Metagenoms: Difference between revisions
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* [http://www.sciencemag.org/cgi/content/abstract/312/5778/1355 Gill] | * [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/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/HGMISeq.pdf Human Gut Microbiome Initiative (HGMI)] | * [http://www.genome.gov/Pages/Research/Sequencing/SeqProposals/HGMISeq.pdf Human Gut Microbiome Initiative (HGMI)] | ||
Revision as of 14:24, 2 June 2008
Articles
Web sites
HMP
- ~10times more bateria 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
- In colon, the differences between individuals are greater than the differences between different sampling sites in one individuall
- Comunirties are usually stable over time