Intestinal dysbiosis in preterm infants preceding necrotizing enterocolitis: a systematic review and meta-analysis
Mohan Pammi, Julia Cope, Phillip I Tarr, Barbara B Warner, Ardythe L Morrow, Volker Mai, Katherine E Gregory, J Simon Kroll, Valerie McMurtry, Michael J Ferris, Lars Engstrand, Helene Engstrand Lilja, Emily B Hollister, James Versalovic, Josef Neu, Mohan Pammi, Julia Cope, Phillip I Tarr, Barbara B Warner, Ardythe L Morrow, Volker Mai, Katherine E Gregory, J Simon Kroll, Valerie McMurtry, Michael J Ferris, Lars Engstrand, Helene Engstrand Lilja, Emily B Hollister, James Versalovic, Josef Neu
Abstract
Background: Necrotizing enterocolitis (NEC) is a catastrophic disease of preterm infants, and microbial dysbiosis has been implicated in its pathogenesis. Studies evaluating the microbiome in NEC and preterm infants lack power and have reported inconsistent results.
Methods and results: Our objectives were to perform a systematic review and meta-analyses of stool microbiome profiles in preterm infants to discern and describe microbial dysbiosis prior to the onset of NEC and to explore heterogeneity among studies. We searched MEDLINE, PubMed, CINAHL, and conference abstracts from the proceedings of Pediatric Academic Societies and reference lists of relevant identified articles in April 2016. Studies comparing the intestinal microbiome in preterm infants who developed NEC to those of controls, using culture-independent molecular techniques and reported α and β-diversity metrics, and microbial profiles were included. In addition, 16S ribosomal ribonucleic acid (rRNA) sequence data with clinical meta-data were requested from the authors of included studies or searched in public data repositories. We reprocessed the 16S rRNA sequence data through a uniform analysis pipeline, which were then synthesized by meta-analysis. We included 14 studies in this review, and data from eight studies were available for quantitative synthesis (106 NEC cases, 278 controls, 2944 samples). The age of NEC onset was at a mean ± SD of 30.1 ± 2.4 weeks post-conception (n = 61). Fecal microbiome from preterm infants with NEC had increased relative abundances of Proteobacteria and decreased relative abundances of Firmicutes and Bacteroidetes prior to NEC onset. Alpha- or beta-diversity indices in preterm infants with NEC were not consistently different from controls, but we found differences in taxonomic profiles related to antibiotic exposure, formula feeding, and mode of delivery. Exploring heterogeneity revealed differences in microbial profiles by study and the target region of the 16S rRNA gene (V1-V3 or V3-V5).
Conclusions: Microbial dysbiosis preceding NEC in preterm infants is characterized by increased relative abundances of Proteobacteria and decreased relative abundances of Firmicutes and Bacteroidetes. Microbiome optimization may provide a novel strategy for preventing NEC.
Keywords: 16S rRNA sequencing; Intestinal; Microbiome; NEC; Neonate; Preterm.
Figures
References
- Neu J, Walker WA. Necrotizing enterocolitis. N Engl J Med. 2011;364:255–264. doi: 10.1056/NEJMra1005408.
- Lin PW, Stoll BJ. Necrotising enterocolitis. Lancet. 2006;368:1271–1283. doi: 10.1016/S0140-6736(06)69525-1.
- Fanaroff AA, Stoll BJ, Wright LL, Carlo WA, Ehrenkranz RA, Stark AR, Bauer CR, Donovan EF, Korones SB, Laptook AR, et al. Trends in neonatal morbidity and mortality for very low birthweight infants. Am J Obstet Gynecol. 2007;196:147. doi: 10.1016/j.ajog.2006.09.014.
- Lemons JA, Bauer CR, Oh W, Korones SB, Papile LA, Stoll BJ, Verter J, Temprosa M, Wright LL, Ehrenkranz RA, et al. Very low birth weight outcomes of the National Institute of Child health and human development neonatal research network, January 1995 through December 1996. NICHD Neonatal Research Network. Pediatrics. 2001;107:E1. doi: 10.1542/peds.107.1.e1.
- Holman RC, Stoll BJ, Curns AT, Yorita KL, Steiner CA, Schonberger LB. Necrotising enterocolitis hospitalisations among neonates in the United States. Paediatr Perinat Epidemiol. 2006;20:498–506. doi: 10.1111/j.1365-3016.2006.00756.x.
- Stoll BJ, Hansen NI, Adams-Chapman I, Fanaroff AA, Hintz SR, Vohr B, Higgins RD. Neurodevelopmental and growth impairment among extremely low-birth-weight infants with neonatal infection. JAMA. 2004;292:2357–2365. doi: 10.1001/jama.292.19.2357.
- Claud EC, Walker WA. Bacterial colonization, probiotics, and necrotizing enterocolitis. J Clin Gastroenterol. 2008;42(Suppl 2):S46–52. doi: 10.1097/MCG.0b013e31815a57a8.
- 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. doi: 10.1073/pnas.97.11.6043.
- Nanthakumar N, Meng D, Goldstein AM, Zhu W, Lu L, Uauy R, Llanos A, Claud EC, Walker WA. The mechanism of excessive intestinal inflammation in necrotizing enterocolitis: an immature innate immune response. PLoS One. 2011;6:e17776. doi: 10.1371/journal.pone.0017776.
- Carlisle EM, Morowitz MJ. The intestinal microbiome and necrotizing enterocolitis. Curr Opin Pediatr. 2013;25:382–387. doi: 10.1097/MOP.0b013e3283600e91.
- 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;3:944–954. doi: 10.1038/ismej.2009.37.
- Afrazi A, Sodhi CP, Richardson W, Neal M, Good M, Siggers R, Hackam DJ. New insights into the pathogenesis and treatment of necrotizing enterocolitis: toll-like receptors and beyond. Pediatr Res. 2011;69:183–188. doi: 10.1203/PDR.0b013e3182093280.
- Musemeche CA, Kosloske AM, Bartow SA, Umland ET. Comparative effects of ischemia, bacteria, and substrate on the pathogenesis of intestinal necrosis. J Pediatr Surg. 1986;21:536–538. doi: 10.1016/S0022-3468(86)80228-7.
- Cotten CM, Taylor S, Stoll B, Goldberg RN, Hansen NI, Sanchez PJ, Ambalavanan N, Benjamin DK., Jr 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. doi: 10.1542/peds.2007-3423.
- Alexander VN, Northrup V, Bizzarro MJ. Antibiotic exposure in the newborn intensive care unit and the risk of necrotizing enterocolitis. J Pediatr. 2011;159:392–397. doi: 10.1016/j.jpeds.2011.02.035.
- Morowitz MJ, Poroyko V, Caplan M, Alverdy J, Liu DC. Redefining the role of intestinal microbes in the pathogenesis of necrotizing enterocolitis. Pediatrics. 2010;125:777–785. doi: 10.1542/peds.2009-3149.
- Sodhi CP, Neal MD, Siggers R, Sho S, Ma C, Branca MF, Prindle T, Jr, Russo AM, Afrazi A, Good M, et al. Intestinal epithelial toll-like receptor 4 regulates goblet cell development and is required for necrotizing enterocolitis in mice. Gastroenterology. 2012;143:708–718. doi: 10.1053/j.gastro.2012.05.053.
- Lu P, Sodhi CP, Hackam DJ. Toll-like receptor regulation of intestinal development and inflammation in the pathogenesis of necrotizing enterocolitis. Pathophysiology. 2014;21:81–93. doi: 10.1016/j.pathophys.2013.11.007.
- Gevers D, Knight R, Petrosino JF, Huang K, McGuire AL, Birren BW, Nelson KE, White O, Methe BA, Huttenhower C. The Human Microbiome Project: a community resource for the healthy human microbiome. PLoS Biol. 2012;10:e1001377. doi: 10.1371/journal.pbio.1001377.
- Human Microbiome Project C Structure, function and diversity of the healthy human microbiome. Nature. 2012;486:207–214. doi: 10.1038/nature11234.
- Sze MA, Schloss PD. Looking for a signal in the noise: revisiting obesity and the microbiome. mBio. 2016;7(4):e01018–16. doi:10.1128/mBio.01018-16.
- Bell MJ, Ternberg JL, Feigin RD, Keating JP, Marshall R, Barton L, Brotherton T. Neonatal necrotizing enterocolitis, therapeutic decisions based upon clinical staging. Ann Surg. 1978;187:1–7. doi: 10.1097/00000658-197801000-00001.
- Moher D, Liberati A, Tetzlaff J, Altman DG, Group P. Preferred reporting items for systematic reviews and meta-analyses: the PRISMA statement. BMJ. 2009;339:b2535. doi: 10.1136/bmj.b2535.
- Stroup DF, Berlin JA, Morton SC, Olkin I, Williamson GD, Rennie D, Moher D, Becker BJ, Sipe TA, Thacker SB. Meta-analysis of observational studies in epidemiology: a proposal for reporting. Meta-analysis of observational studies in epidemiology (MOOSE) group. JAMA. 2000;283:2008–2012. doi: 10.1001/jama.283.15.2008.
- Lozupone CA, Stombaugh J, Gonzalez A, Ackermann G, Wendel D, Vazquez-Baeza Y, Jansson JK, Gordon JI, Knight R. Meta-analyses of studies of the human microbiota. Genome Res. 2013;23:1704–1714. doi: 10.1101/gr.151803.112.
- Viswanathan M, Berkman ND, Dryden DM, Hartling L. Assessing Risk of Bias and Confounding in Observational Studies of Interventions or Exposures: Further Development of the RTI Item Bank. Methods Research Report. (Prepared by RTI–UNC Evidence-based Practice Center under Contract No. 290-2007-10056-I). AHRQ Publication No. 13-EHC106-EF. Rockville: Agency for Healthcare Research and Quality; 2013. . Accessed 27 June 2015.
- Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N, Pena AG, Goodrich JK, Gordon JI, et al. QIIME allows analysis of high-throughput community sequencing data. Nat Methods. 2010;7:335–336. doi: 10.1038/nmeth.f.303.
- McDonald D, Price MN, Goodrich J, Nawrocki EP, DeSantis TZ, Probst A, Andersen GL, Knight R, Hugenholtz P. An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea. ISME J. 2012;6:610–618. doi: 10.1038/ismej.2011.139.
- Edgar RC. Search and clustering orders of magnitude faster than BLAST. Bioinformatics. 2010;26:2460–2461. doi: 10.1093/bioinformatics/btq461.
- 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;156:20–25. doi: 10.1016/j.jpeds.2009.06.063.
- Mai V, Young CM, Ukhanova M, Wang X, Sun Y, Casella G, Theriaque D, Li N, Sharma R, Hudak M, Neu J. Fecal microbiota in premature infants prior to necrotizing enterocolitis. PLoS One. 2011;6:e20647. doi: 10.1371/journal.pone.0020647.
- McMurtry VE, Gupta RW, Tran L, Blanchard EE, Penn D, Taylor CM, Ferris MJ. Bacterial diversity and Clostridia abundance decrease with increasing severity of necrotizing enterocolitis. Microbiome. 2015;3:11. doi: 10.1186/s40168-015-0075-8.
- 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. doi: 10.1186/2049-2618-1-13.
- Normann E, Fahlen A, Engstrand L, Lilja HE. Intestinal microbial profiles in extremely preterm infants with and without necrotizing enterocolitis. Acta Paediatr. 2013;102:129–136. doi: 10.1111/apa.12059.
- Sim K, Shaw AG, Randell P, Cox MJ, McClure ZE, Li MS, Haddad M, Langford PR, Cookson WO, Moffatt MF, Kroll JS. Dysbiosis anticipating necrotizing enterocolitis in very premature infants. Clin Infect Dis. 2015;60:389–397. doi: 10.1093/cid/ciu822.
- 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. doi: 10.1371/journal.pone.0083304.
- Zhou Y, Shan G, Sodergren E, Weinstock G, Walker WA, Gregory KE. Longitudinal analysis of the premature infant intestinal microbiome prior to necrotizing enterocolitis: a case-control study. PLoS One. 2015;10:e0118632. doi: 10.1371/journal.pone.0118632.
- Warner BB, Deych E, Zhou Y, Hall-Moore C, Weinstock GM, Sodergren E, Shaikh N, Hoffmann JA, Linneman LA, Hamvas A, et al. Gut bacteria dysbiosis and necrotising enterocolitis in very low birthweight infants: a prospective case–control study. Lancet. 2016;387(10031):1928–36.
- 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. doi: 10.1203/01.PDR.0000134251.45878.D5.
- Stewart CJ, Marrs EC, 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;101:1121–1127. doi: 10.1111/j.1651-2227.2012.02801.x.
- Yee WH, Soraisham AS, Shah VS, Aziz K, Yoon W, Lee SK. Incidence and timing of presentation of necrotizing enterocolitis in preterm infants. Pediatrics. 2012;129:e298–304. doi: 10.1542/peds.2011-2022.
- Gonzalez-Rivera R, Culverhouse RC, Hamvas A, Tarr PI, Warner BB. The age of necrotizing enterocolitis onset: an application of Sartwell’s incubation period model. J Perinatol. 2011;31:519–523. doi: 10.1038/jp.2010.193.
- Llanos AR, Moss ME, Pinzon MC, Dye T, Sinkin RA, Kendig JW. Epidemiology of neonatal necrotising enterocolitis: a population-based study. Paediatr Perinat Epidemiol. 2002;16:342–349. doi: 10.1046/j.1365-3016.2002.00445.x.
- La Rosa PS, Warner BB, Zhou Y, Weinstock GM, Sodergren E, Hall-Moore CM, Stevens HJ, Bennett WE, Jr, Shaikh N, Linneman LA, et al. Patterned progression of bacterial populations in the premature infant gut. Proc Natl Acad Sci U S A. 2014;111:12522–12527. doi: 10.1073/pnas.1409497111.
- Sodhi C, Richardson W, Gribar S, Hackam DJ. The development of animal models for the study of necrotizing enterocolitis. Dis Model Mech. 2008;1:94–98. doi: 10.1242/dmm.000315.
- Sodhi CP, Shi XH, Richardson WM, Grant ZS, Shapiro RA, Prindle T, Jr, Branca M, Russo A, Gribar SC, Ma C, Hackam DJ. Toll-like receptor-4 inhibits enterocyte proliferation via impaired beta-catenin signaling in necrotizing enterocolitis. Gastroenterology. 2010;138:185–196. doi: 10.1053/j.gastro.2009.09.045.
- Jilling T, Simon D, Lu J, Meng FJ, Li D, Schy R, Thomson RB, Soliman A, Arditi M, Caplan MS. The roles of bacteria and TLR4 in rat and murine models of necrotizing enterocolitis. J Immunol. 2006;177:3273–3282. doi: 10.4049/jimmunol.177.5.3273.
- Ward DV, Scholz M, Zolfo M, Taft DH, Schibler KR, Tett A, Segata N, Morrow AL. Metagenomic sequencing with strain-level resolution implicates uropathogenic E. coli in necrotizing enterocolitis and mortality in preterm infants. Cell Rep. 2016;14:2912–2924. doi: 10.1016/j.celrep.2016.03.015.
- Morowitz MJ, Denef VJ, Costello EK, Thomas BC, Poroyko V, Relman DA, Banfield JF. Strain-resolved community genomic analysis of gut microbial colonization in a premature infant. Proc Natl Acad Sci U S A. 2011;108:1128–1133. doi: 10.1073/pnas.1010992108.
- Zeissig S, Blumberg RS. Life at the beginning: perturbation of the microbiota by antibiotics in early life and its role in health and disease. Nat Immunol. 2014;15:307–310. doi: 10.1038/ni.2847.
- Gibson MK, Wang B, Ahmadi S, Burnham CA, Tarr PI, Warner BB, Dantas G. Developmental dynamics of the preterm infant gut microbiota and antibiotic resistome. Nat Microbiol. 2016;1:16024. doi: 10.1038/nmicrobiol.2016.24.
- Barb JJ, Oler AJ, Kim HS, Chalmers N, Wallen GR, Cashion A, Munson PJ, Ames NJ. Development of an analysis pipeline characterizing multiple hypervariable regions of 16S rRNA using mock samples. PLoS One. 2016;11:e0148047. doi: 10.1371/journal.pone.0148047.
- Zheng W, Tsompana M, Ruscitto A, Sharma A, Genco R, Sun Y, Buck MJ. An accurate and efficient experimental approach for characterization of the complex oral microbiota. Microbiome. 2015;3:48. doi: 10.1186/s40168-015-0110-9.
- Kumar PS, Brooker MR, Dowd SE, Camerlengo T. Target region selection is a critical determinant of community fingerprints generated by 16S pyrosequencing. PLoS One. 2011;6:e20956. doi: 10.1371/journal.pone.0020956.
- Taft DH, Ambalavanan N, Schibler KR, Yu Z, Newburg DS, Ward DV, Morrow AL. Intestinal microbiota of preterm infants differ over time and between hospitals. Microbiome. 2014;2:36. doi: 10.1186/2049-2618-2-36.
- Torrazza RM, Neu J. The altered gut microbiome and necrotizing enterocolitis. Clin Perinatol. 2013;40:93–108. doi: 10.1016/j.clp.2012.12.009.
- Schwiertz A, Gruhl B, Lobnitz 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;54:393–399. doi: 10.1203/01.PDR.0000078274.74607.7A.
- Bjorkstrom MV, Hall L, Soderlund S, Hakansson EG, Hakansson S, Domellof M. Intestinal flora in very low-birth weight infants. Acta Paediatr. 2009;98:1762–1767. doi: 10.1111/j.1651-2227.2009.01471.x.
- Latuga MS, Stuebe A, Seed PC. A review of the source and function of microbiota in breast milk. Semin Reprod Med. 2014;32:68–73. doi: 10.1055/s-0033-1361824.
- Sharon I, Morowitz MJ, Thomas BC, Costello EK, Relman DA, Banfield JF. Time series community genomics analysis reveals rapid shifts in bacterial species, strains, and phage during infant gut colonization. Genome Res. 2013;23:111–120. doi: 10.1101/gr.142315.112.
- Grishin A, Papillon S, Bell B, Wang J, Ford HR. The role of the intestinal microbiota in the pathogenesis of necrotizing enterocolitis. Semin Pediatr Surg. 2013;22:69–75. doi: 10.1053/j.sempedsurg.2013.01.002.
- Raveh-Sadka T, Thomas BC, Singh A, Firek B, Brooks B, Castelle CJ, Sharon I, Baker R, Good M, Morowitz MJ, Banfield JF. Gut bacteria are rarely shared by co-hospitalized premature infants, regardless of necrotizing enterocolitis development. Elife. 2015; 4.
- 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(10):2506–10.
- Smith B, Bodé S, Skov TH, Mirsepasi H, Greisen G, Krogfelt KA. Investigation of the early intestinal microflora in premature infants with/without necrotizing enterocolitis using two different methods. Pediatr Res. 2012;71(1):115–20.
Source: PubMed