Difference between revisions of "Metagenome"

From Opengenome.net
 
(7 intermediate revisions by 6 users not shown)
Line 1: Line 1:
 +
<p><strong>Metagenomics</strong> (also <strong>Environmental Genomics</strong>, <strong>Ecogenomics</strong> or <strong>Community Genomics</strong>) 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.</p>
 +
<p>An interesting overview of metagenomics is &quot;Welcome to life on the tiniest scales&quot;&nbsp;; written by Henry Nicholls, in March 17th 2007 New Scientist magazine (paid).</p>
 +
<p>Early environmental gene sequencing cloned specific genes (often the 16S rRNA gene) to produce a profile of diversity in a natural sample. Such work revealed that the vast majority of microbial diversity had been missed by cultivation-based methods. <sup class="reference" id="cite_ref-Hugenholz1998_0-0">[1]</sup> Recent studies use &quot;shotgun&quot; Sanger sequencing or chip-based pyrosequencing to get (mostly) unbiased samples of all genes from all members of sampled communities.</p>
  
 
+
<p>&nbsp;</p>
 
+
<h2><span class="mw-headline">History</span></h2>
 
+
<p>&nbsp;</p>
 
+
<h3><span class="mw-headline">Origin of the term</span></h3>
 
+
<p>The term &quot;metagenomics&quot; was first used by Jo Handelsman and others in the University of Wisconsin Department of Plant Pathology, and first appeared in publication in 1998. <sup class="reference" id="cite_ref-Handelsman1998_1-0">[2]</sup> The term <strong>metagenome</strong> referenced the idea that a collection of genes sequenced from the environment could be analyzed in way analogous to the study of a single genome. The exploding interest in environmental genetics, along with the buzzword-like nature of the term, has resulted in the broader use of <strong>metagenomics</strong> to describe any sequencing of genetic material from environmental (i.e. uncultured) samples, even work that focuses on one organism or gene. Recently, Kevin Chen and Lior Pachter (researchers at the University of California, Berkeley) defined metagenomics as &quot;the application of modern genomics techniques to the study of communities of microbial organisms directly in their natural environments, bypassing the need for isolation and lab cultivation of individual species.&quot; <sup class="reference" id="cite_ref-Chen2005_2-0">[3]</sup></p>
 
+
<p>&nbsp;</p>
 
+
<h3><span class="mw-headline">Environmental gene surveys</span></h3>
 
+
<p>Conventional sequencing begins with a culture of identical cells as a source of DNA. However, early metagenomic studies revealed that there are probably large groups of microorganisms in many environments that cannot be cultured and thus cannot be sequenced. These early studies focused on 16S ribosomal RNA sequences which are relatively short, often conserved within a species, and generally different between species. Many 16S rRNA sequences have been found which do not belong to any known cultured species, indicating that there are numerous non-isolated organisms out there.</p>
 
+
<p>Early molecular work in the field was conducted by Norman R. Pace and colleagues, who used PCR to explore the diversity of ribosomal RNA sequences. <sup class="reference" id="cite_ref-Lane1985_3-0">[4]</sup> The insights gained from these breakthrough studies led Pace to propose the idea of cloning DNA directly from environmental samples as early as 1985. <sup class="reference" id="cite_ref-Pace1985_4-0">[5]</sup> This led to the first report of isolating and cloning bulk DNA from an environmental sample, published by Pace and colleagues in 1991 <sup class="reference" id="cite_ref-Pace1991_5-0">[6]</sup> while Pace was in the Department of Biology at Indiana University. Considerable efforts ensured that these were not PCR false positives and supported the existence of a complex community of unexplored species. Although this methodology was limited to exploring highly conserved, non-protein coding genes, it did support early microbial morphology-based observations that diversity was far more complex than was known by culturing methods.</p>
 
+
<p>Soon after that, Healy reported the metagenomic isolation of functional genes from &quot;zoolibraries&quot; constructed from a complex culture of environmental organisms grown in the laboratory on dried grasses in 1995. <sup class="reference" id="cite_ref-Healy1995_6-0">[7]</sup> After leaving the Pace laboratory, Ed DeLong continued in the field and has published work that has largely laid the groundwork for environmental phylogenies based on signature 16S sequences, beginning with his group's construction of libraries from marine samples. <sup class="reference" id="cite_ref-Stein1996_7-0">[8]</sup></p>
 
+
<p>&nbsp;</p>
 
+
<h3><span class="mw-headline">Longer sequences from environmental samples</span></h3>
 
+
<p>Recovery of DNA sequences longer than a few thousand base pairs from environmental samples was very difficult until recent advances in molecular biological techniques, particularly related to constructing libraries in bacterial artificial chromosomes (BACs), provided better vectors for molecular cloning. <sup class="reference" id="cite_ref-Beja2000_8-0">[9]</sup></p>
 
+
<p>&nbsp;</p>
 
+
<h3><span class="mw-headline">Shotgun metagenomics</span></h3>
<div id="kbektt12891" style="overflow:auto;height:1px;">
+
<p>Advances in bioinformatics, refinements of DNA amplification, and proliferation of computational power have greatly aided the analysis of DNA sequences recovered from environmental samples. These advances have enabled the adaptation of shotgun sequencing to metagenomic samples. The approach, used to sequence many cultured microorganisms as well as the human genome, randomly shears DNA, sequences many short sequences, and reconstructs them into a consensus sequence. In 2002, Mya Breitbart, Forest Rohwer, and colleagues used environmental shotgun sequencing to show that 200 liters of seawater contains over 5000 different viruses. <sup class="reference" id="cite_ref-Breitbart2002_9-0">[10]</sup> Subsequent studies showed that there are &gt;1000 viral species in human stool and possibly a million different viruses per kilogram of marine sediment, including many bacteriophages. Essentially all of the viruses in these studies were new species. A 2004 metagenomic study of the Sargasso Sea found DNA from nearly 2000 different species including 148 types of bacteria never seen before. <sup class="reference" id="cite_ref-Venter2004_10-0">[11]</sup></p>
[http://www.superiormartialarts.com/Karate_Forum/posts/220.html buy ambien]
+
<p>Also in 2004, Gene Tyson, Jill Banfield, and colleagues at the University of California, Berkeley and the Joint Genome Institute sequenced DNA extracted from an acid mine drainage system. <sup class="reference" id="cite_ref-Tyson2004_11-0">[12]</sup> This effort resulted in the complete, or nearly complete, genomes for a handful of bacteria and archaea that had previously resisted attempts to culture them. It was now possible to study entire genomes without the biases associated with laboratory cultures. <sup class="reference" id="cite_ref-Hugenholz2002_12-0">[13]</sup></p>
[http://www.superiormartialarts.com/Karate_Forum/posts/221.html buy adipex]
+
<p>In 2006 Robert Edwards, Forest Rohwer, and colleagues at San Diego State University published the first sequences of environmental samples generated with so-called next generation sequencing, in this case chip based pyrosequencing developed by 454 Life Sciences. <sup class="reference" id="cite_ref-Edwards2006_13-0">[14]</sup> This technique for sequencing the DNA generates shorter fragments than the conventional techniques, however this limitation is compensated for by the very large number of sequences generated. In addition, this technique does not require cloning the DNA before sequencing, removing one of the main biases in metagenomics.</p>
[http://www.superiormartialarts.com/Karate_Forum/posts/222.html buy xenical]
+
<p>In 2007, Daniel Huson and Stephan Schuster developed and published the first stand-alone metagenome analysis tool, MEGAN, which can be used to perform a first analysis of a metagenomic shotgun dataset. This tool was originally developed to analyse the metagenome of a mammoth sample <sup class="reference" id="cite_ref-14">[15]</sup>.</p>
[http://www.superiormartialarts.com/Karate_Forum/posts/223.html buy valium]
+
<p>In 2007, Folker Meyer and Robert Edwards and a team at Argonne National Laboratory and the University of Chicago released the Metagenomics RAST server (MG-RAST) a community resource for metagenome data set analysis <sup class="reference" id="cite_ref-Meyer2008_15-0">[16]</sup> The SEED based free, public resource contains 158 public metagenome data sets (as of September 2008) and has so far been used for the analysis of several hundred metagenome data sets.</p>
[http://www.superiormartialarts.com/Karate_Forum/posts/224.html buy carisoprodol]
+
<p>&nbsp;</p>
[http://www.superiormartialarts.com/Karate_Forum/posts/225.html buy hydrocodone]
+
<h2><span class="mw-headline">Microbial Diversity</span></h2>
[http://www.superiormartialarts.com/Karate_Forum/posts/226.html order phentermine]
+
<p>Much of the interest in metagenomics comes from the discovery that the vast majority of microorganisms had previously gone unnoticed. Traditional microbiological methods relied upon laboratory cultures of organisms. Surveys of ribosomal RNA (rRNA) genes taken directly from the environment revealed that cultivation based methods find less than 1% of the bacteria and archaea species in a sample. <sup class="reference" id="cite_ref-Hugenholz1998_0-1">[1]</sup></p>
[http://www.superiormartialarts.com/Karate_Forum/posts/227.html anime wallpapers]
+
<p>&nbsp;</p>
[http://www.superiormartialarts.com/Karate_Forum/posts/228.html desktop wallpapers]
+
<h2><span class="mw-headline">Gene Surveys</span></h2>
[http://www.superiormartialarts.com/Karate_Forum/posts/229.html cell phone wallpapers]
+
<p>Shotgun sequencing and screens of clone libraries reveal genes present in environmental samples. This provides information both on which organisms are present and what metabolic processes are possible in the community. This can be helpful in understanding the ecology of a community, particularly if multiple samples are compared to each other. <sup class="reference" id="cite_ref-Allen2005_16-0">[17]</sup></p>
[http://www.superiormartialarts.com/Karate_Forum/posts/230.html wallpaper borders]
+
<p>&nbsp;</p>
[http://www.superiormartialarts.com/Karate_Forum/posts/231.html free ringtones]
+
<h2><span class="mw-headline">Environmental Genomes</span></h2>
[http://www.superiormartialarts.com/Karate_Forum/posts/232.html nextel ringtones]
+
<p>Shotgun metagenomics also is capable of sequencing nearly complete microbial genomes directly from the environment. <sup class="reference" id="cite_ref-Tyson2004_11-1">[12]</sup> Because the collection of DNA from an environment is largely uncontrolled, the most abundant organisms types in a sample are most highly represented in the resulting sequence data. To achieve the high coverage needed to fully resolve the genomes of underrepresented community members, large samples, often prohibitively so, are needed. On the other hand, the random nature of shotgun sequencing ensures that many of these organisms will be represented by at least some small sequence segments. Due to the limitations of microbial isolation methods, the vast majority of these organisms would go unnoticed using traditional culturing techniques.</p>
[http://www.superiormartialarts.com/Karate_Forum/posts/233.html free nokia ringtones]
+
<p>&nbsp;</p>
[http://www.superiormartialarts.com/Karate_Forum/posts/234.html verizon ringtones]
+
<h2><span class="mw-headline">Community metabolism</span></h2>
[http://www.superiormartialarts.com/Karate_Forum/posts/235.html free sprint ringtones]
+
<p>Many bacterial communities show significant division of labor in metabolism. Waste products of some organisms are metabolites for others. Working together they turn raw resources into fully metabolized waste. Using comparative gene studies and expression experiments with microarrays or proteomics researchers can piece together a metabolic network that goes beyond species boundaries. Such studies require detailed knowledge about which versions of which proteins are coded by which species and even by which strains of which species. Therefore, community genomic information is another fundamental part (as metabolomics or proteomics) to be able to estimate how metabolites are possibly transferred and transformed through a community.</p>
[http://www.sc27.org/SC27Crew/posts/6.html motorola ringtones]
+
<p>&nbsp;</p>
[http://www.sc27.org/SC27Crew/posts/7.html toddler beds]
+
<h2><span class="mw-headline">References</span></h2>
[http://www.sc27.org/SC27Crew/posts/8.html download ringtones]
+
<div class="references-small">
[http://www.sc27.org/SC27Crew/posts/9.html cingular ringtones]
+
<ol class="references">
[http://www.sc27.org/SC27Crew/posts/10.html sprint ringtones]
+
    <li id="cite_note-Hugenholz1998-0">^ <sup><em><strong>a</strong></em></sup> <sup><em><strong>b</strong></em></sup> <cite style="FONT-STYLE: normal">Hugenholz, P; Goebel BM, Pace NR (1998). &quot;Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity&quot;. <em>J. Bacteriol</em> <strong>180</strong>: 4765&ndash;4774. PMID 9733676.</cite><span class="Z3988" title="ctx_ver=Z39.88-2004&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rft.genre=article&amp;rft.atitle=Impact+of+culture-independent+studies+on+the+emerging+phylogenetic+view+of+bacterial+diversity&amp;rft.jtitle=J.+Bacteriol&amp;rft.date=1998&amp;rft.volume=180&amp;rft.aulast=Hugenholz&amp;rft.aufirst=P&amp;rft.pages=4765%E2%80%934774&amp;rft_id=info:pmid/9733676&amp;rft_id=http%3A%2F%2Fwww.pubmedcentral.nih.gov%2Farticlerender.fcgi%3Ftool%3Dpubmed%26pubmedid%3D9733676"><span style="DISPLAY: none">&nbsp;</span></span> </li>
[http://www.sc27.org/SC27Crew/posts/11.html laminate flooring]
+
    <li id="cite_note-Handelsman1998-1"><strong>^</strong> <cite style="FONT-STYLE: normal">Handelsman, J; Rondon MR, Brady SF, Clardy J, Goodman RM (1998). &quot;Molecular biological access to the chemistry of unknown soil microbes: a new frontier for natural products&quot;. <em>Chemistry &amp; Biology</em> <strong>5</strong>: 245&ndash;249. doi:<span class="neverexpand">10.1016/S1074-5521(98)90108-9</span>.</cite><span class="Z3988" title="ctx_ver=Z39.88-2004&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rft.genre=article&amp;rft.atitle=Molecular+biological+access+to+the+chemistry+of+unknown+soil+microbes%3A+a+new+frontier+for+natural+products&amp;rft.jtitle=Chemistry+%26amp%3B+Biology&amp;rft.date=1998&amp;rft.volume=5&amp;rft.aulast=Handelsman&amp;rft.aufirst=J&amp;rft.pages=245%26ndash%3B249&amp;rft_id=info:doi/10.1016%2FS1074-5521%2898%2990108-9"><span style="DISPLAY: none">&nbsp;</span></span>. </li>
[http://www.sc27.org/SC27Crew/posts/12.html baby strollers]
+
    <li id="cite_note-Chen2005-2"><strong>^</strong> <cite style="FONT-STYLE: normal">Chen, K; Pachter L (2005). &quot;Bioinformatics for whole-genome shotgun sequencing of microbial communities&quot;. <em>PLoS Comp Biol</em> <strong>1</strong>: 24. doi:<span class="neverexpand">10.1371/journal.pcbi.0010024</span>.</cite><span class="Z3988" title="ctx_ver=Z39.88-2004&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rft.genre=article&amp;rft.atitle=Bioinformatics+for+whole-genome+shotgun+sequencing+of+microbial+communities&amp;rft.jtitle=PLoS+Comp+Biol&amp;rft.date=2005&amp;rft.volume=1&amp;rft.aulast=Chen&amp;rft.aufirst=K&amp;rft.pages=24&amp;rft_id=info:doi/10.1371%2Fjournal.pcbi.0010024"><span style="DISPLAY: none">&nbsp;</span></span>. </li>
[http://www.sc27.org/SC27Crew/posts/13.html free ringtones]
+
    <li id="cite_note-Lane1985-3"><strong>^</strong> <cite style="FONT-STYLE: normal">Lane, DJ; Pace B, Olsen GJ, Stahl DA, Sogin ML, Pace NR (1985). &quot;Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses&quot;. <em>Proceedings of the National Academy of Sciences</em> <strong>82</strong>: 6955. doi:<span class="neverexpand">10.1073/pnas.82.20.6955</span>. PMID 2413450.</cite><span class="Z3988" title="ctx_ver=Z39.88-2004&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rft.genre=article&amp;rft.atitle=Rapid+determination+of+16S+ribosomal+RNA+sequences+for+phylogenetic+analyses&amp;rft.jtitle=%5B%5BProceedings+of+the+National+Academy+of+Sciences%5D%5D&amp;rft.date=1985&amp;rft.volume=82&amp;rft.aulast=Lane&amp;rft.aufirst=DJ&amp;rft.pages=6955&amp;rft_id=info:pmid/2413450&amp;rft_id=info:doi/10.1073%2Fpnas.82.20.6955"><span style="DISPLAY: none">&nbsp;</span></span>. </li>
[http://www.sc27.org/SC27Crew/posts/14.html nextel ringtones]
+
    <li id="cite_note-Pace1985-4"><strong>^</strong> <cite style="FONT-STYLE: normal">Pace, NR; DA Stahl, DJ Lane, GJ Olsen (1985). &quot;Analyzing natural microbial populations by rRNA sequences&quot;. <em>ASM News</em> <strong>51</strong>: 4&ndash;12.</cite><span class="Z3988" title="ctx_ver=Z39.88-2004&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rft.genre=article&amp;rft.atitle=Analyzing+natural+microbial+populations+by+rRNA+sequences&amp;rft.jtitle=ASM+News&amp;rft.date=1985&amp;rft.volume=51&amp;rft.aulast=Pace&amp;rft.aufirst=NR&amp;rft.pages=4%26ndash%3B12"><span style="DISPLAY: none">&nbsp;</span></span>. </li>
[http://www.sc27.org/SC27Crew/posts/15.html buy ambien]
+
    <li id="cite_note-Pace1991-5"><strong>^</strong> <cite style="FONT-STYLE: normal">Pace, NR (1991). &quot;Analysis of a marine picoplankton community by 16S rRNA gene cloning and sequencing&quot;. <em>Journal of Bacteriology</em> <strong>173</strong>: 4371&ndash;4378.</cite><span class="Z3988" title="ctx_ver=Z39.88-2004&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rft.genre=article&amp;rft.atitle=Analysis+of+a+marine+picoplankton+community+by+16S+rRNA+gene+cloning+and+sequencing&amp;rft.jtitle=%5B%5BJournal+of+Bacteriology%5D%5D&amp;rft.date=1991&amp;rft.volume=173&amp;rft.aulast=Pace&amp;rft.aufirst=NR&amp;rft.pages=4371%26ndash%3B4378"><span style="DISPLAY: none">&nbsp;</span></span>. </li>
[http://www.sc27.org/SC27Crew/posts/16.html buy adipex]
+
    <li id="cite_note-Healy1995-6"><strong>^</strong> <cite style="FONT-STYLE: normal">Healy, FG; RM Ray, HC Aldrich, AC Wilkie, LO Ingram, KT Shanmugam (1995). &quot;Direct isolation of functional genes encoding cellulases from the microbial consortia in a thermophilic, anaerobic digester maintained on lignocellulose&quot;. <em>Appl. Microbiol Biotechnol.</em> <strong>43</strong>: 667. doi:<span class="neverexpand">10.1007/BF00164771</span>.</cite><span class="Z3988" title="ctx_ver=Z39.88-2004&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rft.genre=article&amp;rft.atitle=Direct+isolation+of+functional+genes+encoding+cellulases+from+the+microbial+consortia+in+a+thermophilic%2C+anaerobic+digester+maintained+on+lignocellulose&amp;rft.jtitle=Appl.+Microbiol+Biotechnol.&amp;rft.date=1995&amp;rft.volume=43&amp;rft.aulast=Healy&amp;rft.aufirst=FG&amp;rft.pages=667&amp;rft_id=info:doi/10.1007%2FBF00164771"><span style="DISPLAY: none">&nbsp;</span></span>. </li>
[http://www.sc27.org/SC27Crew/posts/17.html buy xenical]
+
    <li id="cite_note-Stein1996-7"><strong>^</strong> <cite style="FONT-STYLE: normal">Stein, JL; TL Marsh, KY Wu, H Shizuya, EF DeLong (1996). &quot;Characterization of uncultivated prokaryotes: isolation and analysis of a 40-kilobase-pair genome fragment from a planktonic marine archaeon&quot;. <em>Journal of Bacteriology</em> <strong>178</strong>: 591&ndash;599.</cite><span class="Z3988" title="ctx_ver=Z39.88-2004&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rft.genre=article&amp;rft.atitle=Characterization+of+uncultivated+prokaryotes%3A+isolation+and+analysis+of+a+40-kilobase-pair+genome+fragment+from+a+planktonic+marine+archaeon&amp;rft.jtitle=Journal+of+Bacteriology&amp;rft.date=1996&amp;rft.volume=178&amp;rft.aulast=Stein&amp;rft.aufirst=JL&amp;rft.pages=591%26ndash%3B599"><span style="DISPLAY: none">&nbsp;</span></span>. </li>
[http://www.sc27.org/SC27Crew/posts/18.html buy valium]
+
    <li id="cite_note-Beja2000-8"><strong>^</strong> <cite style="FONT-STYLE: normal">Beja, O; Suzuki MT, Koonin EV, Aravind L, Hadd A, Nguyen LP, Villacorta R, Amjadi M, Garrigues C, Jovanovich SB, Feldman RA, Delong EF (2000). &quot;Construction and analysis of bacterial artificial chromosome libraries from a marine microbial assemblage&quot; <strong>2</strong>: 516&ndash;529.</cite><span class="Z3988" title="ctx_ver=Z39.88-2004&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rft.genre=article&amp;rft.atitle=Construction+and+analysis+of+bacterial+artificial+chromosome+libraries+from+a+marine+microbial+assemblage&amp;rft.date=2000&amp;rft.volume=2&amp;rft.aulast=Beja&amp;rft.aufirst=O&amp;rft.pages=516%E2%80%93529"><span style="DISPLAY: none">&nbsp;</span></span> </li>
[http://www.sc27.org/SC27Crew/posts/19.html buy carisoprodol]
+
    <li id="cite_note-Breitbart2002-9"><strong>^</strong> <cite style="FONT-STYLE: normal">Breitbart, M; Salamon P, Andresen B, Mahaffy JM, Segall AM, Mead D, Azam F, Rohwer F (2002). &quot;Genomic analysis of uncultured marine viral communities&quot;. <em>Proceedings of the National Academy USA</em> <strong>99</strong>: 14250&ndash;14255. doi:<span class="neverexpand">10.1073/pnas.202488399</span>. PMID 12384570.</cite><span class="Z3988" title="ctx_ver=Z39.88-2004&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rft.genre=article&amp;rft.atitle=Genomic+analysis+of+uncultured+marine+viral+communities&amp;rft.jtitle=Proceedings+of+the+National+Academy+USA&amp;rft.date=2002&amp;rft.volume=99&amp;rft.aulast=Breitbart&amp;rft.aufirst=M&amp;rft.pages=14250%E2%80%9314255&amp;rft_id=info:pmid/12384570&amp;rft_id=info:doi/10.1073%2Fpnas.202488399"><span style="DISPLAY: none">&nbsp;</span></span>. </li>
[http://www.sc27.org/SC27Crew/posts/20.html free nokia ringtones]
+
    <li id="cite_note-Venter2004-10"><strong>^</strong> <cite style="FONT-STYLE: normal">Venter, JC; Remington K, Heidelberg JF, Halpern AL, Rusch D, Eisen JA, Wu D, Paulsen I, Nelson KE, Nelson W, Fouts DE, Levy S, Knap AH, Lomas MW, Nealson K, White O, Peterson J, Hoffman J, Parsons R, Baden-Tillson H, Pfannkoch C, Rogers Y, Smith HO (2004). &quot;Environmental Genome Shotgun Sequencing of the Sargasso Sea&quot;. <em>Science</em> <strong>304</strong>: 66&ndash;74. doi:<span class="neverexpand">10.1126/science.1093857</span>. PMID 15001713.</cite><span class="Z3988" title="ctx_ver=Z39.88-2004&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rft.genre=article&amp;rft.atitle=Environmental+Genome+Shotgun+Sequencing+of+the+Sargasso+Sea&amp;rft.jtitle=Science&amp;rft.date=2004&amp;rft.volume=304&amp;rft.aulast=Venter&amp;rft.aufirst=JC&amp;rft.pages=66%E2%80%9374&amp;rft_id=info:pmid/15001713&amp;rft_id=info:doi/10.1126%2Fscience.1093857"><span style="DISPLAY: none">&nbsp;</span></span>. </li>
[http://www.sc27.org/SC27Crew/posts/21.html verizon ringtones]
+
    <li id="cite_note-Tyson2004-11">^ <sup><em><strong>a</strong></em></sup> <sup><em><strong>b</strong></em></sup> <cite style="FONT-STYLE: normal">Tyson, GW; Chapman J, Hugenholtz P, Allen EE, Ram RJ, Richardson PM, Solovyev VV, Rubin EM, Rokhsar DS, Banfield JF (2004). &quot;Insights into community structure and metabolism by reconstruction of microbial genomes from the environment&quot;. <em>Nature</em> <strong>428</strong>: 37&ndash;43. doi:<span class="neverexpand">10.1038/nature02340</span>.</cite><span class="Z3988" title="ctx_ver=Z39.88-2004&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rft.genre=article&amp;rft.atitle=Insights+into+community+structure+and+metabolism+by+reconstruction+of+microbial+genomes+from+the+environment&amp;rft.jtitle=Nature&amp;rft.date=2004&amp;rft.volume=428&amp;rft.aulast=Tyson&amp;rft.aufirst=GW&amp;rft.pages=37%E2%80%9343&amp;rft_id=info:doi/10.1038%2Fnature02340&amp;rft_id=http%3A%2F%2Fwww.nature.com%2Fnature%2Fjournal%2Fv428%2Fn6978%2Ffull%2Fnature02340.html"><span style="DISPLAY: none">&nbsp;</span></span>. </li>
[http://www.sc27.org/SC27Crew/posts/23.html free sprint ringtones]
+
    <li id="cite_note-Hugenholz2002-12"><strong>^</strong> <cite style="FONT-STYLE: normal">Hugenholz, P (2002). &quot;Exploring prokaryotic diversity in the genomic era&quot;. <em>Genome Biology</em> <strong>3</strong>: 1&ndash;8. doi:<span class="neverexpand">10.1186/gb-2002-3-2-reviews0003</span>.</cite><span class="Z3988" title="ctx_ver=Z39.88-2004&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rft.genre=article&amp;rft.atitle=Exploring+prokaryotic+diversity+in+the+genomic+era&amp;rft.jtitle=Genome+Biology&amp;rft.date=2002&amp;rft.volume=3&amp;rft.aulast=Hugenholz&amp;rft.aufirst=P&amp;rft.pages=1%E2%80%938&amp;rft_id=info:doi/10.1186%2Fgb-2002-3-2-reviews0003"><span style="DISPLAY: none">&nbsp;</span></span>. </li>
[http://www.superiormartialarts.com/Karate_Forum/posts/237.html motorola ringtones]
+
    <li id="cite_note-Edwards2006-13"><strong>^</strong> <cite style="FONT-STYLE: normal">Edwards, RA; Rodriguez-Brito B, Wegley L, Haynes M, Breitbart M, Peterson DM, Saar MO, Alexander S, Alexander EC, Rohwer F (2006). &quot;Using pyrosequencing to shed light on deep mine microbial ecology&quot;. <em>BMC Genomics</em> <strong>7</strong>: 57. doi:<span class="neverexpand">10.1186/1471-2164-7-57</span>.</cite><span class="Z3988" title="ctx_ver=Z39.88-2004&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rft.genre=article&amp;rft.atitle=Using+pyrosequencing+to+shed+light+on+deep+mine+microbial+ecology&amp;rft.jtitle=BMC+Genomics&amp;rft.date=2006&amp;rft.volume=7&amp;rft.aulast=Edwards&amp;rft.aufirst=RA&amp;rft.pages=57&amp;rft_id=info:doi/10.1186%2F1471-2164-7-57"><span style="DISPLAY: none">&nbsp;</span></span>. </li>
[http://www.superiormartialarts.com/Karate_Forum/posts/238.html download ringtones]
+
    <li id="cite_note-14"><strong>^</strong> 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 </li>
[http://www.superiormartialarts.com/Karate_Forum/posts/239.html cingular ringtones]
+
    <li id="cite_note-Meyer2008-15"><strong>^</strong> <cite style="FONT-STYLE: normal">Meyer, F; Paarmann D, D'Souza M, Olson R, Glass EM, Kubal M, Paczian T, Rodriguez A, Stevens R, Wilke A, Wilkening J, Edwards RA (2008). &quot;The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes&quot;. <em>BMC Bioinformatics</em> <strong>9</strong>: 0. doi:<span class="neverexpand">doi:10.1186/1471-2105-9-386</span>.</cite><span class="Z3988" title="ctx_ver=Z39.88-2004&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rft.genre=article&amp;rft.atitle=The+metagenomics+RAST+server+-+a+public+resource+for+the+automatic+phylogenetic+and+functional+analysis+of+metagenomes&amp;rft.jtitle=BMC+Bioinformatics&amp;rft.date=2008&amp;rft.volume=9&amp;rft.aulast=Meyer&amp;rft.aufirst=F&amp;rft.pages=0&amp;rft_id=info:doi/doi%3A10.1186%2F1471-2105-9-386"><span style="DISPLAY: none">&nbsp;</span></span>. </li>
[http://www.superiormartialarts.com/Karate_Forum/posts/240.html sprint ringtones]
+
    <li id="cite_note-Allen2005-16"><strong>^</strong> <cite style="FONT-STYLE: normal">Allen, EE; Banfield, JF (2005). &quot;Community genomics in microbial ecology and evolution&quot;. <em>Nature Reviews Microbiology</em> <strong>3</strong>: 489&ndash;498. doi:<span class="neverexpand">10.1038/nrmicro1157</span>.</cite><span class="Z3988" title="ctx_ver=Z39.88-2004&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rft.genre=article&amp;rft.atitle=Community+genomics+in+microbial+ecology+and+evolution&amp;rft.jtitle=Nature+Reviews+Microbiology&amp;rft.date=2005&amp;rft.volume=3&amp;rft.aulast=Allen&amp;rft.aufirst=EE&amp;rft.pages=489%E2%80%93498&amp;rft_id=info:doi/10.1038%2Fnrmicro1157"><span style="DISPLAY: none">&nbsp;</span></span> </li>
[http://pc-dmis.com/anyboard9/forum/posts/2396.html buy ambien]
+
</ol>
[http://pc-dmis.com/anyboard9/forum/posts/2397.html buy adipex]
 
[http://pc-dmis.com/anyboard9/forum/posts/2398.html buy xenical]
 
[http://pc-dmis.com/anyboard9/forum/posts/2399.html buy valium]
 
[http://pc-dmis.com/anyboard9/forum/posts/2400.html buy carisoprodol]
 
[http://pc-dmis.com/anyboard9/forum/posts/2401.html buy hydrocodone]
 
[http://pc-dmis.com/anyboard9/forum/posts/2402.html free ringtones]
 
[http://pc-dmis.com/anyboard9/forum/posts/2403.html nextel ringtones]
 
[http://pc-dmis.com/anyboard9/forum/posts/2404.html free nokia ringtones]
 
[http://pc-dmis.com/anyboard9/forum/posts/2405.html verizon ringtones]
 
[http://pc-dmis.com/anyboard9/forum/posts/2406.html free sprint ringtones]
 
[http://pc-dmis.com/anyboard9/forum/posts/2407.html motorola ringtones]
 
[http://pc-dmis.com/anyboard9/forum/posts/2408.html download ringtones]
 
[http://pc-dmis.com/anyboard9/forum/posts/2409.html cingular ringtones]
 
[http://pc-dmis.com/anyboard9/forum/posts/2410.html sprint ringtones]
 
[http://pc-dmis.com/anyboard9/forum/posts/2411.html cell phone wallpapers]
 
[http://pc-dmis.com/anyboard9/forum/posts/2412.html polyphonic ringtones]
 
[http://pc-dmis.com/anyboard9/forum/posts/2413.html toddler beds]
 
[http://www.tiggerstales.com/boards/bbs/posts/1213.html buy ambien]
 
[http://www.tiggerstales.com/boards/bbs/posts/1214.html buy adipex]
 
[http://www.tiggerstales.com/boards/bbs/posts/1215.html buy xenical]
 
[http://www.tiggerstales.com/boards/bbs/posts/1216.html buy valium]
 
[http://www.tiggerstales.com/boards/bbs/posts/1217.html buy carisoprodol]
 
[http://www.tiggerstales.com/boards/bbs/posts/1218.html buy hydrocodone]
 
[http://www.tiggerstales.com/boards/bbs/posts/1219.html free ringtones]
 
[http://www.tiggerstales.com/boards/bbs/posts/1220.html nextel ringtones]
 
[http://www.tiggerstales.com/boards/bbs/posts/1221.html free nokia ringtones]
 
[http://www.tiggerstales.com/boards/bbs/posts/1222.html verizon ringtones]
 
[http://www.tiggerstales.com/boards/bbs/posts/1223.html free sprint ringtones]
 
[http://www.tiggerstales.com/boards/bbs/posts/1224.html motorola ringtones]
 
[http://www.tiggerstales.com/boards/bbs/posts/1225.html laminate flooring]
 
[http://www.tiggerstales.com/boards/bbs/posts/1226.html toddler beds]
 
[http://www.tiggerstales.com/boards/bbs/posts/1227.html download ringtones]
 
[http://www.tiggerstales.com/boards/bbs/posts/1228.html cingular ringtones]
 
[http://www.tiggerstales.com/boards/bbs/posts/1229.html sprint ringtones]
 
[http://www.tiggerstales.com/boards/bbs/posts/1230.html cell phone wallpapers]
 
[http://www.tiggerstales.com/boards/bbs/posts/1231.html polyphonic ringtones]
 
[http://www.tiggerstales.com/boards/bbs/posts/1232.html electric wheelchair]
 
[http://smokesigs.com/messageboard1/posts/52013.html buy ambien]
 
[http://smokesigs.com/messageboard1/posts/52014.html buy adipex]
 
[http://smokesigs.com/messageboard1/posts/52015.html buy xenical]
 
[http://smokesigs.com/messageboard1/posts/52016.html buy valium]
 
[http://smokesigs.com/messageboard1/posts/52017.html buy carisoprodol]
 
[http://smokesigs.com/messageboard1/posts/52018.html buy hydrocodone]
 
[http://smokesigs.com/messageboard1/posts/52020.html laminate flooring]
 
[http://smokesigs.com/messageboard1/posts/52021.html toddler beds]
 
[http://smokesigs.com/messageboard1/posts/52022.html cell phone wallpapers]
 
[http://www.indianink.net/forums/Tips/posts/4281.html buy ambien]
 
[http://www.indianink.net/forums/Tips/posts/4283.html buy adipex]
 
[http://www.indianink.net/forums/Tips/posts/4284.html buy xenical]
 
[http://www.indianink.net/forums/Tips/posts/4286.html buy valium]
 
[http://www.indianink.net/forums/Tips/posts/4287.html buy carisoprodol]
 
[http://www.indianink.net/forums/Tips/posts/4289.html buy hydrocodone]
 
[http://www.indianink.net/forums/Tips/posts/4291.html free ringtones]
 
[http://www.indianink.net/forums/Tips/posts/4292.html nextel ringtones]
 
[http://www.indianink.net/forums/Tips/posts/4293.html free nokia ringtones]
 
[http://www.indianink.net/forums/Tips/posts/4295.html verizon ringtones]
 
[http://www.indianink.net/forums/Tips/posts/4296.html free sprint ringtones]
 
[http://www.indianink.net/forums/Tips/posts/4297.html motorola ringtones]
 
[http://www.indianink.net/forums/Tips/posts/4299.html toddler beds]
 
[http://www.indianink.net/forums/Tips/posts/4300.html cingular ringtones]
 
[http://www.indianink.net/forums/Tips/posts/4301.html polyphonic ringtones]
 
[http://www.indianink.net/forums/Tips/posts/4303.html cell phone wallpapers]
 
[http://smokesigs.com/messageboard1/posts/52028.html electric wheelchair]
 
[http://www.indianink.net/forums/Tips/posts/4431.html laminate flooring]
 
[http://www.indianink.net/forums/Tips/posts/4433.html download ringtones]
 
[http://www.indianink.net/forums/Tips/posts/4434.html sprint ringtones]
 
[http://www.indianink.net/forums/Tips/posts/4435.html electric wheelchair]
 
[http://www.desert-tropicals.com/bbs/posts/7322.html buy ambien]
 
[http://www.desert-tropicals.com/bbs/posts/7323.html buy adipex]
 
[http://www.desert-tropicals.com/bbs/posts/7324.html buy xenical]
 
[http://www.desert-tropicals.com/bbs/posts/7325.html buy valium]
 
[http://www.desert-tropicals.com/bbs/posts/7326.html buy carisoprodol]
 
[http://www.desert-tropicals.com/bbs/posts/7327.html buy hydrocodone]
 
[http://www.desert-tropicals.com/bbs/posts/7329.html laminate flooring]
 
[http://www.desert-tropicals.com/bbs/posts/7330.html toddler beds]
 
[http://www.desert-tropicals.com/bbs/posts/7331.html cell phone wallpapers]
 
[http://www.desert-tropicals.com/bbs/posts/7332.html electric wheelchair]
 
[http://www2.fhy.net/forum/XXGC/posts/230.shtml buy ambien]
 
[http://www2.fhy.net/forum/XXGC/posts/231.shtml buy adipex]
 
[http://www2.fhy.net/forum/XXGC/posts/233.shtml buy xenical]
 
[http://www2.fhy.net/forum/XXGC/posts/234.shtml buy valium]
 
[http://www2.fhy.net/forum/XXGC/posts/235.shtml buy carisoprodol]
 
[http://www2.fhy.net/forum/XXGC/posts/236.shtml buy hydrocodone]
 
[http://www2.fhy.net/forum/XXGC/posts/237.shtml free ringtones]
 
[http://www2.fhy.net/forum/XXGC/posts/238.shtml nextel ringtones]
 
[http://www2.fhy.net/forum/XXGC/posts/239.shtml free nokia ringtones]
 
[http://www2.fhy.net/forum/XXGC/posts/240.shtml verizon ringtones]
 
[http://www.finnmark-slekt.com/finnquery/posts/1823.html free ringtones]
 
[http://www.finnmark-slekt.com/finnquery/posts/1824.html nextel ringtones]
 
[http://www.finnmark-slekt.com/finnquery/posts/1825.html free nokia ringtones]
 
[http://www.finnmark-slekt.com/finnquery/posts/1826.html verizon ringtones]
 
[http://www.finnmark-slekt.com/finnquery/posts/1827.html free sprint ringtones]
 
[http://www.finnmark-slekt.com/finnquery/posts/1828.html motorola ringtones]
 
[http://www.finnmark-slekt.com/finnquery/posts/1829.html download ringtones]
 
[http://www.finnmark-slekt.com/finnquery/posts/1830.html cingular ringtones]
 
[http://www.finnmark-slekt.com/finnquery/posts/1831.html sprint ringtones]
 
[http://www.finnmark-slekt.com/finnquery/posts/1832.html polyphonic ringtones]
 
[http://www.finnmark-slekt.com/finnquery/posts/1833.html cell phone wallpapers]
 
[http://www2.fhy.net/forum/XXGC/posts/241.shtml free sprint ringtones]
 
[http://www2.fhy.net/forum/XXGC/posts/242.shtml motorola ringtones]
 
[http://www2.fhy.net/forum/XXGC/posts/243.shtml download ringtones]
 
[http://www2.fhy.net/forum/XXGC/posts/244.shtml cingular ringtones]
 
[http://www2.fhy.net/forum/XXGC/posts/245.shtml sprint ringtones]
 
[http://www2.fhy.net/forum/XXGC/posts/246.shtml polyphonic ringtones]
 
[http://www2.fhy.net/forum/XXGC/posts/247.shtml cell phone wallpapers]
 
[http://www.finnmark-slekt.com/finnquery/posts/1838.html buy ambien]
 
[http://www.finnmark-slekt.com/finnquery/posts/1839.html buy adipex]
 
[http://www.finnmark-slekt.com/finnquery/posts/1840.html buy xenical]
 
[http://www.finnmark-slekt.com/finnquery/posts/1841.html buy carisoprodol]
 
[http://www.finnmark-slekt.com/finnquery/posts/1842.html buy hydrocodone]
 
[http://www.finnmark-slekt.com/finnquery/posts/1843.html didrex]
 
[http://www.finnmark-slekt.com/finnquery/posts/1844.html diazepam]
 
[http://www.finnmark-slekt.com/finnquery/posts/1845.html toddler beds]
 
[http://www.finnmark-slekt.com/finnquery/posts/1846.html laminate flooring]
 
[http://www.finnmark-slekt.com/finnquery/posts/1847.html electric wheelchair]
 
[http://www2.fhy.net/forum/XXGC/posts/248.shtml prepaid cell phones]
 
[http://www2.fhy.net/forum/XXGC/posts/249.shtml laminate flooring]
 
[http://www2.fhy.net/forum/XXGC/posts/250.shtml toddler beds]
 
[http://www2.fhy.net/forum/XXGC/posts/251.shtml mp3 ringtones]
 
[http://www.finnmark-slekt.com/finnquery/posts/1855.html prepaid cell phones]
 
[http://www.finnmark-slekt.com/finnquery/posts/1856.html mp3 ringtones]
 
[http://www.finnmark-slekt.com/finnquery/posts/1858.html cell phone ringtones]
 
[http://www.finnmark-slekt.com/finnquery/posts/1859.html download free ringtones]
 
[http://forum.lantbruksnet.se/batnet/posts/5309.html free ringtones]
 
[http://forum.lantbruksnet.se/batnet/posts/5310.html nextel ringtones]
 
[http://forum.lantbruksnet.se/batnet/posts/5311.html free nokia ringtones]
 
[http://forum.lantbruksnet.se/batnet/posts/5312.html verizon ringtones]
 
[http://forum.lantbruksnet.se/batnet/posts/5313.html free sprint ringtones]
 
[http://forum.lantbruksnet.se/lantbruksnet/posts/11492.html motorola ringtones]
 
[http://forum.lantbruksnet.se/lantbruksnet/posts/11493.html download ringtones]
 
[http://forum.lantbruksnet.se/lantbruksnet/posts/11494.html cingular ringtones]
 
[http://forum.lantbruksnet.se/lantbruksnet/posts/11495.html sprint ringtones]
 
[http://forum.lantbruksnet.se/lantbruksnet/posts/11496.html polyphonic ringtones]
 
[http://forum.lantbruksnet.se/lantbruksnet/posts/11498.html cell phone wallpapers]
 
[http://forum.lantbruksnet.se/lantbruksnet/posts/11499.html prepaid cell phones]
 
[http://forum.lantbruksnet.se/lantbruksnet/posts/11500.html mp3 ringtones]
 
[http://forum.lantbruksnet.se/lantbruksnet/posts/11501.html cell phone ringtones]
 
[http://forum.lantbruksnet.se/lantbruksnet/posts/11502.html download free ringtones]
 
[http://forum.lantbruksnet.se/lantbruksnet/posts/11503.html t-mobile ringtones]
 
[http://forum.lantbruksnet.se/lantbruksnet/posts/11504.html nokia ringtones]
 
[http://forum.lantbruksnet.se/lantbruksnet/posts/11505.html free cingular ringtones]
 
[http://www.sweepersonline.com/virtualsweeperforum/posts/663.html ambien]
 
[http://www.sweepersonline.com/virtualsweeperforum/posts/664.html adipex]
 
[http://www.sweepersonline.com/virtualsweeperforum/posts/665.html xenical]
 
[http://www.sweepersonline.com/virtualsweeperforum/posts/666.html didrex]
 
[http://www.sweepersonline.com/virtualsweeperforum/posts/667.html free ringtones]
 
[http://www.sweepersonline.com/virtualsweeperforum/posts/668.html nextel ringtones]
 
[http://www.sweepersonline.com/virtualsweeperforum/posts/669.html free nokia ringtones]
 
[http://www.sweepersonline.com/virtualsweeperforum/posts/670.html verizon ringtones]
 
[http://www.sweepersonline.com/virtualsweeperforum/posts/671.html free sprint ringtones]
 
[http://www.sweepersonline.com/bidboardforum/posts/1483.html motorola ringtones]
 
[http://www.sweepersonline.com/bidboardforum/posts/1484.html download ringtones]
 
[http://www.sweepersonline.com/bidboardforum/posts/1485.html cingular ringtones]
 
[http://www.sweepersonline.com/bidboardforum/posts/1486.html sprint ringtones]
 
[http://www.sweepersonline.com/bidboardforum/posts/1487.html polyphonic ringtones]
 
[http://www.sweepersonline.com/bidboardforum/posts/1488.html cell phone wallpapers]
 
[http://www.sweepersonline.com/bidboardforum/posts/1489.html prepaid cell phones]
 
[http://www.sweepersonline.com/bidboardforum/posts/1490.html mp3 ringtones]
 
[http://www.sweepersonline.com/bidboardforum/posts/1491.html cell phone ringtones]
 
[http://www.sweepersonline.com/bidboardforum/posts/1492.html download free ringtones]
 
[http://www.sweepersonline.com/bidboardforum/posts/1493.html t-mobile ringtones]
 
[http://www.sweepersonline.com/bidboardforum/posts/1494.html nokia ringtones]
 
[http://www.sweepersonline.com/bidboardforum/posts/1495.html free cingular ringtones]
 
[http://www.humancloning.org/anyboard9/contactus/posts/525.html ambien]
 
[http://www.humancloning.org/anyboard9/contactus/posts/526.html adipex]
 
[http://www.humancloning.org/anyboard9/contactus/posts/527.html xenical]
 
[http://www.humancloning.org/anyboard9/contactus/posts/528.html didrex]
 
[http://www.69indianporn.com/cgi-local/board/69indianporn/posts/1124.html ambien]
 
[http://www.69indianporn.com/cgi-local/board/69indianporn/posts/1135.html adipex]
 
[http://www.69indianporn.com/cgi-local/board/69indianporn/posts/1136.html xenical]
 
[http://www.69indianporn.com/cgi-local/board/69indianporn/posts/1137.html didrex]
 
[http://www.69indianporn.com/cgi-local/board/69indianporn/posts/1138.html free ringtones]
 
[http://www.69indianporn.com/cgi-local/board/69indianporn/posts/1139.html nextel ringtones]
 
[http://www.69indianporn.com/cgi-local/board/69indianporn/posts/1140.html free nokia ringtones]
 
[http://www.69indianporn.com/cgi-local/board/69indianporn/posts/1141.html verizon ringtones]
 
[http://www.69indianporn.com/cgi-local/board/69indianporn/posts/1142.html free sprint ringtones]
 
[http://www.69indianporn.com/cgi-local/board/69indianporn/posts/1143.html motorola ringtones]
 
[http://www.69indianporn.com/cgi-local/board/69indianporn/posts/1144.html download ringtones]
 
[http://www.69indianporn.com/cgi-local/board/69indianporn/posts/1145.html cingular ringtones]
 
[http://www.69indianporn.com/cgi-local/board/69indianporn/posts/1146.html sprint ringtones]
 
[http://www.69indianporn.com/cgi-local/board/69indianporn/posts/1147.html polyphonic ringtones]
 
[http://www.69indianporn.com/cgi-local/board/69indianporn/posts/1148.html cell phone wallpapers]
 
[http://www.69indianporn.com/cgi-local/board/69indianporn/posts/1149.html prepaid cell phones]
 
[http://www.69indianporn.com/cgi-local/board/69indianporn/posts/1150.html mp3 ringtones]
 
[http://www.69indianporn.com/cgi-local/board/69indianporn/posts/1151.html cell phone ringtones]
 
[http://www.69indianporn.com/cgi-local/board/69indianporn/posts/1152.html download free ringtones]
 
[http://www.69indianporn.com/cgi-local/board/69indianporn/posts/1153.html t-mobile ringtones]
 
[http://www.69indianporn.com/cgi-local/board/69indianporn/posts/1154.html nokia ringtones]
 
[http://www.69indianporn.com/cgi-local/board/69indianporn/posts/1155.html free cingular ringtones]
 
[http://www.hartsville.net/betatest/posts/12.html ambien]
 
[http://www.humancloning.org/anyboard9/contactus/posts/529.html free ringtones]
 
[http://www.humancloning.org/anyboard9/contactus/posts/530.html nextel ringtones]
 
[http://www.humancloning.org/anyboard9/contactus/posts/531.html free nokia ringtones]
 
[http://www.humancloning.org/anyboard9/contactus/posts/532.html verizon ringtones]
 
[http://www.humancloning.org/anyboard9/contactus/posts/533.html free sprint ringtones]
 
[http://www.humancloning.org/anyboard9/contactus/posts/534.html motorola ringtones]
 
[http://www.humancloning.org/anyboard9/contactus/posts/535.html download ringtones]
 
[http://www.humancloning.org/anyboard9/contactus/posts/536.html cingular ringtones]
 
[http://www.humancloning.org/anyboard9/contactus/posts/537.html sprint ringtones]
 
[http://www.humancloning.org/anyboard9/contactus/posts/538.html polyphonic ringtones]
 
[http://www.humancloning.org/anyboard9/contactus/posts/539.html cell phone wallpapers]
 
[http://www.humancloning.org/anyboard9/contactus/posts/540.html prepaid cell phones]
 
[http://www.humancloning.org/anyboard9/contactus/posts/541.html mp3 ringtones]
 
[http://www.humancloning.org/anyboard9/contactus/posts/542.html cell phone ringtones]
 
[http://www.humancloning.org/anyboard9/contactus/posts/543.html download free ringtones]
 
[http://www.humancloning.org/anyboard9/contactus/posts/544.html t-mobile ringtones]
 
[http://www.humancloning.org/anyboard9/contactus/posts/545.html nokia ringtones]
 
[http://www.humancloning.org/anyboard9/contactus/posts/546.html free cingular ringtones]
 
[http://www.hartsville.net/betatest/posts/13.html adipex]
 
[http://www.hartsville.net/betatest/posts/14.html xenical]
 
[http://www.hartsville.net/betatest/posts/15.html didrex]
 
[http://www.hartsville.net/betatest/posts/16.html free ringtones]
 
[http://www.hartsville.net/betatest/posts/17.html nextel ringtones]
 
[http://www.hartsville.net/betatest/posts/18.html free nokia ringtones]
 
[http://www.hartsville.net/betatest/posts/19.html verizon ringtones]
 
[http://www.hartsville.net/betatest/posts/20.html free sprint ringtones]
 
[http://www.hartsville.net/betatest/posts/21.html motorola ringtones]
 
[http://www.hartsville.net/betatest/posts/22.html download ringtones]
 
[http://www.hartsville.net/betatest/posts/23.html cingular ringtones]
 
[http://www.hartsville.net/betatest/posts/24.html sprint ringtones]
 
[http://www.hartsville.net/betatest/posts/25.html polyphonic ringtones]
 
[http://www.hartsville.net/betatest/posts/26.html cell phone wallpapers]
 
[http://www.hartsville.net/betatest/posts/27.html prepaid cell phones]
 
[http://www.hartsville.net/betatest/posts/28.html mp3 ringtones]
 
[http://www.hartsville.net/betatest/posts/29.html cell phone ringtones]
 
[http://www.hartsville.net/betatest/posts/30.html download free ringtones]
 
[http://www.hartsville.net/betatest/posts/31.html t-mobile ringtones]
 
[http://www.hartsville.net/betatest/posts/32.html nokia ringtones]
 
[http://www.hartsville.net/betatest/posts/33.html free cingular ringtones]
 
[http://www.hartsville.net/betatest/posts/34.html Justin Timberlake concert tickets]
 
[http://www.hartsville.net/betatest/posts/35.html Shakira concert tickets]
 
[http://www.hartsville.net/betatest/posts/36.html Pink concert tickets]
 
[http://northstar.northseattle.edu/discussions/cis111dl-kent/posts/346.html buy ambien]
 
[http://northstar.northseattle.edu/discussions/cis111dl-kent/posts/347.html buy adipex]
 
[http://northstar.northseattle.edu/discussions/cis111dl-kent/posts/348.html buy xenical]
 
[http://northstar.northseattle.edu/discussions/cis111dl-kent/posts/349.html buy carisoprodol]
 
[http://northstar.northseattle.edu/discussions/cis111dl-kent/posts/350.html buy hydrocodone]
 
[http://northstar.northseattle.edu/discussions/cis111dl-kent/posts/351.html free ringtones]
 
[http://northstar.northseattle.edu/discussions/cis111dl-kent/posts/352.html nextel ringtones]
 
[http://northstar.northseattle.edu/discussions/cis111dl-kent/posts/353.html free nokia ringtones]
 
[http://northstar.northseattle.edu/discussions/cis111dl-kent/posts/354.html verizon ringtones]
 
[http://northstar.northseattle.edu/discussions/cis111dl-kent/posts/355.html free sprint ringtones]
 
[http://northstar.northseattle.edu/discussions/cis111dl-kent/posts/356.html motorola ringtones]
 
[http://northstar.northseattle.edu/discussions/cis111dl-kent/posts/357.html download ringtones]
 
[http://northstar.northseattle.edu/discussions/cis111dl-kent/posts/358.html Justin Timberlake concert tickets]
 
[http://northstar.northseattle.edu/discussions/cis111dl-kent/posts/359.html Shakira concert tickets]
 
[http://northstar.northseattle.edu/discussions/cis111dl-kent/posts/360.html Pink concert tickets]
 
[http://northstar.sccd.ctc.edu/discussions/csc143-goldner/posts/1528.html cingular ringtones]
 
[http://northstar.sccd.ctc.edu/discussions/csc143-goldner/posts/1529.html sprint ringtones]
 
[http://northstar.sccd.ctc.edu/discussions/csc143-goldner/posts/1530.html polyphonic ringtones]
 
[http://northstar.sccd.ctc.edu/discussions/csc143-goldner/posts/1531.html cell phone wallpapers]
 
[http://northstar.sccd.ctc.edu/discussions/csc143-goldner/posts/1532.html prepaid cell phones]
 
[http://northstar.sccd.ctc.edu/discussions/csc143-goldner/posts/1533.html mp3 ringtones]
 
[http://northstar.sccd.ctc.edu/discussions/csc143-goldner/posts/1534.html cell phone ringtones]
 
[http://northstar.sccd.ctc.edu/discussions/csc143-goldner/posts/1535.html download free ringtones]
 
[http://northstar.sccd.ctc.edu/discussions/csc143-goldner/posts/1536.html t-mobile ringtones]
 
[http://northstar.sccd.ctc.edu/discussions/csc143-goldner/posts/1537.html nokia ringtones]
 
[http://northstar.sccd.ctc.edu/discussions/csc143-goldner/posts/1538.html free cingular ringtones]
 
 
</div>
 
</div>
 +
<p>&nbsp;</p>
 +
<h2><span class="mw-headline">Additional References</span></h2>
 +
<p><font size="2"></font></p>
 +
<h3><span class="mw-headline">Review articles</span></h3>
 +
<ul>
 +
    <li>Edwards RA, &amp; Rohwer F. Viral metagenomics. Nat Rev Microbiol. 2005 3(6):504-10. PubMed </li>
 +
    <li>Eisen, J. A. (2007). Environmental shotgun sequencing: its potential and challenges for studying the hidden world of microbes. <em>PLoS Biology 5(3): e82</em> </li>
 +
    <li>Green, B. D. &amp; Keller, M. (2006). Capturing the uncultivated majority. <em>Current Opinion in Biotechnology</em> 17[3], 236-240. </li>
 +
    <li>Handelsman J. (2004). Metagenomics: application of genomics to uncultured microorganisms. <em>Microbiology and Molecular Biology Reviews</em> <strong>68</strong>:669-685. </li>
 +
    <li>Keller, M. &amp; Sengler, K. (2004). Tapping into microbial diversity. Nature Reviews Microbiology 2[2], 141-150. </li>
 +
    <li>Lombard, N. <em>et al.</em> (2006). The metagenomics of microbial communities. <em>Biofutur</em> 24-7. </li>
 +
    <li>Riesenfeld, C. S. <em>et al.</em> (2004). Metagenomics: genomic analysis of microbial communities. <em>Annu Rev Genet</em> <strong>38</strong>: 525-52. </li>
 +
    <li>Rodriguez Valera, F. (2002). Approaches to prokaryotic biodiversity: a population genetics perspective. <em>Environmental Microbiology</em> <strong>4</strong>: 628-33. </li>
 +
    <li>Rodriguez-Valera. (2004). Environmental genomics, the big picture?. <em>FEMS Microbiology Letters</em> <strong>231</strong>:153-158. </li>
 +
    <li>Torsvik, V. &amp; Ovreas, L. (2002). Microbial diversity and function in soil: from genes to ecosystems. <em>Current opinion in Microbiology</em> <strong>5</strong>: 240-5. </li>
 +
    <li>Whitaker, R. J. &amp; Banfield, J. F. (2006). Population genomics in natural microbial communities. <em>Trends in Ecology &amp; Evolution</em> <strong>21</strong>: 508-16. </li>
 +
    <li>Worden, A. Z. <em>et al.</em> (2006). In-depth analyses of marine microbial community genomics. <em>Trends in Microbiology</em> <strong>14</strong>: 331-6. </li>
 +
    <li>Xu, J. P. (2006). Microbial ecology in the age of genomics and metagenomics: concepts, tools, and recent advances. <em>Molecular Ecology</em> <strong>15</strong>: 1713-31. </li>
 +
</ul>
 +
<p>&nbsp;</p>
 +
<h3><span class="mw-headline">Methods</span></h3>
 +
<ul>
 +
    <li>Beja, O. <em>et al.</em> (2000). Construction and analysis of bacterial artificial chromosome libraries from a marine microbial assemblage. <em>Environmental Microbiology</em> <strong>2</strong>: 516-29. </li>
 +
    <li>Sebat, J. L. <em>et al.</em> (2003). Metagenomic profiling: Microarray analysis of an environmental genomic library. <em>Applied and Environmental Microbiology</em> <strong>69</strong>: 4927-34. </li>
 +
    <li>Suzuki, M. T. <em>et al.</em> (2004). Phylogenetic screening of ribosomal RNA gene-containing clones in bacterial artificial chromosome (BAC) libraries from different depths in Monterey Bay. <em>Microbial Ecology</em> <strong>48</strong>: 473-88. </li>
 +
</ul>
 +
<p>&nbsp;</p>
 +
<h3><span class="mw-headline">Bioinformatics</span></h3>
 +
<ul>
 +
    <li>Krause L., Diaz N.N., Goesmann A., Kelley S., Nattkemper T.W., Rohwer F., Edwards R.A., Stoye J. Phylogenetic classification of short environmental DNA fragments. Nucleic Acids Res. 36:2230-9, 2008 </li>
 +
    <li>Huson, D.H., A. Auch, Ji Qi and S.C. Schuster, MEGAN Analysis of Metagenomic Data, Genome Research. 17:377-386, 2007 </li>
 +
    <li>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. </li>
 +
    <li>Rodriguez-Brito B, Rohwer F, Edwards RA. An application of statistics to comparative metagenomics. BMC Bioinformatics. 2006 20;7:162. </li>
 +
    <li>Raes, J., Foerstner, K.U. &amp; Bork, P. (2007) Get the most out of your metagenome: computational analysis of environmental sequence data. Curr Opin Microbiol, in press. </li>
 +
    <li>Harrington, E.D., Singh, A.H., Doerks, T., Letunic, I., von Mering, C., Jensen, L.J., Raes, J. &amp; Bork, P. (2007) Quantitative assessment of protein function predicion from metagenomics shotgun sequences. Proc. Natl. Acad. Sci. USA 104, 13913-8 </li>
 +
    <li>Tress, M. L. <em>et al.</em> (2006). An analysis of the Sargasso Sea resource and the consequences for database composition. <em>Bmc Bioinformatics</em> <strong>7</strong> </li>
 +
    <li>Foerstner KU, von Mering C, Hooper SD, Bork P (2005) Environments shape the nucleotide composition of genomes. EMBO Rep. 6(12): 1208-13 </li>
 +
    <li>Raes, J., Korbel, J.O., Lercher, M.J., Von Mering, C. &amp; Bork, P. (2007) Prediction of effective genome size in metagenomic samples. Genome Biology 8, R10 [1] </li>
 +
    <li>von Mering, C., Hugenholtz, P., Raes, J., Tringe, S.G., Doerks, T., Jensen, L.J., Ward N. &amp; Bork, P. (2007) Quantitative phylogenetic assessment of microbial communities in diverse environments. Science 315, 1126-1130 </li>
 +
    <li>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 </li>
 +
    <li>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 </li>
 +
    <li>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 </li>
 +
    <li>Pushker R., D'Auria G., Alba-Casado J.C. and Rodr&iacute;guez-Valera F. (2005) Micro-Mar: a database for dynamic representation of marine microbial biodiversity. BMC Bioinformatics, 6:222. </li>
 +
</ul>
 +
<p>&nbsp;</p>
 +
<h3><span class="mw-headline">Marine ecosystems</span></h3>
 +
<ul>
 +
    <li>Angly, F. E. <em>et al.</em> (2006). The marine viromes of four oceanic regions. <em>PloS Biology</em> <strong>4</strong>: 2121-31. </li>
 +
    <li>Beja, O. <em>et al.</em> (2000). Bacterial rhodopsin: Evidence for a new type of phototrophy in the sea. <em>Science</em> <strong>289</strong>: 1902-6. </li>
 +
    <li>Beja, O. <em>et al.</em> (2001). Proteorhodopsin phototrophy in the ocean. <em>Nature</em> <strong>411</strong>: 786-9. </li>
 +
    <li>Beja, O. <em>et al.</em> (2002). Unsuspected diversity among marine aerobic anoxygenic phototrophs. <em>Nature</em> <strong>415</strong>: 630-3. </li>
 +
    <li>Culley, A. I. <em>et al.</em> (2006). Metagenomic analysis of coastal RNA virus communities. <em>Science</em> <strong>312</strong>: 1795-8. </li>
 +
    <li>DeLong, E. F. <em>et al.</em> (2006). Community genomics among stratified microbial assemblages in the ocean's interior. <em>Science</em> <strong>311</strong>: 496-503. </li>
 +
    <li>Hallam, S. J. <em>et al.</em> (2006). Genomic analysis of the uncultivated marine crenarchaeote Cenarchaeum symbiosum. <em>Proceedings of the National Academy of Sciences of the United States of America</em> <strong>103</strong>: 18296-301. </li>
 +
    <li>John, D. E. <em>et al.</em> (2006). Gene diversity and organization in rbcL-containing genome fragments from uncultivated <em>Synechococcus</em> in the Gulf of Mexico. <em>Marine Ecology-Progress Series</em> <strong>316</strong>: 23-33. </li>
 +
    <li>Kannan N. <em>et al.</em> (2007). Structural and Functional Diversity of the Microbibial Kinome. <em>PloS Biology</em> <strong>5</strong>: 467-478 </li>
 +
    <li>Rusch D. B. <em>et al.</em> (2007). The Sorcerer II Global Ocean Sampling Expedition: Northwest Atlantic through Eastern Tropical Pacific. <em>PloS Biology</em> <strong>5</strong>: 398-431 </li>
 +
    <li>Tringe, S. G. <em>et al.</em> (2005). Comparative metagenomics of microbial communities. <em>Science</em> <strong>308</strong>: 554-7. </li>
 +
    <li>Woyke, T. <em>et al.</em> (2006). Symbiosis insights through metagenomic analysis of a microbial consortium. <em>Nature</em> <strong>443</strong>: 950-5. </li>
 +
    <li>Yooseph S. <em>et al.</em> (2007). The Sorcerer II Global Ocean Sampling Expedition: Expanding the Universe of Protein Families. 'PloS Biology <em><strong>5</strong>: 432-466</em> </li>
 +
    <li>Yutin, N. &amp; Beja, O. (2005). Putative novel photosynthetic reaction centre organizations in marine aerobic anoxygenic photosynthetic bacteria: insights from metagenomics and environmental genomics. <em>Environmental Microbiology</em> <strong>7</strong>: 2027-33. </li>
 +
</ul>
 +
<p>&nbsp;</p>
 +
<h3><span class="mw-headline">Sediments</span></h3>
 +
<ul>
 +
    <li>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. </li>
 +
    <li>Breitbart et al. (2004). <em>Diversity and population structure of a nearshore marine sediment viral community</em>. Proceedings of the Royal Society B <strong>271</strong>: 565-574. </li>
 +
</ul>
 +
<p>&nbsp;</p>
 +
<h3><span class="mw-headline">Extreme environments</span></h3>
 +
<ul>
 +
    <li>Baker, B. J. <em>et al.</em> (2006). Lineages of acidophilic archaea revealed by community genomic analysis. <em>Science</em> <strong>314</strong>: 1933-5. </li>
 +
</ul>
 +
<p>&nbsp;</p>
 +
<h3><span class="mw-headline">Medical Sciences and biotechnological applications</span></h3>
 +
<ul>
 +
    <li>Breitbart et al. (2003). <em>Metagenomic analyses of an uncultured viral community from human feces</em>. Journal of Bacteriology <strong>185</strong>:6220-6223. </li>
 +
    <li>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. </li>
 +
    <li>Gill, S. R. <em>et al.</em> (2006). Metagenomic analysis of the human distal gut microbiome. <em>Science</em> <strong>312</strong>: 1355-9. </li>
 +
    <li>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. </li>
 +
    <li>Schloss, P. D. &amp; Handelsman, J. (2003). Biotechnological prospects from metagenomics. <em>Current Opinion in Biotechnology</em> <strong>14</strong>: 303-10. </li>
 +
    <li>Zengler, K., Paradkar, A., &amp; Keller, M. (2005). New methods to access microbial diversity for small molecule discovery. Natural Products , 275-293. </li>
 +
    <li>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) <em>RNA viral community in human feces: prevalence of plant pathogenic viruses</em>. PLoS biology, <strong>4</strong>, e3. </li>
 +
</ul>
 +
<p>&nbsp;</p>
 +
<h3><span class="mw-headline">Ancient DNA</span></h3>
 +
<ul>
 +
    <li>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 </li>
 +
</ul>
 +
<p>&nbsp;</p>
 +
<h2><span class="mw-headline">External links</span></h2>
 +
<ul>
 +
    <li><a class="external text" title="http://www-ab.informatik.uni-tuebingen.de/software/megan/" rel="nofollow" href="http://www-ab.informatik.uni-tuebingen.de/software/megan/">MEGAN</a> MEtaGenome ANalyzer. A stand-alone metagenome analysis tool. </li>
 +
    <li><a class="external text" title="http://dels.nas.edu/metagenomics/" rel="nofollow" href="http://dels.nas.edu/metagenomics/">Metagenomics and Our Microbial Planet</a> A website on metagenomics and the vital role of microbes on Earth from the <a class="external text" title="http://nationalacademies.org" rel="nofollow" href="http://nationalacademies.org/">National Academies.</a> </li>
 +
    <li><a class="external text" title="http://books.nap.edu/catalog.php?record_id=11902" rel="nofollow" href="http://books.nap.edu/catalog.php?record_id=11902">The New Science of Metagenomics: Revealing the Secrets of Our Microbial Planet</a> A report released by the National Research Council in March 2007. Also, see the <a class="external text" title="http://dels.nas.edu/dels/rpt_briefs/metagenomics_brief_final.pdf" rel="nofollow" href="http://dels.nas.edu/dels/rpt_briefs/metagenomics_brief_final.pdf">Report In Brief.</a> </li>
 +
    <li><a class="external text" title="http://img.jgi.doe.gov/m" rel="nofollow" href="http://img.jgi.doe.gov/m">IMG/M</a> The Integrated Microbial Genomes system, for metagenome analysis by the DOE-JGI. </li>
 +
    <li><a class="external text" title="http://camera.calit2.net/index.php" rel="nofollow" href="http://camera.calit2.net/index.php">CAMERA</a> Cyberinfrastructure for Metagenomics, data repository and tools for metagenomics research. </li>
 +
    <li><a class="external text" title="http://www.scq.ubc.ca/?p=509" rel="nofollow" href="http://www.scq.ubc.ca/?p=509">A good overview of metagenomics from the Science Creative Quarterly</a> </li>
 +
    <li><a class="external text" title="http://www.genomesonline.org/gold.cgi?want=Metagenomes" rel="nofollow" href="http://www.genomesonline.org/gold.cgi?want=Metagenomes">list of Metagenome Projects from genomesonline.org</a> </li>
 +
    <li><a class="external text" title="http://metagenomics.theseed.org" rel="nofollow" href="http://metagenomics.theseed.org/">The SEED</a> publicly available, free, metagenomics annotation pipeline for pyrosequences, Sanger sequences, and other sequence approaches. </li>
 +
    <li><a title="Human microbiome project" href="http://en.wikipedia.org/wiki/Human_microbiome_project"><font color="#810081">Human microbiome project</font></a> </li>
 +
    <li><a class="external text" title="http://www.metahit.eu/" rel="nofollow" href="http://www.metahit.eu/">MetaHIT</a> official website for the EU-funded project&nbsp;: Metagenomics of the Human Intestinal Tract </li>
 +
    <li><a class="external text" title="http://annotathon.univ-mrs.fr/" rel="nofollow" href="http://annotathon.univ-mrs.fr/">Annotathon</a> Bioinformatics Training Through Metagenomic Sequence Annotation </li>
 +
</ul>
 +
<!--
 +
NewPP limit report
 +
Preprocessor node count: 3716/1000000
 +
Post-expand include size: 35546/2048000 bytes
 +
Template argument size: 12195/2048000 bytes
 +
Expensive parser function count: 0/500
 +
--><!-- Saved in parser cache with key enwiki:pcache:idhash:1408929-0!1!0!default!!en!2 and timestamp 20080924153352 -->
 +
<div class="printfooter">Retrieved from &quot;<a href="http://en.wikipedia.org/wiki/Metagenomics">http://en.wikipedia.org/wiki/Metagenomics</a>&quot;</div>

Latest revision as of 02:44, 25 September 2008

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.

An interesting overview of metagenomics is "Welcome to life on the tiniest scales" ; written by Henry Nicholls, in March 17th 2007 New Scientist magazine (paid).

Early environmental gene sequencing cloned specific genes (often the 16S rRNA gene) to produce a profile of diversity in a natural sample. Such work revealed that the vast majority of microbial diversity had been missed by cultivation-based methods. [1] Recent studies use "shotgun" Sanger sequencing or chip-based pyrosequencing to get (mostly) unbiased samples of all genes from all members of sampled communities.

 

History

 

Origin of the term

The term "metagenomics" was first used by Jo Handelsman and others in the University of Wisconsin Department of Plant Pathology, and first appeared in publication in 1998. [2] The term metagenome referenced the idea that a collection of genes sequenced from the environment could be analyzed in way analogous to the study of a single genome. The exploding interest in environmental genetics, along with the buzzword-like nature of the term, has resulted in the broader use of metagenomics to describe any sequencing of genetic material from environmental (i.e. uncultured) samples, even work that focuses on one organism or gene. Recently, Kevin Chen and Lior Pachter (researchers at the University of California, Berkeley) defined metagenomics as "the application of modern genomics techniques to the study of communities of microbial organisms directly in their natural environments, bypassing the need for isolation and lab cultivation of individual species." [3]

 

Environmental gene surveys

Conventional sequencing begins with a culture of identical cells as a source of DNA. However, early metagenomic studies revealed that there are probably large groups of microorganisms in many environments that cannot be cultured and thus cannot be sequenced. These early studies focused on 16S ribosomal RNA sequences which are relatively short, often conserved within a species, and generally different between species. Many 16S rRNA sequences have been found which do not belong to any known cultured species, indicating that there are numerous non-isolated organisms out there.

Early molecular work in the field was conducted by Norman R. Pace and colleagues, who used PCR to explore the diversity of ribosomal RNA sequences. [4] The insights gained from these breakthrough studies led Pace to propose the idea of cloning DNA directly from environmental samples as early as 1985. [5] This led to the first report of isolating and cloning bulk DNA from an environmental sample, published by Pace and colleagues in 1991 [6] while Pace was in the Department of Biology at Indiana University. Considerable efforts ensured that these were not PCR false positives and supported the existence of a complex community of unexplored species. Although this methodology was limited to exploring highly conserved, non-protein coding genes, it did support early microbial morphology-based observations that diversity was far more complex than was known by culturing methods.

Soon after that, Healy reported the metagenomic isolation of functional genes from "zoolibraries" constructed from a complex culture of environmental organisms grown in the laboratory on dried grasses in 1995. [7] After leaving the Pace laboratory, Ed DeLong continued in the field and has published work that has largely laid the groundwork for environmental phylogenies based on signature 16S sequences, beginning with his group's construction of libraries from marine samples. [8]

 

Longer sequences from environmental samples

Recovery of DNA sequences longer than a few thousand base pairs from environmental samples was very difficult until recent advances in molecular biological techniques, particularly related to constructing libraries in bacterial artificial chromosomes (BACs), provided better vectors for molecular cloning. [9]

 

Shotgun metagenomics

Advances in bioinformatics, refinements of DNA amplification, and proliferation of computational power have greatly aided the analysis of DNA sequences recovered from environmental samples. These advances have enabled the adaptation of shotgun sequencing to metagenomic samples. The approach, used to sequence many cultured microorganisms as well as the human genome, randomly shears DNA, sequences many short sequences, and reconstructs them into a consensus sequence. In 2002, Mya Breitbart, Forest Rohwer, and colleagues used environmental shotgun sequencing to show that 200 liters of seawater contains over 5000 different viruses. [10] Subsequent studies showed that there are >1000 viral species in human stool and possibly a million different viruses per kilogram of marine sediment, including many bacteriophages. Essentially all of the viruses in these studies were new species. A 2004 metagenomic study of the Sargasso Sea found DNA from nearly 2000 different species including 148 types of bacteria never seen before. [11]

Also in 2004, Gene Tyson, Jill Banfield, and colleagues at the University of California, Berkeley and the Joint Genome Institute sequenced DNA extracted from an acid mine drainage system. [12] This effort resulted in the complete, or nearly complete, genomes for a handful of bacteria and archaea that had previously resisted attempts to culture them. It was now possible to study entire genomes without the biases associated with laboratory cultures. [13]

In 2006 Robert Edwards, Forest Rohwer, and colleagues at San Diego State University published the first sequences of environmental samples generated with so-called next generation sequencing, in this case chip based pyrosequencing developed by 454 Life Sciences. [14] This technique for sequencing the DNA generates shorter fragments than the conventional techniques, however this limitation is compensated for by the very large number of sequences generated. In addition, this technique does not require cloning the DNA before sequencing, removing one of the main biases in metagenomics.

In 2007, Daniel Huson and Stephan Schuster developed and published the first stand-alone metagenome analysis tool, MEGAN, which can be used to perform a first analysis of a metagenomic shotgun dataset. This tool was originally developed to analyse the metagenome of a mammoth sample [15].

In 2007, Folker Meyer and Robert Edwards and a team at Argonne National Laboratory and the University of Chicago released the Metagenomics RAST server (MG-RAST) a community resource for metagenome data set analysis [16] The SEED based free, public resource contains 158 public metagenome data sets (as of September 2008) and has so far been used for the analysis of several hundred metagenome data sets.

 

Microbial Diversity

Much of the interest in metagenomics comes from the discovery that the vast majority of microorganisms had previously gone unnoticed. Traditional microbiological methods relied upon laboratory cultures of organisms. Surveys of ribosomal RNA (rRNA) genes taken directly from the environment revealed that cultivation based methods find less than 1% of the bacteria and archaea species in a sample. [1]

 

Gene Surveys

Shotgun sequencing and screens of clone libraries reveal genes present in environmental samples. This provides information both on which organisms are present and what metabolic processes are possible in the community. This can be helpful in understanding the ecology of a community, particularly if multiple samples are compared to each other. [17]

 

Environmental Genomes

Shotgun metagenomics also is capable of sequencing nearly complete microbial genomes directly from the environment. [12] Because the collection of DNA from an environment is largely uncontrolled, the most abundant organisms types in a sample are most highly represented in the resulting sequence data. To achieve the high coverage needed to fully resolve the genomes of underrepresented community members, large samples, often prohibitively so, are needed. On the other hand, the random nature of shotgun sequencing ensures that many of these organisms will be represented by at least some small sequence segments. Due to the limitations of microbial isolation methods, the vast majority of these organisms would go unnoticed using traditional culturing techniques.

 

Community metabolism

Many bacterial communities show significant division of labor in metabolism. Waste products of some organisms are metabolites for others. Working together they turn raw resources into fully metabolized waste. Using comparative gene studies and expression experiments with microarrays or proteomics researchers can piece together a metabolic network that goes beyond species boundaries. Such studies require detailed knowledge about which versions of which proteins are coded by which species and even by which strains of which species. Therefore, community genomic information is another fundamental part (as metabolomics or proteomics) to be able to estimate how metabolites are possibly transferred and transformed through a community.

 

References

  1. ^ a b Hugenholz, P; Goebel BM, Pace NR (1998). "Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity". J. Bacteriol 180: 4765–4774. PMID 9733676. 
  2. ^ Handelsman, J; Rondon MR, Brady SF, Clardy J, Goodman RM (1998). "Molecular biological access to the chemistry of unknown soil microbes: a new frontier for natural products". Chemistry & Biology 5: 245–249. doi:10.1016/S1074-5521(98)90108-9. .
  3. ^ Chen, K; Pachter L (2005). "Bioinformatics for whole-genome shotgun sequencing of microbial communities". PLoS Comp Biol 1: 24. doi:10.1371/journal.pcbi.0010024. .
  4. ^ Lane, DJ; Pace B, Olsen GJ, Stahl DA, Sogin ML, Pace NR (1985). "Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses". Proceedings of the National Academy of Sciences 82: 6955. doi:10.1073/pnas.82.20.6955. PMID 2413450. .
  5. ^ Pace, NR; DA Stahl, DJ Lane, GJ Olsen (1985). "Analyzing natural microbial populations by rRNA sequences". ASM News 51: 4–12. .
  6. ^ Pace, NR (1991). "Analysis of a marine picoplankton community by 16S rRNA gene cloning and sequencing". Journal of Bacteriology 173: 4371–4378. .
  7. ^ Healy, FG; RM Ray, HC Aldrich, AC Wilkie, LO Ingram, KT Shanmugam (1995). "Direct isolation of functional genes encoding cellulases from the microbial consortia in a thermophilic, anaerobic digester maintained on lignocellulose". Appl. Microbiol Biotechnol. 43: 667. doi:10.1007/BF00164771. .
  8. ^ Stein, JL; TL Marsh, KY Wu, H Shizuya, EF DeLong (1996). "Characterization of uncultivated prokaryotes: isolation and analysis of a 40-kilobase-pair genome fragment from a planktonic marine archaeon". Journal of Bacteriology 178: 591–599. .
  9. ^ Beja, O; Suzuki MT, Koonin EV, Aravind L, Hadd A, Nguyen LP, Villacorta R, Amjadi M, Garrigues C, Jovanovich SB, Feldman RA, Delong EF (2000). "Construction and analysis of bacterial artificial chromosome libraries from a marine microbial assemblage" 2: 516–529. 
  10. ^ Breitbart, M; Salamon P, Andresen B, Mahaffy JM, Segall AM, Mead D, Azam F, Rohwer F (2002). "Genomic analysis of uncultured marine viral communities". Proceedings of the National Academy USA 99: 14250–14255. doi:10.1073/pnas.202488399. PMID 12384570. .
  11. ^ Venter, JC; Remington K, Heidelberg JF, Halpern AL, Rusch D, Eisen JA, Wu D, Paulsen I, Nelson KE, Nelson W, Fouts DE, Levy S, Knap AH, Lomas MW, Nealson K, White O, Peterson J, Hoffman J, Parsons R, Baden-Tillson H, Pfannkoch C, Rogers Y, Smith HO (2004). "Environmental Genome Shotgun Sequencing of the Sargasso Sea". Science 304: 66–74. doi:10.1126/science.1093857. PMID 15001713. .
  12. ^ a b Tyson, GW; Chapman J, Hugenholtz P, Allen EE, Ram RJ, Richardson PM, Solovyev VV, Rubin EM, Rokhsar DS, Banfield JF (2004). "Insights into community structure and metabolism by reconstruction of microbial genomes from the environment". Nature 428: 37–43. doi:10.1038/nature02340. .
  13. ^ Hugenholz, P (2002). "Exploring prokaryotic diversity in the genomic era". Genome Biology 3: 1–8. doi:10.1186/gb-2002-3-2-reviews0003. .
  14. ^ Edwards, RA; Rodriguez-Brito B, Wegley L, Haynes M, Breitbart M, Peterson DM, Saar MO, Alexander S, Alexander EC, Rohwer F (2006). "Using pyrosequencing to shed light on deep mine microbial ecology". BMC Genomics 7: 57. doi:10.1186/1471-2164-7-57. .
  15. ^ 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
  16. ^ Meyer, F; Paarmann D, D'Souza M, Olson R, Glass EM, Kubal M, Paczian T, Rodriguez A, Stevens R, Wilke A, Wilkening J, Edwards RA (2008). "The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes". BMC Bioinformatics 9: 0. doi:doi:10.1186/1471-2105-9-386. .
  17. ^ Allen, EE; Banfield, JF (2005). "Community genomics in microbial ecology and evolution". Nature Reviews Microbiology 3: 489–498. doi:10.1038/nrmicro1157. 

 

Additional References

Review articles

  • Edwards RA, & Rohwer F. Viral metagenomics. Nat Rev Microbiol. 2005 3(6):504-10. PubMed
  • Eisen, J. A. (2007). Environmental shotgun sequencing: its potential and challenges for studying the hidden world of microbes. 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

  • Krause L., Diaz N.N., Goesmann A., Kelley S., Nattkemper T.W., Rohwer F., Edwards R.A., Stoye J. Phylogenetic classification of short environmental DNA fragments. Nucleic Acids Res. 36:2230-9, 2008
  • Huson, D.H., A. Auch, Ji Qi and S.C. Schuster, MEGAN Analysis of Metagenomic Data, Genome Research. 17:377-386, 2007
  • 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.
  • Rodriguez-Brito B, Rohwer F, Edwards RA. An application of statistics to comparative metagenomics. BMC Bioinformatics. 2006 20;7:162.
  • 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.
  • 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 [1]
  • 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
  • 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
  • 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
  • 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
  • Pushker R., D'Auria G., Alba-Casado J.C. and Rodríguez-Valera F. (2005) Micro-Mar: a database for dynamic representation of marine microbial biodiversity. BMC Bioinformatics, 6:222.

 

Marine ecosystems

  • 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.
  • Kannan N. et al. (2007). Structural and Functional Diversity of the Microbibial Kinome. PloS Biology 5: 467-478
  • Rusch D. B. et al. (2007). The Sorcerer II Global Ocean Sampling Expedition: Northwest Atlantic through Eastern Tropical Pacific. PloS Biology 5: 398-431
  • 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.
  • 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

  • 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