Metagenoms

Links

• Kurokawa article
• Gill article
• [1]

• JGI FAMeS
• JGI SIMHC
• Human Microbiome Project @ NIH
• {http://www.nature.com/nature/journal/v449/n7164/full/nature06244.html HMP Nature article Oct 2007]

HMP

• ~10X 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