Metagenoms: Difference between revisions

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== Articles ==
* [http://dnaresearch.oxfordjournals.org/cgi/reprint/dsm018v1  Kurokawa]
* [http://www.sciencemag.org/cgi/content/abstract/312/5778/1355 Gill]
* [http://www.nature.com/nmeth/journal/v4/n6/pdf/nmeth1043.pdf JGI]
* [http://www.nature.com/nature/journal/v449/n7164/full/nature06244.html HMP Nature Oct 2007]
* [http://www.genome.gov/Pages/Research/Sequencing/SeqProposals/HMPP_Proposal.pdf HMP Pilot Project Proposal]
* [http://www.genome.gov/Pages/Research/Sequencing/SeqProposals/HGMISeq.pdf 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
* [http://www.nature.com/nrmicro/journal/v6/n6/pdf/nrmicro1901.pdf Nature Reviews: Microbiology in the post-genomic era]
* [http://nar.oxfordjournals.org/cgi/reprint/gkm846v1 IMG NAR 2007]
== Web sites ==  
== Web sites ==  


* [http://www.ncbi.nlm.nih.gov/genomes/lproks.cgi NCBI Bacterial Genomes] 647 Complete, 1067 in Progress
* [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 Fidelity of Analysis of Metagenomic Samples (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]
* [http://nihroadmap.nih.gov/hmp/ Human Microbiome Project @ NIH]
* [http://nihroadmap.nih.gov/hmp/ Human Microbiome Project (HMP) @ NIH]
* [http://genome.wustl.edu/pub/organism/Microbes/Human_Gut_Microbiome/ WUSTL HGMI] 41 genomes
* [http://genome.wustl.edu/pub/organism/Microbes/Human_Gut_Microbiome/ WUSTL HGMI] 41 genomes
* [http://www.hgsc.bcm.tmc.edu/microbiome-index.xsp Baylor HMP] list of 353 genomes targeted for sequencing by the 4 centers
* [http://www.hgsc.bcm.tmc.edu/microbiome-index.xsp Baylor HMP] list of 353 genomes targeted for sequencing by the 4 centers
* [http://www.jcvi.org/cms/research/projects/hmp/overview/ JCVI HMP] 50 genomes (oral,skin,vagina)
* [http://www.jcvi.org/cms/research/projects/hmp/overview/ JCVI HMP] 50 genomes (oral,skin,vagina)
* [http://img.jgi.doe.gov/cgi-bin/pub/main.cgi JGI IMG]
* [http://img.jgi.doe.gov/cgi-bin/pub/main.cgi JGI IMG]
* [http://www.ncbi.nlm.nih.gov/sites/entrez?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=16729 HGMI at NIH]
* [http://www.ncbi.nlm.nih.gov/sites/entrez?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=16729 HGMI at NIH]
* [ftp://ftp.ncbi.nih.gov/pub/TraceDB/16729_uncultured_bacteria/ HGMI TA] ~150K Sanger traces; trimming points are given
* [ftp://ftp.ncbi.nih.gov/pub/TraceDB/16729_uncultured_bacteria/ HGMI TA] ~150K Sanger traces; trimming points are given
== Articles ==
* [http://dnaresearch.oxfordjournals.org/cgi/reprint/dsm018v1  Kurokawa]
* [http://www.sciencemag.org/cgi/content/abstract/312/5778/1355 Gill]
* [http://www.nature.com/nmeth/journal/v4/n6/pdf/nmeth1043.pdf JGI]
* [http://www.nature.com/nature/journal/v449/n7164/full/nature06244.html HMP Nature Oct 2007]
* [http://www.genome.gov/Pages/Research/Sequencing/SeqProposals/HMPP_Proposal.pdf Human Microbiome Pilot Project (HMPP)]
* [http://www.genome.gov/Pages/Research/Sequencing/SeqProposals/HGMISeq.pdf 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
* [http://www.nature.com/nrmicro/journal/v6/n6/pdf/nrmicro1901.pdf Nature Reviews: Microbiology in the post-genomic era]
* [http://nar.oxfordjournals.org/cgi/reprint/gkm846v1 IMG NAR 2007]


== HMP ==
== HMP ==

Revision as of 13:53, 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
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