Metagenoms: Difference between revisions

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== SIMHC ==
== SIMHC ==


* 113 reference genomes  
* 113 reference genomes : 89 complete, 24 incomplete
* 116771 Sanger reads from 3 insert libs (small,med,large)
* 116771 Sanger reads from 3 insert libs (small,med,large)
   #reads  min    max    mean    median  n50    sum
   #reads  min    max    mean    median  n50    sum
Line 72: Line 72:
   ...
   ...
* read coverage of each organism 0.09 ..0.53X
* read coverage of each organism 0.09 ..0.53X
   0.53X: Moorella thermoacetica ATCC 39073 (Firmicutes)
   0.53X: Moorella thermoacetica ATCC 39073 (NC_007644 2,628,784bp 55.79%GC) (Firmicutes)
   0.09X: Xylella fastidiosa Ann-1
   0.09X: Xylella fastidiosa Ann-1

Revision as of 14:40, 5 June 2008

Web sites

Articles

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

SIMHC

  • 113 reference genomes : 89 complete, 24 incomplete
  • 116771 Sanger reads from 3 insert libs (small,med,large)
 #reads  min     max     mean    median  n50     sum
 116771  43      3754    950     968     982     110875383
  • More than 50% of reads are from Proteobacteria; Gammaproteobacteria
 Proteobacteria  73261
 Firmicutes      15707
 Actinobacteria  10744
 ...
  • read coverage of each organism 0.09 ..0.53X
 0.53X: Moorella thermoacetica ATCC 39073 (NC_007644 2,628,784bp 55.79%GC) (Firmicutes)
 0.09X: Xylella fastidiosa Ann-1