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Genomic approaches to studying the human microbiota

Abstract

The human body is colonized by a vast array of microbes, which form communities of bacteria, viruses and microbial eukaryotes that are specific to each anatomical environment. Every community must be studied as a whole because many organisms have never been cultured independently, and this poses formidable challenges. The advent of next-generation DNA sequencing has allowed more sophisticated analysis and sampling of these complex systems by culture-independent methods. These methods are revealing differences in community structure between anatomical sites, between individuals, and between healthy and diseased states, and are transforming our view of human biology.

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Figure 1: Data and analysis workflow for microbiome analysis.

References

  1. 1

    Backhed, F., Ley, R. E., Sonnenburg, J. L., Peterson, D. A. & Gordon, J. I. Host–bacterial mutualism in the human intestine. Science 307, 1915–1920 (2005).

    ADS  Article  Google Scholar 

  2. 2

    Foxman, B., Goldberg, D., Murdock, C., Xi, C. & Gilsdorf, J. R. Conceptualizing human microbiota: from multicelled organ to ecological community. Interdiscip. Perspect. Infect. Dis. 2008, 613979 (2008).

    Article  Google Scholar 

  3. 3

    Possemiers, S., Bolca, S., Verstraete, W. & Heyerick, A. The intestinal microbiome: a separate organ inside the body with the metabolic potential to influence the bioactivity of botanicals. Fitoterapia 82, 53–66 (2011).

    CAS  Article  Google Scholar 

  4. 4

    Shanahan, F. The host–microbe interface within the gut. Best Pract. Res. Clin. Gastroenterol. 16, 915–931 (2002).

    Article  Google Scholar 

  5. 5

    Bruls, T. & Weissenbach, J. The human metagenome: our other genome? Hum. Mol. Genet. 20, R142–R148 (2011).

    CAS  Article  Google Scholar 

  6. 6

    Qin, J. et al. A human gut microbial gene catalogue established by metagenomic sequencing. Nature 464, 59–65 (2010). This paper presents initial findings on the gut microbiome from the MetaHIT project.

    CAS  Article  Google Scholar 

  7. 7

    Human Microbiome Project Consortium. Structure, function and diversity of the healthy human microbiome. Nature 486, 207–214 (2012). This paper presents analysis of data from the HMP.

  8. 8

    Stein, J. L., Marsh, T. L., Wu, K. Y., Shizuya, H. & DeLong, E. F. Characterization of uncultivated prokaryotes: isolation and analysis of a 40-kilobase-pair genome fragment from a planktonic marine archaeon. J. Bacteriol. 178, 591–599 (1996).

    CAS  Article  Google Scholar 

  9. 9

    Vergin, K. L. et al. Screening of a fosmid library of marine environmental genomic DNA fragments reveals four clones related to members of the order Planctomycetales. Appl. Environ. Microbiol. 64, 3075–3078 (1998).

    CAS  PubMed  PubMed Central  Google Scholar 

  10. 10

    Olsen, G. J., Lane, D. J., Giovannoni, S. J., Pace, N. R. & Stahl, D. A. Microbial ecology and evolution: a ribosomal RNA approach. Annu. Rev. Microbiol. 40, 337–365 (1986).

    CAS  Article  Google Scholar 

  11. 11

    Manichanh, C. et al. Reduced diversity of faecal microbiota in Crohn's disease revealed by a metagenomic approach. Gut 55, 205–211 (2006).

    CAS  Article  Google Scholar 

  12. 12

    Fredricks, D. N., Fiedler, T. L. & Marrazzo, J. M. Molecular identification of bacteria associated with bacterial vaginosis. N. Engl. J. Med. 353, 1899–1911 (2005).

    CAS  Article  Google Scholar 

  13. 13

    Flint, H. J., Bayer, E. A., Rincon, M. T., Lamed, R. & White, B. A. Polysaccharide utilization by gut bacteria: potential for new insights from genomic analysis. Nature Rev. Microbiol. 6, 121–131 (2008).

    CAS  Article  Google Scholar 

  14. 14

    Srikanth, C. V. & McCormick, B. A. Interactions of the intestinal epithelium with the pathogen and the indigenous microbiota: a three-way crosstalk. Interdiscip. Perspect. Infect. Dis. 2008, 626827 (2008).

    CAS  Article  Google Scholar 

  15. 15

    Jakobsson, H. E. et al. Short-term antibiotic treatment has differing long-term impacts on the human throat and gut microbiome. PLoS ONE 5, e9836 (2010).

    ADS  Article  Google Scholar 

  16. 16

    Dethlefsen, L., Huse, S., Sogin, M. L. & Relman, D. A. The pervasive effects of an antibiotic on the human gut microbiota, as revealed by deep 16S rRNA sequencing. PLoS Biol. 6, e280 (2008).

    Article  Google Scholar 

  17. 17

    Miller, C. P., Bohnhoff, M. & Rifkind, D. The effect of an antibiotic on the susceptibility of the mouse's intestinal tract to Salmonella infection. Trans. Am. Clin. Climatol. Assoc. 68, 51–55 (1956).

    PubMed  Google Scholar 

  18. 18

    Sekirov, I. et al. Antibiotic-induced perturbations of the intestinal microbiota alter host susceptibility to enteric infection. Infect. Immun. 76, 4726–4736 (2008).

    CAS  Article  Google Scholar 

  19. 19

    Croswell, A., Amir, E., Teggatz, P., Barman, M. & Salzman, N. H. Prolonged impact of antibiotics on intestinal microbial ecology and susceptibility to enteric Salmonella infection. Infect. Immun. 77, 2741–2753 (2009).

    CAS  Article  Google Scholar 

  20. 20

    Mulligan, M. E. Epidemiology of Clostridium difficile-induced intestinal disease. Clin. Infect. Dis. 6, S222–S228 (1984).

    Article  Google Scholar 

  21. 21

    Jarchum, I. & Pamer, E. G. Regulation of innate and adaptive immunity by the commensal microbiota. Curr. Opin. Immunol. 23, 353–360 (2011).

    CAS  Article  Google Scholar 

  22. 22

    Marsland, B. J. Regulation of inflammatory responses by the commensal microbiota. Thorax 67, 93–94 (2012).

    Article  Google Scholar 

  23. 23

    Wang, Z. et al. Gut flora metabolism of phosphatidylcholine promotes cardiovascular disease. Nature 472, 57–63 (2011).

    ADS  CAS  Article  Google Scholar 

  24. 24

    Gough, E., Shaikh, H. & Manges, A. R. Systematic review of intestinal microbiota transplantation (fecal bacteriotherapy) for recurrent Clostridium difficile infection. Clin. Infect. Dis. 53, 994–1002 (2011).

    Article  Google Scholar 

  25. 25

    Brandt, L. J. & Reddy, S. S. Fecal microbiota transplantation for recurrent clostridium difficile infection. J. Clin. Gastroenterol. 45, S159–S167 (2011).

    Article  Google Scholar 

  26. 26

    D'Onofrio, A. et al. Siderophores from neighboring organisms promote the growth of uncultured bacteria. Chem. Biol. 17, 254–264 (2010).

    CAS  Article  Google Scholar 

  27. 27

    Human Microbiome Jumpstart Reference Strains Consortium. A catalog of reference genomes from the human microbiome. Science 328, 994–999 (2010). This paper presents methods and analysis for large-scale production of reference genome sequences from human-microbiome organisms.

  28. 28

    Gans, J., Wolinsky, M. & Dunbar, J. Computational improvements reveal great bacterial diversity and high metal toxicity in soil. Science 309, 1387–1390 (2005).

    ADS  CAS  Article  Google Scholar 

  29. 29

    Nelson, T. A. et al. PhyloChip microarray analysis reveals altered gastrointestinal microbial communities in a rat model of colonic hypersensitivity. Neurogastroenterol. Motil. 23, 169–177 (2011).

    CAS  Article  Google Scholar 

  30. 30

    Bent, S. J. et al. Measuring species richness based on microbial community fingerprints: the emperor has no clothes. Appl. Environ. Microbiol. 73, 2399–2401 (2007).

    CAS  Article  Google Scholar 

  31. 31

    Sogin, M. L. et al. Microbial diversity in the deep sea and the underexplored “rare biosphere”. Proc. Natl Acad. Sci. USA 103, 12115–12120 (2006).

    ADS  CAS  Article  Google Scholar 

  32. 32

    The NIH HMP Working Group et al. The NIH Human Microbiome Project. Genome Res. 19, 2317–2323 (2009).

  33. 33

    Human Microbiome Project Consortium. A framework for human microbiome research. Nature 486, 215–221 (2012). This paper describes the data sets and resources of the HMP.

  34. 34

    Lazarevic, V. et al. Metagenomic study of the oral microbiota by Illumina high-throughput sequencing. J. Microbiol. Methods 79, 266–271 (2009).

    CAS  Article  Google Scholar 

  35. 35

    Claesson, M. J. et al. Comparison of two next-generation sequencing technologies for resolving highly complex microbiota composition using tandem variable 16S rRNA gene regions. Nucleic Acids Res. 38, e200 (2010).

    Article  Google Scholar 

  36. 36

    Gloor, G. B. et al. Microbiome profiling by Illumina sequencing of combinatorial sequence-tagged PCR products. PLoS ONE 5, e15406 (2010).

    ADS  Article  Google Scholar 

  37. 37

    Hummelen, R. et al. Deep sequencing of the vaginal microbiota of women with HIV. PLoS ONE 5, e12078 (2010).

    ADS  Article  Google Scholar 

  38. 38

    Zubrzycki, L. & Spaulding, E. H. Studies on the stability of the normal human fecal flora. J. Bacteriol. 83, 968–974 (1962).

    CAS  PubMed  PubMed Central  Google Scholar 

  39. 39

    Luckey, T. D. Introduction to intestinal microecology. Am. J. Clin. Nutr. 25, 1292–1294 (1972).

    CAS  Article  Google Scholar 

  40. 40

    Arumugam, M. et al. Enterotypes of the human gut microbiome. Nature 473, 174–180 (2011).

    CAS  Article  Google Scholar 

  41. 41

    Martin, J. et al. Optimizing read mapping to reference genomes to determine composition and species prevalence in microbial communities. PloS ONE 7, e36427 (2012).

    ADS  CAS  Article  Google Scholar 

  42. 42

    Wu, G. D. et al. Linking long-term dietary patterns with gut microbial enterotypes. Science 334, 105–108 (2011).

    ADS  CAS  Article  Google Scholar 

  43. 43

    Ravel, J. et al. Vaginal microbiome of reproductive-age women. Proc. Natl Acad. Sci. USA 108, S4680–S4687 (2011).

    ADS  Article  Google Scholar 

  44. 44

    Proctor, L. M. The Human Microbiome Project in 2011 and beyond. Cell Host Microbe 10, 287–291 (2011).

    CAS  Article  Google Scholar 

  45. 45

    DOE Joint Genome Institute. A Genomic Encyclopedia of Bacteria and Archaea. http://www.jgi.doe.gov/programs/GEBA/ (US Department of Energy, 2012).

  46. 46

    Parfrey, L. W., Walters, W. A. & Knight, R. Microbial eukaryotes in the human microbiome: ecology, evolution, and future directions. Front. Microbiol. 2, 153 (2011).

    Article  Google Scholar 

  47. 47

    Wylie, K. M., Weinstock, G. M. & Storch, G. A. Emerging view of the human virome. Transl. Res. http://dx.doi.org/10.1016/j.trsl.2012.03.006 (24 April 2012).

  48. 48

    Breitbart, M. et al. Metagenomic analyses of an uncultured viral community from human feces. J. Bacteriol. 185, 6220–6223 (2003).

    CAS  Article  Google Scholar 

  49. 49

    Palacios, G. et al. Panmicrobial oligonucleotide array for diagnosis of infectious diseases. Emerg. Infect. Dis. 13, 73–81 (2007).

    CAS  Article  Google Scholar 

  50. 50

    Wang, D. et al. Viral discovery and sequence recovery using DNA microarrays. PLoS Biol. 1, E2 (2003).

    Article  Google Scholar 

  51. 51

    Casas, V. & Rohwer, F. Phage metagenomics. Methods Enzymol. 421, 259–268 (2007).

    CAS  Article  Google Scholar 

  52. 52

    Allander, T. et al. Cloning of a human parvovirus by molecular screening of respiratory tract samples. Proc. Natl Acad. Sci. USA 102, 12891–12896 (2005).

    ADS  CAS  Article  Google Scholar 

  53. 53

    Finkbeiner, S. R. et al. Metagenomic analysis of human diarrhea: viral detection and discovery. PLoS Pathogens. 4, e1000011 (2008).

    Article  Google Scholar 

  54. 54

    Breitbart, M. & Rohwer, F. Method for discovering novel DNA viruses in blood using viral particle selection and shotgun sequencing. Biotechniques 39, 729–736 (2005).

    CAS  Article  Google Scholar 

  55. 55

    Wylie, K. M., Mihindukulasuriya, K. A., Sodergren, E., Weinstock, G. M. & Storch, G. A. Sequence analysis of the human virome in febrile and afebrile children. PLoS ONE 7, e27735 (2012).

    ADS  CAS  Article  Google Scholar 

  56. 56

    Pride, D. T. et al. Evidence of a robust resident bacteriophage population revealed through analysis of the human salivary virome. ISME J. 6, 915–926 (2011).

    Article  Google Scholar 

  57. 57

    Minot, S., Grunberg, S., Wu, G. D., Lewis, J. D. & Bushman, F. D. Hypervariable loci in the human gut virome. Proc. Natl Acad. Sci. USA 109, 3962–3966 (2012).

    ADS  CAS  Article  Google Scholar 

  58. 58

    Breitbart, M. et al. Viral diversity and dynamics in an infant gut. Res. Microbiol. 159, 367–373 (2008).

    CAS  Article  Google Scholar 

  59. 59

    Minot, S. et al. The human gut virome: inter-individual variation and dynamic response to diet. Genome Res. 21, 1616–1625 (2011).

    CAS  Article  Google Scholar 

  60. 60

    Willner, D. & Furlan, M. Deciphering the role of phage in the cystic fibrosis airway. Virulence 1, 309–313 (2010).

    Article  Google Scholar 

  61. 61

    Lepage, P. et al. Dysbiosis in inflammatory bowel disease: a role for bacteriophages? Gut 57, 424–425 (2008).

    CAS  Article  Google Scholar 

  62. 62

    Kanehisa, M., Goto, S., Furumichi, M., Tanabe, M. & Hirakawa, M. KEGG for representation and analysis of molecular networks involving diseases and drugs. Nucleic Acids Res. 38, D355–D360 (2010).

    CAS  Article  Google Scholar 

  63. 63

    Abubucker, S. et al. Metabolic reconstruction for metagenomic data and its application to the human microbiome. PLoS Comput. Biol. 8, e1002358 (2012).

    CAS  Article  Google Scholar 

  64. 64

    Cantarel, B. L. et al. The Carbohydrate-Active EnZymes database (CAZy): an expert resource for glycogenomics. Nucleic Acids Res. 37, D233–D238 (2009).

    CAS  Article  Google Scholar 

  65. 65

    Cantarel, B. L., Lombard, V. & Henrissat, B. Complex carbohydrate utilization by the healthy human microbiome. PLoS ONE 7, e28742 (2012).

    ADS  CAS  Article  Google Scholar 

  66. 66

    Turnbaugh, P. J. & Gordon, J. I. The core gut microbiome, energy balance and obesity. J. Physiol. (Lond.) 587, 4153–4158 (2009).

    CAS  Article  Google Scholar 

  67. 67

    Raes, J., Foerstner, K. U. & Bork, P. Get the most out of your metagenome: computational analysis of environmental sequence data. Curr. Opin. Microbiol. 10, 490–498 (2007).

    CAS  Article  Google Scholar 

  68. 68

    Wooley, J. C., Godzik, A. & Friedberg, I. A primer on metagenomics. PLoS Comput. Biol. 6, e1000667 (2010).

    ADS  Article  Google Scholar 

  69. 69

    Edgar, R. C., Haas, B. J., Clemente, J. C., Quince, C. & Knight, R. UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 27, 2194–2200 (2011).

    CAS  Article  Google Scholar 

  70. 70

    Haas, B. J. et al. Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons. Genome Res. 21, 494–504 (2011).

    CAS  Article  Google Scholar 

  71. 71

    Jumpstart Consortium Human Microbiome Project Data Generation Working Group. Evaluation of 16S rDNA-based community profiling for human microbiome research. PLoS ONE 7, e39315 (2012).

  72. 72

    Schloss, P. D., Gevers, D. & Westcott, S. L. Reducing the effects of PCR amplification and sequencing artifacts on 16S rRNA-based studies. PLoS ONE 6, e27310 (2011).

    ADS  CAS  Article  Google Scholar 

  73. 73

    Wright, E. S., Yilmaz, L. S. & Noguera, D. R. DECIPHER, a search-based approach to chimera identification for 16S rRNA sequences. Appl. Environ. Microbiol. 78, 717–725 (2012).

    CAS  Article  Google Scholar 

  74. 74

    Lozupone, C., Lladser, M. E., Knights, D., Stombaugh, J. & Knight, R. UniFrac: an effective distance metric for microbial community comparison. ISME J. 5, 169–172 (2011).

    Article  Google Scholar 

  75. 75

    Schloss, P. D. et al. Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl. Environ. Microbiol. 75, 7537–7541 (2009).

    CAS  Article  Google Scholar 

  76. 76

    Caporaso, J. G. et al. Moving pictures of the human microbiome. Genome Biol. 12, R50 (2011).

    Article  Google Scholar 

  77. 77

    Angiuoli, S. V., White, J. R., Matalka, M., White, O. & Fricke, W. F. Resources and costs for microbial sequence analysis evaluated using virtual machines and cloud computing. PLoS ONE 6, e26624 (2011).

    ADS  CAS  Article  Google Scholar 

  78. 78

    Chitsaz, H. et al. Efficient de novo assembly of single-cell bacterial genomes from short-read data sets. Nature Biotechnol. 29, 915–921 (2011).

    CAS  Article  Google Scholar 

  79. 79

    Dichosa, A. E. et al. Artificial polyploidy improves bacterial single cell genome recovery. PLoS ONE 7, e37387 (2012).

    ADS  CAS  Article  Google Scholar 

  80. 80

    Benson, A. K. et al. Individuality in gut microbiota composition is a complex polygenic trait shaped by multiple environmental and host genetic factors. Proc. Natl Acad. Sci. USA 107, 18933–18938 (2010).

    ADS  CAS  Article  Google Scholar 

  81. 81

    Elinav, E. et al. NLRP6 inflammasome regulates colonic microbial ecology and risk for colitis. Cell 145, 745–757 (2011).

    CAS  Article  Google Scholar 

  82. 82

    Hooper, L. V., Littman, D. R. & Macpherson, A. J. Interactions between the microbiota and the immune system. Science 336, 1268–1273 (2012).

    ADS  CAS  Article  Google Scholar 

  83. 83

    Handelsman, J., Rondon, M. R., Brady, S. F., Clardy, J. & Goodman, R. M. Molecular biological access to the chemistry of unknown soil microbes: a new frontier for natural products. Chem. Biol. 5, R245–R249 (1998).

    CAS  Article  Google Scholar 

  84. 84

    Riesenfeld, C. S., Schloss, P. D. & Handelsman, J. Metagenomics: genomic analysis of microbial communities. Annu. Rev. Genet. 38, 525–552 (2004).

    CAS  Article  Google Scholar 

  85. 85

    Hooper, L. V. & Gordon, J. I. Commensal host–bacterial relationships in the gut. Science 292, 1115–1118 (2001).

    ADS  CAS  Article  Google Scholar 

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Acknowledgements

The author gratefully acknowledges generous support from the National Institutes of Health.

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Weinstock, G. Genomic approaches to studying the human microbiota. Nature 489, 250–256 (2012). https://doi.org/10.1038/nature11553

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