The neonatal bowel microbiome in health and infection

Current Opinion in Infectious Diseases

Volumn 27, Issue 3, 2014, Pages 236-243

  Berrington, Janet E ^a   Stewart, Christopher J ^b   Cummings, Stephen P ^b   Embleton, Nicholas D ^a  

^a NEWCASTLE UNIVERSITY   (United Kingdom)

^b NORTHUMBRIA UNIVERSITY   (United Kingdom)

Author keywords

health; infection; microbiome; necrotizing enterocolitis; neonatal

Indexed keywords

ARCHAEON; CAUSE OF DEATH; CLINICAL PRACTICE; DISEASE PREDISPOSITION; DYSBIOSIS; FIRMICUTES; HEALTH STATUS; HUMAN; IMMUNITY; IMMUNOMODULATION; INFECTION; INFORMATION PROCESSING; INTESTINE FLORA; MICROBIAL COMMUNITY; MICROBIOME; MOLECULAR GENETICS; MORBIDITY; NECROTIZING ENTEROCOLITIS; NEWBORN SEPSIS; NONHUMAN; OUTCOME ASSESSMENT; PREMATURITY; PROTEOBACTERIA; REVIEW; SEQUENCE ANALYSIS; VIRUS; BACTEREMIA; ENTEROCOLITIS, NECROTIZING; FECES; GASTROINTESTINAL TRACT; HOST PATHOGEN INTERACTION; IMMUNOLOGY; MICROBIOLOGY; MICROFLORA; NEWBORN; SEPSIS;

PROBIOTIC AGENT;

BACTEREMIA; ENTEROCOLITIS, NECROTIZING; FECES; GASTROINTESTINAL TRACT; HOST-PATHOGEN INTERACTIONS; HUMANS; INFANT, NEWBORN; MICROBIOTA; PROBIOTICS; SEPSIS;

EID: 84900518093     PISSN: 09517375     EISSN: 14736527     Source Type: Journal    
DOI: 10.1097/QCO.0000000000000061     Document Type: Review

References (57)

1. Kinross JM, Darzi AW, Nicholson JK. Gut microbiome-host interactions in health and disease. Genome Med 2011; 3:14.
2. Wardwell LH, Huttenhower C, Garrett WS. Current concepts of the intestinal microbiota and the pathogenesis of infection. Curr Infect Dis Rep 2011; 13:28-34.
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. Eggesbø M, Moen B, Peddada S, et al. Development of gut microbiota in infants not exposed to medical interventions. Acta Pathol Microbiol Immunol Scand 2011; 119:17-35.
5. Dominguez-Bello MG, Blaser MJ, Ley RE, et al. Development of the human gastrointestinal microbiota and insights from high-throughput sequencing. Gastroenterology 2011; 140:1713-1719.
6. Berrington JE, Hearn RI, Bythell M, et al. Deaths in preterm infants: changing pathology over 2 decades. J Pediatr 2012; 160:49-53.
7. Lauber CL, Zhou N, Gordon JI, et al. Effect of storage conditions on the assessment of bacterial community structure in soil and human-associated samples. FEMS Microbiol Lett 2010; 307:80-86.
8. Loman NJ, Misra RV, Dallman TJ, et al. Performance comparison of benchtop high-throughput sequencing platforms. Nature Biotechnol 2012; 30:434-439.
9. Amend SA, Seifert KA, Bruns TD. Quantifying microbial communities with 454 pyrosequencing: does read abundance count? Mol Ecol 2010; 19:5555-5556.
10. Mussap M, Noto A, Cibecchini F, Fanos V. The importance of biomarkers in neonatology. Semin Fetal Neonatal Med 2013; 18:56-64.
11. Mardis ER. The $1, 000 genome, the $100, 000 analysis? Genome Med 2010; 2:84.
12. Rushton SP, Shirley MDF, Sheridan EA, et al. The transmission of nosocomial pathogens in an intensive care unit: a space-time clustering and structural equation modelling approach. Epidemiol Infect 2010; 138:915-926.
13. Langille MGI, Zaneveld J, Caporaso JG, et al. Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences. Nature Biotechnol 2013; 31:814-821.
14. Round JL, Mazmanian SK. The gut microbiota shapes intestinal immune responses during health and disease. Nat Rev Immunol 2009; 9:313-323.
15. Kamada N, Kim YG, Sham HP, et al. Regulated virulence controls the ability of a pathogen to compete with the gut microbiota. Science 2012; 336:1325-1329.
16. Fukuda S, Toh H, Hase K, et al. Bifidobacteria can protect from enteropatho-genic infection through production of acetate. Nature 2011; 469:543-547.
17. McElroy SJ, Underwood MA, Sherman MP. Paneth cells and necrotizing enterocolitis: a novel hypothesis for disease pathogenesis. Neonatology 2013; 103:10-20.
18. Vaishnava S, Yamamoto M, Severson KM, et al. The antibacterial lectin RegIIIgamma promotes the spatial segregation of microbiota and host in the intestine. Science (New York) 2011; 334:255-258.
19. Tourner E, Chassin C. Neonatal immune adaptation of the gut and its role during infections. Clin Dev Immunol 2013; 2013:270301.
20. Lopez P, Gonzalez-Rodríguez I, Gueimonde M, et al. Immune response to Bifidobacterium bifidum strains support Treg/Th17 plasticity. PloS one 2011; 6:e24776.
21. Round JL, Lee SM, Li J, et al. The Toll-like receptor 2 pathway establishes colonization by a commensal of the human microbiota. Science 2011; 332:974-977.
22. Furusawa Y, Obata Y, Fukuda S, et al. Commensal microbe-derived butyrate induces the differentiation of colonic regulatory T cells. Nature 2013; 504:446-450.
23. Arpaia N, Campbell C, Fan X, et al. Metabolites produced by commensal bacteria promote peripheral regulatory T-cell generation. Nature 2013;504:451-455.
24. Echarri PP, Graciá CM, Berruezo GR, et al. Assessment of intestinal micro-biota of full-term breast-fed infants from two different geographical locations. Early Hum Dev 2011; 87:511-513.
25. Palmer C, Bik EM, DiGiulio DB, et al. Development of the human infant intestinal microbiota. PLoS Biol 2007; 5:1556-1573.
26. White R, Bjørnholt JV, Baird DD, et al. Novel developmental analyses identify longitudinal patterns of early gut microbiota that affect infant growth. PLoS Comput Biol 2013; 9:e1003042.
27. Musso G, Gambino R, Cassader M. Obesity, diabetes, and gut microbiota: the hygiene hypothesis expanded? Diabetes Care 2010; 33:2277-2284.
28. Trosvik P, Stenseth NC, Rudi K. Convergent temporal dynamics of the human infant gut microbiota. ISME J 2010; 4:151-158.
29. Arboleya S, Ruas-Madiedo P, Margolles A, et al. Characterization and in vitro properties of potentially probiotic Bifidobacterium strains isolated from breast-milk. Int J Food Microbiol 2011; 149:28-36.
30. Arboleya S, González S, Salazar N, et al. Development of probiotic products for nutritional requirements of specific human populations. Eng Life Sci 2012; 12:368-376.
31. Westerbeek EAM, Van den Berg A, Lafeber HN, et al. The intestinal bacterial colonisation in preterm infants: a review of the literature. Clin Nutr 2006; 25:361-368.
32. Arboleya S, Binetti A, Salazar N, et al. Establishment and development of intestinal microbiota in preterm neonates. FEMS Microbiol Ecol 2012; 79:763-772.
33. Stewart C, Marrs E, Magorrian S, et al. The preterm gut microbiota: changes associated with necrotizing enterocolitis and infection. Acta Paediatr 2012;101:1121-1127.
34. Hickey L, Jacobs SE, Garland SM. Probiotics in neonatology. J Paediatr Child Health 2012; 48:777-783.
35. Mai V, Young CM, Ukhanova M, et al. Fecal microbiota in premature infants prior to necrotizing enterocolitis. PLoS One 2011; 6:e20647.
36. Tran L, Ferris M, Norori J, et al. Necrotizing enterocolitis and cytomegalovirus infection in a premature infant. Pediatrics 2013; 131:e318-e322.
37. Jenke AC, Postberg J, Mariel B, et al. S100A12 and hBD2 correlate with the composition of the fecal microflora in ELBW infants and expansion of E. coli is associated with NEC. BioMed Res Int 2013; i:150372.
38. Morrow AL, Lagomarcino AJ, Schibler KR, et al. Early microbial and meta-bolomic signatures predict later onset of necrotizing enterocolitis in preterm infants. Biomed Central 2013; 1:13.
39. Stewart CJ, Marrs ECL, Nelson A, et al. Development of the preterm gut microbiome in twins at risk of necrotising enterocolitis and sepsis. PLoS ONE 2013; 8:e73465.
40. Smith S, Bode S, Skov T, et al. Investigation of the early intestinal microflora in premature infants with/without necrotizing enterocolitis using two different methods. Ped Res 2012; 71:115-120.
41. Madan JC, Salari RC, Saxena D, et al. Gut microbial colonisation in premature neonates predicts neonatal sepsis. Arch Dis Child Fetal Neonatal Ed 2012;97:F456-F462.
42. Mai V, Torrazza RM, Ukhanova M, et al. Distortions in development of intestinal microbiota associated with late onset sepsis in preterm infants. PLoS One 2013; 8:e52876.
43. Smith S, Bode S, Petersen B, et al. Community analysis of bacteria colonising intestinal tissue of neonates with necrotising enterocilitis. BMC Microbiol 2011; 11:73.
44. Scanlan PD, Shanahan F, Marchesi JR. Human methanogen diversity and incidence in healthy and diseased colonic groups using mcrA gene analysis. BMC Microbiol 2008; 8:79.
45. Lodha A, de Silva N, Petric M, et al. Human torovirus: a new virus associated with neonatal necrotizing enterocolitis. Acta Paediatr 2005; 94:1085-1088.
46. Bagci S, Eis-Hübinger A. Detection of astrovirus in premature infants with necrotizing enterocolitis. Pediatr Infect Dis J 2008; 27:347-350.
47. LaTuga MS, Ellis JC, Cotton CM, et al. Beyond bacteria: a study of the enteric microbial consortium in extremely low birth weight infants. PLoS One 2011; 6:e27858.
48. Thingstad T, Lignell R. Theoretical models for the control of bacterial growth rate, abundance, diversity and carbon demand. Aquat Microb Ecol 1997; 13:19-27.
49. Stewart C, Nelson A, Scribbins D, et al. Bacterial and fungal viability in the preterm gut: NEC and sepsis. Arch Dis Child Fetal Neonatal Ed 2013;98:F298-F303.
50. Cotton MC, Taylor S, Stoll B, et al. Prolonged duration of initial empiric antibiotic treatment is associated with increased rates of necrotising enter-ocolitis and death for extremely low birth weight infants. Pediatrics 2009; 123:58-66.
51. Bury RG, Tudehope D. Enteral antibiotics for preventing necrotizing enter-ocolitic in low birthweight or preterm infants. Cochrane Database Syst Rev 2007; CD000405.
52. Embleton N, Berrington JE. Probiotics reduce the risk of necrotising enter-ocolitis (NEC) in preterm infants. Evid Based Med 2013; 18:219-220.
53. Manzoni P, Rinaldi M, Cattani S, et al. Bovine lactoferrin supplementation for prevention of late-onset sepsis in very low-birth-weight neonates: a randomized trial. JAMA 2009; 302:1421-1428.
54. Venkatesh MP, Abrams S. Oral lactoferrin for the prevention of sepsis and necrotizing enterocolitis in preterm infants. Cochrane Database Syst Rev 2010; 5:CD007137.
55. Deshpande G, Rao S, Patole S, et al. Probiotics for prevention of necrotising enterocolitis in preterm neonates with very low birthweight: a systematic review of randomised controlled trials. Lancet 2007; 369:1614-1620.
56. Riskin A, Hochwald O, Bader D, et al. The effects of lactulose supplementation to enteral feedings in premature infants: a pilot study. J Pediatr 2010; 156:209-214.
57. Embleton ND, Berrington JE, McGuire W. Lactoferrin: antimicrobial activity and therapeutic potential. Semin Fetal Neonatal Med 2013. [Epub ahead of print]