Metagenoms

Web sites

• NCBI Bacterial Genomes 647 Complete, 1067 in Progress
• JGI Fidelity of Analysis of Metagenomic Samples (FAMeS)
• JGI Simultaed High Complexity (SIMHC)
• Human Microbiome Project (HMP) @ NIH
• WUSTL Human Gut Microbiome (HGMI) 41 genomes
• Baylor HMP list of 353 genomes targeted for sequencing by the 4 centers
• JCVI HMP 50 genomes (oral,skin,vagina)
• JGI IMG
• HGMI at NIH
• HGMI TA ~150K Sanger traces; trimming points are given

Articles

• Kurokawa
• Gill
• JGI
• HMP Nature Oct 2007
• Human Microbiome Pilot Project (HMPP)
• Human Gut Microbiome Initiative (HGMI) Need for more RefSeqs; sequence the genomes of 100 cultured representatives of the phylogenetic diversity in the human gut microbiota
• Nature Reviews: Microbiology in the post-genomic era
• IMG NAR 2007

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
• 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 (Firmicutes)
 0.09X: Xylella fastidiosa Ann-1