Metagenoms: Difference between revisions

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== Web sites ==  
== Web sites ==  
* [http://www.ncbi.nlm.nih.gov/genomes/lproks.cgi NCBI Bacterial Genomes] 647 Complete, 1067 in Progress
* [http://fames.jgi-psf.org/ JGI FAMeS]
* [http://fames.jgi-psf.org/ JGI FAMeS]
* [http://fames.jgi-psf.org/cgi-bin/dataset_desc.pl?dataset=soil JGI SIMHC]
* [http://fames.jgi-psf.org/cgi-bin/dataset_desc.pl?dataset=soil JGI SIMHC]

Revision as of 13:44, 5 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

  • Baylor HMP list of 353 genomes targeted for sequencing by the 4 centers
  • JCVI HMP 50 genomes (oral,skin,vagina)

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 cells 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