Metagenoms: Difference between revisions
Jump to navigation
Jump to search
No edit summary |
No edit summary |
||
| Line 7: | Line 7: | ||
* [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)] | ||
* 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] | |||
== Web sites == | == Web sites == | ||
| Line 12: | Line 13: | ||
* [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] | ||
* [http://genome.wustl.edu/pub/organism/Microbes/Human_Gut_Microbiome/ WUSTL HGMI] | * [http://genome.wustl.edu/pub/organism/Microbes/Human_Gut_Microbiome/ WUSTL HGMI] 41 genomes | ||
== HMP == | == HMP == | ||
Revision as of 14:47, 2 June 2008
Articles
* Need for more RefSeqs; sequence the genomes of 100 cultured representatives of the phylogenetic diversity in the human gut microbiota
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
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