Metagenoms: Difference between revisions

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NIH Roadmap
NIH Roadmap
1. Sequence the genomes of 200 microbes that have been isolated from the human body;
# Sequence the genomes of 200 microbes that have been isolated from the human body;
2. Recruit a set of healthy donors and obtain samples from a set of body regions  
# Recruit a set of healthy donors and obtain samples from a set of body regions  
3. Perform initial 16S rDNA gene metagenomic sequence analyses to estimate the complexity of the microbiota at these sites.
# Perform initial 16S rDNA gene metagenomic sequence analyses to estimate the complexity of the microbiota at these sites.
Centers: Baylor, Broad, JCVI, WUSTL
Centers: Baylor, Broad, JCVI, WUSTL



Revision as of 14:50, 2 June 2008

Articles

 * Need for more RefSeqs; sequence the genomes of 100 cultured representatives of the phylogenetic diversity in the human gut microbiota

Web sites

HMP

NIH Roadmap

  1. Sequence the genomes of 200 microbes that have been isolated from the human body;
  2. Recruit a set of healthy donors and obtain samples from a set of body regions
  3. Perform initial 16S rDNA gene metagenomic sequence analyses to estimate the complexity of the microbiota at these sites.

Centers: Baylor, Broad, JCVI, WUSTL

  • ~10times more bateria than human cells in the body
  • small-subunit (16S) ribosomal RNA gene-sequence-based surveys:
 * found in all microorganisms 
 * has enough sequence conservation for accurate alignment 
 * has enough variation for phylogenetic analyses.
  • skin, mouth, oesophagus, stomach, colon and vagina
  • largest reported data sets are for the gut
  • most of the 10–100 trillion microorganisms in the human gastrointestinal tract live in the colon.
  • more than 90% of all phylogenetic types (phylotypes) of colonic bacteria belong to just 2 of the 70 known divisions (phyla) in the domain Bacteria: the Firmicutes and the Bacteroidetes.

Firmicutes (Gram-positive bacteria) : 639 Genome Sequences

   * Bacilli    472
   * Clostridia    106
   * Erysipelotrichi    1
   * Mollicutes    60
   * Thermolithobacteria   
   * unclassified Firmicutes sensu stricto   
   * environmental samples    

Bacteroidetes : 53 Genome Sequences

   * Bacteroidetes (class)    22
   * Flavobacteria    21
   * Sphingobacteria    8
   * unclassified Bacteroidetes    1
   * environmental samples    1

Actinobacteria

  • In colon, the differences between individuals are greater than the differences between different sampling sites in one individuall
  • Comunirties are usually stable over time