The Bacterial Microbiome and Virome Milestones of Infant Development

Trends in Microbiology

Volumn 24, Issue 10, 2016, Pages 801-810

  Lim, Efrem S ^a   Wang, David ^a   Holtz, Lori R ^a  

^a WASHINGTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

infant; microbiome; virome

Indexed keywords

ARTIFICIAL MILK; BACTERIAL COLONIZATION; BREAST MILK; CESAREAN SECTION; CHILD DEVELOPMENT; GESTATIONAL AGE; HOST PATHOGEN INTERACTION; HUMAN; INTESTINE FLORA; MICROBIAL COMMUNITY; MICROBIAL DIVERSITY; MICROBIOME; NONHUMAN; PLACENTAL TRANSFER; PRENATAL EXPOSURE; PRIORITY JOURNAL; REVIEW; VAGINAL DELIVERY; BACTERIUM; CHILD HEALTH; FECES; GASTROINTESTINAL TRACT; INFANT; METABOLISM; MICROBIOLOGY; VIROLOGY; VIRUS;

BACTERIA; CHILD DEVELOPMENT; FECES; GASTROINTESTINAL MICROBIOME; GASTROINTESTINAL TRACT; HUMANS; INFANT; INFANT HEALTH; VIRUSES;

EID: 84977660014     PISSN: 0966842X     EISSN: 18784380     Source Type: Journal    
DOI: 10.1016/j.tim.2016.06.001     Document Type: Review

References (82)

1. 1 Pettker, C.M., et al. Value of placental microbial evaluation in diagnosing intra-amniotic infection. Obstet. Gynecol. 109 (2007), 739–749.
2. 2 Stout, M.J., et al. Identification of intracellular bacteria in the basal plate of the human placenta in term and preterm gestations. Am. J. Obstet. Gynecol., 208, 2013 226 e221-e227.
3. 3 Aagaard, K., et al. The placenta harbors a unique microbiome. Sci. Transl. Med, 6, 2014, 237ra265.
4. 4 DiGiulio, D.B., Diversity of microbes in amniotic fluid. Semin. Fetal Neonatal Med. 17 (2012), 2–11.
5. 5 Jimenez, E., et al. Isolation of commensal bacteria from umbilical cord blood of healthy neonates born by cesarean section. Curr. Microbiol. 51 (2005), 270–274.
6. 6 Jimenez, E., et al. Is meconium from healthy newborns actually sterile?. Res. Microbiol. 159 (2008), 187–193.
7. 7 Han, Y.W., et al. Fusobacterium nucleatum induces premature and term stillbirths in pregnant mice: implication of oral bacteria in preterm birth. Infect. Immun. 72 (2004), 2272–2279.
8. 8 Perez, P.F., et al. Bacterial imprinting of the neonatal immune system: lessons from maternal cells?. Pediatrics 119 (2007), e724–e732.
9. 9 Andrews, W.W., et al. Endometrial microbial colonization and plasma cell endometritis after spontaneous or indicated preterm versus term delivery. Am. J. Obstet. Gynecol. 193 (2005), 739–745.
10. 10 Ardissone, A.N., et al. Meconium microbiome analysis identifies bacteria correlated with premature birth. PLoS ONE, 9, 2014, e90784.
11. 11 Dominguez-Bello, M.G., et al. Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns. Proc. Natl. Acad. Sci. U.S.A. 107 (2010), 11971–11975.
12. 12 Backhed, F., et al. Dynamics and stabilization of the human gut microbiome during the first year of life. Cell Host Microbe, 17, 2015, 852.
13. 13 Jakobsson, H.E., et al. Decreased gut microbiota diversity, delayed Bacteroidetes colonisation and reduced Th1 responses in infants delivered by caesarean section. Gut 63 (2014), 559–566.
14. 14 Kuhle, S., et al. Association between caesarean section and childhood obesity: a systematic review and meta-analysis. Obes. Rev. 16 (2015), 295–303.
15. 15 Huang, L., et al. Is elective cesarean section associated with a higher risk of asthma?. A meta-analysis. J. Asthma 52 (2015), 16–25.
16. 16 Dominguez-Bello, M.G., et al. Partial restoration of the microbiota of cesarean-born infants via vaginal microbial transfer. Nat. Med. 22 (2016), 250–253.
17. 17 Cunnington, A.J., et al. “Vaginal seeding” of infants born by caesarean section. BMJ, 352, 2016, i227.
18. 18 La Rosa, P.S., et al. Patterned progression of bacterial populations in the premature infant gut. Proc. Natl. Acad. Sci. U.S.A. 111 (2014), 12522–12527.
19. 19 Gibson, M., et al. Developmental dynamics of the preterm infant gut microbiota and antibiotic resistome. Nat. Microbiol., 1, 2016, 16024.
20. 20 Dogra, S., et al. Dynamics of infant gut microbiota are influenced by delivery mode and gestational duration and are associated with subsequent adiposity. mBio 6 (2015), e02419–e2514.
21. 21 Arboleya, S., et al. Deep 16S rRNA metagenomics and quantitative PCR analyses of the premature infant fecal microbiota. Anaerobe 18 (2012), 378–380.
22. 22 Harmsen, H.J., 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. 30 (2000), 61–67.
23. 23 Martin, V., et al. Sharing of bacterial strains between breast milk and infant feces. J. Hum. Lact. 28 (2012), 36–44.
24. 24 Koenig, J.E., et al. Succession of microbial consortia in the developing infant gut microbiome. Proc. Natl. Acad. Sci. U.S.A. 108:Suppl. 1 (2011), 4578–4585.
25. 25 Yatsunenko, T., et al. Human gut microbiome viewed across age and geography. Nature 486 (2012), 222–227.
26. 26 Palmer, C., et al. Development of the human infant intestinal microbiota. PLoS Biol., 5, 2007, e177.
27. 27 Laursen, M.F., et al. Having older siblings is associated with gut microbiota development during early childhood. BMC Microbiol., 15, 2015, 154.
28. 28 Clemente, J.C., et al. The microbiome of uncontacted Amerindians. Sci. Adv., 1, 2015, e1500183.
29. 29 De Filippo, C., et al. Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa. Proc. Natl. Acad. Sci. U.S.A. 107 (2010), 14691–14696.
30. 30 Fallani, M., et al. Intestinal microbiota of 6-week-old infants across Europe: geographic influence beyond delivery mode, breast-feeding, and antibiotics. J. Pediatr. Gastroenterol. Nutr. 51 (2010), 77–84.
31. 31 Konya, T., et al. Associations between bacterial communities of house dust and infant gut. Environ. Res. 131 (2014), 25–30.
32. 32 Shin, H., et al. The first microbial environment of infants born by C-section: the operating room microbes. Microbiome, 3, 2015, 59.
33. 33 Turnbaugh, P.J., et al. A core gut microbiome in obese and lean twins. Nature 457 (2009), 480–484.
34. 34 Spor, A., et al. Unravelling the effects of the environment and host genotype on the gut microbiome. Nat. Rev. Microbiol. 9 (2011), 279–290.
35. 35 Goodrich, J.K., et al. Human genetics shape the gut microbiome. Cell 159 (2014), 789–799.
36. 36 Lozupone, C.A., et al. Diversity, stability and resilience of the human gut microbiota. Nature 489 (2012), 220–230.
37. 37 Fouhy, F., et al. High-throughput sequencing reveals the incomplete, short-term recovery of infant gut microbiota following parenteral antibiotic treatment with ampicillin and gentamicin. Antimicrob. Agents Chemother. 56 (2012), 5811–5820.
38. 38 Dethlefsen, L., et al. The pervasive effects of an antibiotic on the human gut microbiota, as revealed by deep 16S rRNA sequencing. PLoS Biol., 6, 2008, e280.
39. 39 Nobel, Y.R., et al. Metabolic and metagenomic outcomes from early-life pulsed antibiotic treatment. Nat. Commun., 6, 2015, 7486.
40. 40 Reyes, A., et al. Gut DNA viromes of Malawian twins discordant for severe acute malnutrition. Proc. Natl. Acad. Sci. U.S.A. 112 (2015), 11941–11946.
41. 41 Lim, E.S., et al. Early life dynamics of the human gut virome and bacterial microbiome in infants. Nat. Med. 21 (2015), 1228–1234.
42. 42 Calvet, G., et al. Detection and sequencing of Zika virus from amniotic fluid of fetuses with microcephaly in Brazil: a case study. Lancet Infect. Dis., 2016, 10.1016/S1473-3099(16)00095-5 Published online February 17, 2016.
43. 43 Wenstrom, K.D., et al. Intrauterine viral infection at the time of second trimester genetic amniocentesis. Obstet. Gynecol. 92 (1998), 420–424.
44. 44 Baschat, A.A., et al. Prevalence of viral DNA in amniotic fluid of low-risk pregnancies in the second trimester. J. Matern. Fetal Neonatal Med. 13 (2003), 381–384.
45. 45 Minot, S., et al. The human gut virome: inter-individual variation and dynamic response to diet. Genome Res. 21 (2011), 1616–1625.
46. 46 Holtz, L.R., et al. Geographic variation in the eukaryotic virome of human diarrhea. Virology 468-470 (2014), 556–564.
47. 47 Reyes, A., et al. Viruses in the faecal microbiota of monozygotic twins and their mothers. Nature 466 (2010), 334–338.
48. 48 Wylie, K.M., et al. Metagenomic analysis of double-stranded DNA viruses in healthy adults. BMC Biol., 12, 2014, 71.
49. 49 Norman, J.M., et al. Disease-specific alterations in the enteric virome in inflammatory bowel disease. Cell 160 (2015), 447–460.
50. 50 Rivera, L., et al. Horizontal transmission of a human rotavirus vaccine strain–a randomized, placebo-controlled study in twins. Vaccine 29 (2011), 9508–9513.
51. 51 Penders, J., et al. Establishment of the intestinal microbiota and its role for atopic dermatitis in early childhood. J. Allergy Clin. Immunol., 132, 2013 601-607 e608.
52. 52 Cheng, J., et al. Discordant temporal development of bacterial phyla and the emergence of core in the fecal microbiota of young children. ISME J. 10 (2016), 1002–1014.
53. 53 Smith, M.I., et al. Gut microbiomes of Malawian twin pairs discordant for kwashiorkor. Science 339 (2013), 548–554.
54. 54 Subramanian, S., et al. Persistent gut microbiota immaturity in malnourished Bangladeshi children. Nature 510 (2014), 417–421.
55. 55 Kapusinszky, B., et al. Nearly constant shedding of diverse enteric viruses by two healthy infants. J. Clin. Microbiol. 50 (2012), 3427–3434.
56. 56 Kramna, L., et al. Gut virome sequencing in children with early islet autoimmunity. Diabetes Care 38 (2015), 930–933.
57. 57 Lambert, L., et al. Immunity to RSV in early-life. Front. Immunol., 5, 2014, 466.
58. 58 Grassly, N.C., Fraser, C., Seasonal infectious disease epidemiology. Proc. Biol. Sci. 273 (2006), 2541–2550.
59. 59 Lofgren, E., et al. Influenza seasonality: underlying causes and modeling theories. J. Virol. 81 (2007), 5429–5436.
60. 60 Tapia, G., et al. Longitudinal observation of parechovirus in stool samples from Norwegian infants. J. Med. Virol. 80 (2008), 1835–1842.
61. 61 Arrieta, M.C., et al. Early infancy microbial and metabolic alterations affect risk of childhood asthma. Sci. Transl. Med., 7, 2015, 307ra152.
62. 62 Russell, S.L., et al. Early life antibiotic-driven changes in microbiota enhance susceptibility to allergic asthma. EMBO Rep. 13 (2012), 440–447.
63. 63 Cahenzli, J., et al. Intestinal microbial diversity during early-life colonization shapes long-term IgE levels. Cell Host Microbe 14 (2013), 559–570.
64. 64 Pfeiffer, J.K., Virgin, H.W., Viral immunity. Transkingdom control of viral infection and immunity in the mammalian intestine. Science, 2016, 10.1126/science.aad5872 Published online January 14, 2016.
65. 65 Virgin, H.W., The virome in mammalian physiology and disease. Cell 157 (2014), 142–150.
66. 66 Sansone, C.L., et al. Microbiota-dependent priming of antiviral intestinal immunity in Drosophila. Cell Host Microbe 18 (2015), 571–581.
67. 67 Kernbauer, E., et al. An enteric virus can replace the beneficial function of commensal bacteria. Nature 516 (2014), 94–98.
68. 68 Kane, M., et al. Successful transmission of a retrovirus depends on the commensal microbiota. Science 334 (2011), 245–249.
69. 69 Kuss, S.K., et al. Intestinal microbiota promote enteric virus replication and systemic pathogenesis. Science 334 (2011), 249–252.
70. 70 Uchiyama, R., et al. Antibiotic treatment suppresses rotavirus infection and enhances specific humoral immunity. J. Infect. Dis. 210 (2014), 171–182.
71. 71 Jones, M.K., et al. Enteric bacteria promote human and mouse norovirus infection of B cells. Science 346 (2014), 755–759.
72. 72 Baldridge, M.T., et al. Commensal microbes and interferon-lambda determine persistence of enteric murine norovirus infection. Science 347 (2015), 266–269.
73. 73 Rodriguez-Valera, F., et al. Explaining microbial population genomics through phage predation. Nat. Rev. Microbiol. 7 (2009), 828–836.
74. 74 Lugli, G.A., et al. Prophages of the genus Bifidobacterium as modulating agents of the infant gut microbiota. Environ. Microbiol., 2015, 10.1111/1462-2920.13154 Published online December 2, 2015.
75. 75 Cortez, M.H., Weitz, J.S., Coevolution can reverse predator–prey cycles. Proc. Natl. Acad. Sci. U.S.A. 111 (2014), 7486–7491.
76. 76 Gosalbes, M.J., et al. Meconium microbiota types dominated by lactic acid or enteric bacteria are differentially associated with maternal eczema and respiratory problems in infants. Clin. Exp. Allergy 43 (2013), 198–211.
77. 77 Johansson, M.A., et al. Early colonization with a group of lactobacilli decreases the risk for allergy at five years of age despite allergic heredity. PLoS ONE, 6, 2011, e23031.
78. 78 Ley, R.E., et al. Obesity alters gut microbial ecology. Proc. Natl. Acad. Sci. U.S.A. 102 (2005), 11070–11075.
79. 79 Blanton, L.V., et al. Gut bacteria that prevent growth impairments transmitted by microbiota from malnourished children. Science, 2016, 10.1126/science.aad3311 Published online February 19, 2016.
80. 80 Rosenfeld, C.S., Microbiome disturbances and autism spectrum disorders. Drug Metab. Dispos. 43 (2015), 1557–1571.
81. 81 SM, O.M., et al. The microbiome and childhood diseases: Focus on brain–gut axis. Birth Defects Res. C Embryo Today 105 (2015), 296–313.
82. 82 Pantoja-Feliciano, I.G., et al. Biphasic assembly of the murine intestinal microbiota during early development. ISME J. 7 (2013), 1112–1115.