Metagenomics - Revision history

Christoph at 23:59, 23 July 2012

2012-07-23T23:59:57Z

Christoph at 23:05, 23 July 2012

2012-07-23T23:05:31Z

Christoph at 23:02, 23 July 2012

2012-07-23T23:02:34Z

Christoph at 00:01, 16 July 2008

2008-07-16T00:01:22Z

New page

'''Metagenomics''' (also '''Environmental Genomics''', '''Ecogenomics''' or '''Community Genomics''') is the study of genetic material recovered directly from environmental samples. Traditional microbiology and microbial genome sequencing rely upon cultivated clonal cultures. This relatively new field of genetic research enables studies of organisms that are not easily cultured in a laboratory as well as studies of organisms in their natural environment.

I did some research in metagenomics whilst in Denmark.

==Further reading==

=== Review articles ===
* Edwards RA, & Rohwer F. Viral metagenomics. Nat Rev Microbiol. 2005 3(6):504-10. [http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=pubmed&dopt=AbstractPlus&list_uids=15886693 PubMed]
* Eisen, J. A. (2007). Environmental shotgun sequencing: its potential and challenges for studying the hidden world of microbes. [http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pbio.0050082 ''PLoS Biology 5(3): e82'']
* Green, B. D. & Keller, M. (2006). Capturing the uncultivated majority. ''Current Opinion in Biotechnology'' 17[3], 236-240.
* Handelsman J. (2004). Metagenomics: application of genomics to uncultured microorganisms. ''Microbiology and Molecular Biology Reviews'' '''68''':669-685.
* Keller, M. & Sengler, K. (2004). Tapping into microbial diversity. Nature Reviews Microbiology 2[2], 141-150.
* Lombard, N. ''et al.'' (2006). The metagenomics of microbial communities. ''Biofutur'' 24-7.
* Riesenfeld, C. S. ''et al.'' (2004). Metagenomics: genomic analysis of microbial communities. ''Annu Rev Genet'' '''38''': 525-52.
* Rodriguez Valera, F. (2002). Approaches to prokaryotic biodiversity: a population genetics perspective. ''Environmental Microbiology'' '''4''': 628-33.
* Rodriguez-Valera. (2004). Environmental genomics, the big picture?. ''FEMS Microbiology Letters'' '''231''':153-158.
* Torsvik, V. & Ovreas, L. (2002). Microbial diversity and function in soil: from genes to ecosystems. ''Current opinion in Microbiology'' '''5''': 240-5.
* Whitaker, R. J. & Banfield, J. F. (2006). Population genomics in natural microbial communities. ''Trends in Ecology & Evolution'' '''21''': 508-16.
* Worden, A. Z. ''et al.'' (2006). In-depth analyses of marine microbial community genomics. ''Trends in Microbiology'' '''14''': 331-6.
* Xu, J. P. (2006). Microbial ecology in the age of genomics and metagenomics: concepts, tools, and recent advances. ''Molecular Ecology'' '''15''': 1713-31.

=== Methods ===
* Beja, O. ''et al.'' (2000). Construction and analysis of bacterial artificial chromosome libraries from a marine microbial assemblage. ''Environmental Microbiology'' '''2''': 516-29.
* Sebat, J. L. ''et al.'' (2003). Metagenomic profiling: Microarray analysis of an environmental genomic library. ''Applied and Environmental Microbiology'' '''69''': 4927-34.
* Suzuki, M. T. ''et al.'' (2004). Phylogenetic screening of ribosomal RNA gene-containing clones in bacterial artificial chromosome (BAC) libraries from different depths in Monterey Bay. ''Microbial Ecology'' '''48''': 473-88.

=== Bioinformatics ===
* [http://www.genome.org/cgi/reprint/gr.5969107v1 Huson, D.H., A. Auch, Ji Qi and S.C. Schuster, MEGAN Analysis of Metagenomic Data, Genome Research. 17:377-386, 2007]
* [http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=pubmed&dopt=AbstractPlus&list_uids=16873483 Krause L, Diaz NN, Bartels D, Edwards RA, Puhler A, Rohwer F, Meyer F, Stoye J. Finding novel genes in bacterial communities isolated from the environment. Bioinformatics. 2006 15;22(14):e281-9.]
* [http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=pubmed&dopt=AbstractPlus&list_uids=16549025 Rodriguez-Brito B, Rohwer F, Edwards RA. An application of statistics to comparative metagenomics. BMC Bioinformatics. 2006 20;7:162].
* [http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=pubmed&dopt=AbstractPlus&list_uids=17936679 Raes, J., Foerstner, K.U. & Bork, P. (2007) Get the most out of your metagenome: computational analysis of environmental sequence data. Curr Opin Microbiol, in press.]
* [http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=pubmed&dopt=AbstractPlus&list_uids=17717083 Harrington, E.D., Singh, A.H., Doerks, T., Letunic, I., von Mering, C., Jensen, L.J., Raes, J. & Bork, P. (2007) Quantitative assessment of protein function predicion from metagenomics shotgun sequences. Proc. Natl. Acad. Sci. USA 104, 13913-8]
* Tress, M. L. ''et al.'' (2006). An analysis of the Sargasso Sea resource and the consequences for database composition. ''Bmc Bioinformatics'' '''7'''
* Foerstner KU, von Mering C, Hooper SD, Bork P (2005) Environments shape the nucleotide composition of genomes. EMBO Rep. 6(12): 1208-13
* Raes, J., Korbel, J.O., Lercher, M.J., Von Mering, C. & Bork, P. (2007) Prediction of effective genome size in metagenomic samples. Genome Biology 8, R10 [http://genomebiology.com/2007/8/1/R10]
* von Mering, C., Hugenholtz, P., Raes, J., Tringe, S.G., Doerks, T., Jensen, L.J., Ward N. & Bork, P. (2007) Quantitative phylogenetic assessment of microbial communities in diverse environments. Science 315, 1126-1130
* [http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=17468765 Mavromatis K, Ivanova N, Barry K, Shapiro H, Goltsman E, McHardy AC, Rigoutsos I, Salamov A, Korzeniewski F, Land M, Lapidus A, Grigoriev I, Richardson P, Hugenholtz P, Kyrpides NC. (2007) Use of simulated data sets to evaluate the fidelity of metagenomic processing methods. Nat Methods. 4(6):495-500]
* [http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=16873494 Markowitz VM, Ivanova N, Palaniappan K, Szeto E, Korzeniewski F, Lykidis A, Anderson I, Mavromatis K, Kunin V, Garcia Martin H, Dubchak I, Hugenholtz P, Kyrpides NC. (2006) An experimental metagenome data management and analysis system. Bioinformatics. 22(14):e359-67]
* [http://nar.oxfordjournals.org/cgi/content/full/gkm869v1 Markowitz VM, Ivanova NN, Szeto E, Palaniappan K, Chu K, Dalevi D, Chen IM, Grechkin Y, Dubchak I, Anderson I, Lykidis A, Mavromatis K, Hugenholtz P, Kyrpides NC. (2007) IMG/M: a data management and analysis system for metagenomes. Nucleic Acids Res. Epub]

=== Marine ecosystems ===
* [http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pbio.0040368 Angly, F. E. ''et al.'' (2006). The marine viromes of four oceanic regions. ''PloS Biology'' '''4''': 2121-31.]
* Beja, O. ''et al.'' (2000). Bacterial rhodopsin: Evidence for a new type of phototrophy in the sea. ''Science'' '''289''': 1902-6.
* Beja, O. ''et al.'' (2001). Proteorhodopsin phototrophy in the ocean. ''Nature'' '''411''': 786-9.
* Beja, O. ''et al.'' (2002). Unsuspected diversity among marine aerobic anoxygenic phototrophs. ''Nature'' '''415''': 630-3.
* Culley, A. I. ''et al.'' (2006). Metagenomic analysis of coastal RNA virus communities. ''Science'' '''312''': 1795-8.
* DeLong, E. F. ''et al.'' (2006). Community genomics among stratified microbial assemblages in the ocean's interior. ''Science'' '''311''': 496-503.
* Hallam, S. J. ''et al.'' (2006). Genomic analysis of the uncultivated marine crenarchaeote Cenarchaeum symbiosum. ''Proceedings of the National Academy of Sciences of the United States of America'' '''103''': 18296-301.
* John, D. E. ''et al.'' (2006). Gene diversity and organization in rbcL-containing genome fragments from uncultivated ''Synechococcus'' in the Gulf of Mexico. ''Marine Ecology-Progress Series'' '''316''': 23-33.
* [http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pbio.0050017 Kannan N. ''et al.'' (2007). Structural and Functional Diversity of the Microbibial Kinome. ''PloS Biology'' '''5''': 467-478]
* [http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pbio.0050077 Rusch D. B. ''et al.'' (2007). The Sorcerer II Global Ocean Sampling Expedition: Northwest Atlantic through Eastern Tropical Pacific. ''PloS Biology'' '''5''': 398-431]
* [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=15845853&query_hl=3&itool=pubmed_docsum Tringe, S. G. ''et al.'' (2005). Comparative metagenomics of microbial communities. ''Science'' '''308''': 554-7.]
* Woyke, T. ''et al.'' (2006). Symbiosis insights through metagenomic analysis of a microbial consortium. ''Nature'' '''443''': 950-5.
* [http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pbio.0050016 Yooseph S. ''et al.'' (2007). The Sorcerer II Global Ocean Sampling Expedition: Expanding the Universe of Protein Families. 'PloS Biology'' '''5''': 432-466]
* Yutin, N. & Beja, O. (2005). Putative novel photosynthetic reaction centre organizations in marine aerobic anoxygenic photosynthetic bacteria: insights from metagenomics and environmental genomics. ''Environmental Microbiology'' '''7''': 2027-33.

=== Sediments ===
* Abulencia, C. B., Wyborski, D. L., Garcia, J. A., Podar, M., Chen, W., Chang, S. H. et al. (2006). Environmental whole-genome amplification to access microbial populations in contaminated sediments. Applied and Environmental Microbiology 72[5], 3291-3301.
* Breitbart et al. (2004). ''Diversity and population structure of a nearshore marine sediment viral community''. Proceedings of the Royal Society B '''271''': 565-574.

=== Extreme environments ===
* Baker, B. J. ''et al.'' (2006). Lineages of acidophilic archaea revealed by community genomic analysis. ''Science'' '''314''': 1933-5.

=== Medical Sciences and biotechnological applications ===
* Breitbart et al. (2003). ''Metagenomic analyses of an uncultured viral community from human feces''. Journal of Bacteriology '''185''':6220-6223.
* Breitbart, M. and Rohwer, F. (2005) Method for discovering novel DNA viruses in blood using viral particle selection and shotgun sequencing. BioTechniques, 39, 729-736.
* Gill, S. R. ''et al.'' (2006). Metagenomic analysis of the human distal gut microbiome. ''Science'' '''312''': 1355-9.
* Mathur, E., Toledo, G., Green, B. D., Podar, M., Richardson, T. H., Kulwiec (2005). A biodiversity-based approach to development of performance enzymes: Applied metagenomics and directed evolution. Industrial Biotechnology, 1, 283-287.
* Schloss, P. D. & Handelsman, J. (2003). Biotechnological prospects from metagenomics. ''Current Opinion in Biotechnology'' '''14''': 303-10.
* Zengler, K., Paradkar, A., & Keller, M. (2005). New methods to access microbial diversity for small molecule discovery. Natural Products , 275-293.
* Zhang, T., Breitbart, M., Lee, W.H., Run, J.Q., Wei, C.L., Soh, S.W., Hibberd, M.L., Liu, E.T., Rohwer, F. and Ruan, Y. (2006) ''RNA viral community in human feces: prevalence of plant pathogenic viruses''. PLoS biology, '''4''', e3.

=== Ancient DNA===
* [http://www.sciencemag.org/cgi/content/abstract/1123360v1?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&fulltext=wooly+mammoth&searchid=1135358119618_7589&FIRSTINDEX=0&journalcode=sci H. N. Poinar, C. Schwarz, Ji Qi, B. Shapiro, R. D. E. MacPhee, B. Buigues, A. Tikhonov, D. H. Huson, L. P. Tomsho, A. Auch, M. Rampp, W. Miller, S. C. Schuster, Metagenomics to Paleogenomics: Large-Scale Sequencing of Mammoth DNA, Science 311:392-394, 2006]

==External links==
* [http://www-ab.informatik.uni-tuebingen.de/software/megan/ MEGAN] MEtaGenome ANalyzer. A stand-alone metagenome analysis tool.
* [http://dels.nas.edu/metagenomics/ Metagenomics and Our Microbial Planet] A website on metagenomics and the vital role of microbes on Earth from the [http://nationalacademies.org National Academies.]
* [http://books.nap.edu/catalog.php?record_id=11902 The New Science of Metagenomics: Revealing the Secrets of Our Microbial Planet] A report released by the National Research Council in March 2007. Also, see the [http://dels.nas.edu/dels/rpt_briefs/metagenomics_brief_final.pdf Report In Brief.]
* [http://img.jgi.doe.gov/m IMG/M] The Integrated Microbial Genomes system, for metagenome analysis by the DOE-JGI.
* [http://camera.calit2.net/index.php CAMERA] Cyberinfrastructure for Metagenomics, data repository and tools for metagenomics research.
*[http://www.scq.ubc.ca/?p=509 A good overview of metagenomics from the Science Creative Quarterly]
*[http://www.genomesonline.org/gold.cgi?want=Metagenomes list of Metagenome Projects from genomesonline.org]
* [http://metagenomics.theseed.org The SEED] publicly available, free, metagenomics annotation pipeline for pyrosequences, Sanger sequences, and other sequence approaches.
* [http://nihroadmap.nih.gov/hmp/ Human microbiome project]
* [http://www.metahit.eu/ MetaHIT] official website for the EU-funded project : Metagenomics of the Human Intestinal Tract
* [http://annotathon.univ-mrs.fr/ Annotathon] Bioinformatics Training Through Metagenomic Sequence Annotation
*[[wikipedia:Metagenomics]]

[[Category:Bioinformatics]]

@@ Line 7: / Line 7: @@
 Metagenomics is the study of the DNA from all the genomes in an environment. The term ''meta'' implies that this transcends traditional genomics. Most of the bacteria living in an environment will not grow in standard laboratory media. This is true for more than 99% of the species present in a typical soil sample, and similar numbers are likely to hold for bacteria growing in different environmental niches. Thus, by sampling all of the DNA from a given environment, it is possible to gain much additional information that would not be available from traditional methods that depend on single, pure monocultures of a well-characterized bacterium. The area of metagenomics is relatively new and rapidly changes as technology allows more and better sampling of the environmental DNA. The consequences of current improvements in speed and output of genome technology to future research are discussed.<ref>David Wayne Ussery, Trudy M. Wassenaar, Stefano Borini (2009). ''Computing for Comparative Microbial Genomics: Bioinformatics for Microbiologists''. Springer. ISBN 978-1849967631.</ref>
 </blockquote>
 ==References==

@@ Line 17: / Line 17: @@
 ==Further reading==
 === Review articles ===
 * Edwards RA, & Rohwer F. "Viral metagenomics". Nat Rev Microbiol. 2005 3(6):504-10. [http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=pubmed&dopt=AbstractPlus&list_uids=15886693 PubMed]

@@ Line 2: / Line 2: @@
 I did some research in metagenomics whilst in Denmark.
 ==Further reading==
 === Review articles ===
-* Edwards RA, & Rohwer F.	Viral metagenomics. Nat Rev Microbiol. 2005 3(6):504-10. [http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=pubmed&dopt=AbstractPlus&list_uids=15886693 PubMed]
+* Edwards RA, & Rohwer F. "Viral metagenomics". Nat Rev Microbiol. 2005 3(6):504-10. [http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=pubmed&dopt=AbstractPlus&list_uids=15886693 PubMed]
 * Eisen, J. A. (2007). Environmental shotgun sequencing: its potential and challenges for studying the hidden world of microbes. [http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pbio.0050082 ''PLoS Biology 5(3): e82'']
 * Green, B. D. & Keller, M. (2006). Capturing the uncultivated majority. ''Current Opinion in Biotechnology'' 17[3], 236-240.