Metagenoms: Difference between revisions
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* Need for more RefSeqs; sequence the genomes of 100 cultured representatives of the phylogenetic diversity in the human gut microbiota | * 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://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://fames.jgi-psf.org/ JGI FAMeS] | * [http://fames.jgi-psf.org/ JGI FAMeS] | ||
Revision as of 15:03, 3 June 2008
Articles
- Kurokawa
- Gill
- JGI
- HMP Nature Oct 2007
- HMP Pilot Project Proposal
- 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
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
- Sequence the genomes of 200 microbes that have been isolated from the human body;
- Recruit a set of healthy donors and obtain samples from a set of body regions
- 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