• Metagenomics
  • Whole-genome shotgun sequencing
  • Environmental metagenomics
  • Human microbiome
    –Precision medicine
  • Conclusion
        Metagenomics
  • Environmental genomics.
  • DNA analysis without lab-based cultivation.
  • Better  understanding  of  community-based 
   microbial biology, ecology, and evolution.
   Whole-genome shotgun sequencing
    Environmental Genome Shotgun Sequencing of 
         the Sargasso Sea. Venter et al. (2004) 
   • 1.045 billion base pairs of nonredundant sequence. 
    – Gene content, diversity, and relative abundance of the 
      organisms.  
    – At  least  1.800  genomic  species  based  on  sequence 
      relatedness.
    – At least 148 previously unknown bacterial phylotypes. 
    – Over 1.2 million previously unknown genes . 
   • Quantitative picture.
   • Limitations.
    – Well-conserved regions may assemble across species. 
    – Closely related organisms may contain stretches of high 
      similarity that co-assemble.
    – At  lower  coverage  less  statistical  support  for  the 
      scaffolds.
    – Sequencing cost.
    Environmental Genome Shotgun Sequencing of 
         the Sargasso Sea. Venter et al. (2004) 
   • 1.045 billion base pairs of nonredundant sequence. 
    – Gene content, diversity, and relative abundance of the 
      organisms.  
    – At  least  1.800  genomic  species  based  on  sequence 
      relatedness.
    – At least 148 previously unknown bacterial phylotypes. 
    – Over 1.2 million previously unknown genes . 
   • Quantitative picture.
   • Limitations.
    – Well-conserved regions may assemble across species. 
    – Closely related organisms may contain stretches of high 
      similarity that co-assemble.
    – At  lower  coverage  less  statistical  support  for  the 
      scaffolds.
    – Sequencing cost.