The development of gut microbiota in critically ill extremely low birth weight infants assessed with 16S rRNA gene based sequencing

Gut Microbes

Volumn 5, Issue 3, 2014, Pages 304-503

  Drell, Tiina ^a,b,c   Lutsar, Irja ^a   Štšepetova, Jelena ^a   Parm, Ülle ^a   Metsvaht, Tuuli ^a,d   Ilmoja, Mari Liis ^e   Simm, Jaak ^b   Sepp, Eepp ^a  

^a UNIVERSITY OF TARTU   (Estonia)

^b TALLINN UNIVERSITY OF TECHNOLOGY   (Estonia)

^c Competence Centre on Rreproductive Medicine and Biology ^*  (Estonia)

^d TARTU UNIVERSITY HOSPITAL   (Estonia)

^e TALLINN CHILDREN S HOSPITAL   (Estonia)

Author keywords

16S rRNA gene sequencing; Extremely low birth weight; Gut microbiota; Microbiome profiling; Preterm neonates

Indexed keywords

RNA 16S; BACTERIAL DNA; RIBOSOME DNA;

ACTINOBACTERIA; ADOLESCENT; ADULT; ARTICLE; BACTERIAL COLONIZATION; BACTEROIDES; BACTEROIDETES; CHORIOAMNIONITIS; CLINICAL ARTICLE; CRITICALLY ILL PATIENT; ENTEROBACTERIACEAE; ENTEROCOCCUS; ESCHERICHIA COLI; EXTREMELY LOW BIRTH WEIGHT; FEMALE; FIRMICUTES; GENE SEQUENCE; HUMAN; INFANT; INTESTINE FLORA; LACTOBACILLUS; NEWBORN; NUCLEOTIDE SEQUENCE; PREVALENCE; PREVOTELLA; PROTEOBACTERIA; PYROSEQUENCING; SHIGELLA; STAPHYLOCOCCUS; VEILLONELLA; VERRUCOMICROBIA; BACTERIUM; BIOTA; CHEMISTRY; CLASSIFICATION; CLUSTER ANALYSIS; CRITICAL ILLNESS; DNA SEQUENCE; FECES; GASTROINTESTINAL TRACT; GENETICS; MALE; MICROBIOLOGY; MOLECULAR GENETICS; PHYLOGENY; RNA GENE;

BACTERIA; BIOTA; CLUSTER ANALYSIS; CRITICAL ILLNESS; DNA, BACTERIAL; DNA, RIBOSOMAL; FECES; FEMALE; GASTROINTESTINAL TRACT; GENES, RRNA; HUMANS; INFANT; INFANT, EXTREMELY LOW BIRTH WEIGHT; INFANT, NEWBORN; MALE; MOLECULAR SEQUENCE DATA; PHYLOGENY; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA;

EID: 84901370914     PISSN: 19490976     EISSN: 19490984     Source Type: Journal    
DOI: 10.4161/gmic.28849     Document Type: Article

References (36)

1. 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; PMID:20333224; http://dx.doi.org/10.1093/gbe/evp057
2. Eggesbø M, Moen B, Peddada S, Baird D, Rugtveit J, Midtvedt T, Bushel PR, Sekelja M, Rudi K. Development of gut microbiota in infants not exposed to medical interventions. APMIS 2011; 119:17-35; PMID:21143523; http://dx.doi.org/10.1111/j.1600-0463.2010.02688.x
3. Palmer C, Bik EM, DiGiulio DB, Relman DA, Brown PO. Development of the human infant intestinal microbiota. PLoS Biol 2007; 5:e177; PMID:17594176; http://dx.doi.org/10.1371/journal.pbio.0050177
4. Parm Ü, Metsvaht T, Sepp E, Ilmoja M-L, Pisarev H, Pauskar M, Lutsar I. Mucosal surveillance cultures in predicting Gram-negative late-onset sepsis in neonatal intensive care units. J Hosp Infect 2011; 78:327-32; PMID:21684633; http://dx.doi.org/10.1016/j.jhin.2011.03.025
5. Mshvildadze M, Neu J, Mai V. Intestinal microbiota development in the premature neonate: establishment of a lasting commensal relationship? Nutr Rev 2008; 66:658-63; PMID:19019028; http://dx.doi.org/10.1111/j.1753-4887.2008.00119.x
6. 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; 57:128-38; PMID:16819956; http://dx.doi.org/10.1111/j.1574-6941.2006.00097.x
7. Schwiertz A, Gruhl B, Löbnitz M, Michel P, Radke M, Blaut M. Development of the intestinal bacterial composition in hospitalized preterm infants in comparison with breast-fed, full-term infants. Pediatr Res 2003; 54:393-9; PMID:12788986; http://dx.doi.org/10.1203/01.PDR.0000078274.74607.7A
8. 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:F167-73; PMID:10212075; http://dx.doi.org/10.1136/fn.80.3.F167
9. Mshvildadze M, Neu J, Shuster J, Theriaque D, Li N, Mai V. Intestinal microbial ecology in premature infants assessed with non-culture-based techniques. J Pediatr 2010; 156:20-5; PMID:19783002; http://dx.doi.org/10.1016/j.jpeds.2009.06.063
10. LaTuga MS, Ellis JC, Cotton CM, Goldberg RN, Wynn JL, Jackson RB, Seed PC. Beyond bacteria: a study of the enteric microbial consortium in extremely low birth weight infants. PLoS One 2011; 6:e27858; PMID:22174751; http://dx.doi.org/10.1371/journal.pone.0027858
11. Mai V, Torrazza RM, Ukhanova M, Wang X, Sun Y, Li N, Shuster J, Sharma R, Hudak ML, Neu J. Distortions in development of intestinal microbiota associated with late onset sepsis in preterm infants. PLoS One 2013; 8:e52876; PMID:23341915; http://dx.doi.org/10.1371/journal.pone.0052876
12. Stewart CJ, Marrs EC, Nelson A, Lanyon C, Perry JD, Embleton ND, Cummings SP, Berrington JE. Development of the preterm gut microbiome in twins at risk of necrotising enterocolitis and sepsis. PLoS One 2013; 8:e73465; PMID:24023682; http://dx.doi.org/10.1371/journal.pone.0073465
13. Torrazza RM, Ukhanova M, Wang X, Sharma R, Hudak ML, Neu J, Mai V. Intestinal microbial ecology and environmental factors affecting necrotizing enterocolitis. PLoS One 2013; 8:e83304; PMID:24386174; http://dx.doi.org/10.1371/journal.pone.0083304
14. Claud EC, Keegan KP, Brulc JM, Lu L, Bartels D, Glass E, Chang EB, Meyer F, Antonopoulos DA. Bacterial community structure and functional contributions to emergence of health or necrotizing enterocolitis in preterm infants. Microbiome 2013; 1:20; PMID:24450928; http://dx.doi.org/10.1186/2049-2618-1-20
15. Stewart CJ, Marrs ECL, Magorrian S, Nelson A, Lanyon C, Perry JD, Embleton ND, Cummings SP, Berrington JE. The preterm gut microbiota: changes associated with necrotizing enterocolitis and infection. Acta Paediatr 2012; 101:1121-7; PMID:22845166; http://dx.doi.org/10.1111/j.1651-2227.2012.02801.x
16. Koenig JE, Spor A, Scalfone N, Fricker AD, Stombaugh J, Knight R, Angenent LT, Ley RE. Succession of microbial consortia in the developing infant gut microbiome. Proc Natl Acad Sci U S A 2011; 108(Suppl 1):4578-85; PMID:20668239; http://dx.doi.org/10.1073/pnas.1000081107
17. Jacquot A, Neveu D, Aujoulat F, Mercier G, Marchandin H, Jumas-Bilak E, Picaud J-C. Dynamics and clinical evolution of bacterial gut microflora in extremely premature patients. J Pediatr 2011; 158:390-6; PMID:20961563; http://dx.doi.org/10.1016/j.jpeds.2010.09.007
18. Madan JC, Salari RC, Saxena D, Davidson L, O'Toole GA, Moore JH, Sogin ML, Foster JA, Edwards WH, Palumbo P, et al. Gut microbial colonisation in premature neonates predicts neonatal sepsis. Arch Dis Child Fetal Neonatal Ed 2012; 97:F456-62; PMID:22562869
19. Tita ATN, Andrews WW. Diagnosis and management of clinical chorioamnionitis. Clin Perinatol 2010; 37:339-54; PMID:20569811; http://dx.doi.org/10.1016/j.clp.2010.02.003
20. Barrett E, Kerr C, Murphy K, O'Sullivan O, Ryan CA, Dempsey EM, Murphy BP, O'Toole PW, Cotter PD, Fitzgerald GF, et al. The individual-specific and diverse nature of the preterm infant microbiota. Arch Dis Child Fetal Neonatal Ed 2013; 98:F334-40; PMID:23303303; http://dx.doi.org/10.1136/archdischild-2012-303035
21. Chang JY, Shin SM, Chun J, Lee J-H, Seo J-K. Pyrosequencing-based molecular monitoring of the intestinal bacterial colonization in preterm infants. J Pediatr Gastroenterol Nutr 2011; 53:512-9; PMID:21734604
22. Wang Y, Hoenig JD, Malin KJ, Qamar S, Petrof EO, Sun J, Antonopoulos DA, Chang EB, Claud EC. 16S rRNA gene-based analysis of fecal microbiota from preterm infants with and without necrotizing enterocolitis. ISME J 2009; 3:944-54; PMID:19369970; http://dx.doi.org/10.1038/ismej.2009.37
23. Mai V, Young CM, Ukhanova M, Wang X, Sun Y, Casella G, Theriaque D, Li N, Sharma R, Hudak M, et al. Fecal microbiota in premature infants prior to necrotizing enterocolitis. PLoS One 2011; 6:e20647; PMID:21674011; http://dx.doi.org/10.1371/journal.pone.0020647
24. Adlerberth I, Lindberg E, Aberg N, Hesselmar B, Saalman R, Strannegård I-L, Wold AE. Reduced enterobacterial and increased staphylococcal colonization of the infantile bowel: an effect of hygienic lifestyle? Pediatr Res 2006; 59:96-101; PMID:16380405; http://dx.doi.org/10.1203/01.pdr.0000191137.12774.b2
25. Stoll BJ, Hansen N. Infections in VLBW infants: studies from the NICHD Neonatal Research Network. Semin Perinatol 2003; 27:293-301; PMID:14510320; http://dx.doi.org/10.1016/S0146-0005(03)00046-6
26. Arboleya S, Binetti A, Salazar N, Fernández N, Solís G, Hernández-Barranco A, Margolles A, de Los Reyes-Gavilán CG, Gueimonde M. Establishment and development of intestinal microbiota in preterm neonates. FEMS Microbiol Ecol 2012; 79:763-72; PMID:22126419; http://dx.doi.org/10.1111/j.1574-6941.2011.01261.x
27. Morrow AL, Lagomarcino AJ, Schibler KR, Taft DH, Yu Z, Wang B, Altaye M, Wagner M, Gevers D, Ward DV, et al. Early microbial and metabolomic signatures predict later onset of necrotizing enterocolitis in preterm infants. Microbiome 2013; 1:13; PMID:24450576; http://dx.doi.org/10.1186/2049-2618-1-13
28. Butel M-J, Suau A, Campeotto F, Magne F, Aires J, Ferraris L, Kalach N, Leroux B, Dupont C. Conditions of bifidobacterial colonization in preterm infants: a prospective analysis. J Pediatr Gastroenterol Nutr 2007; 44:577-82; PMID:17460489; http://dx.doi.org/10.1097/MPG.0b013e3180406b20
29. Adlerberth I, Wold AE. Establishment of the gut microbiota in Western infants. Acta Paediatr 2009; 98:229-38; PMID:19143664; http://dx.doi.org/10.1111/j.1651-2227.2008.01060.x
30. Sim K, Cox MJ, Wopereis H, Martin R, Knol J, Li M-S, Cookson WO, Moffatt MF, Kroll JS. Improved detection of bifidobacteria with optimised 16S rRNA-gene based pyrosequencing. PLoS One 2012; 7:e32543; PMID:22470420; http://dx.doi.org/10.1371/journal.pone.0032543
31. Metsvaht T, Ilmoja M-L, Parm U, Maipuu L, Merila M, Lutsar I. Comparison of ampicillin plus gentamicin vs. penicillin plus gentamicin in empiric treatment of neonates at risk of early onset sepsis. Acta Paediatr 2010; 99:665-72; PMID:20096030
32. Keinänen-Toivola MM, Revetta RP, Santo Domingo JW. Identification of active bacterial communities in a model drinking water biofilm system using 16S rRNA-based clone libraries. FEMS Microbiol Lett 2006; 257:182-8; PMID:16553851; http://dx.doi.org/10.1111/j.1574-6968.2006.00167.x
33. Hamady M, Walker JJ, Harris JK, Gold NJ, Knight R. Error-correcting barcoded primers for pyrosequencing hundreds of samples in multiplex. Nat Methods 2008; 5:235-7; PMID:18264105; http://dx.doi.org/10.1038/nmeth.1184
34. Pruesse E, Quast C, Knittel K, Fuchs BM, Ludwig W, Peplies J, Glöckner FO. SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res 2007; 35:7188-96; PMID:17947321; http://dx.doi.org/10.1093/nar/gkm864
35. Wang Q, Garrity GM, Tiedje JM, Cole JR. Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol 2007; 73:5261-7; PMID:17586664; http://dx.doi.org/10.1128/AEM.00062-07
36. Magurran AE. Chapter four: An index of diversity. In: Measuring biological diversity. Malden, MA: Blackwell Publishing; 2004: 100-130.