Metagenoms: Difference between revisions
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= Web sites = | |||
* [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 | ||
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* [ftp://ftp.ncbi.nih.gov/pub/TraceDB/16729_uncultured_bacteria/ HGMI TA] ~150K Sanger traces; trimming points are given | * [ftp://ftp.ncbi.nih.gov/pub/TraceDB/16729_uncultured_bacteria/ HGMI TA] ~150K Sanger traces; trimming points are given | ||
= Articles = | |||
* [http://dnaresearch.oxfordjournals.org/cgi/reprint/dsm018v1 Kurokawa] | * [http://dnaresearch.oxfordjournals.org/cgi/reprint/dsm018v1 Kurokawa] | ||
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* [http://nar.oxfordjournals.org/cgi/reprint/gkm846v1 IMG NAR 2007] | * [http://nar.oxfordjournals.org/cgi/reprint/gkm846v1 IMG NAR 2007] | ||
= HMP = | |||
NIH Roadmap | NIH Roadmap | ||
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* Comunirties are usually stable over time | * Comunirties are usually stable over time | ||
= SIMHC = | |||
=== | == Data == | ||
=== Online === | |||
* 113 reference genomes : 89 complete, 24 incomplete | * 113 reference genomes : 89 complete, 24 incomplete | ||
* 118084 Sanger reads from 3 insert libs (small,med,large) | * 118084 Sanger reads from 3 insert libs (small,med,large) | ||
| Line 76: | Line 78: | ||
0.09X: Xylella fastidiosa Ann-1 | 0.09X: Xylella fastidiosa Ann-1 | ||
=== | === Local === | ||
* 113 reference genomes : 89 complete, 24 incomplete | * 113 reference genomes : 89 complete, 24 incomplete | ||
Revision as of 15:46, 6 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
SIMHC
Data
Online
- 113 reference genomes : 89 complete, 24 incomplete
- 118084 Sanger reads from 3 insert libs (small,med,large)
#reads min max mean median n50 sum 116771 43 3754 950 968 982 110875383
- More than 50% of reads are from Proteobacteria; Gammaproteobacteria
Proteobacteria 73261 Firmicutes 15707 Actinobacteria 10744 ...
- read coverage of each organism 0.09 ..0.53X
0.53X: Moorella thermoacetica ATCC 39073 (1426 reads; NC_007644 2,628,784bp 55.79%GC) (Firmicutes) 0.09X: Xylella fastidiosa Ann-1
Local
- 113 reference genomes : 89 complete, 24 incomplete
- 116771 Sanger reads from 3 insert libs (small,med,large)
- 118084-116771=1313 Moorella and Xylella were discarded !!!
- read coverage of each organism ...
0.23X: Moorella thermoacetica ATCC 39073 (740 reads; NC_007644 2,628,784bp 55.79%GC) (Firmicutes)
Assemblies
Contig stats
#elem min max mean median n50 sum singl
phrap-ctg 23398 73 8603 1289 1194 1341 30,163,430 66524 arachne-ctg 578 240 6300 1878 1822 1985 1,085,508 115300 jazz-scaff 860 1000 39837 3236 1105 7278 2,783,247 109080
CA-scaff 4327 1000 48,861 1682 1342 1456 7,278,044 76270 # OBT trimming of the reads CA-ctg 4491 1000 5252 1419 1340 1388 6,374,863 CA-deg 11611 66 5920 850 833 898 9,865,902
AMOS-ctg 95372 72 7426 975 916 964 92,959,055 5661 # alignment based trimming of the reads; casm-layout "-S -r" have been used minimus2-ctg 15211 85 4699 1257 1205 1305 19,119,413 82535 # alignment based trimming of the reads