Metagenoms: Difference between revisions
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* [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 Fidelity of Analysis of Metagenomic Samples (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 Simultaed High Complexity (SIMHC)] | ||
* [http://nihroadmap.nih.gov/hmp/ Human Microbiome Project (HMP) @ 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 Human Gut Microbiome (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) | ||
Revision as of 13:54, 5 June 2008
Web sites
- NCBI Bacterial Genomes 647 Complete, 1067 in Progress
- JGI Fidelity of Analysis of Metagenomic Samples (FAMeS)
- JGI Simultaed High Complexity (SIMHC)
- Human Microbiome Project (HMP) @ NIH
- WUSTL Human Gut Microbiome (HGMI) 41 genomes
- Baylor HMP list of 353 genomes targeted for sequencing by the 4 centers
- JCVI HMP 50 genomes (oral,skin,vagina)
- JGI IMG
- HGMI at NIH
- HGMI TA ~150K Sanger traces; trimming points are given
Articles
- Kurokawa
- Gill
- JGI
- HMP Nature Oct 2007
- Human Microbiome Pilot Project (HMPP)
- 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
- Nature Reviews: Microbiology in the post-genomic era
- IMG NAR 2007
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