-culture-based techniques. J Pediatr 2010;156:20-5.
17. Favier CF, Vaughan EE, De Vos WM, et al. Molecular monitoring of succession of bacterial communities in human neonates. Appl Environ Microbiol 2002;68:219-26. (Pubitemid 34031183)
18. Morelli L. Postnatal development of intestinal microflora as influenced by infant nutrition. J Nutr 2008;138:1791S-5.
19. Li F, Hullar MA, Lampe JW. Optimization of terminal restriction fragment polymorphism (TRFLP) analysis of human gut microbiota. J Microbiol Methods 2007;68:303-11. (Pubitemid 46149943)
20. McKenna P, Hoffmann C, Minkah N, et al. The macaque gut microbiome in health, lentiviral infection, and chronic enterocolitis. PLoS Pathog 2008;4:e20.
21. Hamady M, Walker JJ, Harris JK, et al. Error-correcting barcoded primers for pyrosequencing hundreds of samples in multiplex. Nat Methods 2008;5:235-7. (Pubitemid 351325646)
22. Chun J, Kim KY, Lee JH, et al. The analysis of oral microbial communities of wild-type and Toll-like receptor 2-deficient mice using a 454 GS FLX titanium pyrosequencer. BMC Microbiol 2010;10:101.
23. Chun J, Lee JH, Jung Y, et al. EzTaxon: a web-based tool for the identification of prokaryotes based on 16S ribosomal RNA gene sequences. Int J Syst Evol Microbiol 2007;57:2259-61. (Pubitemid 350031697)
24. Schwiertz A, Gruhl B, Lobnitz M, et al. Development of the intestinal bacterial composition in hospitalized preterm infants in comparison with breast-fed, full-term infants. Pediatr Res 2003;54:393-9. (Pubitemid 37013203)
25. Palmer C, Bik EM, DiGiulio DB, et al. Development of the human infant intestinal microbiota. PLoS Biol 2007;5:e177.
26. Qin J, Li R, Raes J, et al. A human gut microbial gene catalogue established by metagenomic sequencing. Nature 2010;464:59-65.
27. Westerbeek EA, van den Berg A, Lafeber HN, et al. The intestinal bacterial colonisation in preterm infants: a review of the literature. Clin Nutr 2006;25:361-8. (Pubitemid 43843032)
28. Chang JY, Antonopoulos DA, Kalra A, et al. Decreased diversity of the fecal microbiome in recurrent Clostridium difficile-associated diarrhea. J Infect Dis 2008;197:435-8. (Pubitemid 351263426)
29. Feder HM Jr, Roberts JC, Salazar JC, et al. HACEK endocarditis in infants and children: two cases and a literature review. Pediatr Infect Dis J 2003;22:557-62. (Pubitemid 36782198)
30. Muytjens HL, Zanen HC, Sonderkamp HJ, et al Analysis of eight cases of neonatal meningitis and sepsis due to Enterobacter sakazakii. J Clin Microbiol 1983;18:115-20. (Pubitemid 13056820)
31. Friedemann M. Epidemiology of invasive neonatal Cronobacter (Enterobacter sakazakii) infections. Eur J Clin Microbiol Infect Dis 2009;28:1297-304.
32. Rinttila T, Kassinen A, Malinen E, et al. Development of an extensive set of 16S rDNA-targeted primers for quantification of pathogenic and indigenous bacteria in faecal samples by real-time PCR. J Appl Microbiol 2004;97:1166-77. (Pubitemid 39573940)
33. Hall MA, Cole CB, Smith SL, et al. Factors influencing the presence of faecal lactobacilli in early infancy. Arch Dis Child 1990;65:185-8. (Pubitemid 20057808)
34. Harmsen HJ, Wildeboer-Veloo AC, Raangs GC, et al. Analysis of intestinal flora development in breast-fed and formula-fed infants by using molecular identification and detection methods. J Pediatr Gastroenterol Nutr 2000;30:61-7.