Development of the Preterm Gut Microbiome in Twins at Risk of Necrotising Enterocolitis and Sepsis

PLoS ONE

Volumn 8, Issue 8, 2013, Pages

  Stewart, Christopher J ^a   Marrs, Emma C L ^b   Nelson, Andrew ^a   Lanyon, Clare ^a   Perry, John D ^b   Embleton, Nicholas D ^c   Cummings, Stephen P ^b   Berrington, Janet E ^c  

^a NORTHUMBRIA UNIVERSITY   (United Kingdom)

^b FREEMAN HOSPITAL   (United Kingdom)

^c ROYAL VICTORIA INFIRMARY   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ANTIBIOTIC THERAPY; ARTICLE; BIRTH; BREAST MILK MICROBIOME; CLINICAL ARTICLE; COMMUNITY STRUCTURE; DENATURING GRADIENT GEL ELECTROPHORESIS; DRUG EXPOSURE; ENTEROBACTERIACEAE; ENTEROCOCCACEAE; ENVIRONMENTAL FACTOR; ESCHERICHIA; EXPOSURE; FECES ANALYSIS; FEEDING; FEMALE; HEREDITY; HOST; HUMAN; HUMAN TRIPLETS; INFECTION RISK; INTESTINE FLORA; LONGITUDINAL STUDY; MALE; MICROBIAL COMMUNITY; MICROBIOME; NECROTIZING ENTEROCOLITIS; NEWBORN; NEWBORN INTENSIVE CARE; NEWBORN SEPSIS; PATHOGENESIS; POLYMERASE CHAIN REACTION; PREMATURITY; PYROSEQUENCING; SIBLING; STAPHYLOCOCCACEAE; TWINS;

BACTERIA; DEMOGRAPHY; ENTEROCOLITIS, NECROTIZING; FECES; FEMALE; GASTROINTESTINAL TRACT; HUMANS; INFANT, NEWBORN; MALE; MICROBIOTA; MILK, HUMAN; PREMATURE BIRTH; RISK FACTORS; SEPSIS; TWINS;

EID: 84883362657     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0073465     Document Type: Article

References (41)

1. Sekirov I, Russell SL, Antunes LC, Finlay BB, (2010) Gut microbiota in health and disease. Physiol Rev 90: 859-904. doi:10.1152/physrev.00045.2009. PubMed: 20664075.
2. Palmer C, Bik EM, DiGiulio DB, Relman DA, Brown PO, (2007) Development of the human infant intestinal microbiota. PLOS Biol 5: 1556-1573. PubMed: 17594176.
3. Stewart JA, Chadwick VS, Murray A, (2005) Investigations into the influence of host genetics on the predominant eubacteria in the faecal microflora of children. J Med Microbiol 54: 1239-1242. doi:10.1099/jmm.0.46189-0. PubMed: 16278440.
4. Zoetendal E, Akkermans A, Akkermans-van Vliet W, Visser J, Vos W, (2001) The host genotype affects the bacterial community in the human gastronintestinal tract. Microb Ecol Health Dis 13: 129-134. doi:10.1080/089106001750462669.
5. Berrington J, Stewart C, Embleton N, Cummings S, (2012) Gut microbiota in preterm infants: assessment and relevance to health and disease. Arch Dis Child Fetal Neonatal Ed. Available: http://fn.bmj.com/content/early/2012/09/24/archdischild-2012-302134.short. Accessed 2013 February 27.
6. Mai V, Young CM, Ukhanova M, Wang X, Sun Y, et al. (2011) Fecal microbiota in premature infants prior to necrotizing enterocolitis. PLOS ONE 6: e20647. doi:10.1371/journal.pone.0020647. PubMed: 21674011.
7. Stewart CJ, Marrs EC, Magorrian S, Nelson A, Lanyon C, et al. (2012) The preterm gut microbiota: changes associated with necrotizing enterocolitis and infection. Acta Paediatr 101: 1121-1127. doi:10.1111/j.1651-2227.2012.02801.x. PubMed: 22845166.
8. Wang Y, Hoenig JD, Malin KJ, Qamar S, Petrof EO, et al. (2009) 16S rRNA gene-based analysis of fecal microbiota from preterm infants with and without necrotizing enterocolitis. ISME J 3: 944-954. doi:10.1038/ismej.2009.37. PubMed: 19369970.
9. Martín R, Langa S, Reviriego C, Jimínez E, Marín ML, et al. (2003) Human milk is a source of lactic acid bacteria for the infant gut. J Pediatr 143: 754-758. Available: http://www.ncbi.nlm.nih.gov/pubmed/14657823. doi:10.1016/j.jpeds.2003.09.028. PubMed: 14657823.
10. Martín R, Jiménez E, Heilig H, Fernández L, Marín ML, et al. (2009) Isolation of bifidobacteria from breast milk and assessment of the bifidobacterial population by PCR-denaturing gradient gel electrophoresis and quantitative real-time PCR. Appl Environ Microbiol 75: 965-969. doi:10.1128/AEM.02063-08. PubMed: 19088308.
11. Muyzer G, De Waal EC, Uitterlinden AG, (1993) Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl Environ Microbiol 59: 695-700. PubMed: 7683183.
12. Baxter J, Cummings SP, (2006) The current and future applications of microorganism in the bioremediation of cyanide contamination. Antonie Van Leeuwenhoek 90: 1-17. doi:10.1007/s10482-006-9057-y. PubMed: 16683094.
13. Stewart CJ, Nelson A, Scribbins D, Marrs EC, Lanyon C, et al. (2013) Bacterial and fungal viability in the preterm gut: NEC and sepsis. Arch Dis Child Fetal Neonatal Ed, 98: F298-303. PubMed: 23426613.
14. Sim K, Cox MJ, Wopereis H, Martin R, Knol J, et al. (2012) Improved Detection of Bifidobacteria with Optimised 16S rRNA-Gene Based Pyrosequencing. PLOS ONE 7: e32543. doi:10.1371/journal.pone.0032543. PubMed: 22470420.
15. Dowd SE, Sun Y, Secor PR, Rhoads DD, (2008) Survey of bacterial diversity in chronic wounds using pyrosequencing, DGGE, and full ribosome shotgun sequencing. BMC Microbiol 8: 43. doi:10.1186/1471-2180-8-43. PubMed: 18325110.
16. Caporaso JG, Kuczynski J, Stombaugh J, (2010) QIIME allows analysis of high-throughput community sequencing data. Nature 7: 335-336. PubMed: 20383131.
17. Edgar RC, (2010) Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26: 2460-2461. doi:10.1093/bioinformatics/btq461. PubMed: 20709691.
18. Caporaso JG, Bittinger K, (2010) PyNAST: a flexible tool for aligning sequences to a template alignment. Bioinformatics 26: 266-267. doi:10.1093/bioinformatics/btp636. PubMed: 19914921.
19. Wang Q, Garrity GM, Tiedje JM, Cole JR, (2007) Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol 73: 5261-5267. doi:10.1128/AEM.00062-07. PubMed: 17586664.
20. Haas BJ, Gevers D, Earl AM, (2011) Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons. Genome Res 21: 494-504. doi:10.1101/gr.112730.110. PubMed: 21212162.
21. Price MN, Dehal PS, Arkin AP, (2010) FastTree 2-approximately maximum-likelihood trees for large alignments. PLOS ONE 5: e9490. doi:10.1371/journal.pone.0009490. PubMed: 20224823.
22. Eriksson L, Johansson E, Kettaneh-Wold N, (2006) Multi- and Megavariate Data Analysis, Part 2, Advanced Applications and Method Extensions. MKS Umetrics AB.
23. Hammer Ø, Harper D, (2001) PAST: Paleontological statistics software package for education and data analysis. Palaeo Electronica 4: 1-9.
24. Hamady M, Lozupone C, Knight R, (2009) Fast UniFrac: facilitating high-throughput phylogenetic analyses of microbial communities including analysis of pyrosequencing and PhyloChip data. ISME J 4: 17-27. PubMed: 19710709.
25. Martin AP, (2002) Phylogenetic approaches for describing and comparing the diversity of microbial communities. Appl Environ Microbiol 68: 3673-3682. doi:10.1128/AEM.68.8.3673-3682.2002. PubMed: 12147459.
26. Hamady M, Lozupone C, Knight R, (2009) Fast UniFrac: facilitating high-throughput phylogenetic analyses of microbial communities including analysis of pyrosequencing and PhyloChip data. ISME J 4: 17-27. PubMed: 19710709.
27. Ley RE, Bäckhed F, Turnbaugh P, Lozupone CA, Knight RD, et al. (2005) Obesity alters gut microbial ecology. Proc Natl Acad Sci U S A 102: 11070-11075. doi:10.1073/pnas.0504978102. PubMed: 16033867.
28. Mshvildadze M, Neu J, Shuster J, Theriaque D, Li N, et al. (2010) Intestinal microbial ecology in premature infants assessed with non-culture-based techniques. J Pediatr 156: 20-25. doi:10.1016/j.jpeds.2009.06.063. PubMed: 19783002.
29. Collado MC, Delgado S, Maldonado A, Rodríguez JM, (2009) Assessment of the bacterial diversity of breast milk of healthy women by quantitative real-time PCR. Lett Appl Microbiol 48: 523-528. doi:10.1111/j.1472-765X.2009.02567.x. PubMed: 19228290.
30. Hunt KM, Foster JA, Forney LJ, Schütte UME, Beck DL, et al. (2011) Characterization of the diversity and temporal stability of bacterial communities in human milk. PLOS ONE 6: e21313. doi:10.1371/journal.pone.0021313. PubMed: 21695057.
31. Penders J, Thijs C, Vink C, Stelma FF, Snijders B, et al. (2006) Factors influencing the composition of the intestinal microbiota in early infancy. Pediatrics 118: 511-521. doi:10.1542/peds.2005-2824. PubMed: 16882802.
32. Cogen AL, Nizet V, Gallo RL, (2008) Skin microbiota: a source of disease or defence? Br J Dermatol 158: 442-455. doi:10.1111/j.1365-2133.2008.08437.x. PubMed: 18275522.
33. Madan JC, Salari RC, Saxena D, Davidson L, O'Toole GA, et al. (2012) Gut microbial colonisation in premature neonates predicts neonatal sepsis. Arch Dis Child Fetal Neonatal Ed 97: pp. F456-F462. PubMed: 22562869.
34. Lepage P, Häsler R, Spehlmann ME, Rehman A, Zvirbliene A, et al. (2011) Twin study indicates loss of interaction between microbiota and mucosa of patients with ulcerative colitis. Gastroenterology 141: 227-236. doi:10.1053/j.gastro.2011.04.011. PubMed: 21621540.
35. Gophna U, Sommerfeld K, Gophna S, Doolittle WF, Veldhuyzen van Zanten SJO, (2006) Differences between tissue-associated intestinal microfloras of patients with Crohn's disease and ulcerative colitis. J Clin Microbiol 44: 4136-4141. doi:10.1128/JCM.01004-06. PubMed: 16988016.
36. Darfeuille-Michaud A, Boudeau J, Bulois P, Neut C, Glasser AL, et al. (2004) High prevalence of adherent-invasive Escherichia coli associated with ileal mucosa in Crohn's disease. Gastroenterology 127: 412-421. doi:10.1053/j.gastro.2004.04.061. PubMed: 15300573.
37. Sasaki M, Sitaraman SV, Babbin BA, Gerner-Smidt P, Ribot EM, et al. (2007) Invasive Escherichia coli are a feature of Crohn's disease. Lab Invest 87: 1042-1054. doi:10.1038/labinvest.3700661. PubMed: 17660846.
38. Kaper JB, Nataro JP, Mobley HL, (2004) Pathogenic Escherichia coli. Nat Rev Microbiol 2: 123-140. doi:10.1038/nrmicro818. PubMed: 15040260.
39. Eckburg PB, Bik EM, Bernstein CN, Purdom E, Dethlefsen L, et al. (2005) Diversity of the human intestinal microbial flora. Science 308: 1635-1638. doi:10.1126/science.1110591. PubMed: 15831718.
40. Embleton ND, Yates R, (2008) Probiotics and other preventative strategies for necrotising enterocolitis. Semin Fetal Neonatal Med 13: 35-43. doi:10.1016/j.siny.2007.09.003. PubMed: 17974513.
41. Simões CD, Maukonen J, (2013) Habitual Dietary Intake Is Associated with Stool Microbiota Composition in Monozygotic Twins. J Nutr, 143: 417-23. doi:10.3945/jn.112.166322. PubMed: 23343669. PubMed: 23343669.