metagenome all kinds of fun

from wikipedia of course:

Origin of the term

The term "metagenomics" was first used by Jo Handelsman, Jon Clardy, Robert M. Goodman, and others, and first appeared in publication in 1998.[5] The term metagenome referenced the idea that a collection of genes sequenced from the environment could be analyzed in a 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."[6]

[edit] 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.[7] The insights gained from these breakthrough studies led Pace to propose the idea of cloning DNA directly from environmental samples as early as 1985.[8] This led to the first report of isolating and cloning bulk DNA from an environmental sample, published by Pace and colleagues in 1991[9] 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.[10] 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.[11]

[edit] 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.[12]

[edit] 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.[13] 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. 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.[14] 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.[15]

 

2.

Metagenomic analysis of a permafrost microbial community reveals a rapid response to thaw.

Mackelprang R, Waldrop MP, Deangelis KM, David MM, Chavarria KL, Blazewicz SJ, Rubin EM, Jansson JK.

Nature. 2011 Nov 6. doi: 10.1038/nature10576. [Epub ahead of print]

PMID:
22056985
[PubMed - as supplied by publisher]

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3.

Resources and costs for microbial sequence analysis evaluated using virtual machines and cloud computing.

Angiuoli SV, White JR, Matalka M, White O, Fricke WF.

PLoS One. 2011;6(10):e26624. Epub 2011 Oct 19.

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4.

Accurate and fast estimation of taxonomic profiles from metagenomic shotgun sequences.

Liu B, Gibbons T, Ghodsi M, Treangen T, Pop M.

BMC Genomics. 2011;12 Suppl 2:S4. Epub 2011 Jul 27.

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5.

Functional metagenomic investigations of the human intestinal microbiota.

Moore AM, Munck C, Sommer MO, Dantas G.

Front Microbiol. 2011;2:188. Epub 2011 Oct 17.

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6.

Plasmid metagenome reveals high levels of antibiotic resistance genes and mobile genetic elements in activated sludge.

Zhang T, Zhang XX, Ye L.

PLoS One. 2011;6(10):e26041. Epub 2011 Oct 10.

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7.

Raw sewage harbors diverse viral populations.

Cantalupo PG, Calgua B, Zhao G, Hundesa A, Wier AD, Katz JP, Grabe M, Hendrix RW, Girones R, Wang D, Pipas JM.

MBio. 2011 Oct 4;2(5). pii: e00180-11. doi: 10.1128/mBio.00180-11. Print 2011.

PMID:
21972239
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8.

Selection in coastal Synechococcus (cyanobacteria) populations evaluated from environmental metagenomes.

Tai V, Poon AF, Paulsen IT, Palenik B.

PLoS One. 2011;6(9):e24249. Epub 2011 Sep 9.

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21931665
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9.

Phosphate transporters in marine phytoplankton and their viruses: cross-domain commonalities in viral-host gene exchanges.

Monier A, Welsh RM, Gentemann C, Weinstock G, Sodergren E, Armbrust EV, Eisen JA, Worden AZ.

Environ Microbiol. 2011 Sep 14. doi: 10.1111/j.1462-2920.2011.02576.x. [Epub ahead of print]

PMID:
21914098
[PubMed - as supplied by publisher]

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10.

Human Microbiome in Health and Disease.

Pflughoeft KJ, Versalovic J.

Annu Rev Pathol. 2011 Jan 25. [Epub ahead of print]

PMID:
21910623
[PubMed - as supplied by publisher]

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11.

Identification and characterization of alkaline serine protease from goat skin surface metagenome.

Pushpam PL, Rajesh T, Gunasekaran P.

AMB Express. 2011 Mar 28;1(1):3.

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12.

TheViral MetaGenome Annotation Pipeline(VMGAP):an automated tool for the functional annotation of viral Metagenomic shotgun sequencing data.

Lorenzi HA, Hoover J, Inman J, Safford T, Murphy S, Kagan L, Williamson SJ.

Stand Genomic Sci. 2011 Jul 1;4(3):418-29. Epub 2011 Jun 30.

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13.

Linking long-term dietary patterns with gut microbial enterotypes.

Wu GD, Chen J, Hoffmann C, Bittinger K, Chen YY, Keilbaugh SA, Bewtra M, Knights D, Walters WA, Knight R, Sinha R, Gilroy E, Gupta K, Baldassano R, Nessel L, Li H, Bushman FD, Lewis JD.

Science. 2011 Oct 7;334(6052):105-8. Epub 2011 Sep 1.

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14.

CloVR: a virtual machine for automated and portable sequence analysis from the desktop using cloud computing.

Angiuoli SV, Matalka M, Gussman A, Galens K, Vangala M, Riley DR, Arze C, White JR, White O, Fricke WF.

BMC Bioinformatics. 2011 Aug 30;12:356.

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15.

Hydrogen is an energy source for hydrothermal vent symbioses.

Petersen JM, Zielinski FU, Pape T, Seifert R, Moraru C, Amann R, Hourdez S, Girguis PR, Wankel SD, Barbe V, Pelletier E, Fink D, Borowski C, Bach W, Dubilier N.

Nature. 2011 Aug 10;476(7359):176-80. doi: 10.1038/nature10325.

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16.

Taxonomic and functional assignment of cloned sequences from high Andean forest soil metagenome.

Montaña JS, Jiménez DJ, Hernández M, Angel T, Baena S.

Antonie Van Leeuwenhoek. 2011 Jul 27. [Epub ahead of print]

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17.

Biochemical and kinetic characterization of GH43 β-D: -xylosidase/α-L: -arabinofuranosidase and GH30 α-L: -arabinofuranosidase/β-D: -xylosidase from rumen metagenome.

Zhou J, Bao L, Chang L, Zhou Y, Lu H.

J Ind Microbiol Biotechnol. 2011 Jul 2. [Epub ahead of print]

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18.

The intestinal microbiota, gastrointestinal environment and colorectal cancer: a putative role for probiotics in prevention of colorectal cancer?

Azcárate-Peril MA, Sikes M, Bruno-Bárcena JM.

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19.

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Klatt CG, Wood JM, Rusch DB, Bateson MM, Hamamura N, Heidelberg JF, Grossman AR, Bhaya D, Cohan FM, Kühl M, Bryant DA, Ward DM.

ISME J. 2011 Aug;5(8):1262-78. doi: 10.1038/ismej.2011.73. Epub 2011 Jun 23.

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20.

Temporal analysis of the honey bee microbiome reveals four novel viruses and seasonal prevalence of known viruses, Nosema, and Crithidia.

Runckel C, Flenniken ML, Engel JC, Ruby JG, Ganem D, Andino R, DeRisi JL.

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