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Pyrosequencing as a tool for better understanding of human microbiomes

By José F. Siqueira, Ashraf F. Fouad and Isabela N. Rôças

Abstract

Next-generation sequencing technologies have revolutionized the analysis of microbial communities in diverse environments, including the human body. This article reviews several aspects of one of these technologies, the pyrosequencing technique, including its principles, applications, and significant contribution to the study of the human microbiome, with especial emphasis on the oral microbiome. The results brought about by pyrosequencing studies have significantly contributed to refining and augmenting the knowledge of the community membership and structure in and on the human body in healthy and diseased conditions. Because most oral infectious diseases are currently regarded as biofilm-related polymicrobial infections, high-throughput sequencing technologies have the potential to disclose specific patterns related to health or disease. Further advances in technology hold the perspective to have important implications in terms of accurate diagnosis and more effective preventive and therapeutic measures for common oral diseases

Topics: Invited Review Article
Publisher: Co-Action Publishing
OAI identifier: oai:pubmedcentral.nih.gov:3266102
Provided by: PubMed Central

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Citations

  1. (2009). A core gut microbiome in obese and lean twins. Nature
  2. (2007). A pyrosequencing-tailored nucleotide barcode design unveils opportunities for large-scale sample multiplexing. Nucleic Acids Res
  3. (2008). A renaissance for the pioneering 16S rRNA gene. Curr Opin Microbiol
  4. (2011). Alves FR, Ro ˆc ¸as IN. Pyrosequencing analysis of the apical root canal microbiota.
  5. (2010). Analysis of microbiota associated with peri-implantitis using 16S rRNA gene clone library.
  6. (2010). Analyzing endodontic infections by deep coverage pyrosequencing. J Dent Res
  7. (2008). Bacteria of dental caries in primary and permanent teeth in children and young adults.
  8. (2009). Bacterial community variation in human body habitats across space and time. Science
  9. (2001). Bacterial diversity in human subgingival plaque.
  10. (2002). Bacterial diversity in necrotizing ulcerative periodontitis in HIV-positive subjects. Ann Periodontol
  11. (2009). Bacterial diversity in persistent periapical lesions on root-filled teeth.
  12. (2010). Bacterial diversity in the oral cavity of 10 healthy individuals.
  13. (2007). Bacterial flora-typing with targeted, chip-based pyrosequencing.
  14. (2006). Beyond diversity: functional microbiomics of the human colon. Trends Microbiol
  15. Characterization of the oral fungal microbiome (mycobiome) in healthy individuals. PLoS Pathog 2010; 6: e1000713. *Jose ´ F. Siqueira, Jr Faculty of Dentistry Esta ´cio de Sa ´ University Av. Alfredo Baltazar da Silveira 580/cobertura,
  16. (2010). Clonal analysis of the microbiota of severe early childhood caries. Caries Res
  17. (2010). Community and gene composition of a human dental plaque microbiota obtained by metagenomic sequencing. Mol Oral Microbiol
  18. (2008). Comparative analysis of human gut microbiota by barcoded pyrosequencing. PLoS ONE
  19. (2009). Comparative analysis of human saliva microbiome diversity by barcoded pyrosequencing and cloning approaches. Anal Biochem
  20. (2011). CORE: a phylogenetically-curated 16S rDNA database of the core oral microbiome. PLoS One
  21. (2009). Cultivated and notyet-cultivated bacteria in oral biofilms. Microb Ecol Health Dis
  22. (2009). Defining the healthy core microbiome of oral microbial communities.
  23. (2005). Defining the normal bacterial flora of the oral cavity.
  24. (2010). Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns.
  25. (2010). Direct sequencing of the human microbiome readily reveals community differences. Genome Biol
  26. (2010). Disordered microbial communities in the upper respiratory tract of cigarette smokers. PLoS One
  27. (2003). Diversity of bacterial populations on the tongue dorsa of patients with halitosis and healthy patients.
  28. (2007). DNA pyrosequencing-based bacterial pathogen identification in a pediatric hospital setting.
  29. (2009). Evaluation of the bacterial diversity among and within individual venous leg ulcers using bacterial tag-encoded FLX and titanium amplicon pyrosequencing and metagenomic approaches.
  30. Evaluation of the bacterial diversity of pressure ulcers using bTEFAP pyrosequencing.
  31. (2010). Experimental factors affecting PCR-based estimates of microbial species richness and evenness.
  32. (2011). Exploring bacterial diversity of endodontic microbiota by cloning and sequencing 16S rRNA.
  33. (2008). Exploring microbial diversity and taxonomy using SSU rRNA hypervariable tag sequencing. PLoS Genet
  34. (2011). Exploring the oral microbiota of children at various developmental stages of their dentition in the relation to their oral health.
  35. (2010). Forensic identification using skin bacterial communities.
  36. (2006). Gonc ¸alves RB. Identification of bacteria in endodontic infections by sequence analysis of 16S rDNA clone libraries.
  37. (2006). Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol
  38. (2010). Gut microbiota in human adults with type 2 diabetes differs from non-diabetic adults. PLoS One
  39. (2011). Human oral, gut, and plaque microbiota in patients with atherosclerosis.
  40. (2005). Identifi-cation of candidate periodontal pathogens and beneficial species by quantitative 16S clonal analysis.
  41. (2007). Identification of oral bacterial species associated with halitosis. J Am Dent Assoc
  42. (2004). Impact of 16S rRNA gene sequence analysis for identification of bacteria on clinical microbiology and infectious diseases. Clin Microbiol Rev
  43. (2010). Impact of diet in shaping gut microbiota revealed by a comparative study
  44. (2011). Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation.
  45. (2005). Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness. Appl Environ Microbiol
  46. (2008). Metagenomic diagnosis of bacterial infections. Emerg Infect Dis
  47. (2009). Metagenomic study of the oral microbiota by Illumina high-throughput sequencing.
  48. (2010). Metagenomics and Ecosystems Biology: conceptual frameworks, tools and methods.
  49. (2006). Microbial diversity in the deep sea and the underexplored rare biosphere.
  50. (2006). Microbial ecology: human gut microbes associated with obesity. Nature
  51. (2011). Microbial genomics and infectious diseases.
  52. (2005). Microbial risk indicators of early childhood caries.
  53. (2008). Microbiological diversity of generalized aggressive periodontitis by 16S rRNA clonal analysis. Oral Microbiol Immunol
  54. (2006). Molecular analysis of bacteria in asymptomatic and symptomatic endodontic infections. Oral Microbiol Immunol
  55. (2002). Molecular analysis of bacterial species associated with childhood caries.
  56. (2010). Molecular analysis of the diversity of vaginal microbiota associated with bacterial vaginosis.
  57. (2004). Molecular analysis of the microflora associated with dental caries.
  58. (2002). Molecular and cultural analysis of the microflora associated with endodontic infections.
  59. (2003). New bacterial species associated with chronic periodontitis.
  60. (2011). Next-generation DNA sequencing and microbiology.
  61. (2008). Next-generation DNA sequencing methods. Annu Rev Genomics Hum Genet
  62. (2008). Next-generation DNA sequencing.
  63. (2009). Next-generation sequencing: from basic research to diagnostics. Clin Chem
  64. (2009). Nextgeneration sequencing technologies and their implications Pyrosequencing and the oral microbiome Citation:
  65. (2006). Novel subgingival bacterial phylotypes detected using multiple universal polymerase chain reaction primer sets. Oral Microbiol Immunol
  66. (2011). Oral Microbiome Profiles: 16S rRNA pyrosequencing and microarray assay comparison. PLoS ONE
  67. (2010). Organismal, genetic, and transcriptional variation in the deeply sequenced gut microbiomes of identical twins.
  68. (2011). Our microbial selves: what ecology can teach us. EMBO Rep
  69. (2008). Polymicrobial nature of chronic diabetic foot ulcer biofilm infections determined using bacterial tag encoded FLX amplicon pyrosequencing (bTEFAP). PLoS One
  70. (1998). Prokaryotes: the unseen majority.
  71. (2008). Pyrosequencing analysis of the oral microflora of healthy adults.
  72. (2010). Pyrosequencing study of fecal microflora of autistic and control children. Anaerobe
  73. (2010). Rapidly denoising pyrosequencing amplicon reads by exploiting rank-abundance distributions. Nat Methods
  74. (2009). Realtime DNA sequencing from single polymerase molecules. Science
  75. (2011). Rethinking microbial diversity analysis in the high throughput sequencing era.
  76. (2011). Ro ˆc ¸as
  77. (2008). Ro ˆc ¸as IN, Benno Y. Molecular analysis of the root canal microbiota associated with endodontic treatment failures. Oral Microbiol Immunol
  78. (2009). Ro ˆc ¸as IN. Molecular analysis of endodontic infections.
  79. (2009). Ro ˆc ¸as IN. The microbiota of acute apical abscesses.
  80. (2010). Sampling and pyrosequencing methods for characterizing bacterial communities in the human gut using 16S sequence tags.
  81. (2010). Sequencing technologiesthe next generation. Nat Rev Genet
  82. (2010). Short-term antibiotic treatment has differing long-term impacts on the human throat and gut microbiome. PLoS One
  83. (2010). Study of inter- and intra-individual variations in the salivary microbiota.
  84. (2008). Survey of bacterial diversity in chronic wounds using pyrosequencing, DGGE, and full ribosome shotgun sequencing.
  85. (2000). The breadth of bacterial diversity in the human periodontal pocket and other oral sites. Periodontol
  86. (2008). The development and impact of 454 sequencing.
  87. (2009). The expansion of the microbiological spectrum of brain abscesses with use of multiple 16S ribosomal DNA sequencing. Clin Infect Dis
  88. (2007). The human microbiome project. Nature
  89. (2010). The human oral microbiome.
  90. (2008). The influence of sex, handedness, and washing on the diversity of hand surface bacteria.
  91. (2008). The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes.
  92. (2011). The microbial challenge to pulp regeneration. Adv Dent Res
  93. (2008). The pervasive effects of an antibiotic on the human gut microbiota, as revealed by deep 16S rRNA sequencing. PLoS Biol
  94. (2005). The Ribosomal Database Project (RDP-II): sequences and tools for high-throughput rRNA analysis. Nucleic Acids Res
  95. (2005). UniFrac: a new phylogenetic method for comparing microbial communities. Appl Environ Microbiol
  96. (2008). Use of pyrosequencing and DNA barcodes to monitor variations in Firmicutes and Bacteroidetes communities in the gut microbiota of obese humans.
  97. (2005). Use of pyrosequencing of 16S rRNA fragments to differentiate between bacteria responsible for neonatal sepsis.
  98. (2006). Using pyrosequencing to shed light on deep mine microbial ecology.
  99. (2011). Vaginal microbiome of reproductive-age women.
  100. (2010). Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates. Environ Microbiol

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