Research on neonatal microbiomes: What neonatologists need to know

Neonatology

Volumn 105, Issue 1, 2013, Pages 14-24

  Sherman, Michael P ^a   Minnerly, John ^b   Curtiss, William ^b   Rangwala, Shaukat ^b   Kelley, Scott T ^c  

^a UNIVERSITY OF MISSOURI   (United States)

^b MOgene Green Chemicals   (United States)

^c SAN DIEGO STATE UNIVERSITY   (United States)

Author keywords

Biodiversity; Bioinformatics; Genome analyzers; Pyrosequencing; Taxonomy

Indexed keywords

AMPLICON; BACTERIAL COLONIZATION; BACTERIAL VIRULENCE; BIOINFORMATICS; CAREGIVER; CELL FUNCTION; CHIMERA; DNA SEQUENCE; DNA STRAND; GENE AMPLIFICATION; GENE EXPRESSION; GENE SEQUENCE; GENETIC ANALYZER; HISTORY; HUMAN; METAGENOMICS; MICROBIAL COLONIZATION; MICROBIAL COMMUNITY; MICROBIOME; NANOPORE; NEONATOLOGIST; NEWBORN INTENSIVE CARE; NONHUMAN; PHYLOGENETIC TREE; PHYLOGENY; PRIORITY JOURNAL; PYROSEQUENCING; QUALITY CONTROL; REVIEW; SOIL MICROFLORA; WORKFLOW;

BIOMEDICAL RESEARCH; HUMANS; INFANT, NEWBORN; METAGENOMICS; MICROBIOTA; NEONATOLOGY; PHYLOGENY; SEQUENCE ANALYSIS, DNA;

EID: 84886744199     PISSN: 16617800     EISSN: 16617819     Source Type: Journal    
DOI: 10.1159/000354944     Document Type: Review

References (86)

1. Ursell LK, Clemente JC, Rideout JR, Gevers D, Caporaso JG, Knight R: The interpersonal and intrapersonal diversity of human-associated microbiota in key body sites. J Allergy Clin Immunol 2012; 129: 1204-1208.
2. Madan JC, Salari RC, Saxena D, Davidson L, O'Toole GA, Moore JH, Sogin ML, Foster JA, Edwards WH, Palumbo P, Hibberd PL: Gut microbial colonisation in premature neonates predicts neonatal sepsis. Arch Dis Child Fetal Neonatal Ed 2012; 97:F456-F462.
3. 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.
4. Hooper LV, Gordon JI: Commensal host-bacterial relationships in the gut. Science 2001; 292: 1115-1118.
5. Palmer C, Bik EM, DiGiulio DB, Relman DA, Brown PO: Development of the human infant intestinal microbiota. PLoS Biol 2007; 5:e177.
6. Dominguez-Bello MG, Costello EK, Contreras M, Magris M, Hidalgo G, Fierer N, Knight R: Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns. Proc Natl Acad Sci USA 2010; 107: 11971-11975.
7. 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.
8. 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.
9. Hewitt KM, Mannino FL, Gonzalez A, Chase JH, Caporaso JG, Knight R, Kelley ST: Bacterial diversity in two neonatal intensive care units (NICUs). PLoS One 2013; 8:e54703.
10. Tanaka S, Kobayashi T, Songjinda P, Tateyama A, Tsubouchi M, Kiyohara C, Shirakawa T, Sonomoto K, Nakayama J: Influence of antibiotic exposure in the early postnatal period on the development of intestinal microbiota. FEMS Immunol Med Microbiol 2009; 56: 80-87.
11. Dethlefsen L, Relman DA: Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation. Proc Natl Acad Sci USA 2011; 108(suppl 1):4554-4561.
12. Morowitz MJ, Carlisle EM, Alverdy JC: Contributions of intestinal bacteria to nutrition and metabolism in the critically ill. Surg Clin North Am 2011; 91: 771-785.
13. Jacquot A, Neveu D, Aujoulat F, Mercier G, Marchandin H, Jumas-Bilak E, Picaud JC: Dynamics and clinical evolution of bacterial gut microflora in extremely premature patients. J Pediatr 2011; 158: 390-396.
14. Sherman MP: New concepts of microbial translocation in the neonatal intestine: mechanisms and prevention. Clin Perinatol 2010; 37: 565-579.
15. Schwartz S, Friedberg I, Ivanov IV, Davidson LA, Goldsby JS, Dahl DB, Herman D, Wang M, Donovan SM, Chapkin RS: A metagenomic study of diet-dependent interaction between gut microbiota and host in infants reveals differences in immune response. Genome Biol 2012; 13:r32.
16. Sherman MP: Lactoferrin and necrotizing enterocolitis. Clin Perinatol 2013; 40: 79-91.
17. Sherman MP: Intestinal microbes and obesity: a reality check. Commentary on F.B. Morel et al: Can antibiotic treatment in preweaning rats alter body composition in adulthood? (Neonatology 2013; 103: 182-189). Neonatology 2013; 103: 190-192.
18. Trasande L, Blustein J, Liu M, Corwin E, Cox LM, Blaser MJ: Infant antibiotic exposures and early-life body mass. Int J Obes (Lond) 2013; 37: 16-23.
19. Brown CT, Davis-Richardson AG, Giongo A, Gano KA, Crabb DB, Mukherjee N, Casella G, Drew JC, Ilonen J, Knip M, Hyöty H, Veijola R, Simell T, Simell O, Neu J, Wasserfall CH, Schatz D, Atkinson MA, Triplett EW: Gut microbiome metagenomics analysis suggests a functional model for the development of autoimmunity for type 1 diabetes. PLoS One 2011; 6:e25792.
20. Vaarala O: Is the origin of type 1 diabetes in the gut? Immunol Cell Biol 2012; 90: 271-276.
21. Russell SL, Gold MJ, Hartmann M, Willing BP, Thorson L, Wlodarska M, Gill N, Blanchet MR, Mohn WW, McNagny KM, Finlay BB: Early life antibiotic-driven changes in microbiota enhance susceptibility to allergic asthma. EMBO Rep 2012; 13: 440-447.
22. Isolauri E: Development of healthy gut microbiota early in life. J Paediatr Child Health 2012; 48(suppl 3):1-6.
23. Weinstock GM: Genomic approaches to studying the human microbiota. Nature 2012; 489: 250-256.
24. Cabellos-Ruiz A, Janca H, Baena S, Venegas I, Zambrano MM: Beyond metagenomics: integration of complementary approaches for the study of microbial communities; in Marco D (ed): Metagenomics: Theory, Methods, and Applications. Norfolk, Caister Academic Press, 2010, pp 15-37.
25. Blevins SM, Bronze MS: Robert Koch and the 'golden age' of bacteriology. Int J Infect Dis 2010; 14:e744-e751.
26. Dunne WM Jr, Pinckard JK, Hooper LV: Clinical microbiology in the year 2025. J Clin Microbiol 2002; 40: 3889-3893.
27. Woese CR, Fox GE: Phylogenetic structure of the prokaryotic domain: the primary kingdoms. Proc Natl Acad Sci USA 1977; 74: 5088-5090.
28. Woese CR, Kandler O, Wheelis ML: Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Proc Natl Acad Sci USA 1990; 87: 4576-4579.
29. Pace NR, Stahl DA, Lane DJ, Olsen GJ: The analysis of natural microbial populations by ribosomal RNA sequences. Am Soc Microbiol News 1985; 51: 4-12.
30. Schmidt TM, DeLong EF, Pace NR: Analysis of a marine picoplankton community by 16S rRNA gene cloning and sequencing. J Bacteriol 1991; 173: 4371-4378.
31. Handelsman J, Rondon MR, Brady SF, Clardy J, Goodman RM: Molecular biological access to the chemistry of unknown soil microbes: a new frontier for natural products. Chem Biol 1998; 5:R245-R249.
32. Tyson GW, Chapman J, Hugenholtz P, Allen EE, Ram RJ, Richardson PM, Solovyev VV, Rubin EM, Rokhsar DS, Banfield JF: Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature 2004; 428: 37-43.
33. Venter JC, Remington K, Heidelberg JF, Halpern AL, Rusch D, Eisen JA, Wu D, Paulsen I, Nelson KE, Nelson W, Fouts DE, Levy S, Knap AH, Lomas MW, Nealson K, White O, Peterson J, Hoffman J, Parsons R, Baden-Tillson H, Pfannkoch C, Rogers YH, Smith HO: Environmental genome shotgun sequencing of the Sargasso Sea. Science 2004; 304: 66-74.
34. Gilbert W, Maxam A: The nucleotide sequence of the lac operator. Proc Natl Acad Sci USA 1973; 70: 3581-3584.
35. Sanger F, Donelson JE, Coulson AR, Kössel H, Fischer D: Use of DNA polymerase I primed by a synthetic oligonucleotide to determine a nucleotide sequence in phage fl DNA. Proc Natl Acad Sci USA 1973; 70: 1209-1213.
36. Sanger F, Nicklen S, Coulson AR: DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci USA 1977; 74: 5463-5467.
37. Mullis KB, Faloona FA: Specific synthesis of DNA in vitro via a polymerase-catalyzed chain reaction. Methods Enzymol 1987; 155: 335-350.
38. Ronaghi M, Karamohamed S, Pettersson B, Uhlen M, Nyren P: Real-time DNA sequencing using detection of pyrophosphate release. Anal Biochem 1996; 242: 84-89.
39. Ronaghi M: Pyrosequencing sheds light on DNA sequencing. Genome Res 2001; 11: 3-11.
40. Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, Berka J, Braverman MS, Chen YJ, Chen Z, Dewell SB, Du L, Fierro JM, Gomes XV, Godwin BC, He W, Helgesen S, Ho CH, Irzyk GP, Jando SC, Alenquer ML, Jarvie TP, Jirage KB, Kim JB, Knight JR, Lanza JR, Leamon JH, Lefkowitz SM, Lei M, Li J, Lohman KL, Lu H, Makhijani VB, McDade KE, McKenna MP, Myers EW, Nickerson E, Nobile JR, Plant R, Puc BP, Ronan MT, Roth GT, Sarkis GJ, Simons JF, Simpson JW, Srinivasan M, Tartaro KR, Tomasz A, Vogt KA, Volkmer GA, Wang SH, Wang Y, Weiner MP, Yu P, Begley RF, Rothberg JM: Genome sequencing in microfabricated high-density picolitre reactors. Nature 2005; 437: 376-380.
41. Lederberg J, McCray AT: 'Ome sweet' omics-a genealogical treasury of words. Scientist 2001; 15: 8.
42. Relman DA, Falkow S: The meaning and impact of the human genome sequence for microbiology. Trends Microbiol 2001; 9: 206-208.
43. Turnbaugh PJ, Ley RE, Hamady M, Fraser-Liggett CM, Knight R, Gordon JI: The Human Microbiome Project. Nature 2007; 449: 804-810.
44. Lauber CL, Zhou N, Gordon JI, Knight R, Fierer N: Effect of storage conditions on the assessment of bacterial community structure in soil and human-associated samples. FEMS Microbiol Lett 2010; 307: 80-86.
45. Cardona S, Eck A, Cassellas M, Gallart M, Alastrue C, Dore J, Azpiroz F, Roca J, Guarner F, Manichanh C: Storage conditions of intestinal microbiota matter in metagenomic analysis. BMC Microbiol 2012; 12: 158.
46. Wu GD, Lewis JD, Hoffmann C, Chen YY, Knight R, Bittinger K, Hwang J, Chen J, Berkowsky R, Nessel L, Li H, Bushman FD: Sampling and pyrosequencing methods for characterizing bacterial communities in the human gut using 16S sequence tags. BMC Microbiol 2010; 10: 206.
47. Knierim E, Lucke B, Schwarz JM, Schuelke M, Seelow D: Systematic comparison of three methods for fragmentation of long-range PCR products for next generation sequencing. PLoS One 2011; 6:e28240.
48. Tamaki H, Wright CL, Li X, Lin Q, Hwang C, Wang S, Thimmapuram J, Kamagata Y, Liu WT: Analysis of 16S rRNA amplicon sequencing options on the Roche/454 next-generation titanium sequencing platform. PLoS One 2011; 6:e25263.
49. Gilles A, Meglécz E, Pech N, Ferreira S, Malausa T, Martin JF: Accuracy and quality assessment of 454 GS-FLX Titanium pyrosequencing. BMC Genomics 2011; 12: 245.
50. Angiuoli SV, White JR, Matalka M, White O, Fricke WF: Resources and costs for microbial sequence analysis evaluated using virtual machines and cloud computing. PLoS One 2011; 6:e26624.
51. Thomas T, Gilbert J, Meyer F: Metagenomics-a guide from sampling to data analysis. Microb Inform Exp 2012; 2: 3.
52. Petrosino JF, Highlander S, Luna RA, Gibbs RA, Versalovic J: Metagenomic pyrosequencing and microbial identification. Clin Chem 2009; 55: 856-866.
53. Chakravorty S, Helb D, Burday M, Connell N, Alland D: A detailed analysis of 16S ribosomal RNA gene segments for the diagnosis of pathogenic bacteria. J Microbiol Methods 2007; 69: 330-339.
54. Liu Z, Lozupone C, Hamady M, Bushman FD, Knight R: Short pyrosequencing reads suffice for accurate microbial community analysis. Nucleic Acids Res 2007; 35:e120.
55. Luna RA, Fasciano LR, Jones SC, Boyanton BL Jr, Ton TT, Versalovic J: DNA pyrosequencing-based bacterial pathogen identification in a pediatric hospital setting. J Clin Microbiol 2007; 45: 2985-2992.
56. Andersson AF, Lindberg M, Jakobsson H, Bäckhed F, Nyrén P, Engstrand L: Comparative analysis of human gut microbiota by barcoded pyrosequencing. PLoS One 2008; 3:e2836.
57. Quail MA, Smith M, Coupland P, Otto TD, Harris SR, Connor TR, Bertoni A, Swerdlow HP, Gu Y: A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers. BMC Genomics 2012; 13: 341.
58. Sherry NL, Porter JL, Seemann T, Watkins A, Stinear TP, Howden BP: Outbreak investigation using high-throughput genome sequencing within a diagnostic microbiology laboratory. J Clin Microbiol 2013; 51: 1396-1401.
59. Chin CS, Sorenson J, Harris JB, Robins WP, Charles RC, Jean-Charles RR, Bullard J, Webster DR, Kasarskis A, Peluso P, Paxinos EE, Yamaichi Y, Calderwood SB, Mekalanos JJ, Schadt EE, Waldor MK: The origin of the Haitian cholera outbreak strain. N Engl J Med 2011; 364: 33-42.
60. Hammerstein AF, Jayasinghe L, Bayley H: Subunit dimers of alpha-hemolysin expand the engineering toolbox for protein nanopores. J Biol Chem 2011; 286: 14324-14334.
61. Wu HC, Astier Y, Maglia G, Mikhailova E, Bayley H: Protein nanopores with covalently attached molecular adapters. J Am Chem Soc 2007; 129: 16142-16148.
62. Hayden EC: Nanopore genome sequencer makes its debut. http://www.nature.com/news/nanopore-genome-sequencer-makesits-debut-1.10051.
63. Suzuki S, Ono N, Furusawa C, Ying BW, Yomo T: Comparison of sequence reads obtained from three next-generation sequencing platforms. PLoS One 2011; 6:e19534.
64. Loman NJ, Misra RV, Dallman TJ, Constantinidou C, Gharbia SE, Wain J, Pallen MJ: Performance comparison of benchtop highthroughput sequencing platforms. Nat Biotechnol 2012; 30: 434-439.
65. Schloss PD, Gevers D, Westcott SL: Reducing the effects of PCR amplification and sequencing artifacts on 16S rRNA-based studies. PLoS One 2011; 6:e27310.
66. Edgar RC, Haas BJ, Clemente JC, Quince C, Knight R: UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 2011; 27: 2194-2200.
67. Jumpstart Consortium Human Microbiome Project Data Generation Working Group: Evaluation of 16S rDNA-based community profiling for human microbiome research. PLoS One 2012; 7:e39315.
68. Keegan KP, Trimble WL, Wilkening J, Wilke A, Harrison T, D'Souza M, Meyer F: A platform-independent method for detecting errors in metagenomic sequencing data: DRISEE. PLoS Comput Biol 2012; 8:e1002541.
69. Balzer S, Malde K, Lanzén A, Sharma A, Jonassen I: Characteristics of 454 pyrosequencing data-enabling realistic simulation with flowsim. Bioinformatics 2010; 26:i420-i425.
70. Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, Lesniewski RA, Oakley BB, Parks DH, Robinson CJ, Sahl JW, Stres B, Thallinger GG, Van Horn DJ, Weber CF: Introducing mothur: open-source, platform- independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 2009; 75: 7537-7541.
71. 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.
72. Schloss PD, Westcott SL: Assessing and improving methods used in operational taxonomic unit-based approaches for 16S rRNA gene sequence analysis. Appl Environ Microbiol 2011; 77: 3219-3226.
73. Wooley JC, Godzik A, Friedberg I: A primer on metagenomics. PLoS Comput Biol 2010; 6:e1000667.
74. Kembel SW, Eisen JA, Pollard KS, Green JL: The phylogenetic diversity of metagenomes. PLoS One 2011; 6:e23214.
75. Hughes JB, Hellmann JJ, Ricketts TH, Bohannan BJ: Counting the uncountable: statistical approaches to estimating microbial diversity. Appl Environ Microbiol 2001; 67: 4399-4406.
76. Hill TC, Walsh KA, Harris JA, Moffett BF: Using ecological diversity measures with bacterial communities. FEMS Microbiol Ecol 2003; 43: 1-11.
77. Schloss PD: The effects of alignment quality, distance calculation method, sequence filtering, and region on the analysis of 16S rRNA gene-based studies. PLoS Comput Biol 2010; 6:e1000844.
78. Gotelli NJ, Colwell RK: Estimating species richness; in Magurran AE, McGill BJ (eds): Biological Diversity, Frontiers in Measurement and Assessment. New York, Oxford University Press, 2010, pp 39-54.
79. Kuczynski J, Stombaugh J, Walters WA, González A, Caporaso JG, Knight R: Using QIIME to analyze 16S rRNA gene sequences from microbial communities. Curr Protoc Microbiol 2012;Chapter 1:Unit 1E.5.
80. Hamady M, Lozupone C, Knight R: Fast Uni-Frac: facilitating high-throughput phylogenetic analyses of microbial communities including analysis of pyrosequencing and PhyloChip data. ISME J 2010; 4: 17-27.
81. 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.
82. Human Microbiome Project Consortium: A framework for human microbiome research. Nature 2012; 486: 215-221.
83. Duerkop BA, Clements CV, Rollins D, Rodrigues JL, Hooper LV: A composite bacteriophage alters colonization by an intestinal commensal bacterium. Proc Natl Acad Sci USA 2012; 109: 17621-17626.
84. Reyes A, Semenkovich NP, Whiteson K, Rohwer F, Gordon JI: Going viral: next-generation sequencing applied to phage populations in the human gut. Nat Rev Microbiol 2012; 10: 607-617.
85. Fortier LC, Sekulovic O: Importance of prophages to evolution and virulence of bacterial pathogens. Virulence 2013; 4: 5,1-12.
86. Zarraonaindia I, Smith DP, Gilbert JA: Beyond the genome: community-level analysis of the microbial world. Biol Philos 2013; 28: 261-282.