Metagenoms: Difference between revisions
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== | == Articles == | ||
* [http://dnaresearch.oxfordjournals.org/cgi/reprint/dsm018v1 Kurokawa | * [http://dnaresearch.oxfordjournals.org/cgi/reprint/dsm018v1 Kurokawa] | ||
* [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] | * [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)] | |||
== Web sites == | |||
* [http://fames.jgi-psf.org/ JGI FAMeS] | * [http://fames.jgi-psf.org/ JGI 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 @ NIH] | ||
== HMP == | == HMP == | ||
* ~ | * ~10times more bateria than human cells in the body | ||
* small-subunit (16S) ribosomal RNA gene-sequence-based surveys : | * small-subunit (16S) ribosomal RNA gene-sequence-based surveys: | ||
* found in all microorganisms | * found in all microorganisms | ||
* has enough sequence conservation for accurate alignment | * has enough sequence conservation for accurate alignment | ||
| Line 21: | Line 23: | ||
* 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. | * 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) | Firmicutes (Gram-positive bacteria) : 639 Genome Sequences | ||
* Bacilli 472 | * Bacilli 472 | ||
* Clostridia 106 | * Clostridia 106 | ||
| Line 29: | Line 31: | ||
* unclassified Firmicutes sensu stricto | * unclassified Firmicutes sensu stricto | ||
* environmental samples | * environmental samples | ||
Bacteroidetes : 53 Genome Sequences | |||
Bacteroidetes | |||
* Bacteroidetes (class) 22 | * Bacteroidetes (class) 22 | ||
* Flavobacteria 21 | * Flavobacteria 21 | ||
| Line 36: | Line 37: | ||
* unclassified Bacteroidetes 1 | * unclassified Bacteroidetes 1 | ||
* environmental samples 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 | |||
Revision as of 14:24, 2 June 2008
Articles
- Kurokawa
- Gill
- JGI
- {http://www.nature.com/nature/journal/v449/n7164/full/nature06244.html HMP Nature Oct 2007]
- Human Gut Microbiome Initiative (HGMI)
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